Starting phenix.real_space_refine on Sun Jun 15 11:17:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d3l_27159/06_2025/8d3l_27159.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d3l_27159/06_2025/8d3l_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d3l_27159/06_2025/8d3l_27159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d3l_27159/06_2025/8d3l_27159.map" model { file = "/net/cci-nas-00/data/ceres_data/8d3l_27159/06_2025/8d3l_27159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d3l_27159/06_2025/8d3l_27159.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.17, per 1000 atoms: 0.64 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: 4.17 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 6.46 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: 5.71 Time building geometry restraints manager: 4.92 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=" CA TYR F 7 " pdb=" C TYR F 7 " ideal model delta sigma weight residual 1.523 1.488 0.034 1.25e-02 6.40e+03 7.61e+00 bond pdb=" CA ALA C 204 " pdb=" CB ALA C 204 " ideal model delta sigma weight residual 1.532 1.491 0.040 1.57e-02 4.06e+03 6.62e+00 bond pdb=" CA ASN C 203 " pdb=" C ASN C 203 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.31e-02 5.83e+03 6.48e+00 bond pdb=" C TYR E 7 " pdb=" O TYR E 7 " ideal model delta sigma weight residual 1.234 1.204 0.030 1.28e-02 6.10e+03 5.64e+00 ... (remaining 17938 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 24353 3.21 - 6.41: 103 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=" CA GLU E 62 " pdb=" CB GLU E 62 " pdb=" CG GLU E 62 " ideal model delta sigma weight residual 114.10 121.67 -7.57 2.00e+00 2.50e-01 1.43e+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: 2632 0.108 - 0.216: 52 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 219 or resid 301 through 302)) selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 48.470 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 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= 0.331 Angle : 1.658 84.418 24489 Z= 0.373 Chirality : 0.041 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 : 9.01 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (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 TRP 0.015 0.001 TRP B 296 HIS 0.010 0.001 HIS D 130 PHE 0.026 0.001 PHE D 232 TYR 0.027 0.001 TYR E 7 ARG 0.006 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.14998 ( 840) hydrogen bonds : angle 6.08121 ( 2413) metal coordination : bond 0.46753 ( 8) metal coordination : angle 49.16666 ( 24) covalent geometry : bond 0.00306 (17943) covalent geometry : angle 0.61689 (24465) *********************** 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 : 1.823 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: 0.3963 time to fit residues: 154.7973 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 : 3.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 8.9990 chunk 153 optimal weight: 0.0020 chunk 84 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN C 39 HIS ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN J 24 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 = 0.170145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133157 restraints weight = 22843.964| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.44 r_work: 0.3444 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 17951 Z= 0.156 Angle : 1.500 87.110 24489 Z= 0.334 Chirality : 0.040 0.148 2687 Planarity : 0.005 0.115 2912 Dihedral : 16.968 154.091 2901 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.55 % Favored : 93.25 % Rotamer: Outliers : 1.03 % Allowed : 8.29 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.19), residues: 1985 helix: 1.82 (0.18), residues: 912 sheet: -0.05 (0.33), residues: 242 loop : -2.03 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 342 HIS 0.005 0.001 HIS C 39 PHE 0.015 0.001 PHE J 20 TYR 0.018 0.001 TYR C 95 ARG 0.003 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.04524 ( 840) hydrogen bonds : angle 4.31431 ( 2413) metal coordination : bond 0.01663 ( 8) metal coordination : angle 44.21898 ( 24) covalent geometry : bond 0.00360 (17943) covalent geometry : angle 0.57844 (24465) *********************** 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 226 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 1.872 Fit side-chains REVERT: B 12 GLN cc_start: 0.7756 (mp10) cc_final: 0.7441 (mp10) REVERT: B 150 MET cc_start: 0.5256 (tpp) cc_final: 0.4951 (tpp) REVERT: B 180 MET cc_start: 0.5375 (mpp) cc_final: 0.4115 (mmt) REVERT: B 313 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.8038 (ptt) REVERT: D 125 ARG cc_start: 0.6340 (tpp-160) cc_final: 0.5483 (tmt170) REVERT: D 126 MET cc_start: 0.8212 (tmm) cc_final: 0.7888 (tpp) REVERT: D 178 ASP cc_start: 0.7298 (t0) cc_final: 0.7056 (t0) REVERT: D 197 PRO cc_start: 0.3809 (Cg_exo) cc_final: 0.3523 (Cg_endo) REVERT: D 200 ASP cc_start: 0.7618 (m-30) cc_final: 0.6085 (p0) REVERT: D 336 GLU cc_start: 0.8403 (pm20) cc_final: 0.8113 (pm20) REVERT: E 62 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7996 (pm20) REVERT: I 48 LYS cc_start: 0.7553 (tptt) cc_final: 0.6701 (mttt) REVERT: I 147 ASN cc_start: 0.7929 (t0) cc_final: 0.7651 (t0) REVERT: J 44 GLN cc_start: 0.7813 (tp-100) cc_final: 0.7519 (tt0) REVERT: J 154 GLU cc_start: 0.7871 (pp20) cc_final: 0.7671 (pp20) REVERT: J 175 TYR cc_start: 0.8130 (m-10) cc_final: 0.7782 (m-10) outliers start: 18 outliers final: 13 residues processed: 215 average time/residue: 0.3011 time to fit residues: 97.6558 Evaluate side-chains 210 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 1.909 ------------------------------------------------------------------------------- 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 B residue 313 MET Chi-restraints excluded: chain C residue 53 SER 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 F residue 0 SER Chi-restraints excluded: chain I residue 130 CYS Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 71 GLN 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 60 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 99 optimal weight: 0.0040 chunk 74 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 86 optimal weight: 0.0060 chunk 37 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 overall best weight: 0.7812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN C 39 HIS ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4050 r_free = 0.4050 target = 0.178860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.154265 restraints weight = 21821.468| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.48 r_work: 0.3658 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 17951 Z= 0.132 Angle : 1.317 88.291 24489 Z= 0.311 Chirality : 0.038 0.145 2687 Planarity : 0.004 0.114 2912 Dihedral : 16.992 155.255 2901 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.20 % Favored : 93.65 % Rotamer: Outliers : 1.03 % Allowed : 12.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.19), residues: 1985 helix: 2.04 (0.18), residues: 912 sheet: 0.08 (0.33), residues: 248 loop : -2.07 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 296 HIS 0.003 0.001 HIS D 234 PHE 0.026 0.001 PHE D 111 TYR 0.010 0.001 TYR D 337 ARG 0.003 0.000 ARG J 162 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 840) hydrogen bonds : angle 4.05861 ( 2413) metal coordination : bond 0.02171 ( 8) metal coordination : angle 38.11024 ( 24) covalent geometry : bond 0.00300 (17943) covalent geometry : angle 0.55892 (24465) *********************** 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 227 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 1.964 Fit side-chains REVERT: B 12 GLN cc_start: 0.7892 (mp10) cc_final: 0.7675 (mp10) REVERT: B 125 ARG cc_start: 0.7444 (tmm-80) cc_final: 0.6928 (ttt90) REVERT: B 180 MET cc_start: 0.5719 (mpp) cc_final: 0.5407 (mmt) REVERT: C 131 PRO cc_start: 0.8283 (Cg_endo) cc_final: 0.8030 (Cg_exo) REVERT: D 125 ARG cc_start: 0.6971 (tpp-160) cc_final: 0.6320 (tmt170) REVERT: D 126 MET cc_start: 0.8032 (tmm) cc_final: 0.7820 (tpp) REVERT: D 191 HIS cc_start: 0.7664 (t-90) cc_final: 0.7089 (t-90) REVERT: D 197 PRO cc_start: 0.3720 (Cg_exo) cc_final: 0.3427 (Cg_endo) REVERT: D 200 ASP cc_start: 0.7490 (m-30) cc_final: 0.6524 (p0) REVERT: D 342 TRP cc_start: 0.8402 (OUTLIER) cc_final: 0.7823 (m-10) REVERT: E 38 VAL cc_start: 0.8719 (p) cc_final: 0.8411 (t) REVERT: E 62 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7986 (pm20) REVERT: I 48 LYS cc_start: 0.8146 (tptt) cc_final: 0.7590 (ttmm) outliers start: 18 outliers final: 7 residues processed: 220 average time/residue: 0.2894 time to fit residues: 96.2374 Evaluate side-chains 205 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 196 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 193 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN C 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 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 = 0.4020 r_free = 0.4020 target = 0.176036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152090 restraints weight = 21861.783| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.32 r_work: 0.3588 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 17951 Z= 0.146 Angle : 1.165 84.538 24489 Z= 0.310 Chirality : 0.039 0.144 2687 Planarity : 0.004 0.112 2912 Dihedral : 17.099 156.017 2901 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.80 % Favored : 93.10 % Rotamer: Outliers : 1.37 % Allowed : 14.80 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.19), residues: 1985 helix: 2.04 (0.18), residues: 916 sheet: 0.24 (0.34), residues: 236 loop : -2.07 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 165 HIS 0.004 0.001 HIS D 234 PHE 0.033 0.001 PHE D 232 TYR 0.013 0.001 TYR C 320 ARG 0.003 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.04271 ( 840) hydrogen bonds : angle 3.97432 ( 2413) metal coordination : bond 0.02314 ( 8) metal coordination : angle 32.71313 ( 24) covalent geometry : bond 0.00337 (17943) covalent geometry : angle 0.55496 (24465) *********************** 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: 24 poor density : 202 time to evaluate : 1.912 Fit side-chains REVERT: A 268 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7998 (mm-30) REVERT: B 12 GLN cc_start: 0.7917 (mp10) cc_final: 0.7612 (mp10) REVERT: B 125 ARG cc_start: 0.7650 (tmm-80) cc_final: 0.7211 (ttt90) REVERT: B 155 ASN cc_start: 0.7199 (t0) cc_final: 0.5765 (p0) REVERT: B 180 MET cc_start: 0.5920 (mpp) cc_final: 0.4216 (mmt) REVERT: D 125 ARG cc_start: 0.7183 (tpp-160) cc_final: 0.6542 (tmt170) REVERT: D 200 ASP cc_start: 0.7630 (m-30) cc_final: 0.6614 (p0) REVERT: D 342 TRP cc_start: 0.8499 (OUTLIER) cc_final: 0.7909 (m-10) REVERT: E 38 VAL cc_start: 0.8719 (p) cc_final: 0.8456 (t) REVERT: E 62 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8017 (pm20) REVERT: F 9 VAL cc_start: 0.9038 (OUTLIER) cc_final: 0.8642 (m) REVERT: I 48 LYS cc_start: 0.8229 (tptt) cc_final: 0.7542 (mttt) REVERT: I 147 ASN cc_start: 0.8242 (t0) cc_final: 0.7949 (t0) outliers start: 24 outliers final: 13 residues processed: 217 average time/residue: 0.2955 time to fit residues: 96.7967 Evaluate side-chains 206 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 1.718 ------------------------------------------------------------------------------- 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 176 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 162 LEU 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 F residue 9 VAL Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 191 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 148 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 146 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 HIS ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN J 16 GLN J 32 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 = 0.3936 r_free = 0.3936 target = 0.167847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.142707 restraints weight = 22453.816| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.42 r_work: 0.3509 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 17951 Z= 0.227 Angle : 1.170 83.341 24489 Z= 0.362 Chirality : 0.043 0.147 2687 Planarity : 0.005 0.111 2912 Dihedral : 17.459 158.239 2901 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.56 % Favored : 92.19 % Rotamer: Outliers : 2.17 % Allowed : 16.34 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.19), residues: 1985 helix: 1.67 (0.18), residues: 911 sheet: 0.02 (0.32), residues: 249 loop : -2.26 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 342 HIS 0.006 0.001 HIS J 180 PHE 0.025 0.002 PHE C 340 TYR 0.020 0.002 TYR C 320 ARG 0.006 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.05777 ( 840) hydrogen bonds : angle 4.35499 ( 2413) metal coordination : bond 0.03087 ( 8) metal coordination : angle 30.83545 ( 24) covalent geometry : bond 0.00541 (17943) covalent geometry : angle 0.66224 (24465) *********************** 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 235 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 1.866 Fit side-chains REVERT: A 190 PHE cc_start: 0.7759 (t80) cc_final: 0.7102 (t80) REVERT: A 268 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8009 (mm-30) REVERT: B 125 ARG cc_start: 0.7560 (tmm-80) cc_final: 0.7102 (ttt90) REVERT: B 183 GLN cc_start: 0.6791 (OUTLIER) cc_final: 0.6430 (tm-30) REVERT: C 131 PRO cc_start: 0.8242 (Cg_endo) cc_final: 0.7951 (Cg_exo) REVERT: D 41 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8443 (mp) REVERT: D 125 ARG cc_start: 0.7213 (tpp-160) cc_final: 0.6519 (tmt170) REVERT: D 129 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6775 (tp30) REVERT: D 200 ASP cc_start: 0.7816 (m-30) cc_final: 0.6892 (p0) REVERT: D 342 TRP cc_start: 0.8679 (OUTLIER) cc_final: 0.8086 (m-10) REVERT: E 38 VAL cc_start: 0.8736 (p) cc_final: 0.8466 (t) REVERT: E 62 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8008 (pm20) REVERT: I 147 ASN cc_start: 0.8273 (t0) cc_final: 0.7916 (t0) outliers start: 38 outliers final: 21 residues processed: 226 average time/residue: 0.2878 time to fit residues: 99.0130 Evaluate side-chains 211 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 1.728 ------------------------------------------------------------------------------- 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 176 VAL Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 223 THR 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 159 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 127 THR 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 284 MET Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain J residue 71 GLN Chi-restraints excluded: chain J residue 191 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 56 optimal weight: 0.7980 chunk 154 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 33 optimal weight: 0.3980 chunk 132 optimal weight: 0.8980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 30 GLN C 39 HIS ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.169823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145200 restraints weight = 22191.182| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.41 r_work: 0.3526 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17951 Z= 0.170 Angle : 1.088 79.983 24489 Z= 0.329 Chirality : 0.040 0.143 2687 Planarity : 0.004 0.111 2912 Dihedral : 17.338 159.669 2901 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.95 % Favored : 92.85 % Rotamer: Outliers : 2.34 % Allowed : 17.20 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.19), residues: 1985 helix: 1.73 (0.18), residues: 912 sheet: -0.11 (0.32), residues: 249 loop : -2.19 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 165 HIS 0.004 0.001 HIS D 306 PHE 0.033 0.001 PHE D 232 TYR 0.015 0.001 TYR C 320 ARG 0.004 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.04909 ( 840) hydrogen bonds : angle 4.19827 ( 2413) metal coordination : bond 0.02632 ( 8) metal coordination : angle 28.97711 ( 24) covalent geometry : bond 0.00401 (17943) covalent geometry : angle 0.60123 (24465) *********************** 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 233 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 1.756 Fit side-chains REVERT: A 190 PHE cc_start: 0.7744 (t80) cc_final: 0.7118 (t80) REVERT: A 268 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8065 (mm-30) REVERT: B 125 ARG cc_start: 0.7482 (tmm-80) cc_final: 0.7050 (ttt90) REVERT: B 155 ASN cc_start: 0.7334 (OUTLIER) cc_final: 0.5950 (p0) REVERT: B 180 MET cc_start: 0.6101 (mpp) cc_final: 0.4294 (mmt) REVERT: B 183 GLN cc_start: 0.6777 (OUTLIER) cc_final: 0.6382 (tm-30) REVERT: D 125 ARG cc_start: 0.7186 (tpp-160) cc_final: 0.6452 (tmt170) REVERT: D 129 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6724 (tp30) REVERT: D 342 TRP cc_start: 0.8639 (OUTLIER) cc_final: 0.7990 (m-10) REVERT: E 22 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7935 (mtpp) REVERT: E 38 VAL cc_start: 0.8662 (p) cc_final: 0.8393 (t) REVERT: E 62 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8055 (pm20) REVERT: I 48 LYS cc_start: 0.8248 (tptt) cc_final: 0.7669 (ttmm) REVERT: I 68 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.6575 (tpt) REVERT: I 147 ASN cc_start: 0.8266 (t0) cc_final: 0.7891 (t0) outliers start: 41 outliers final: 28 residues processed: 222 average time/residue: 0.2991 time to fit residues: 100.6655 Evaluate side-chains 217 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 215 ASN 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 E residue 62 GLU Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 91 GLU 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 134 MET Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 71 GLN Chi-restraints excluded: chain J residue 198 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 83 optimal weight: 0.6980 chunk 151 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 161 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 39 HIS ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN ** D 203 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.171112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.144968 restraints weight = 22128.530| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.56 r_work: 0.3543 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2618 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= 0.143 Angle : 1.044 77.800 24489 Z= 0.314 Chirality : 0.039 0.139 2687 Planarity : 0.004 0.111 2912 Dihedral : 17.248 159.851 2901 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.80 % Favored : 93.05 % Rotamer: Outliers : 2.57 % Allowed : 17.54 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.19), residues: 1985 helix: 1.82 (0.18), residues: 916 sheet: -0.01 (0.33), residues: 245 loop : -2.13 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 165 HIS 0.003 0.001 HIS D 306 PHE 0.031 0.001 PHE D 232 TYR 0.011 0.001 TYR C 320 ARG 0.005 0.000 ARG D 252 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 840) hydrogen bonds : angle 4.07571 ( 2413) metal coordination : bond 0.02384 ( 8) metal coordination : angle 27.76485 ( 24) covalent geometry : bond 0.00329 (17943) covalent geometry : angle 0.57860 (24465) *********************** 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 238 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 1.970 Fit side-chains REVERT: A 268 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8035 (mm-30) REVERT: B 125 ARG cc_start: 0.7417 (tmm-80) cc_final: 0.6984 (ttt90) REVERT: B 155 ASN cc_start: 0.7292 (OUTLIER) cc_final: 0.5936 (p0) REVERT: B 180 MET cc_start: 0.6013 (mpp) cc_final: 0.4235 (mmt) REVERT: B 183 GLN cc_start: 0.6691 (OUTLIER) cc_final: 0.6196 (tm-30) REVERT: D 129 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6775 (tp30) REVERT: D 154 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7328 (ttm-80) REVERT: D 190 PHE cc_start: 0.5817 (t80) cc_final: 0.5566 (t80) REVERT: D 200 ASP cc_start: 0.7745 (m-30) cc_final: 0.6739 (p0) REVERT: D 342 TRP cc_start: 0.8619 (OUTLIER) cc_final: 0.7985 (m-10) REVERT: E 22 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7910 (mtpp) REVERT: E 38 VAL cc_start: 0.8622 (p) cc_final: 0.8375 (t) REVERT: E 62 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: I 48 LYS cc_start: 0.8189 (tptt) cc_final: 0.7636 (ttmm) REVERT: I 68 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.6476 (tpt) REVERT: I 147 ASN cc_start: 0.8286 (t0) cc_final: 0.7894 (t0) REVERT: J 129 MET cc_start: 0.8527 (mmm) cc_final: 0.8264 (mtp) REVERT: J 217 LEU cc_start: 0.4597 (OUTLIER) cc_final: 0.4330 (mm) outliers start: 45 outliers final: 26 residues processed: 226 average time/residue: 0.2967 time to fit residues: 102.1721 Evaluate side-chains 222 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 1.945 ------------------------------------------------------------------------------- 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 153 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 155 ASN 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 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 122 MET Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 91 GLU 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 38 VAL Chi-restraints excluded: chain J residue 71 GLN Chi-restraints excluded: chain J residue 198 ILE 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 182 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 129 optimal weight: 0.0010 chunk 23 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 39 HIS ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.168982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.142005 restraints weight = 22186.437| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.43 r_work: 0.3520 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17951 Z= 0.191 Angle : 1.064 78.450 24489 Z= 0.334 Chirality : 0.041 0.144 2687 Planarity : 0.005 0.110 2912 Dihedral : 17.325 160.317 2901 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.61 % Favored : 92.24 % Rotamer: Outliers : 2.91 % Allowed : 17.71 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 1985 helix: 1.70 (0.18), residues: 916 sheet: -0.15 (0.32), residues: 255 loop : -2.21 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 342 HIS 0.004 0.001 HIS C 39 PHE 0.033 0.002 PHE D 232 TYR 0.016 0.001 TYR C 320 ARG 0.004 0.000 ARG D 252 Details of bonding type rmsd hydrogen bonds : bond 0.04979 ( 840) hydrogen bonds : angle 4.17512 ( 2413) metal coordination : bond 0.02754 ( 8) metal coordination : angle 27.65885 ( 24) covalent geometry : bond 0.00456 (17943) covalent geometry : angle 0.61850 (24465) *********************** 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 238 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 187 time to evaluate : 1.986 Fit side-chains REVERT: A 190 PHE cc_start: 0.7720 (t80) cc_final: 0.7092 (t80) REVERT: A 267 LYS cc_start: 0.8329 (mttp) cc_final: 0.8059 (mttm) REVERT: B 125 ARG cc_start: 0.7373 (tmm-80) cc_final: 0.6967 (ttt90) REVERT: B 149 MET cc_start: 0.7351 (ttp) cc_final: 0.7070 (tmm) REVERT: B 155 ASN cc_start: 0.7255 (OUTLIER) cc_final: 0.5932 (p0) REVERT: B 180 MET cc_start: 0.5985 (mpp) cc_final: 0.4236 (mmt) REVERT: B 183 GLN cc_start: 0.6634 (OUTLIER) cc_final: 0.6265 (tm-30) REVERT: D 126 MET cc_start: 0.7920 (tpp) cc_final: 0.7293 (tpp) REVERT: D 129 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6804 (tp30) REVERT: D 190 PHE cc_start: 0.5826 (t80) cc_final: 0.5564 (t80) REVERT: D 342 TRP cc_start: 0.8651 (OUTLIER) cc_final: 0.8079 (m-10) REVERT: E 22 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7919 (mtpp) REVERT: E 38 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8443 (t) REVERT: E 62 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: I 48 LYS cc_start: 0.8225 (tptt) cc_final: 0.7645 (ttmm) REVERT: I 68 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.6485 (tpt) REVERT: I 147 ASN cc_start: 0.8306 (t0) cc_final: 0.7902 (t0) REVERT: J 129 MET cc_start: 0.8569 (mmm) cc_final: 0.8369 (mtp) REVERT: J 217 LEU cc_start: 0.4685 (OUTLIER) cc_final: 0.4381 (mm) outliers start: 51 outliers final: 31 residues processed: 225 average time/residue: 0.3569 time to fit residues: 122.1596 Evaluate side-chains 224 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 1.980 ------------------------------------------------------------------------------- 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 97 ILE Chi-restraints excluded: chain A residue 153 ILE 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 155 ASN Chi-restraints excluded: chain B residue 176 VAL 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 105 THR Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 91 GLU 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 38 VAL 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 56 optimal weight: 4.9990 chunk 86 optimal weight: 0.0670 chunk 193 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 39 HIS ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN ** D 203 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.169586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.143303 restraints weight = 22161.123| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.52 r_work: 0.3549 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17951 Z= 0.171 Angle : 1.043 76.771 24489 Z= 0.328 Chirality : 0.040 0.143 2687 Planarity : 0.004 0.109 2912 Dihedral : 17.312 161.263 2901 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.90 % Favored : 92.95 % Rotamer: Outliers : 2.63 % Allowed : 18.17 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 1985 helix: 1.73 (0.18), residues: 915 sheet: -0.13 (0.32), residues: 255 loop : -2.24 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 165 HIS 0.005 0.001 HIS C 39 PHE 0.032 0.001 PHE D 232 TYR 0.014 0.001 TYR C 320 ARG 0.003 0.000 ARG D 252 Details of bonding type rmsd hydrogen bonds : bond 0.04809 ( 840) hydrogen bonds : angle 4.14229 ( 2413) metal coordination : bond 0.02628 ( 8) metal coordination : angle 27.15294 ( 24) covalent geometry : bond 0.00406 (17943) covalent geometry : angle 0.60541 (24465) *********************** 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 242 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 2.117 Fit side-chains REVERT: A 190 PHE cc_start: 0.7739 (t80) cc_final: 0.7145 (t80) REVERT: A 267 LYS cc_start: 0.8340 (mttp) cc_final: 0.8073 (mttm) REVERT: B 125 ARG cc_start: 0.7336 (tmm-80) cc_final: 0.6940 (ttt90) REVERT: B 155 ASN cc_start: 0.7212 (OUTLIER) cc_final: 0.5905 (p0) REVERT: B 180 MET cc_start: 0.6012 (mpp) cc_final: 0.4351 (mmt) REVERT: B 183 GLN cc_start: 0.6626 (OUTLIER) cc_final: 0.6271 (tm-30) REVERT: D 126 MET cc_start: 0.7882 (tpp) cc_final: 0.7253 (tpp) REVERT: D 129 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6811 (tp30) REVERT: D 154 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7476 (ttm-80) REVERT: D 190 PHE cc_start: 0.5952 (t80) cc_final: 0.5631 (t80) REVERT: D 342 TRP cc_start: 0.8645 (OUTLIER) cc_final: 0.8009 (m-10) REVERT: E 38 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8428 (t) REVERT: E 62 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8021 (pm20) REVERT: I 48 LYS cc_start: 0.8279 (tptt) cc_final: 0.7682 (ttmm) REVERT: I 68 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.6477 (tpt) REVERT: I 147 ASN cc_start: 0.8315 (t0) cc_final: 0.7911 (t0) REVERT: J 217 LEU cc_start: 0.4674 (OUTLIER) cc_final: 0.4364 (mm) outliers start: 46 outliers final: 31 residues processed: 228 average time/residue: 0.3297 time to fit residues: 114.0172 Evaluate side-chains 232 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 1.776 ------------------------------------------------------------------------------- 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 97 ILE Chi-restraints excluded: chain A residue 153 ILE 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 155 ASN 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 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 122 MET Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 91 GLU 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 38 VAL Chi-restraints excluded: chain J residue 71 GLN Chi-restraints excluded: chain J residue 198 ILE 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 150 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 47 optimal weight: 0.0270 chunk 42 optimal weight: 0.1980 chunk 89 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 190 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 3 optimal weight: 0.0370 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 39 HIS ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** D 203 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.166177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130335 restraints weight = 23018.236| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.39 r_work: 0.3410 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 17951 Z= 0.120 Angle : 0.988 71.354 24489 Z= 0.307 Chirality : 0.038 0.197 2687 Planarity : 0.004 0.108 2912 Dihedral : 17.151 161.699 2901 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.99 % Favored : 93.85 % Rotamer: Outliers : 2.00 % Allowed : 19.03 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 1985 helix: 1.95 (0.18), residues: 916 sheet: -0.07 (0.32), residues: 268 loop : -2.11 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 165 HIS 0.008 0.001 HIS C 39 PHE 0.027 0.001 PHE D 232 TYR 0.010 0.001 TYR D 275 ARG 0.003 0.000 ARG D 252 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 840) hydrogen bonds : angle 3.92731 ( 2413) metal coordination : bond 0.01996 ( 8) metal coordination : angle 25.84326 ( 24) covalent geometry : bond 0.00269 (17943) covalent geometry : angle 0.56724 (24465) ********************** 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 240 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 1.827 Fit side-chains REVERT: A 30 GLN cc_start: 0.6773 (tp40) cc_final: 0.6279 (mt0) REVERT: A 268 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7409 (mm-30) REVERT: B 12 GLN cc_start: 0.7665 (mp10) cc_final: 0.7360 (mp10) REVERT: B 155 ASN cc_start: 0.6633 (OUTLIER) cc_final: 0.5080 (p0) REVERT: B 180 MET cc_start: 0.5314 (mpp) cc_final: 0.4310 (mmt) REVERT: B 183 GLN cc_start: 0.6286 (OUTLIER) cc_final: 0.5661 (tm-30) REVERT: D 30 GLN cc_start: 0.7003 (pm20) cc_final: 0.6558 (pm20) REVERT: D 129 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6566 (tp30) REVERT: D 183 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6962 (mp10) REVERT: D 191 HIS cc_start: 0.7798 (t-90) cc_final: 0.6911 (t-90) REVERT: D 342 TRP cc_start: 0.8378 (OUTLIER) cc_final: 0.7560 (m-10) REVERT: E 62 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7848 (pm20) REVERT: I 48 LYS cc_start: 0.7702 (tptt) cc_final: 0.7035 (ttmm) REVERT: I 68 MET cc_start: 0.6474 (OUTLIER) cc_final: 0.5431 (tpt) REVERT: I 147 ASN cc_start: 0.8035 (t0) cc_final: 0.7542 (t0) outliers start: 35 outliers final: 20 residues processed: 231 average time/residue: 0.3524 time to fit residues: 122.4121 Evaluate side-chains 223 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 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 155 ASN 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 127 THR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 91 GLU 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 70 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 66 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 81 optimal weight: 0.0670 chunk 94 optimal weight: 0.0670 chunk 197 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 HIS ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** D 203 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.166089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130378 restraints weight = 23043.662| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.38 r_work: 0.3410 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.203 17951 Z= 0.183 Angle : 1.130 71.413 24489 Z= 0.453 Chirality : 0.039 0.462 2687 Planarity : 0.005 0.108 2912 Dihedral : 17.150 161.705 2901 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.05 % Favored : 93.80 % Rotamer: Outliers : 1.60 % Allowed : 19.54 % Favored : 78.86 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 1985 helix: 1.94 (0.18), residues: 916 sheet: -0.06 (0.32), residues: 268 loop : -2.10 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 165 HIS 0.006 0.001 HIS C 39 PHE 0.025 0.001 PHE D 232 TYR 0.010 0.001 TYR D 275 ARG 0.004 0.000 ARG C 125 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 840) hydrogen bonds : angle 3.92588 ( 2413) metal coordination : bond 0.02053 ( 8) metal coordination : angle 25.82876 ( 24) covalent geometry : bond 0.00400 (17943) covalent geometry : angle 0.78953 (24465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8601.08 seconds wall clock time: 150 minutes 24.15 seconds (9024.15 seconds total)