Starting phenix.real_space_refine on Fri Jun 5 13:49:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oym_71026/06_2026/9oym_71026.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oym_71026/06_2026/9oym_71026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oym_71026/06_2026/9oym_71026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oym_71026/06_2026/9oym_71026.map" model { file = "/net/cci-nas-00/data/ceres_data/9oym_71026/06_2026/9oym_71026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oym_71026/06_2026/9oym_71026.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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 Zn 4 6.06 5 P 55 5.49 5 Mg 3 5.21 5 S 112 5.16 5 C 12940 2.51 5 N 3722 2.21 5 O 3983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20819 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2726 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "B" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2849 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 16, 'TRANS': 349} Chain: "C" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2865 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "D" Number of atoms: 2807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2807 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 14, 'TRANS': 346} Chain: "E" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2601 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "F" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2844 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 345} Chain: "G" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2844 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 345} Chain: "H" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 529 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "I" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "J" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 243 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3209 SG CYS B 64 74.481 86.037 114.999 1.00 79.55 S ATOM 3269 SG CYS B 73 78.220 85.491 115.048 1.00 78.36 S ATOM 3286 SG CYS B 76 76.061 82.515 115.766 1.00 80.81 S ATOM 3308 SG CYS B 79 75.964 83.882 112.317 1.00 69.05 S ATOM 6058 SG CYS C 64 97.768 56.231 86.669 1.00 56.25 S ATOM 6118 SG CYS C 73 99.529 53.565 84.800 1.00 74.23 S ATOM 6135 SG CYS C 76 96.604 52.440 86.913 1.00 64.28 S ATOM 6157 SG CYS C 79 95.806 54.438 83.968 1.00 58.79 S ATOM 8931 SG CYS D 64 75.277 28.557 56.529 1.00 79.91 S ATOM 8991 SG CYS D 73 73.203 26.189 54.427 1.00 97.22 S ATOM 9008 SG CYS D 76 72.045 26.801 57.957 1.00 90.70 S ATOM 9030 SG CYS D 79 71.774 29.579 55.559 1.00 76.75 S ATOM 11654 SG CYS E 50 27.926 35.463 50.214 1.00100.41 S ATOM 11723 SG CYS E 59 24.448 34.501 51.234 1.00108.49 S ATOM 11743 SG CYS E 62 26.931 34.917 53.984 1.00104.45 S ATOM 11764 SG CYS E 65 25.896 37.999 51.995 1.00104.86 S Time building chain proxies: 4.97, per 1000 atoms: 0.24 Number of scatterers: 20819 At special positions: 0 Unit cell: (109.296, 122.544, 149.04, 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) Zn 4 29.99 S 112 16.00 P 55 15.00 Mg 3 11.99 O 3983 8.00 N 3722 7.00 C 12940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 942.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 79 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 76 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 64 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 79 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 73 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 76 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 64 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 79 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 73 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 76 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 64 " pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 59 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 65 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 62 " Number of angles added : 24 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4764 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 13 sheets defined 55.4% alpha, 15.5% beta 19 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 5 through 7 No H-bonds generated for 'chain 'A' and resid 5 through 7' Processing helix chain 'A' and resid 8 through 15 removed outlier: 3.540A pdb=" N GLN A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 45 Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.542A pdb=" N ILE A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.752A pdb=" N GLU A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 198 through 204 removed outlier: 3.706A pdb=" N GLN A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 225 through 240 Processing helix chain 'A' and resid 242 through 264 removed outlier: 3.667A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 282 through 293 Processing helix chain 'A' and resid 294 through 314 Processing helix chain 'A' and resid 319 through 332 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 14 through 18 Processing helix chain 'B' and resid 21 through 35 removed outlier: 4.032A pdb=" N ALA B 27 " --> pdb=" O HIS B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 63 Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 128 through 131 Processing helix chain 'B' and resid 132 through 145 removed outlier: 4.092A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 removed outlier: 3.834A pdb=" N LYS B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 199 through 211 removed outlier: 4.048A pdb=" N GLU B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.644A pdb=" N LEU B 244 " --> pdb=" O MET B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 258 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 277 through 296 Processing helix chain 'B' and resid 298 through 302 removed outlier: 3.504A pdb=" N LEU B 302 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 321 through 338 Processing helix chain 'B' and resid 339 through 342 Processing helix chain 'B' and resid 344 through 358 Processing helix chain 'C' and resid 5 through 10 Processing helix chain 'C' and resid 14 through 18 removed outlier: 3.632A pdb=" N VAL C 18 " --> pdb=" O PHE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 35 removed outlier: 3.722A pdb=" N ALA C 27 " --> pdb=" O HIS C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 64 Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 100 through 110 removed outlier: 3.781A pdb=" N ASN C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 131 Processing helix chain 'C' and resid 132 through 139 Processing helix chain 'C' and resid 139 through 145 Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 163 through 169 removed outlier: 3.667A pdb=" N ARG C 169 " --> pdb=" O THR C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 195 Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.927A pdb=" N GLU C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.673A pdb=" N ALA C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.570A pdb=" N LEU C 252 " --> pdb=" O GLN C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 274 removed outlier: 3.563A pdb=" N ARG C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 298 removed outlier: 3.588A pdb=" N LEU C 282 " --> pdb=" O TRP C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 removed outlier: 3.816A pdb=" N ALA C 307 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 321 through 339 Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 344 through 359 Processing helix chain 'D' and resid 5 through 10 Processing helix chain 'D' and resid 14 through 18 Processing helix chain 'D' and resid 21 through 35 removed outlier: 3.703A pdb=" N ALA D 27 " --> pdb=" O HIS D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 63 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 100 through 110 removed outlier: 3.627A pdb=" N ASN D 110 " --> pdb=" O ASP D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 131 Processing helix chain 'D' and resid 132 through 145 removed outlier: 3.579A pdb=" N LEU D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N THR D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 163 through 170 removed outlier: 3.572A pdb=" N ARG D 169 " --> pdb=" O THR D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 195 Processing helix chain 'D' and resid 199 through 210 Processing helix chain 'D' and resid 213 through 228 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 247 through 258 Processing helix chain 'D' and resid 260 through 274 Processing helix chain 'D' and resid 277 through 298 Processing helix chain 'D' and resid 299 through 302 removed outlier: 3.965A pdb=" N LEU D 302 " --> pdb=" O PRO D 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 299 through 302' Processing helix chain 'D' and resid 303 through 307 Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 321 through 339 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 344 through 357 Processing helix chain 'E' and resid 4 through 6 No H-bonds generated for 'chain 'E' and resid 4 through 6' Processing helix chain 'E' and resid 7 through 20 Processing helix chain 'E' and resid 36 through 50 Processing helix chain 'E' and resid 62 through 71 Processing helix chain 'E' and resid 89 through 101 removed outlier: 3.599A pdb=" N VAL E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN E 101 " --> pdb=" O THR E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 121 through 134 removed outlier: 3.814A pdb=" N LEU E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LYS E 130 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 152 through 158 Processing helix chain 'E' and resid 168 through 178 removed outlier: 3.576A pdb=" N ARG E 178 " --> pdb=" O THR E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 197 through 206 removed outlier: 3.691A pdb=" N PHE E 205 " --> pdb=" O ALA E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 227 Proline residue: E 225 - end of helix Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 240 through 260 Processing helix chain 'E' and resid 270 through 281 Processing helix chain 'E' and resid 282 through 303 Processing helix chain 'E' and resid 307 through 323 Processing helix chain 'F' and resid 7 through 18 removed outlier: 4.359A pdb=" N LYS F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) Proline residue: F 13 - end of helix Processing helix chain 'F' and resid 27 through 30 Processing helix chain 'F' and resid 72 through 82 Processing helix chain 'F' and resid 112 through 116 Processing helix chain 'F' and resid 131 through 141 Processing helix chain 'F' and resid 142 through 146 removed outlier: 3.522A pdb=" N SER F 145 " --> pdb=" O THR F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 207 removed outlier: 3.612A pdb=" N LEU F 207 " --> pdb=" O LEU F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 removed outlier: 3.615A pdb=" N ILE F 272 " --> pdb=" O ALA F 268 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 332 Processing helix chain 'G' and resid 7 through 18 removed outlier: 4.120A pdb=" N LYS G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) Proline residue: G 13 - end of helix Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 72 through 82 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'G' and resid 132 through 141 Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.602A pdb=" N MET G 146 " --> pdb=" O GLN G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 155 Processing helix chain 'G' and resid 197 through 207 removed outlier: 3.534A pdb=" N LEU G 207 " --> pdb=" O LEU G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 247 Processing helix chain 'G' and resid 260 through 271 Processing helix chain 'G' and resid 321 through 332 removed outlier: 3.753A pdb=" N LYS G 332 " --> pdb=" O LEU G 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 12 Processing helix chain 'J' and resid 21 through 25 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 54 removed outlier: 6.637A pdb=" N GLU A 49 " --> pdb=" O THR A 79 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU A 81 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N HIS A 51 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU A 83 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N PHE A 53 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TYR A 21 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY A 114 " --> pdb=" O TYR A 21 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 23 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 162 removed outlier: 6.523A pdb=" N GLU A 161 " --> pdb=" O LEU A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.080A pdb=" N LYS B 121 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU B 153 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR B 123 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA B 155 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE B 125 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N TYR B 41 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N THR B 156 " --> pdb=" O TYR B 41 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N PHE B 43 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ALA B 40 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N PHE B 173 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU B 42 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 359 through 361 Processing sheet with id=AA5, first strand: chain 'C' and resid 90 through 94 removed outlier: 6.162A pdb=" N TYR C 41 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 90 through 94 removed outlier: 6.409A pdb=" N ILE D 91 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASP D 126 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE D 93 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LYS D 121 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU D 153 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ALA D 155 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE D 125 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR D 41 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N THR D 156 " --> pdb=" O TYR D 41 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE D 43 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 76 through 79 removed outlier: 6.668A pdb=" N TYR E 77 " --> pdb=" O TRP E 113 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS E 110 " --> pdb=" O TRP E 140 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE E 142 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL E 112 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA E 144 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL E 114 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 2 through 6 removed outlier: 4.588A pdb=" N ASN G 295 " --> pdb=" O GLY G 280 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLY G 280 " --> pdb=" O ASN G 295 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 66 through 71 removed outlier: 3.620A pdb=" N GLY F 66 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASN F 32 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THR F 47 " --> pdb=" O ASN F 32 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 309 through 310 removed outlier: 4.590A pdb=" N ASP F 351 " --> pdb=" O ALA F 357 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ALA F 357 " --> pdb=" O ASP F 351 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N GLU F 165 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLN F 186 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLU F 163 " --> pdb=" O GLN F 186 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N LEU F 188 " --> pdb=" O GLU F 161 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N GLU F 161 " --> pdb=" O LEU F 188 " (cutoff:3.500A) removed outlier: 13.522A pdb=" N SER F 190 " --> pdb=" O LEU F 159 " (cutoff:3.500A) removed outlier: 14.100A pdb=" N LEU F 159 " --> pdb=" O SER F 190 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 315 through 320 removed outlier: 6.289A pdb=" N GLY F 280 " --> pdb=" O ASN F 295 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ASN F 295 " --> pdb=" O GLY F 280 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.796A pdb=" N ASN G 32 " --> pdb=" O THR G 47 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N THR G 47 " --> pdb=" O ASN G 32 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR G 41 " --> pdb=" O ALA G 38 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASN G 222 " --> pdb=" O GLY G 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 309 through 310 removed outlier: 4.457A pdb=" N ASP G 351 " --> pdb=" O ALA G 357 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ALA G 357 " --> pdb=" O ASP G 351 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU G 165 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N GLN G 186 " --> pdb=" O GLU G 163 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLU G 163 " --> pdb=" O GLN G 186 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N LEU G 188 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 10.315A pdb=" N GLU G 161 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 13.024A pdb=" N SER G 190 " --> pdb=" O LEU G 159 " (cutoff:3.500A) removed outlier: 14.108A pdb=" N LEU G 159 " --> pdb=" O SER G 190 " (cutoff:3.500A) removed outlier: 12.995A pdb=" N SER G 192 " --> pdb=" O GLY G 157 " (cutoff:3.500A) removed outlier: 12.790A pdb=" N GLY G 157 " --> pdb=" O SER G 192 " (cutoff:3.500A) 1102 hydrogen bonds defined for protein. 3114 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 3.74 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7124 1.36 - 1.51: 5500 1.51 - 1.65: 8474 1.65 - 1.80: 109 1.80 - 1.95: 77 Bond restraints: 21284 Sorted by residual: bond pdb=" O3B AGS B 702 " pdb=" PG AGS B 702 " ideal model delta sigma weight residual 1.559 1.628 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O2B AGS C 702 " pdb=" PB AGS C 702 " ideal model delta sigma weight residual 1.531 1.481 0.050 1.60e-02 3.91e+03 9.92e+00 bond pdb=" O2A AGS C 702 " pdb=" PA AGS C 702 " ideal model delta sigma weight residual 1.531 1.481 0.050 1.60e-02 3.91e+03 9.67e+00 bond pdb=" O3B AGS C 702 " pdb=" PG AGS C 702 " ideal model delta sigma weight residual 1.559 1.620 -0.061 2.00e-02 2.50e+03 9.34e+00 bond pdb=" O2G AGS C 702 " pdb=" PG AGS C 702 " ideal model delta sigma weight residual 1.557 1.498 0.059 2.00e-02 2.50e+03 8.80e+00 ... (remaining 21279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 28948 2.97 - 5.94: 126 5.94 - 8.92: 11 8.92 - 11.89: 2 11.89 - 14.86: 3 Bond angle restraints: 29090 Sorted by residual: angle pdb=" PA AGS B 702 " pdb=" O3A AGS B 702 " pdb=" PB AGS B 702 " ideal model delta sigma weight residual 119.76 134.62 -14.86 3.00e+00 1.11e-01 2.45e+01 angle pdb=" PB AGS B 702 " pdb=" O3B AGS B 702 " pdb=" PG AGS B 702 " ideal model delta sigma weight residual 120.12 134.84 -14.72 3.00e+00 1.11e-01 2.41e+01 angle pdb=" PB AGS C 702 " pdb=" O3B AGS C 702 " pdb=" PG AGS C 702 " ideal model delta sigma weight residual 120.12 132.80 -12.68 3.00e+00 1.11e-01 1.79e+01 angle pdb=" CA THR B 99 " pdb=" CB THR B 99 " pdb=" OG1 THR B 99 " ideal model delta sigma weight residual 109.60 103.71 5.89 1.50e+00 4.44e-01 1.54e+01 angle pdb=" PA AGS C 702 " pdb=" O3A AGS C 702 " pdb=" PB AGS C 702 " ideal model delta sigma weight residual 119.76 129.77 -10.01 3.00e+00 1.11e-01 1.11e+01 ... (remaining 29085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.85: 12410 33.85 - 67.71: 432 67.71 - 101.56: 23 101.56 - 135.41: 1 135.41 - 169.27: 2 Dihedral angle restraints: 12868 sinusoidal: 5527 harmonic: 7341 Sorted by residual: dihedral pdb=" O1A AGS D 702 " pdb=" O3A AGS D 702 " pdb=" PA AGS D 702 " pdb=" PB AGS D 702 " ideal model delta sinusoidal sigma weight residual -67.73 101.54 -169.27 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CA TYR C 3 " pdb=" C TYR C 3 " pdb=" N GLN C 4 " pdb=" CA GLN C 4 " ideal model delta harmonic sigma weight residual 180.00 157.18 22.82 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" O1A AGS B 702 " pdb=" O3A AGS B 702 " pdb=" PA AGS B 702 " pdb=" PB AGS B 702 " ideal model delta sinusoidal sigma weight residual -67.73 55.23 -122.96 1 3.00e+01 1.11e-03 1.65e+01 ... (remaining 12865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3305 0.107 - 0.214: 51 0.214 - 0.321: 0 0.321 - 0.429: 0 0.429 - 0.536: 3 Chirality restraints: 3359 Sorted by residual: chirality pdb=" P DC I 7 " pdb=" OP1 DC I 7 " pdb=" OP2 DC I 7 " pdb=" O5' DC I 7 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.54 2.00e-01 2.50e+01 7.18e+00 chirality pdb=" P DG I 6 " pdb=" OP1 DG I 6 " pdb=" OP2 DG I 6 " pdb=" O5' DG I 6 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.53 2.00e-01 2.50e+01 6.89e+00 chirality pdb=" P DC I 5 " pdb=" OP1 DC I 5 " pdb=" OP2 DC I 5 " pdb=" O5' DC I 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.83 -0.49 2.00e-01 2.50e+01 5.96e+00 ... (remaining 3356 not shown) Planarity restraints: 3618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 98 " -0.272 9.50e-02 1.11e+02 1.22e-01 9.18e+00 pdb=" NE ARG B 98 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 98 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 98 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 98 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 70 " 0.030 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO F 71 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO F 71 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 71 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 56 " -0.024 5.00e-02 4.00e+02 3.55e-02 2.01e+00 pdb=" N PRO A 57 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " -0.020 5.00e-02 4.00e+02 ... (remaining 3615 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 95 2.54 - 3.13: 15219 3.13 - 3.72: 33103 3.72 - 4.31: 47171 4.31 - 4.90: 79447 Nonbonded interactions: 175035 Sorted by model distance: nonbonded pdb=" OG1 THR B 52 " pdb="MG MG B 703 " model vdw 1.950 2.170 nonbonded pdb=" O2G AGS D 702 " pdb="MG MG D 703 " model vdw 1.950 2.170 nonbonded pdb=" O3G AGS B 702 " pdb="MG MG B 703 " model vdw 2.043 2.170 nonbonded pdb=" OG1 THR C 52 " pdb="MG MG C 703 " model vdw 2.063 2.170 nonbonded pdb=" OG1 THR D 52 " pdb="MG MG D 703 " model vdw 2.104 2.170 ... (remaining 175030 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 'B' and (resid 2 through 361 or resid 701 through 703)) selection = (chain 'C' and (resid 2 through 361 or resid 701 through 703)) selection = (chain 'D' and resid 2 through 703) } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.250 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 : 0.004 0.069 21300 Z= 0.187 Angle : 0.614 14.859 29114 Z= 0.323 Chirality : 0.041 0.536 3359 Planarity : 0.004 0.122 3618 Dihedral : 15.546 169.265 8104 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.17), residues: 2518 helix: 1.37 (0.15), residues: 1241 sheet: 1.09 (0.24), residues: 437 loop : 0.50 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 47 TYR 0.011 0.001 TYR F 153 PHE 0.012 0.001 PHE A 74 TRP 0.012 0.001 TRP B 10 HIS 0.003 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (21284) covalent geometry : angle 0.60393 / 0.32 (29090) hydrogen bonds : bond 0.15308 / 10.01 ( 1152) hydrogen bonds : angle 5.30530 / 3.77 ( 3214) metal coordination : bond 0.00351 / 0.20 ( 16) metal coordination : angle 3.86610 / 2.23 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 519 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.7468 (tp-100) cc_final: 0.7253 (tp-100) REVERT: A 149 ARG cc_start: 0.7726 (ttp-110) cc_final: 0.7255 (ttp80) REVERT: A 159 ASN cc_start: 0.8187 (m110) cc_final: 0.7867 (m110) REVERT: A 208 ASP cc_start: 0.7757 (t0) cc_final: 0.7387 (t0) REVERT: A 239 GLU cc_start: 0.7280 (tp30) cc_final: 0.6942 (mt-10) REVERT: A 242 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7564 (mm-30) REVERT: A 244 VAL cc_start: 0.8552 (t) cc_final: 0.8318 (p) REVERT: A 286 MET cc_start: 0.7576 (mmm) cc_final: 0.7107 (tpp) REVERT: A 325 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7349 (pt0) REVERT: B 39 HIS cc_start: 0.8130 (m-70) cc_final: 0.7151 (p90) REVERT: B 102 GLU cc_start: 0.6386 (mp0) cc_final: 0.6055 (pm20) REVERT: B 133 ARG cc_start: 0.7721 (mtm110) cc_final: 0.7487 (ptp90) REVERT: B 161 LYS cc_start: 0.8155 (mmpt) cc_final: 0.7431 (mmmt) REVERT: B 201 ARG cc_start: 0.8032 (tpt-90) cc_final: 0.7807 (tpt170) REVERT: B 208 ARG cc_start: 0.8095 (ttp-110) cc_final: 0.7333 (ttp80) REVERT: B 231 GLN cc_start: 0.8118 (mt0) cc_final: 0.7889 (mt0) REVERT: B 245 ASP cc_start: 0.7241 (m-30) cc_final: 0.6838 (m-30) REVERT: B 263 ARG cc_start: 0.8332 (tpt-90) cc_final: 0.6808 (ttt180) REVERT: B 284 GLU cc_start: 0.7977 (tt0) cc_final: 0.7566 (mt-10) REVERT: C 103 ASP cc_start: 0.7901 (m-30) cc_final: 0.7358 (m-30) REVERT: C 157 THR cc_start: 0.8647 (m) cc_final: 0.8329 (p) REVERT: C 193 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7695 (mm-30) REVERT: C 235 GLN cc_start: 0.8142 (tt0) cc_final: 0.7760 (tm-30) REVERT: C 262 GLU cc_start: 0.6968 (mp0) cc_final: 0.6533 (tt0) REVERT: C 277 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6918 (tm-30) REVERT: C 284 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7543 (mp0) REVERT: D 14 THR cc_start: 0.7981 (m) cc_final: 0.7708 (p) REVERT: D 112 GLN cc_start: 0.8307 (pt0) cc_final: 0.7855 (pm20) REVERT: D 141 LYS cc_start: 0.8505 (tptp) cc_final: 0.8276 (tptp) REVERT: D 148 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7679 (mm-30) REVERT: D 161 LYS cc_start: 0.8318 (mtpt) cc_final: 0.7869 (mtpp) REVERT: D 174 HIS cc_start: 0.8721 (m90) cc_final: 0.8493 (m90) REVERT: D 208 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7469 (ttm110) REVERT: D 247 ASP cc_start: 0.7463 (p0) cc_final: 0.7146 (p0) REVERT: D 258 GLU cc_start: 0.7716 (tt0) cc_final: 0.7498 (tt0) REVERT: D 315 GLU cc_start: 0.7825 (tp30) cc_final: 0.7575 (tm-30) REVERT: E 8 ARG cc_start: 0.6948 (tpp-160) cc_final: 0.6719 (ttp-110) REVERT: E 35 MET cc_start: 0.9208 (mmm) cc_final: 0.9008 (mmm) REVERT: E 46 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.7586 (mmm-85) REVERT: F 16 GLN cc_start: 0.8211 (tp40) cc_final: 0.7922 (mm-40) REVERT: F 50 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6997 (tm-30) REVERT: F 64 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7728 (tt0) REVERT: F 279 ARG cc_start: 0.7610 (mmm160) cc_final: 0.7248 (mmm160) REVERT: F 282 ARG cc_start: 0.7181 (mtm-85) cc_final: 0.6889 (mtt180) REVERT: F 284 TYR cc_start: 0.7222 (m-80) cc_final: 0.6621 (m-80) REVERT: F 300 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7767 (mp0) REVERT: F 303 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6665 (tm-30) REVERT: F 317 ILE cc_start: 0.7675 (mt) cc_final: 0.7222 (tp) REVERT: F 326 ASP cc_start: 0.7778 (m-30) cc_final: 0.7533 (m-30) REVERT: G 50 GLU cc_start: 0.6286 (mm-30) cc_final: 0.5529 (tm-30) REVERT: G 53 MET cc_start: 0.7654 (tpt) cc_final: 0.7376 (tpt) REVERT: G 56 ARG cc_start: 0.6875 (mmm-85) cc_final: 0.6658 (ttm-80) REVERT: G 79 CYS cc_start: 0.7428 (m) cc_final: 0.6946 (m) REVERT: G 96 ARG cc_start: 0.6597 (mmt180) cc_final: 0.6174 (mmm160) REVERT: G 100 ARG cc_start: 0.7526 (ptp-170) cc_final: 0.7259 (ptp-170) REVERT: G 105 ARG cc_start: 0.7070 (ttp80) cc_final: 0.6853 (ttp-170) REVERT: G 127 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6633 (tm-30) REVERT: G 198 LYS cc_start: 0.7994 (mttp) cc_final: 0.7350 (tttm) REVERT: G 277 LYS cc_start: 0.8230 (ttpt) cc_final: 0.7682 (tttp) REVERT: G 334 GLU cc_start: 0.7696 (tp30) cc_final: 0.7174 (mp0) outliers start: 0 outliers final: 0 residues processed: 519 average time/residue: 0.8861 time to fit residues: 503.7609 Evaluate side-chains 372 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 0.0370 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN ** A 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 GLN A 146 GLN A 168 GLN B 110 ASN B 172 GLN B 330 GLN C 112 GLN C 231 GLN E 259 HIS F 91 GLN G 143 GLN G 295 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.184268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.149024 restraints weight = 19375.572| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.43 r_work: 0.3632 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21300 Z= 0.164 Angle : 0.574 8.752 29114 Z= 0.287 Chirality : 0.039 0.152 3359 Planarity : 0.005 0.041 3618 Dihedral : 14.823 142.242 3303 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.27 % Allowed : 8.64 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.17), residues: 2518 helix: 1.50 (0.15), residues: 1274 sheet: 1.05 (0.23), residues: 443 loop : 0.63 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 201 TYR 0.013 0.001 TYR F 153 PHE 0.012 0.002 PHE G 3 TRP 0.012 0.001 TRP B 10 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (21284) covalent geometry : angle 0.55823 / 0.29 (29090) hydrogen bonds : bond 0.04069 / 2.74 ( 1152) hydrogen bonds : angle 4.04791 / 2.93 ( 3214) metal coordination : bond 0.00330 / 0.19 ( 16) metal coordination : angle 4.68165 / 2.65 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 394 time to evaluate : 0.822 Fit side-chains REVERT: A 107 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6931 (t0) REVERT: A 149 ARG cc_start: 0.7869 (ttp-110) cc_final: 0.7430 (ttp80) REVERT: A 159 ASN cc_start: 0.8154 (m110) cc_final: 0.7928 (m110) REVERT: A 208 ASP cc_start: 0.7654 (t0) cc_final: 0.7359 (t0) REVERT: A 242 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7566 (mm-30) REVERT: A 244 VAL cc_start: 0.8776 (t) cc_final: 0.8561 (p) REVERT: A 325 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7495 (pt0) REVERT: B 39 HIS cc_start: 0.8215 (m-70) cc_final: 0.7423 (p90) REVERT: B 161 LYS cc_start: 0.8286 (mmpt) cc_final: 0.7723 (mmmt) REVERT: B 208 ARG cc_start: 0.8170 (ttp-110) cc_final: 0.7503 (ttp80) REVERT: B 231 GLN cc_start: 0.8208 (mt0) cc_final: 0.8006 (mt0) REVERT: B 263 ARG cc_start: 0.8522 (tpt-90) cc_final: 0.7184 (ttt180) REVERT: B 284 GLU cc_start: 0.8071 (tt0) cc_final: 0.7754 (mt-10) REVERT: C 103 ASP cc_start: 0.8200 (m-30) cc_final: 0.7633 (m-30) REVERT: C 157 THR cc_start: 0.8540 (m) cc_final: 0.8328 (m) REVERT: C 193 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7781 (mm-30) REVERT: C 284 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7680 (mp0) REVERT: D 14 THR cc_start: 0.8076 (m) cc_final: 0.7859 (p) REVERT: D 133 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8262 (ttm110) REVERT: D 141 LYS cc_start: 0.8643 (tptp) cc_final: 0.8061 (mptm) REVERT: D 148 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7747 (mm-30) REVERT: D 161 LYS cc_start: 0.8336 (mtpt) cc_final: 0.7961 (mtpp) REVERT: D 204 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7311 (mp10) REVERT: D 247 ASP cc_start: 0.7317 (p0) cc_final: 0.6973 (p0) REVERT: D 315 GLU cc_start: 0.7585 (tp30) cc_final: 0.7332 (tm-30) REVERT: D 344 ASP cc_start: 0.8329 (p0) cc_final: 0.8114 (p0) REVERT: E 46 ARG cc_start: 0.7921 (mmm-85) cc_final: 0.7700 (mmm-85) REVERT: E 211 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: E 276 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: F 50 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7243 (tm-30) REVERT: F 64 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7653 (tt0) REVERT: F 150 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7017 (t70) REVERT: F 165 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7289 (tt0) REVERT: F 279 ARG cc_start: 0.7583 (mmm160) cc_final: 0.7312 (mmm160) REVERT: F 284 TYR cc_start: 0.7682 (m-80) cc_final: 0.7220 (m-80) REVERT: F 300 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7671 (mp0) REVERT: F 303 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6871 (tm-30) REVERT: G 48 ASP cc_start: 0.6928 (t0) cc_final: 0.6602 (t70) REVERT: G 50 GLU cc_start: 0.6720 (mm-30) cc_final: 0.5760 (mp0) REVERT: G 56 ARG cc_start: 0.7160 (mmm-85) cc_final: 0.6664 (mmt-90) REVERT: G 79 CYS cc_start: 0.7264 (m) cc_final: 0.6957 (m) REVERT: G 100 ARG cc_start: 0.7591 (ptp-170) cc_final: 0.7218 (mtt180) REVERT: G 105 ARG cc_start: 0.7126 (ttp80) cc_final: 0.6911 (ttp-170) REVERT: G 127 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7090 (tm-30) REVERT: G 203 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8045 (tt) REVERT: G 277 LYS cc_start: 0.8348 (ttpt) cc_final: 0.7847 (tttp) REVERT: G 301 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7125 (tm-30) REVERT: G 334 GLU cc_start: 0.7666 (tp30) cc_final: 0.7302 (mp0) REVERT: J 6 ASP cc_start: 0.8034 (m-30) cc_final: 0.7690 (m-30) outliers start: 48 outliers final: 16 residues processed: 418 average time/residue: 0.8725 time to fit residues: 401.4022 Evaluate side-chains 375 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 351 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 311 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 28 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 232 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 GLN A 146 GLN B 172 GLN C 78 ASN C 112 GLN C 137 ASN C 231 GLN F 91 GLN F 299 GLN G 255 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.183235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.148038 restraints weight = 19433.644| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.42 r_work: 0.3621 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21300 Z= 0.168 Angle : 0.557 8.083 29114 Z= 0.278 Chirality : 0.039 0.153 3359 Planarity : 0.004 0.042 3618 Dihedral : 14.827 139.891 3303 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.98 % Allowed : 11.20 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.17), residues: 2518 helix: 1.59 (0.15), residues: 1273 sheet: 0.94 (0.23), residues: 449 loop : 0.60 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 246 TYR 0.013 0.001 TYR F 153 PHE 0.012 0.001 PHE G 3 TRP 0.013 0.001 TRP B 10 HIS 0.005 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (21284) covalent geometry : angle 0.54430 / 0.28 (29090) hydrogen bonds : bond 0.03836 / 2.60 ( 1152) hydrogen bonds : angle 3.87001 / 2.80 ( 3214) metal coordination : bond 0.00308 / 0.18 ( 16) metal coordination : angle 4.22485 / 2.40 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 369 time to evaluate : 0.897 Fit side-chains REVERT: A 107 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7002 (t0) REVERT: A 149 ARG cc_start: 0.7895 (ttp-110) cc_final: 0.7461 (ttp80) REVERT: A 159 ASN cc_start: 0.8140 (m110) cc_final: 0.7934 (m110) REVERT: A 208 ASP cc_start: 0.7624 (t0) cc_final: 0.7360 (t0) REVERT: A 242 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7601 (mm-30) REVERT: A 244 VAL cc_start: 0.8822 (t) cc_final: 0.8540 (p) REVERT: A 325 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7506 (pt0) REVERT: B 39 HIS cc_start: 0.8279 (m-70) cc_final: 0.7435 (p90) REVERT: B 126 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8395 (t70) REVERT: B 161 LYS cc_start: 0.8273 (mmpt) cc_final: 0.7652 (mmmt) REVERT: B 172 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8702 (tt0) REVERT: B 208 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7482 (ttp80) REVERT: B 231 GLN cc_start: 0.8274 (mt0) cc_final: 0.8036 (mt0) REVERT: B 245 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6783 (t0) REVERT: B 263 ARG cc_start: 0.8573 (tpt-90) cc_final: 0.7179 (ttt180) REVERT: B 284 GLU cc_start: 0.8046 (tt0) cc_final: 0.7723 (mt-10) REVERT: B 327 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8327 (tp) REVERT: B 344 ASP cc_start: 0.7990 (t0) cc_final: 0.7566 (t70) REVERT: C 193 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7832 (mm-30) REVERT: C 284 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7611 (mp0) REVERT: D 14 THR cc_start: 0.8081 (m) cc_final: 0.7839 (p) REVERT: D 133 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8211 (ttm110) REVERT: D 141 LYS cc_start: 0.8631 (tptp) cc_final: 0.8054 (mptm) REVERT: D 161 LYS cc_start: 0.8381 (mtpt) cc_final: 0.8006 (mtpp) REVERT: D 247 ASP cc_start: 0.7326 (p0) cc_final: 0.7001 (p0) REVERT: D 315 GLU cc_start: 0.7642 (tp30) cc_final: 0.7377 (tm-30) REVERT: E 46 ARG cc_start: 0.7900 (mmm-85) cc_final: 0.7685 (mmm-85) REVERT: E 276 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: F 12 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7525 (ttmt) REVERT: F 64 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7584 (tt0) REVERT: F 150 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7062 (t70) REVERT: F 165 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7254 (tt0) REVERT: F 221 ASN cc_start: 0.8526 (m110) cc_final: 0.8319 (m-40) REVERT: F 230 PHE cc_start: 0.7214 (m-80) cc_final: 0.6880 (m-80) REVERT: F 264 LYS cc_start: 0.8184 (ttmt) cc_final: 0.7962 (ttmt) REVERT: F 279 ARG cc_start: 0.7560 (mmm160) cc_final: 0.7244 (mmm160) REVERT: F 284 TYR cc_start: 0.7709 (m-80) cc_final: 0.7222 (m-80) REVERT: F 300 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7640 (mp0) REVERT: F 301 GLU cc_start: 0.7470 (mt-10) cc_final: 0.6765 (tp30) REVERT: F 303 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6884 (tm-30) REVERT: G 48 ASP cc_start: 0.6964 (t70) cc_final: 0.6729 (t70) REVERT: G 50 GLU cc_start: 0.6833 (mm-30) cc_final: 0.5809 (mp0) REVERT: G 53 MET cc_start: 0.7789 (tpt) cc_final: 0.7531 (tpt) REVERT: G 56 ARG cc_start: 0.7098 (mmm-85) cc_final: 0.6650 (mmt-90) REVERT: G 79 CYS cc_start: 0.7328 (m) cc_final: 0.6905 (m) REVERT: G 96 ARG cc_start: 0.6619 (mmt180) cc_final: 0.6217 (mmp-170) REVERT: G 100 ARG cc_start: 0.7520 (ptp-170) cc_final: 0.7264 (mtt180) REVERT: G 105 ARG cc_start: 0.7233 (ttp80) cc_final: 0.6998 (ttp-170) REVERT: G 127 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7274 (tm-30) REVERT: G 186 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6924 (pt0) REVERT: G 277 LYS cc_start: 0.8403 (ttpt) cc_final: 0.7948 (tttp) REVERT: G 301 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: G 334 GLU cc_start: 0.7608 (tp30) cc_final: 0.7298 (mp0) outliers start: 63 outliers final: 20 residues processed: 405 average time/residue: 0.8653 time to fit residues: 386.9303 Evaluate side-chains 374 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 343 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 186 GLN Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 311 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 179 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 238 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 218 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 234 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 165 optimal weight: 0.0070 chunk 2 optimal weight: 0.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 GLN A 146 GLN A 291 ASN B 172 GLN C 112 GLN C 231 GLN F 91 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.172273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.135235 restraints weight = 18866.282| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.40 r_work: 0.3341 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21300 Z= 0.113 Angle : 0.502 7.448 29114 Z= 0.251 Chirality : 0.037 0.138 3359 Planarity : 0.004 0.045 3618 Dihedral : 14.685 138.925 3303 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.36 % Allowed : 12.66 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.17), residues: 2518 helix: 1.81 (0.15), residues: 1275 sheet: 0.95 (0.24), residues: 442 loop : 0.61 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 246 TYR 0.010 0.001 TYR B 341 PHE 0.011 0.001 PHE F 3 TRP 0.013 0.001 TRP B 10 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (21284) covalent geometry : angle 0.48779 / 0.25 (29090) hydrogen bonds : bond 0.03170 / 2.15 ( 1152) hydrogen bonds : angle 3.68723 / 2.67 ( 3214) metal coordination : bond 0.00222 / 0.12 ( 16) metal coordination : angle 4.10325 / 2.33 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 377 time to evaluate : 0.842 Fit side-chains REVERT: A 107 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7165 (t0) REVERT: A 149 ARG cc_start: 0.7900 (ttp-110) cc_final: 0.7323 (ttp80) REVERT: A 208 ASP cc_start: 0.7699 (t0) cc_final: 0.7366 (t0) REVERT: A 242 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7666 (mm-30) REVERT: A 244 VAL cc_start: 0.8766 (t) cc_final: 0.8430 (p) REVERT: A 286 MET cc_start: 0.7458 (mmm) cc_final: 0.7092 (tpt) REVERT: A 325 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7531 (pt0) REVERT: B 39 HIS cc_start: 0.8273 (m-70) cc_final: 0.7291 (p90) REVERT: B 161 LYS cc_start: 0.8200 (mmpt) cc_final: 0.7498 (mmmt) REVERT: B 172 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8802 (tt0) REVERT: B 208 ARG cc_start: 0.8164 (ttp-110) cc_final: 0.7441 (ttp80) REVERT: B 231 GLN cc_start: 0.8230 (mt0) cc_final: 0.7830 (mt0) REVERT: B 245 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6804 (t0) REVERT: B 284 GLU cc_start: 0.8215 (tt0) cc_final: 0.7815 (mt-10) REVERT: B 350 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8576 (mt-10) REVERT: C 110 ASN cc_start: 0.8685 (m-40) cc_final: 0.8471 (m110) REVERT: C 193 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7834 (mm-30) REVERT: C 258 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6862 (mm-30) REVERT: C 284 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7575 (mp0) REVERT: C 345 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8112 (mtt-85) REVERT: D 14 THR cc_start: 0.8026 (m) cc_final: 0.7746 (p) REVERT: D 141 LYS cc_start: 0.8489 (tptp) cc_final: 0.7914 (mptm) REVERT: D 161 LYS cc_start: 0.8342 (mtpt) cc_final: 0.7892 (mtpp) REVERT: D 204 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.7159 (mp10) REVERT: D 247 ASP cc_start: 0.7336 (p0) cc_final: 0.7035 (OUTLIER) REVERT: D 315 GLU cc_start: 0.7569 (tp30) cc_final: 0.7286 (tm-30) REVERT: E 46 ARG cc_start: 0.7856 (mmm-85) cc_final: 0.7628 (mmm-85) REVERT: F 64 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7522 (tt0) REVERT: F 198 LYS cc_start: 0.8283 (mtpt) cc_final: 0.7312 (mptt) REVERT: F 221 ASN cc_start: 0.8561 (m110) cc_final: 0.8324 (m-40) REVERT: F 230 PHE cc_start: 0.7481 (m-80) cc_final: 0.6958 (m-80) REVERT: F 279 ARG cc_start: 0.7516 (mmm160) cc_final: 0.7088 (mmm160) REVERT: F 284 TYR cc_start: 0.7628 (m-80) cc_final: 0.7153 (m-80) REVERT: F 300 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7510 (mp0) REVERT: F 301 GLU cc_start: 0.7533 (mt-10) cc_final: 0.6749 (tp30) REVERT: F 303 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6764 (tm-30) REVERT: G 36 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6920 (mp10) REVERT: G 48 ASP cc_start: 0.6931 (t70) cc_final: 0.6636 (t70) REVERT: G 50 GLU cc_start: 0.6754 (mm-30) cc_final: 0.5713 (mp0) REVERT: G 53 MET cc_start: 0.7657 (tpt) cc_final: 0.7298 (tpt) REVERT: G 56 ARG cc_start: 0.7117 (mmm-85) cc_final: 0.6564 (mmt-90) REVERT: G 79 CYS cc_start: 0.7303 (m) cc_final: 0.6824 (m) REVERT: G 96 ARG cc_start: 0.6511 (mmt180) cc_final: 0.6105 (mmp-170) REVERT: G 105 ARG cc_start: 0.7123 (ttp80) cc_final: 0.6888 (ttp-170) REVERT: G 127 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7255 (tm-30) REVERT: G 277 LYS cc_start: 0.8370 (ttpt) cc_final: 0.7855 (tttp) REVERT: G 301 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7090 (tm-30) REVERT: G 334 GLU cc_start: 0.7543 (tp30) cc_final: 0.7047 (tm-30) REVERT: J 6 ASP cc_start: 0.8005 (m-30) cc_final: 0.7643 (m-30) outliers start: 50 outliers final: 16 residues processed: 403 average time/residue: 0.8492 time to fit residues: 377.6159 Evaluate side-chains 377 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 355 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 306 MET Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 311 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 80 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 245 optimal weight: 0.2980 chunk 114 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 64 optimal weight: 0.0170 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 146 GLN B 172 GLN C 78 ASN C 112 GLN C 137 ASN C 231 GLN D 137 ASN F 91 GLN G 186 GLN G 295 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.185582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.151889 restraints weight = 19470.365| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.37 r_work: 0.3645 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21300 Z= 0.103 Angle : 0.482 6.653 29114 Z= 0.242 Chirality : 0.036 0.157 3359 Planarity : 0.004 0.045 3618 Dihedral : 14.583 139.058 3303 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.55 % Allowed : 13.42 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.17), residues: 2518 helix: 2.01 (0.15), residues: 1276 sheet: 1.12 (0.24), residues: 430 loop : 0.66 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 201 TYR 0.009 0.001 TYR B 341 PHE 0.011 0.001 PHE F 3 TRP 0.013 0.001 TRP B 10 HIS 0.004 0.000 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (21284) covalent geometry : angle 0.46981 / 0.24 (29090) hydrogen bonds : bond 0.02929 / 1.98 ( 1152) hydrogen bonds : angle 3.57188 / 2.60 ( 3214) metal coordination : bond 0.00180 / 0.10 ( 16) metal coordination : angle 3.85233 / 2.17 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 372 time to evaluate : 0.921 Fit side-chains REVERT: A 12 GLN cc_start: 0.7338 (tm-30) cc_final: 0.7030 (tm130) REVERT: A 107 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.6968 (t0) REVERT: A 149 ARG cc_start: 0.7933 (ttp-110) cc_final: 0.7463 (ttp80) REVERT: A 208 ASP cc_start: 0.7582 (t0) cc_final: 0.7348 (t0) REVERT: A 242 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7589 (mm-30) REVERT: A 286 MET cc_start: 0.7611 (mmm) cc_final: 0.7280 (tpt) REVERT: A 325 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7515 (pt0) REVERT: B 39 HIS cc_start: 0.8318 (m-70) cc_final: 0.7501 (p90) REVERT: B 161 LYS cc_start: 0.8209 (mmpt) cc_final: 0.7538 (mmmt) REVERT: B 208 ARG cc_start: 0.8158 (ttp-110) cc_final: 0.7737 (tpp-160) REVERT: B 231 GLN cc_start: 0.8246 (mt0) cc_final: 0.7869 (tt0) REVERT: B 245 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6805 (t0) REVERT: B 279 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: B 284 GLU cc_start: 0.8057 (tt0) cc_final: 0.7763 (mt-10) REVERT: B 318 ARG cc_start: 0.7684 (ttm110) cc_final: 0.7353 (ttm110) REVERT: C 110 ASN cc_start: 0.8689 (m-40) cc_final: 0.8489 (m110) REVERT: C 193 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7798 (mm-30) REVERT: C 258 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7033 (mm-30) REVERT: C 284 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7543 (mp0) REVERT: D 112 GLN cc_start: 0.8405 (pt0) cc_final: 0.7992 (pm20) REVERT: D 141 LYS cc_start: 0.8583 (tptp) cc_final: 0.7993 (mptm) REVERT: D 161 LYS cc_start: 0.8375 (mtpt) cc_final: 0.7990 (mtpp) REVERT: D 247 ASP cc_start: 0.7341 (p0) cc_final: 0.7089 (p0) REVERT: D 315 GLU cc_start: 0.7690 (tp30) cc_final: 0.7429 (tm-30) REVERT: E 46 ARG cc_start: 0.7957 (mmm-85) cc_final: 0.7754 (mmm-85) REVERT: F 64 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7545 (tt0) REVERT: F 198 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7520 (mptt) REVERT: F 206 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7902 (mtm) REVERT: F 227 VAL cc_start: 0.8591 (t) cc_final: 0.8271 (p) REVERT: F 230 PHE cc_start: 0.7597 (m-80) cc_final: 0.7001 (m-80) REVERT: F 279 ARG cc_start: 0.7593 (mmm160) cc_final: 0.7352 (mmm160) REVERT: F 284 TYR cc_start: 0.7722 (m-80) cc_final: 0.7278 (m-80) REVERT: F 300 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7624 (mp0) REVERT: F 301 GLU cc_start: 0.7498 (mt-10) cc_final: 0.6845 (tp30) REVERT: F 303 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6832 (tm-30) REVERT: F 316 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6836 (tm-30) REVERT: G 48 ASP cc_start: 0.6974 (t70) cc_final: 0.6644 (t70) REVERT: G 50 GLU cc_start: 0.6778 (mm-30) cc_final: 0.5915 (mp0) REVERT: G 53 MET cc_start: 0.7706 (tpt) cc_final: 0.7432 (tpt) REVERT: G 56 ARG cc_start: 0.7155 (mmm-85) cc_final: 0.6694 (mmt-90) REVERT: G 79 CYS cc_start: 0.7353 (m) cc_final: 0.6917 (m) REVERT: G 96 ARG cc_start: 0.6597 (mmt180) cc_final: 0.6255 (mmp-170) REVERT: G 100 ARG cc_start: 0.7781 (mtt180) cc_final: 0.7502 (mtt-85) REVERT: G 127 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7339 (tm-30) REVERT: G 169 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8293 (t) REVERT: G 203 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7858 (tt) REVERT: G 277 LYS cc_start: 0.8428 (ttpt) cc_final: 0.7946 (tttp) REVERT: G 301 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7195 (tm-30) REVERT: G 334 GLU cc_start: 0.7518 (tp30) cc_final: 0.7091 (tm-30) outliers start: 54 outliers final: 13 residues processed: 400 average time/residue: 0.8217 time to fit residues: 363.2709 Evaluate side-chains 378 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 357 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 301 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 250 optimal weight: 4.9990 chunk 113 optimal weight: 0.4980 chunk 187 optimal weight: 0.9980 chunk 202 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 227 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 210 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 146 GLN B 172 GLN C 112 GLN C 231 GLN F 91 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.172814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.135687 restraints weight = 18890.141| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.40 r_work: 0.3326 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21300 Z= 0.116 Angle : 0.495 7.544 29114 Z= 0.248 Chirality : 0.037 0.151 3359 Planarity : 0.004 0.046 3618 Dihedral : 14.603 139.642 3303 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.46 % Allowed : 14.22 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.17), residues: 2518 helix: 2.02 (0.15), residues: 1275 sheet: 1.15 (0.24), residues: 430 loop : 0.66 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 263 TYR 0.009 0.001 TYR B 341 PHE 0.011 0.001 PHE F 3 TRP 0.011 0.001 TRP B 10 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (21284) covalent geometry : angle 0.48378 / 0.25 (29090) hydrogen bonds : bond 0.03029 / 2.05 ( 1152) hydrogen bonds : angle 3.54674 / 2.58 ( 3214) metal coordination : bond 0.00200 / 0.11 ( 16) metal coordination : angle 3.73114 / 2.10 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 375 time to evaluate : 0.897 Fit side-chains REVERT: A 12 GLN cc_start: 0.7093 (tm-30) cc_final: 0.6828 (tm-30) REVERT: A 14 ASN cc_start: 0.8022 (m-40) cc_final: 0.7770 (m-40) REVERT: A 107 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7171 (t0) REVERT: A 149 ARG cc_start: 0.7878 (ttp-110) cc_final: 0.7275 (ttp80) REVERT: A 208 ASP cc_start: 0.7693 (t0) cc_final: 0.7373 (t0) REVERT: A 242 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7677 (mm-30) REVERT: A 244 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8366 (p) REVERT: A 286 MET cc_start: 0.7468 (mmm) cc_final: 0.7120 (tpt) REVERT: A 325 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7537 (pt0) REVERT: B 39 HIS cc_start: 0.8296 (m-70) cc_final: 0.7313 (p90) REVERT: B 124 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8455 (tt) REVERT: B 126 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8372 (t0) REVERT: B 161 LYS cc_start: 0.8227 (mmpt) cc_final: 0.7496 (mmmt) REVERT: B 208 ARG cc_start: 0.8180 (ttp-110) cc_final: 0.7682 (tpp-160) REVERT: B 231 GLN cc_start: 0.8256 (mt0) cc_final: 0.7823 (tt0) REVERT: B 245 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6757 (t0) REVERT: B 279 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: B 284 GLU cc_start: 0.8249 (tt0) cc_final: 0.7867 (mt-10) REVERT: B 318 ARG cc_start: 0.7819 (ttm110) cc_final: 0.7520 (ttm110) REVERT: B 327 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8246 (tp) REVERT: C 110 ASN cc_start: 0.8689 (m-40) cc_final: 0.8468 (m110) REVERT: C 193 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7855 (mm-30) REVERT: C 258 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6963 (mm-30) REVERT: C 284 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7523 (mp0) REVERT: D 112 GLN cc_start: 0.8349 (pt0) cc_final: 0.7876 (pm20) REVERT: D 141 LYS cc_start: 0.8480 (tptp) cc_final: 0.7895 (mptm) REVERT: D 161 LYS cc_start: 0.8320 (mtpt) cc_final: 0.7892 (mtpp) REVERT: D 247 ASP cc_start: 0.7342 (p0) cc_final: 0.7089 (p0) REVERT: D 315 GLU cc_start: 0.7630 (tp30) cc_final: 0.7358 (tm-30) REVERT: E 46 ARG cc_start: 0.7888 (mmm-85) cc_final: 0.7647 (mmm-85) REVERT: F 64 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7446 (tt0) REVERT: F 166 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6900 (tt0) REVERT: F 198 LYS cc_start: 0.8267 (mtpt) cc_final: 0.7324 (mptt) REVERT: F 206 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7803 (mtm) REVERT: F 221 ASN cc_start: 0.8519 (m110) cc_final: 0.8308 (m-40) REVERT: F 227 VAL cc_start: 0.8489 (t) cc_final: 0.8145 (p) REVERT: F 230 PHE cc_start: 0.7687 (m-80) cc_final: 0.6906 (m-80) REVERT: F 235 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8275 (mtmt) REVERT: F 279 ARG cc_start: 0.7527 (mmm160) cc_final: 0.7239 (mmm160) REVERT: F 284 TYR cc_start: 0.7627 (m-80) cc_final: 0.7191 (m-80) REVERT: F 300 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7731 (mp0) REVERT: F 301 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6721 (tp30) REVERT: F 303 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6781 (tm-30) REVERT: F 316 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6778 (tm-30) REVERT: G 48 ASP cc_start: 0.7000 (t70) cc_final: 0.6513 (t70) REVERT: G 50 GLU cc_start: 0.6717 (mm-30) cc_final: 0.5769 (mp0) REVERT: G 53 MET cc_start: 0.7617 (tpt) cc_final: 0.7309 (tpt) REVERT: G 56 ARG cc_start: 0.7037 (mmm-85) cc_final: 0.6505 (mmt-90) REVERT: G 79 CYS cc_start: 0.7269 (m) cc_final: 0.6850 (m) REVERT: G 96 ARG cc_start: 0.6460 (mmt180) cc_final: 0.6051 (mmp-170) REVERT: G 100 ARG cc_start: 0.7728 (mtt180) cc_final: 0.7416 (mtt-85) REVERT: G 105 ARG cc_start: 0.7126 (ttp80) cc_final: 0.6864 (ttp-170) REVERT: G 127 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7265 (tm-30) REVERT: G 169 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8220 (t) REVERT: G 198 LYS cc_start: 0.7947 (mttp) cc_final: 0.7436 (tttm) REVERT: G 203 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7688 (tt) REVERT: G 277 LYS cc_start: 0.8394 (ttpt) cc_final: 0.7890 (tttp) REVERT: G 301 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: G 334 GLU cc_start: 0.7528 (tp30) cc_final: 0.7013 (tm-30) outliers start: 52 outliers final: 20 residues processed: 401 average time/residue: 0.8039 time to fit residues: 358.0044 Evaluate side-chains 390 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 357 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 311 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 142 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 175 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 146 GLN B 172 GLN C 78 ASN C 112 GLN C 137 ASN C 231 GLN F 91 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.182135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.147535 restraints weight = 19548.065| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.50 r_work: 0.3594 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21300 Z= 0.182 Angle : 0.568 7.729 29114 Z= 0.281 Chirality : 0.040 0.186 3359 Planarity : 0.004 0.045 3618 Dihedral : 14.739 140.098 3303 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.65 % Allowed : 14.36 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.17), residues: 2518 helix: 1.74 (0.15), residues: 1279 sheet: 1.17 (0.24), residues: 428 loop : 0.56 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 263 TYR 0.015 0.001 TYR F 153 PHE 0.012 0.001 PHE G 3 TRP 0.009 0.001 TRP B 10 HIS 0.005 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (21284) covalent geometry : angle 0.55779 / 0.28 (29090) hydrogen bonds : bond 0.03672 / 2.49 ( 1152) hydrogen bonds : angle 3.69074 / 2.68 ( 3214) metal coordination : bond 0.00264 / 0.15 ( 16) metal coordination : angle 3.80665 / 2.18 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 361 time to evaluate : 0.841 Fit side-chains REVERT: A 1 MET cc_start: 0.5625 (mpm) cc_final: 0.5212 (mmt) REVERT: A 12 GLN cc_start: 0.7376 (tm-30) cc_final: 0.7094 (tm-30) REVERT: A 14 ASN cc_start: 0.8104 (m-40) cc_final: 0.7846 (m-40) REVERT: A 107 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7041 (t0) REVERT: A 149 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7421 (ttp80) REVERT: A 156 LYS cc_start: 0.7788 (mtmt) cc_final: 0.7582 (tmtm) REVERT: A 208 ASP cc_start: 0.7681 (t0) cc_final: 0.7444 (t0) REVERT: A 242 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7698 (mm-30) REVERT: A 244 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8481 (p) REVERT: A 286 MET cc_start: 0.7621 (mmm) cc_final: 0.7310 (tpt) REVERT: B 39 HIS cc_start: 0.8381 (m-70) cc_final: 0.7487 (p90) REVERT: B 110 ASN cc_start: 0.8057 (OUTLIER) cc_final: 0.7718 (m-40) REVERT: B 124 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8528 (tt) REVERT: B 126 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8325 (t70) REVERT: B 161 LYS cc_start: 0.8334 (mmpt) cc_final: 0.7633 (mmmt) REVERT: B 208 ARG cc_start: 0.8188 (ttp-110) cc_final: 0.7720 (ttm-80) REVERT: B 231 GLN cc_start: 0.8365 (mt0) cc_final: 0.7955 (tt0) REVERT: B 279 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: B 284 GLU cc_start: 0.8090 (tt0) cc_final: 0.7760 (mt-10) REVERT: B 344 ASP cc_start: 0.8045 (t0) cc_final: 0.7656 (t0) REVERT: C 193 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7850 (mm-30) REVERT: C 258 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7138 (mm-30) REVERT: C 284 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7620 (mp0) REVERT: D 112 GLN cc_start: 0.8402 (pt0) cc_final: 0.7991 (pm20) REVERT: D 133 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8291 (ttm110) REVERT: D 141 LYS cc_start: 0.8641 (tptp) cc_final: 0.8073 (mptm) REVERT: D 161 LYS cc_start: 0.8348 (mtpt) cc_final: 0.7981 (mtpp) REVERT: D 247 ASP cc_start: 0.7417 (p0) cc_final: 0.7161 (p0) REVERT: D 315 GLU cc_start: 0.7673 (tp30) cc_final: 0.7418 (tm-30) REVERT: E 46 ARG cc_start: 0.7997 (mmm-85) cc_final: 0.7696 (mmm-85) REVERT: E 276 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7685 (tt0) REVERT: F 64 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7542 (tt0) REVERT: F 150 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7085 (t0) REVERT: F 165 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7282 (tt0) REVERT: F 198 LYS cc_start: 0.8423 (mtpt) cc_final: 0.7552 (mptt) REVERT: F 227 VAL cc_start: 0.8572 (t) cc_final: 0.8298 (p) REVERT: F 284 TYR cc_start: 0.7763 (m-80) cc_final: 0.7484 (m-80) REVERT: F 301 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6815 (tp30) REVERT: F 303 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7011 (tm-30) REVERT: F 316 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6883 (tm-30) REVERT: G 48 ASP cc_start: 0.7082 (t70) cc_final: 0.6793 (t70) REVERT: G 50 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6049 (mp0) REVERT: G 56 ARG cc_start: 0.7153 (mmm-85) cc_final: 0.6568 (mmt-90) REVERT: G 79 CYS cc_start: 0.7378 (m) cc_final: 0.7014 (m) REVERT: G 96 ARG cc_start: 0.6458 (mmt180) cc_final: 0.6094 (mmp-170) REVERT: G 100 ARG cc_start: 0.7885 (mtt180) cc_final: 0.7659 (mtt-85) REVERT: G 105 ARG cc_start: 0.7260 (ttp80) cc_final: 0.7049 (ttp-170) REVERT: G 127 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7336 (tm-30) REVERT: G 169 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8192 (t) REVERT: G 198 LYS cc_start: 0.8122 (mttp) cc_final: 0.7660 (tttm) REVERT: G 203 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7854 (tt) REVERT: G 223 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7979 (mt) REVERT: G 277 LYS cc_start: 0.8446 (ttpt) cc_final: 0.8051 (tttm) REVERT: G 301 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: G 334 GLU cc_start: 0.7632 (tp30) cc_final: 0.7168 (tm-30) outliers start: 56 outliers final: 24 residues processed: 394 average time/residue: 0.8183 time to fit residues: 357.1044 Evaluate side-chains 379 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 341 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 311 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 GLN A 146 GLN B 172 GLN C 112 GLN C 231 GLN D 160 GLN F 91 GLN F 149 GLN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.183010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.148787 restraints weight = 19359.213| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.48 r_work: 0.3608 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21300 Z= 0.146 Angle : 0.540 8.498 29114 Z= 0.268 Chirality : 0.038 0.140 3359 Planarity : 0.004 0.067 3618 Dihedral : 14.643 139.672 3303 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.36 % Allowed : 15.21 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.17), residues: 2518 helix: 1.79 (0.15), residues: 1279 sheet: 1.13 (0.24), residues: 428 loop : 0.57 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 86 TYR 0.014 0.001 TYR B 341 PHE 0.014 0.001 PHE B 173 TRP 0.012 0.001 TRP B 10 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (21284) covalent geometry : angle 0.52587 / 0.27 (29090) hydrogen bonds : bond 0.03356 / 2.27 ( 1152) hydrogen bonds : angle 3.63798 / 2.64 ( 3214) metal coordination : bond 0.00564 / 0.20 ( 16) metal coordination : angle 4.30558 / 2.44 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 348 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5611 (mpm) cc_final: 0.5150 (mmt) REVERT: A 12 GLN cc_start: 0.7341 (tm-30) cc_final: 0.7030 (tm-30) REVERT: A 14 ASN cc_start: 0.8176 (m-40) cc_final: 0.7921 (m-40) REVERT: A 107 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.6976 (t0) REVERT: A 149 ARG cc_start: 0.7946 (ttp-110) cc_final: 0.7463 (ttp80) REVERT: A 156 LYS cc_start: 0.7788 (mtmt) cc_final: 0.7575 (tmtm) REVERT: A 208 ASP cc_start: 0.7667 (t0) cc_final: 0.7409 (t0) REVERT: A 242 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7661 (mm-30) REVERT: A 244 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8461 (p) REVERT: A 286 MET cc_start: 0.7567 (mmm) cc_final: 0.7259 (tpt) REVERT: A 325 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7619 (pt0) REVERT: B 39 HIS cc_start: 0.8368 (m-70) cc_final: 0.7495 (p90) REVERT: B 86 ARG cc_start: 0.7902 (mtp-110) cc_final: 0.7377 (mtt-85) REVERT: B 110 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7721 (m-40) REVERT: B 126 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8352 (t70) REVERT: B 161 LYS cc_start: 0.8369 (mmpt) cc_final: 0.7671 (mmmt) REVERT: B 208 ARG cc_start: 0.8182 (ttp-110) cc_final: 0.7473 (ttp80) REVERT: B 231 GLN cc_start: 0.8353 (mt0) cc_final: 0.7952 (tt0) REVERT: B 279 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: B 284 GLU cc_start: 0.8031 (tt0) cc_final: 0.7724 (mt-10) REVERT: B 344 ASP cc_start: 0.7937 (t0) cc_final: 0.7538 (t70) REVERT: C 84 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.7151 (mt0) REVERT: C 193 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7868 (mm-30) REVERT: C 258 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7119 (mm-30) REVERT: C 284 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7613 (mp0) REVERT: D 112 GLN cc_start: 0.8393 (pt0) cc_final: 0.7983 (pm20) REVERT: D 141 LYS cc_start: 0.8639 (tptp) cc_final: 0.8045 (mptm) REVERT: D 161 LYS cc_start: 0.8331 (mtpt) cc_final: 0.7954 (mtpp) REVERT: D 247 ASP cc_start: 0.7407 (p0) cc_final: 0.7164 (p0) REVERT: D 315 GLU cc_start: 0.7682 (tp30) cc_final: 0.7429 (tm-30) REVERT: F 64 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7528 (tt0) REVERT: F 150 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7139 (t0) REVERT: F 165 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7160 (tt0) REVERT: F 198 LYS cc_start: 0.8400 (mtpt) cc_final: 0.7559 (mptt) REVERT: F 227 VAL cc_start: 0.8598 (t) cc_final: 0.8331 (p) REVERT: F 230 PHE cc_start: 0.7625 (m-80) cc_final: 0.7019 (m-80) REVERT: F 284 TYR cc_start: 0.7762 (m-80) cc_final: 0.7508 (m-80) REVERT: F 300 GLU cc_start: 0.7997 (mp0) cc_final: 0.7546 (mp0) REVERT: F 301 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6912 (tp30) REVERT: F 303 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7018 (tm-30) REVERT: F 316 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6909 (tm-30) REVERT: G 48 ASP cc_start: 0.7096 (t70) cc_final: 0.6851 (t70) REVERT: G 50 GLU cc_start: 0.6878 (mm-30) cc_final: 0.6087 (mp0) REVERT: G 56 ARG cc_start: 0.7083 (mmm-85) cc_final: 0.6533 (mmt180) REVERT: G 79 CYS cc_start: 0.7362 (m) cc_final: 0.7015 (m) REVERT: G 96 ARG cc_start: 0.6425 (mmt180) cc_final: 0.6075 (mmp-170) REVERT: G 100 ARG cc_start: 0.7865 (mtt180) cc_final: 0.7660 (mtt-85) REVERT: G 127 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7312 (tm-30) REVERT: G 169 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8175 (t) REVERT: G 198 LYS cc_start: 0.8120 (mttp) cc_final: 0.7709 (tttm) REVERT: G 203 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7874 (tt) REVERT: G 277 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8061 (tttm) REVERT: G 301 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: G 334 GLU cc_start: 0.7657 (tp30) cc_final: 0.7212 (tm-30) outliers start: 50 outliers final: 23 residues processed: 375 average time/residue: 0.8188 time to fit residues: 339.9675 Evaluate side-chains 386 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 351 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 311 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 88 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 20 optimal weight: 0.0670 chunk 65 optimal weight: 0.9980 chunk 209 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 146 GLN B 172 GLN C 78 ASN C 110 ASN C 112 GLN C 231 GLN D 160 GLN F 118 ASN F 149 GLN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.183408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.148899 restraints weight = 19498.178| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.41 r_work: 0.3626 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21300 Z= 0.134 Angle : 0.528 7.659 29114 Z= 0.263 Chirality : 0.038 0.136 3359 Planarity : 0.004 0.056 3618 Dihedral : 14.590 139.682 3303 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.13 % Allowed : 15.40 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.17), residues: 2518 helix: 1.84 (0.15), residues: 1281 sheet: 1.12 (0.24), residues: 428 loop : 0.59 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 86 TYR 0.014 0.001 TYR B 341 PHE 0.012 0.001 PHE F 3 TRP 0.012 0.001 TRP B 10 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (21284) covalent geometry : angle 0.51478 / 0.26 (29090) hydrogen bonds : bond 0.03236 / 2.19 ( 1152) hydrogen bonds : angle 3.59988 / 2.62 ( 3214) metal coordination : bond 0.00428 / 0.16 ( 16) metal coordination : angle 4.06238 / 2.31 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 357 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5581 (mpm) cc_final: 0.5125 (mmt) REVERT: A 12 GLN cc_start: 0.7298 (tm-30) cc_final: 0.6945 (tm-30) REVERT: A 14 ASN cc_start: 0.8169 (m-40) cc_final: 0.7915 (m-40) REVERT: A 107 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.6938 (t0) REVERT: A 149 ARG cc_start: 0.7911 (ttp-110) cc_final: 0.7426 (ttp80) REVERT: A 156 LYS cc_start: 0.7776 (mtmt) cc_final: 0.7567 (tmtm) REVERT: A 208 ASP cc_start: 0.7671 (t0) cc_final: 0.7385 (t0) REVERT: A 242 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7595 (mm-30) REVERT: A 244 VAL cc_start: 0.8763 (OUTLIER) cc_final: 0.8433 (p) REVERT: A 286 MET cc_start: 0.7554 (mmm) cc_final: 0.7256 (tpt) REVERT: A 288 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7258 (mm-30) REVERT: A 325 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7602 (pt0) REVERT: B 39 HIS cc_start: 0.8369 (m-70) cc_final: 0.7504 (p90) REVERT: B 86 ARG cc_start: 0.7906 (mtp-110) cc_final: 0.7399 (mtt-85) REVERT: B 126 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8337 (t70) REVERT: B 161 LYS cc_start: 0.8373 (mmpt) cc_final: 0.7680 (mmmt) REVERT: B 208 ARG cc_start: 0.8140 (ttp-110) cc_final: 0.7463 (ttp80) REVERT: B 231 GLN cc_start: 0.8344 (mt0) cc_final: 0.7949 (tt0) REVERT: B 279 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: B 284 GLU cc_start: 0.8020 (tt0) cc_final: 0.7709 (mt-10) REVERT: C 84 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7155 (mt0) REVERT: C 193 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7850 (mm-30) REVERT: C 258 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7068 (mm-30) REVERT: C 284 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7573 (mp0) REVERT: D 112 GLN cc_start: 0.8378 (pt0) cc_final: 0.7972 (pm20) REVERT: D 141 LYS cc_start: 0.8598 (tptp) cc_final: 0.8025 (mptm) REVERT: D 161 LYS cc_start: 0.8337 (mtpt) cc_final: 0.7967 (mtpp) REVERT: D 247 ASP cc_start: 0.7402 (p0) cc_final: 0.7148 (p0) REVERT: D 315 GLU cc_start: 0.7634 (tp30) cc_final: 0.7382 (tm-30) REVERT: F 64 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7522 (tt0) REVERT: F 165 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7135 (tt0) REVERT: F 166 GLU cc_start: 0.7264 (mt-10) cc_final: 0.7031 (tt0) REVERT: F 198 LYS cc_start: 0.8375 (mtpt) cc_final: 0.7531 (mptt) REVERT: F 227 VAL cc_start: 0.8595 (t) cc_final: 0.8337 (p) REVERT: F 230 PHE cc_start: 0.7712 (m-80) cc_final: 0.7046 (m-80) REVERT: F 284 TYR cc_start: 0.7791 (m-80) cc_final: 0.7565 (m-80) REVERT: F 301 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6823 (tp30) REVERT: F 316 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6906 (tm-30) REVERT: G 48 ASP cc_start: 0.7087 (t70) cc_final: 0.6722 (t70) REVERT: G 50 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6123 (mp0) REVERT: G 56 ARG cc_start: 0.7100 (mmm-85) cc_final: 0.6561 (mmt180) REVERT: G 79 CYS cc_start: 0.7373 (m) cc_final: 0.7032 (m) REVERT: G 96 ARG cc_start: 0.6420 (mmt180) cc_final: 0.6060 (mmp-170) REVERT: G 105 ARG cc_start: 0.7647 (ttp-170) cc_final: 0.7311 (ttp-170) REVERT: G 127 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7308 (tm-30) REVERT: G 169 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8165 (t) REVERT: G 198 LYS cc_start: 0.8118 (mttp) cc_final: 0.7739 (tttm) REVERT: G 202 GLU cc_start: 0.7588 (mm-30) cc_final: 0.6757 (mm-30) REVERT: G 203 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7827 (tt) REVERT: G 223 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7988 (mt) REVERT: G 277 LYS cc_start: 0.8422 (ttpt) cc_final: 0.8020 (tttm) REVERT: G 301 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7174 (tm-30) REVERT: G 334 GLU cc_start: 0.7678 (tp30) cc_final: 0.7258 (tm-30) outliers start: 45 outliers final: 25 residues processed: 382 average time/residue: 0.8036 time to fit residues: 339.5809 Evaluate side-chains 373 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 337 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 337 LYS Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 311 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 68 optimal weight: 0.3980 chunk 117 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 144 optimal weight: 8.9990 chunk 251 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 162 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 GLN A 146 GLN B 172 GLN C 110 ASN C 112 GLN C 231 GLN E 19 GLN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.171944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134822 restraints weight = 18914.905| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.56 r_work: 0.3325 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21300 Z= 0.114 Angle : 0.510 7.528 29114 Z= 0.256 Chirality : 0.037 0.137 3359 Planarity : 0.004 0.052 3618 Dihedral : 14.494 139.245 3303 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.79 % Allowed : 16.01 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.17), residues: 2518 helix: 1.98 (0.15), residues: 1278 sheet: 1.09 (0.24), residues: 440 loop : 0.69 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 86 TYR 0.013 0.001 TYR B 341 PHE 0.010 0.001 PHE F 3 TRP 0.013 0.001 TRP B 10 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (21284) covalent geometry : angle 0.49732 / 0.26 (29090) hydrogen bonds : bond 0.03017 / 2.04 ( 1152) hydrogen bonds : angle 3.54520 / 2.58 ( 3214) metal coordination : bond 0.00377 / 0.14 ( 16) metal coordination : angle 3.97076 / 2.27 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 356 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5526 (mpm) cc_final: 0.5069 (mmt) REVERT: A 14 ASN cc_start: 0.8117 (m-40) cc_final: 0.7873 (m-40) REVERT: A 107 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7120 (t0) REVERT: A 149 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7309 (ttp80) REVERT: A 156 LYS cc_start: 0.7758 (mtmt) cc_final: 0.7428 (tmtm) REVERT: A 208 ASP cc_start: 0.7773 (t0) cc_final: 0.7455 (t0) REVERT: A 242 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7682 (mm-30) REVERT: A 244 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8365 (p) REVERT: A 286 MET cc_start: 0.7519 (mmm) cc_final: 0.7206 (tpt) REVERT: A 288 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7222 (mm-30) REVERT: B 39 HIS cc_start: 0.8363 (m-70) cc_final: 0.7363 (p90) REVERT: B 86 ARG cc_start: 0.7807 (mtp-110) cc_final: 0.7227 (mtt-85) REVERT: B 126 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8370 (t0) REVERT: B 161 LYS cc_start: 0.8316 (mmpt) cc_final: 0.7558 (mmmt) REVERT: B 208 ARG cc_start: 0.8217 (ttp-110) cc_final: 0.7450 (ttp80) REVERT: B 231 GLN cc_start: 0.8328 (mt0) cc_final: 0.7801 (tt0) REVERT: B 284 GLU cc_start: 0.8274 (tt0) cc_final: 0.7881 (mt-10) REVERT: C 193 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7881 (mm-30) REVERT: C 258 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6992 (mm-30) REVERT: C 284 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7597 (mp0) REVERT: D 112 GLN cc_start: 0.8335 (pt0) cc_final: 0.7882 (pm20) REVERT: D 141 LYS cc_start: 0.8531 (tptp) cc_final: 0.7931 (mptm) REVERT: D 161 LYS cc_start: 0.8339 (mtpt) cc_final: 0.7916 (mtpp) REVERT: D 247 ASP cc_start: 0.7445 (p0) cc_final: 0.7200 (p0) REVERT: D 315 GLU cc_start: 0.7646 (tp30) cc_final: 0.7371 (tm-30) REVERT: F 64 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7442 (tt0) REVERT: F 166 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6984 (tt0) REVERT: F 198 LYS cc_start: 0.8328 (mtpt) cc_final: 0.7393 (mptt) REVERT: F 227 VAL cc_start: 0.8531 (t) cc_final: 0.8261 (p) REVERT: F 230 PHE cc_start: 0.7662 (m-80) cc_final: 0.6857 (m-80) REVERT: F 284 TYR cc_start: 0.7745 (m-80) cc_final: 0.7444 (m-80) REVERT: F 298 GLU cc_start: 0.7610 (mp0) cc_final: 0.7236 (mm-30) REVERT: F 301 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6818 (tp30) REVERT: F 316 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6906 (tm-30) REVERT: F 338 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7392 (mtt) REVERT: G 12 LYS cc_start: 0.7022 (mmmt) cc_final: 0.6762 (mppt) REVERT: G 48 ASP cc_start: 0.7020 (t70) cc_final: 0.6627 (t70) REVERT: G 50 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6010 (mp0) REVERT: G 56 ARG cc_start: 0.7135 (mmm-85) cc_final: 0.6524 (mmt180) REVERT: G 79 CYS cc_start: 0.7330 (m) cc_final: 0.6924 (m) REVERT: G 96 ARG cc_start: 0.6361 (mmt180) cc_final: 0.5921 (mmp-170) REVERT: G 127 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7153 (tm-30) REVERT: G 169 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8133 (t) REVERT: G 198 LYS cc_start: 0.8047 (mttp) cc_final: 0.7675 (tttm) REVERT: G 202 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6554 (mm-30) REVERT: G 203 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7738 (tt) REVERT: G 277 LYS cc_start: 0.8399 (ttpt) cc_final: 0.7956 (tttm) REVERT: G 301 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: G 334 GLU cc_start: 0.7729 (tp30) cc_final: 0.7270 (tm-30) outliers start: 38 outliers final: 24 residues processed: 378 average time/residue: 0.8016 time to fit residues: 335.6630 Evaluate side-chains 371 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 339 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 337 LYS Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 204 MET Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 311 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 224 optimal weight: 2.9990 chunk 122 optimal weight: 0.2980 chunk 146 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 201 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 144 GLN A 146 GLN A 204 GLN C 78 ASN C 110 ASN C 112 GLN C 231 GLN E 19 GLN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.184270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.150411 restraints weight = 19428.653| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.47 r_work: 0.3627 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 21300 Z= 0.147 Angle : 0.682 59.200 29114 Z= 0.377 Chirality : 0.039 0.505 3359 Planarity : 0.004 0.048 3618 Dihedral : 14.493 139.288 3303 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.65 % Allowed : 16.53 % Favored : 81.81 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.17), residues: 2518 helix: 1.98 (0.15), residues: 1278 sheet: 1.10 (0.24), residues: 441 loop : 0.69 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 86 TYR 0.013 0.001 TYR B 341 PHE 0.023 0.001 PHE B 173 TRP 0.012 0.001 TRP B 10 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (21284) covalent geometry : angle 0.67242 / 0.38 (29090) hydrogen bonds : bond 0.03055 / 2.07 ( 1152) hydrogen bonds : angle 3.54965 / 2.59 ( 3214) metal coordination : bond 0.00375 / 0.15 ( 16) metal coordination : angle 3.95334 / 2.26 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10210.35 seconds wall clock time: 173 minutes 42.57 seconds (10422.57 seconds total)