Starting phenix.real_space_refine on Sat Jul 4 13:51:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyj_71023/07_2026/9oyj_71023.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyj_71023/07_2026/9oyj_71023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oyj_71023/07_2026/9oyj_71023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyj_71023/07_2026/9oyj_71023.map" model { file = "/net/cci-nas-00/data/ceres_data/9oyj_71023/07_2026/9oyj_71023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyj_71023/07_2026/9oyj_71023.cif" } resolution = 2.53 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= 0.019 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 111 5.16 5 C 12924 2.51 5 N 3719 2.21 5 O 3978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20794 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: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2840 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 16, 'TRANS': 348} 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: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2799 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain: "E" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2602 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "F" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2835 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 20, 'TRANS': 344} 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 78.473 85.516 114.109 1.00 65.01 S ATOM 3269 SG CYS B 73 82.139 84.866 114.254 1.00 74.65 S ATOM 3286 SG CYS B 76 79.912 81.916 114.818 1.00 66.92 S ATOM 3308 SG CYS B 79 79.934 83.222 111.417 1.00 61.50 S ATOM 6049 SG CYS C 64 100.966 55.837 86.770 1.00 51.28 S ATOM 6109 SG CYS C 73 102.510 53.076 84.666 1.00 54.02 S ATOM 6126 SG CYS C 76 99.693 52.081 86.990 1.00 51.70 S ATOM 6148 SG CYS C 79 98.843 54.178 84.141 1.00 43.77 S ATOM 8914 SG CYS D 64 78.219 28.276 56.433 1.00 64.99 S ATOM 8974 SG CYS D 73 76.316 25.909 54.227 1.00 73.81 S ATOM 8991 SG CYS D 76 75.160 26.233 57.812 1.00 75.73 S ATOM 9013 SG CYS D 79 74.573 29.104 55.675 1.00 52.65 S ATOM 11637 SG CYS E 50 32.185 34.266 50.176 1.00 45.18 S ATOM 11706 SG CYS E 59 28.640 33.360 50.958 1.00 57.98 S ATOM 11726 SG CYS E 62 30.853 33.906 53.884 1.00 55.74 S ATOM 11747 SG CYS E 65 30.018 36.904 51.785 1.00 50.93 S Time building chain proxies: 4.85, per 1000 atoms: 0.23 Number of scatterers: 20794 At special positions: 0 Unit cell: (112.608, 123.372, 151.524, 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 111 16.00 P 55 15.00 Mg 3 11.99 O 3978 8.00 N 3719 7.00 C 12924 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: 1.92 Conformation dependent library (CDL) restraints added in 859.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " 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 ZN B 701 " - pdb=" SG CYS B 79 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 79 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 76 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 73 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 64 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 76 " 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 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 62 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 50 " Number of angles added : 24 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 15 sheets defined 55.4% alpha, 14.6% beta 15 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 removed outlier: 3.529A pdb=" N GLN A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 44 Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.720A pdb=" N GLY A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 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 206 removed outlier: 3.756A pdb=" N ALA A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 225 through 239 Processing helix chain 'A' and resid 242 through 264 removed outlier: 3.683A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' 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 338 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: 4.153A 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 99 removed outlier: 3.804A pdb=" N THR B 99 " --> pdb=" O ALA B 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 96 through 99' Processing helix chain 'B' and resid 100 through 110 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 132 through 145 removed outlier: 3.791A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 163 through 169 removed outlier: 3.962A pdb=" N LEU B 167 " --> pdb=" O VAL B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.871A 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 Processing helix chain 'B' and resid 247 through 258 removed outlier: 3.880A pdb=" N SER B 251 " --> pdb=" O ASP B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 277 through 298 Processing helix chain 'B' and resid 299 through 302 removed outlier: 3.651A pdb=" N LEU B 302 " --> pdb=" O PRO B 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 299 through 302' Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.572A pdb=" N MET B 306 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 307 " --> pdb=" O ASN B 304 " (cutoff:3.500A) No H-bonds generated for '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: 3.553A pdb=" N VAL C 18 " --> pdb=" O PHE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 35 Processing helix chain 'C' and resid 50 through 63 Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 100 through 110 removed outlier: 3.632A 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 145 removed outlier: 4.478A pdb=" N LYS C 141 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 163 through 168 Processing helix chain 'C' and resid 179 through 195 Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.896A pdb=" N GLU C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 247 through 258 Processing helix chain 'C' and resid 260 through 275 Processing helix chain 'C' and resid 277 through 298 Processing helix chain 'C' and resid 299 through 302 removed outlier: 4.306A pdb=" N LEU C 302 " --> pdb=" O PRO C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 299 through 302' Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.732A pdb=" N ALA C 307 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ALA C 308 " --> pdb=" O ASP C 305 " (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 removed outlier: 3.535A pdb=" N VAL D 18 " --> pdb=" O PHE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 35 Processing helix chain 'D' and resid 50 through 63 Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 128 through 131 Processing helix chain 'D' and resid 132 through 145 removed outlier: 4.659A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 4.654A 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: 3.626A pdb=" N ARG D 169 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS D 170 " --> pdb=" O ILE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 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 259 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: 4.160A 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 removed outlier: 3.534A pdb=" N ALA D 307 " --> pdb=" O ASN D 304 " (cutoff:3.500A) 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 49 Processing helix chain 'E' and resid 62 through 71 Processing helix chain 'E' and resid 89 through 100 removed outlier: 3.622A pdb=" N VAL E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 128 through 134 Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 152 through 157 Processing helix chain 'E' and resid 168 through 178 removed outlier: 3.519A 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 204 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 261 Processing helix chain 'E' and resid 270 through 281 removed outlier: 3.514A pdb=" N VAL E 274 " --> pdb=" O VAL E 270 " (cutoff:3.500A) 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: 4.173A 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 131 through 143 removed outlier: 3.846A pdb=" N THR F 142 " --> pdb=" O LEU F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 146 No H-bonds generated for 'chain 'F' and resid 144 through 146' Processing helix chain 'F' and resid 196 through 207 removed outlier: 3.611A pdb=" N LEU F 207 " --> pdb=" O LEU F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 247 removed outlier: 3.529A pdb=" N ARG F 246 " --> pdb=" O ASP F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 271 Processing helix chain 'F' and resid 321 through 330 Processing helix chain 'G' and resid 7 through 18 removed outlier: 4.304A 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 71 through 81 removed outlier: 3.651A pdb=" N PHE G 75 " --> pdb=" O PRO G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 141 Processing helix chain 'G' and resid 142 through 146 Processing helix chain 'G' and resid 152 through 155 Processing helix chain 'G' and resid 197 through 207 Processing helix chain 'G' and resid 243 through 248 removed outlier: 3.999A pdb=" N VAL G 247 " --> pdb=" O ASP G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 271 Processing helix chain 'G' and resid 321 through 332 Processing helix chain 'J' and resid 4 through 13 Processing helix chain 'J' and resid 21 through 25 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 6.701A pdb=" N ALA A 20 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL A 137 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A 22 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N CYS A 139 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 24 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 47 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N THR A 79 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU A 49 " --> pdb=" O THR A 79 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N LEU A 81 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N HIS A 51 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU A 83 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE A 53 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 162 removed outlier: 6.169A 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: 3.577A pdb=" N ASP B 126 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYS B 121 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU B 153 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYR B 123 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA B 155 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE B 125 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR B 41 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N THR B 156 " --> pdb=" O TYR B 41 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE B 43 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA B 40 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N PHE B 173 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.095A 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 93 removed outlier: 6.225A pdb=" N LYS C 121 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU C 153 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N TYR C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ALA C 155 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE C 125 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ALA C 40 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N PHE C 173 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU C 42 " --> pdb=" O PHE C 173 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 197 through 198 removed outlier: 6.652A pdb=" N ALA C 197 " --> pdb=" O VAL C 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 90 through 94 removed outlier: 6.099A pdb=" N LYS D 121 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU D 153 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ALA D 155 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE D 125 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY D 45 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA D 40 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N PHE D 173 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU D 42 " --> pdb=" O PHE D 173 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU D 175 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER D 44 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 76 through 79 Processing sheet with id=AA9, first strand: chain 'F' and resid 2 through 6 removed outlier: 3.581A pdb=" N ARG F 96 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU G 301 " --> pdb=" O SER F 107 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN G 295 " --> pdb=" O GLY G 280 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLY G 280 " --> pdb=" O ASN G 295 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.603A pdb=" N ASN F 32 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N THR F 47 " --> pdb=" O ASN F 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 192 through 195 removed outlier: 4.811A pdb=" N GLU F 165 " --> pdb=" O ILE F 184 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 305 through 307 removed outlier: 3.751A pdb=" N MET F 315 " --> pdb=" O VAL F 285 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 2 through 6 Processing sheet with id=AB5, first strand: chain 'G' and resid 67 through 68 Processing sheet with id=AB6, first strand: chain 'G' and resid 309 through 310 removed outlier: 4.329A pdb=" N ASP G 351 " --> pdb=" O ALA G 357 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ALA G 357 " --> pdb=" O ASP G 351 " (cutoff:3.500A) removed outlier: 15.886A pdb=" N SER G 181 " --> pdb=" O THR G 172 " (cutoff:3.500A) removed outlier: 16.026A pdb=" N THR G 172 " --> pdb=" O SER G 181 " (cutoff:3.500A) removed outlier: 14.565A pdb=" N VAL G 170 " --> pdb=" O PRO G 183 " (cutoff:3.500A) removed outlier: 13.605A pdb=" N GLY G 185 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 13.184A pdb=" N ARG G 168 " --> pdb=" O GLY G 185 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N SER G 187 " --> pdb=" O GLU G 166 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLU G 166 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLY G 164 " --> pdb=" O PRO G 189 " (cutoff:3.500A) 1106 hydrogen bonds defined for protein. 3147 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7114 1.36 - 1.51: 5463 1.51 - 1.65: 8498 1.65 - 1.80: 101 1.80 - 1.95: 83 Bond restraints: 21259 Sorted by residual: bond pdb=" O2G AGS B 702 " pdb=" PG AGS B 702 " ideal model delta sigma weight residual 1.604 1.504 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" O2G AGS D 702 " pdb=" PG AGS D 702 " ideal model delta sigma weight residual 1.604 1.507 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" O3B AGS C 702 " pdb=" PB AGS C 702 " ideal model delta sigma weight residual 1.673 1.588 0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" O3A AGS C 702 " pdb=" PA AGS C 702 " ideal model delta sigma weight residual 1.664 1.584 0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" O3B AGS D 702 " pdb=" PB AGS D 702 " ideal model delta sigma weight residual 1.673 1.600 0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 21254 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 28350 1.77 - 3.55: 603 3.55 - 5.32: 71 5.32 - 7.10: 25 7.10 - 8.87: 8 Bond angle restraints: 29057 Sorted by residual: angle pdb=" N3 DT I 16 " pdb=" C4 DT I 16 " pdb=" O4 DT I 16 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT I 4 " pdb=" C4 DT I 4 " pdb=" O4 DT I 4 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT H 25 " pdb=" C4 DT H 25 " pdb=" O4 DT H 25 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT I 8 " pdb=" C4 DT I 8 " pdb=" O4 DT I 8 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT H 27 " pdb=" C4 DT H 27 " pdb=" O4 DT H 27 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 ... (remaining 29052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.84: 12440 31.84 - 63.67: 437 63.67 - 95.51: 26 95.51 - 127.34: 0 127.34 - 159.18: 2 Dihedral angle restraints: 12905 sinusoidal: 5573 harmonic: 7332 Sorted by residual: 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 180.00 158.06 21.94 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA VAL C 19 " pdb=" C VAL C 19 " pdb=" N GLY C 20 " pdb=" CA GLY C 20 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" C4' DT H 26 " pdb=" C3' DT H 26 " pdb=" O3' DT H 26 " pdb=" P DT H 27 " ideal model delta sinusoidal sigma weight residual 220.00 60.82 159.18 1 3.50e+01 8.16e-04 1.52e+01 ... (remaining 12902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 3300 0.114 - 0.227: 34 0.227 - 0.341: 3 0.341 - 0.455: 0 0.455 - 0.568: 12 Chirality restraints: 3349 Sorted by residual: chirality pdb=" P DT H 42 " pdb=" OP1 DT H 42 " pdb=" OP2 DT H 42 " pdb=" O5' DT H 42 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.57 2.00e-01 2.50e+01 8.08e+00 chirality pdb=" P DC H 40 " pdb=" OP1 DC H 40 " pdb=" OP2 DC H 40 " pdb=" O5' DC H 40 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.57 2.00e-01 2.50e+01 7.98e+00 chirality pdb=" P DA I 9 " pdb=" OP1 DA I 9 " pdb=" OP2 DA I 9 " pdb=" O5' DA I 9 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.56 2.00e-01 2.50e+01 7.98e+00 ... (remaining 3346 not shown) Planarity restraints: 3614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 215 " -0.256 9.50e-02 1.11e+02 1.15e-01 8.11e+00 pdb=" NE ARG B 215 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG B 215 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 215 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 215 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 56 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.73e+00 pdb=" N PRO A 57 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 258 " -0.129 9.50e-02 1.11e+02 5.83e-02 2.96e+00 pdb=" NE ARG E 258 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG E 258 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG E 258 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG E 258 " 0.001 2.00e-02 2.50e+03 ... (remaining 3611 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 7 2.48 - 3.09: 13649 3.09 - 3.69: 31650 3.69 - 4.30: 47938 4.30 - 4.90: 79053 Nonbonded interactions: 172297 Sorted by model distance: nonbonded pdb=" OG1 THR C 52 " pdb="MG MG C 703 " model vdw 1.876 2.170 nonbonded pdb=" OG1 THR D 52 " pdb="MG MG D 703 " model vdw 2.019 2.170 nonbonded pdb=" OG1 THR B 52 " pdb="MG MG B 703 " model vdw 2.083 2.170 nonbonded pdb=" S1G AGS C 702 " pdb="MG MG C 703 " model vdw 2.203 2.530 nonbonded pdb=" O2G AGS B 702 " pdb="MG MG B 703 " model vdw 2.230 2.170 ... (remaining 172292 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' } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 1 through 365) } 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 24.510 Find NCS groups from input model: 0.440 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:7.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 0.100 21275 Z= 0.250 Angle : 0.632 8.870 29081 Z= 0.357 Chirality : 0.052 0.568 3349 Planarity : 0.005 0.115 3614 Dihedral : 15.446 159.180 8147 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.15 % Favored : 97.81 % Rotamer: Outliers : 0.05 % Allowed : 0.52 % Favored : 99.43 % 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: 1.97 (0.17), residues: 2515 helix: 2.04 (0.15), residues: 1251 sheet: 1.29 (0.25), residues: 401 loop : 0.31 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG E 258 TYR 0.010 0.001 TYR B 341 PHE 0.012 0.001 PHE B 136 TRP 0.011 0.001 TRP C 10 HIS 0.011 0.001 HIS E 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.25 (21259) covalent geometry : angle 0.61962 / 0.36 (29057) hydrogen bonds : bond 0.13975 / 9.50 ( 1145) hydrogen bonds : angle 5.43748 / 3.94 ( 3225) metal coordination : bond 0.00272 / 0.21 ( 16) metal coordination : angle 4.31682 / 2.61 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 541 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 149 ARG cc_start: 0.7910 (ttp-110) cc_final: 0.7349 (ttp-110) REVERT: A 157 GLN cc_start: 0.7804 (tt0) cc_final: 0.7554 (tt0) REVERT: A 219 ASP cc_start: 0.8257 (m-30) cc_final: 0.8050 (m-30) REVERT: A 242 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7917 (tp30) REVERT: B 36 ARG cc_start: 0.7757 (ttm170) cc_final: 0.7316 (mtm180) REVERT: B 77 ASP cc_start: 0.6981 (m-30) cc_final: 0.6742 (m-30) REVERT: B 176 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8482 (mtpp) REVERT: B 208 ARG cc_start: 0.7970 (mmt180) cc_final: 0.7615 (ttp-110) REVERT: B 215 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8229 (ttm110) REVERT: B 274 ARG cc_start: 0.7400 (ttp80) cc_final: 0.6975 (ttt90) REVERT: B 350 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8336 (mt-10) REVERT: C 112 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7989 (tt0) REVERT: C 126 ASP cc_start: 0.7850 (t0) cc_final: 0.7470 (m-30) REVERT: C 148 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8126 (mm-30) REVERT: C 176 LYS cc_start: 0.8767 (mttt) cc_final: 0.8170 (mmtt) REVERT: C 265 MET cc_start: 0.6892 (mmt) cc_final: 0.6678 (mmt) REVERT: D 26 THR cc_start: 0.8194 (m) cc_final: 0.7973 (t) REVERT: D 65 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7329 (mt-10) REVERT: D 112 GLN cc_start: 0.8257 (pt0) cc_final: 0.7450 (mm-40) REVERT: D 263 ARG cc_start: 0.7919 (ttt90) cc_final: 0.7234 (ttp-170) REVERT: D 338 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7605 (pt0) REVERT: E 37 ASP cc_start: 0.7538 (p0) cc_final: 0.7304 (p0) REVERT: E 38 ASP cc_start: 0.8349 (p0) cc_final: 0.8140 (p0) REVERT: E 56 HIS cc_start: 0.7247 (m-70) cc_final: 0.6606 (p-80) REVERT: E 95 GLU cc_start: 0.7901 (tt0) cc_final: 0.7660 (tm-30) REVERT: E 138 GLU cc_start: 0.8175 (mp0) cc_final: 0.7835 (mm-30) REVERT: E 147 GLU cc_start: 0.8239 (tp30) cc_final: 0.8021 (tp30) REVERT: E 169 GLU cc_start: 0.8065 (tt0) cc_final: 0.7762 (tt0) REVERT: E 211 GLN cc_start: 0.8057 (tp40) cc_final: 0.7551 (mp10) REVERT: E 274 VAL cc_start: 0.8131 (m) cc_final: 0.7910 (t) REVERT: F 73 ARG cc_start: 0.7672 (tpt-90) cc_final: 0.7313 (tpp-160) REVERT: F 105 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7780 (ttp-110) REVERT: F 149 GLN cc_start: 0.7436 (pt0) cc_final: 0.6936 (mm-40) REVERT: F 198 LYS cc_start: 0.8122 (mttt) cc_final: 0.7785 (mtpt) REVERT: F 215 ARG cc_start: 0.7096 (ttt180) cc_final: 0.6843 (ttp-110) REVERT: G 50 GLU cc_start: 0.6107 (mm-30) cc_final: 0.5862 (tm-30) REVERT: G 51 MET cc_start: 0.8047 (ptp) cc_final: 0.7326 (ptt) REVERT: G 53 MET cc_start: 0.7157 (ptm) cc_final: 0.6436 (ptm) REVERT: G 126 VAL cc_start: 0.8048 (t) cc_final: 0.7781 (p) REVERT: G 161 GLU cc_start: 0.7751 (tt0) cc_final: 0.7528 (tt0) REVERT: G 265 GLN cc_start: 0.7884 (mt0) cc_final: 0.7368 (mm-40) REVERT: G 278 PHE cc_start: 0.7018 (m-80) cc_final: 0.6723 (m-10) REVERT: G 300 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7467 (mt-10) REVERT: G 303 GLU cc_start: 0.7584 (tt0) cc_final: 0.7317 (tm-30) REVERT: G 326 ASP cc_start: 0.7761 (m-30) cc_final: 0.7428 (m-30) REVERT: G 350 GLU cc_start: 0.7663 (pt0) cc_final: 0.7268 (pm20) outliers start: 1 outliers final: 0 residues processed: 542 average time/residue: 0.8376 time to fit residues: 500.0371 Evaluate side-chains 354 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 353 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 247 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN A 40 GLN A 136 GLN A 144 GLN A 146 GLN A 234 GLN A 235 GLN B 172 GLN B 174 HIS B 330 GLN C 39 HIS C 78 ASN C 160 GLN D 4 GLN D 204 GLN D 248 GLN E 51 GLN E 240 GLN E 259 HIS E 307 ASN E 333 HIS F 212 ASN F 221 ASN F 329 ASN G 143 GLN G 156 ASN ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.188702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.150493 restraints weight = 19868.642| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.49 r_work: 0.3669 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21275 Z= 0.152 Angle : 0.570 8.330 29081 Z= 0.294 Chirality : 0.041 0.287 3349 Planarity : 0.005 0.067 3614 Dihedral : 13.967 160.697 3358 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.22 % Allowed : 10.08 % Favored : 87.70 % 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: 1.97 (0.17), residues: 2515 helix: 2.02 (0.15), residues: 1266 sheet: 1.16 (0.25), residues: 396 loop : 0.41 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 258 TYR 0.019 0.001 TYR G 284 PHE 0.017 0.002 PHE G 230 TRP 0.013 0.001 TRP C 10 HIS 0.010 0.001 HIS D 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (21259) covalent geometry : angle 0.55527 / 0.29 (29057) hydrogen bonds : bond 0.03985 / 2.66 ( 1145) hydrogen bonds : angle 4.32844 / 3.17 ( 3225) metal coordination : bond 0.00287 / 0.19 ( 16) metal coordination : angle 4.58068 / 2.78 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 358 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ARG cc_start: 0.7968 (ttp-110) cc_final: 0.7493 (ttp80) REVERT: B 176 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8447 (mtpp) REVERT: B 208 ARG cc_start: 0.8044 (mmt180) cc_final: 0.7633 (ttp-110) REVERT: B 274 ARG cc_start: 0.7207 (ttp80) cc_final: 0.6828 (ttt90) REVERT: B 279 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7899 (tp30) REVERT: B 311 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8174 (tp) REVERT: B 350 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8565 (mt-10) REVERT: C 86 ARG cc_start: 0.7368 (mtm180) cc_final: 0.7116 (mtm110) REVERT: C 102 GLU cc_start: 0.7864 (tp30) cc_final: 0.7296 (pm20) REVERT: C 126 ASP cc_start: 0.8112 (t0) cc_final: 0.7565 (m-30) REVERT: C 145 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: C 148 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8170 (mm-30) REVERT: C 161 LYS cc_start: 0.8948 (mtpp) cc_final: 0.8618 (mttm) REVERT: C 176 LYS cc_start: 0.8748 (mttt) cc_final: 0.8159 (mmtt) REVERT: D 26 THR cc_start: 0.8190 (m) cc_final: 0.7954 (t) REVERT: D 65 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7387 (mt-10) REVERT: D 112 GLN cc_start: 0.8251 (pt0) cc_final: 0.7503 (mm-40) REVERT: D 141 LYS cc_start: 0.8460 (tptt) cc_final: 0.8142 (tmtt) REVERT: D 145 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7979 (mt-10) REVERT: D 263 ARG cc_start: 0.7857 (ttt90) cc_final: 0.7160 (ttp-170) REVERT: D 274 ARG cc_start: 0.7517 (mtm-85) cc_final: 0.7167 (mtt90) REVERT: D 277 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: E 56 HIS cc_start: 0.7315 (m-70) cc_final: 0.6728 (p-80) REVERT: E 97 THR cc_start: 0.8808 (m) cc_final: 0.8512 (m) REVERT: E 138 GLU cc_start: 0.8284 (mp0) cc_final: 0.7834 (mm-30) REVERT: E 211 GLN cc_start: 0.8036 (tp40) cc_final: 0.7636 (mp10) REVERT: E 274 VAL cc_start: 0.8192 (m) cc_final: 0.7954 (t) REVERT: E 308 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8189 (ttp80) REVERT: F 53 MET cc_start: 0.8221 (mtt) cc_final: 0.7991 (mmt) REVERT: F 64 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8153 (mt-10) REVERT: F 73 ARG cc_start: 0.7702 (tpt-90) cc_final: 0.7331 (tpp-160) REVERT: F 105 ARG cc_start: 0.8082 (ttp80) cc_final: 0.7875 (ttp-110) REVERT: F 149 GLN cc_start: 0.7525 (pt0) cc_final: 0.7069 (mm110) REVERT: F 198 LYS cc_start: 0.8184 (mttt) cc_final: 0.7799 (mtmt) REVERT: F 339 MET cc_start: 0.5638 (mmt) cc_final: 0.5175 (mmt) REVERT: G 53 MET cc_start: 0.7080 (ptm) cc_final: 0.6437 (ttp) REVERT: G 126 VAL cc_start: 0.8117 (t) cc_final: 0.7833 (p) REVERT: G 182 MET cc_start: 0.7506 (mtp) cc_final: 0.6830 (mtp) REVERT: G 265 GLN cc_start: 0.7968 (mt0) cc_final: 0.7419 (mm-40) REVERT: G 278 PHE cc_start: 0.7003 (m-80) cc_final: 0.6707 (m-10) REVERT: G 303 GLU cc_start: 0.7851 (tt0) cc_final: 0.7612 (tm-30) REVERT: G 326 ASP cc_start: 0.7848 (m-30) cc_final: 0.7513 (m-30) REVERT: G 350 GLU cc_start: 0.7769 (pt0) cc_final: 0.7360 (pm20) outliers start: 47 outliers final: 17 residues processed: 388 average time/residue: 0.8448 time to fit residues: 360.7358 Evaluate side-chains 359 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 336 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 218 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 203 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 233 optimal weight: 9.9990 chunk 131 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 GLN B 330 GLN C 160 GLN D 4 GLN D 204 GLN D 248 GLN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 HIS F 221 ASN F 329 ASN G 143 GLN ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.189846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.147640 restraints weight = 19816.453| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.62 r_work: 0.3662 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21275 Z= 0.124 Angle : 0.517 7.546 29081 Z= 0.268 Chirality : 0.039 0.286 3349 Planarity : 0.004 0.059 3614 Dihedral : 13.922 161.194 3354 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.60 % Allowed : 11.07 % Favored : 86.33 % 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: 2.03 (0.17), residues: 2515 helix: 2.10 (0.15), residues: 1271 sheet: 1.10 (0.25), residues: 399 loop : 0.41 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 252 TYR 0.015 0.001 TYR G 284 PHE 0.013 0.001 PHE G 230 TRP 0.013 0.001 TRP C 10 HIS 0.007 0.001 HIS D 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (21259) covalent geometry : angle 0.50077 / 0.27 (29057) hydrogen bonds : bond 0.03499 / 2.35 ( 1145) hydrogen bonds : angle 4.05014 / 2.96 ( 3225) metal coordination : bond 0.00261 / 0.19 ( 16) metal coordination : angle 4.43330 / 2.66 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 346 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ARG cc_start: 0.7898 (ttp-110) cc_final: 0.7388 (ttp80) REVERT: A 252 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7456 (mtt180) REVERT: B 176 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8435 (mtpp) REVERT: B 208 ARG cc_start: 0.7881 (mmt180) cc_final: 0.7602 (ttp-110) REVERT: B 279 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7735 (tp30) REVERT: B 350 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8458 (mt-10) REVERT: B 363 MET cc_start: 0.5961 (mpp) cc_final: 0.5674 (mpp) REVERT: C 102 GLU cc_start: 0.7736 (tp30) cc_final: 0.7179 (pm20) REVERT: C 126 ASP cc_start: 0.7955 (t0) cc_final: 0.7403 (m-30) REVERT: C 145 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: C 148 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8180 (mm-30) REVERT: C 176 LYS cc_start: 0.8766 (mttt) cc_final: 0.8124 (mmtt) REVERT: C 216 ASP cc_start: 0.8177 (m-30) cc_final: 0.7976 (m-30) REVERT: D 2 SER cc_start: 0.6150 (OUTLIER) cc_final: 0.5784 (t) REVERT: D 26 THR cc_start: 0.8217 (m) cc_final: 0.7967 (t) REVERT: D 65 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7363 (mt-10) REVERT: D 112 GLN cc_start: 0.8205 (pt0) cc_final: 0.7519 (mm-40) REVERT: D 141 LYS cc_start: 0.8354 (tptt) cc_final: 0.8048 (tmtt) REVERT: D 145 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: D 180 VAL cc_start: 0.8197 (t) cc_final: 0.7836 (m) REVERT: D 231 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7308 (mt0) REVERT: D 263 ARG cc_start: 0.7772 (ttt90) cc_final: 0.7085 (ttp-170) REVERT: D 277 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7454 (tm-30) REVERT: E 8 ARG cc_start: 0.7997 (tpm170) cc_final: 0.7474 (ttp80) REVERT: E 56 HIS cc_start: 0.7287 (m-70) cc_final: 0.6697 (p-80) REVERT: E 97 THR cc_start: 0.8678 (m) cc_final: 0.8399 (m) REVERT: E 134 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7796 (mm-30) REVERT: E 138 GLU cc_start: 0.8090 (mp0) cc_final: 0.7756 (mm-30) REVERT: E 211 GLN cc_start: 0.8021 (tp40) cc_final: 0.7586 (mp10) REVERT: E 308 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8109 (ttp80) REVERT: F 64 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8133 (mt-10) REVERT: F 73 ARG cc_start: 0.7558 (tpt-90) cc_final: 0.7252 (tpp-160) REVERT: F 140 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6601 (tm-30) REVERT: F 149 GLN cc_start: 0.7461 (pt0) cc_final: 0.7081 (mm-40) REVERT: F 198 LYS cc_start: 0.8115 (mttt) cc_final: 0.7769 (mtpt) REVERT: F 339 MET cc_start: 0.6083 (mmt) cc_final: 0.5508 (mmt) REVERT: G 53 MET cc_start: 0.7000 (ptm) cc_final: 0.6346 (ttt) REVERT: G 182 MET cc_start: 0.7396 (mtp) cc_final: 0.6661 (mtp) REVERT: G 236 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8243 (mt) REVERT: G 265 GLN cc_start: 0.7909 (mt0) cc_final: 0.7381 (mm-40) REVERT: G 303 GLU cc_start: 0.7741 (tt0) cc_final: 0.7187 (tm-30) REVERT: G 326 ASP cc_start: 0.7701 (m-30) cc_final: 0.7364 (m-30) REVERT: G 350 GLU cc_start: 0.7619 (pt0) cc_final: 0.7247 (pm20) outliers start: 55 outliers final: 21 residues processed: 377 average time/residue: 0.8551 time to fit residues: 354.9551 Evaluate side-chains 364 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 332 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 236 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 142 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 212 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.0470 chunk 97 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 253 optimal weight: 0.0050 chunk 175 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 overall best weight: 0.5292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 HIS B 13 GLN C 78 ASN C 160 GLN D 4 GLN D 204 GLN D 248 GLN D 290 HIS F 221 ASN F 329 ASN G 143 GLN ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.191232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.154131 restraints weight = 19782.440| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.43 r_work: 0.3681 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21275 Z= 0.103 Angle : 0.489 7.314 29081 Z= 0.253 Chirality : 0.038 0.284 3349 Planarity : 0.004 0.056 3614 Dihedral : 13.899 161.011 3354 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.08 % Allowed : 12.91 % Favored : 85.00 % 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: 2.16 (0.17), residues: 2515 helix: 2.24 (0.15), residues: 1272 sheet: 1.05 (0.25), residues: 398 loop : 0.46 (0.23), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 252 TYR 0.013 0.001 TYR B 341 PHE 0.018 0.001 PHE A 65 TRP 0.012 0.001 TRP C 10 HIS 0.003 0.001 HIS D 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (21259) covalent geometry : angle 0.47328 / 0.25 (29057) hydrogen bonds : bond 0.03101 / 2.08 ( 1145) hydrogen bonds : angle 3.84037 / 2.81 ( 3225) metal coordination : bond 0.00217 / 0.15 ( 16) metal coordination : angle 4.28631 / 2.57 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 356 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ARG cc_start: 0.7980 (ttp-110) cc_final: 0.7423 (ttp-110) REVERT: B 176 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8513 (mtpp) REVERT: B 208 ARG cc_start: 0.7902 (mmt180) cc_final: 0.7619 (ttp-110) REVERT: B 279 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7756 (tp30) REVERT: B 350 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8468 (mt-10) REVERT: C 145 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: C 148 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8182 (mm-30) REVERT: C 176 LYS cc_start: 0.8721 (mttt) cc_final: 0.8116 (mmtt) REVERT: C 181 GLU cc_start: 0.7968 (tp30) cc_final: 0.7630 (mp0) REVERT: C 216 ASP cc_start: 0.8189 (m-30) cc_final: 0.7979 (m-30) REVERT: D 2 SER cc_start: 0.6175 (m) cc_final: 0.5781 (t) REVERT: D 26 THR cc_start: 0.8220 (m) cc_final: 0.7952 (t) REVERT: D 65 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7351 (mt-10) REVERT: D 112 GLN cc_start: 0.8252 (pt0) cc_final: 0.7579 (mm-40) REVERT: D 141 LYS cc_start: 0.8313 (tptt) cc_final: 0.8023 (tmtt) REVERT: D 145 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: D 180 VAL cc_start: 0.8217 (t) cc_final: 0.7873 (m) REVERT: D 231 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7325 (mt0) REVERT: D 263 ARG cc_start: 0.7838 (ttt90) cc_final: 0.7154 (ttp-170) REVERT: D 274 ARG cc_start: 0.7596 (mtm-85) cc_final: 0.7371 (mtt90) REVERT: D 277 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: E 56 HIS cc_start: 0.7250 (m-70) cc_final: 0.6708 (p-80) REVERT: E 97 THR cc_start: 0.8693 (m) cc_final: 0.8380 (m) REVERT: E 138 GLU cc_start: 0.8181 (mp0) cc_final: 0.7807 (mm-30) REVERT: E 211 GLN cc_start: 0.7935 (tp40) cc_final: 0.7568 (mp10) REVERT: E 274 VAL cc_start: 0.8163 (m) cc_final: 0.7889 (t) REVERT: F 53 MET cc_start: 0.8032 (mtt) cc_final: 0.7798 (mmt) REVERT: F 64 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8206 (mt-10) REVERT: F 73 ARG cc_start: 0.7551 (tpt-90) cc_final: 0.7286 (tpp-160) REVERT: F 149 GLN cc_start: 0.7432 (pt0) cc_final: 0.7084 (mm-40) REVERT: F 198 LYS cc_start: 0.8187 (mttt) cc_final: 0.7836 (mtmt) REVERT: F 339 MET cc_start: 0.6203 (OUTLIER) cc_final: 0.5520 (mmt) REVERT: G 53 MET cc_start: 0.7046 (ptm) cc_final: 0.6364 (ttp) REVERT: G 176 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7466 (ptt90) REVERT: G 182 MET cc_start: 0.7432 (mtp) cc_final: 0.6715 (mtp) REVERT: G 265 GLN cc_start: 0.7974 (mt0) cc_final: 0.7414 (mm-40) REVERT: G 298 GLU cc_start: 0.7040 (mp0) cc_final: 0.6645 (mt-10) REVERT: G 303 GLU cc_start: 0.7677 (tt0) cc_final: 0.7165 (tm-30) REVERT: G 326 ASP cc_start: 0.7725 (m-30) cc_final: 0.7388 (m-30) REVERT: G 332 LYS cc_start: 0.7160 (pttt) cc_final: 0.6813 (pptt) REVERT: G 350 GLU cc_start: 0.7593 (pt0) cc_final: 0.7209 (pm20) outliers start: 44 outliers final: 16 residues processed: 380 average time/residue: 0.8248 time to fit residues: 347.3332 Evaluate side-chains 354 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 331 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 176 ARG Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 227 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 103 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 185 optimal weight: 6.9990 chunk 159 optimal weight: 0.0670 chunk 201 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN B 330 GLN C 160 GLN D 4 GLN D 248 GLN F 221 ASN F 329 ASN G 143 GLN ** G 221 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 = 0.4221 r_free = 0.4221 target = 0.189506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.152382 restraints weight = 19709.113| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.41 r_work: 0.3659 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21275 Z= 0.129 Angle : 0.523 7.692 29081 Z= 0.266 Chirality : 0.039 0.280 3349 Planarity : 0.004 0.052 3614 Dihedral : 13.935 160.259 3354 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.37 % Allowed : 13.20 % Favored : 84.44 % 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: 2.05 (0.17), residues: 2515 helix: 2.14 (0.15), residues: 1277 sheet: 1.01 (0.25), residues: 391 loop : 0.43 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 80 TYR 0.015 0.001 TYR B 341 PHE 0.017 0.001 PHE G 230 TRP 0.011 0.001 TRP C 10 HIS 0.005 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (21259) covalent geometry : angle 0.50759 / 0.27 (29057) hydrogen bonds : bond 0.03288 / 2.21 ( 1145) hydrogen bonds : angle 3.80255 / 2.78 ( 3225) metal coordination : bond 0.00256 / 0.20 ( 16) metal coordination : angle 4.43965 / 2.64 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 332 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7186 (mtt-85) REVERT: A 149 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7513 (ttp-110) REVERT: B 176 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8511 (mtpp) REVERT: B 208 ARG cc_start: 0.7954 (mmt180) cc_final: 0.7643 (ttp-110) REVERT: B 279 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7738 (tp30) REVERT: B 350 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8469 (mt-10) REVERT: C 145 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: C 148 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8190 (mm-30) REVERT: C 176 LYS cc_start: 0.8764 (mttt) cc_final: 0.8145 (mmtt) REVERT: C 216 ASP cc_start: 0.8183 (m-30) cc_final: 0.7968 (m-30) REVERT: C 345 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7661 (mtt-85) REVERT: D 2 SER cc_start: 0.6224 (OUTLIER) cc_final: 0.5864 (t) REVERT: D 26 THR cc_start: 0.8186 (m) cc_final: 0.7969 (t) REVERT: D 65 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7335 (mt-10) REVERT: D 112 GLN cc_start: 0.8304 (pt0) cc_final: 0.7621 (mm-40) REVERT: D 145 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: D 180 VAL cc_start: 0.8248 (t) cc_final: 0.7902 (m) REVERT: D 231 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7333 (mt0) REVERT: D 263 ARG cc_start: 0.7834 (ttt90) cc_final: 0.7148 (ttp-170) REVERT: D 277 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: E 56 HIS cc_start: 0.7281 (m-70) cc_final: 0.6733 (p-80) REVERT: E 97 THR cc_start: 0.8668 (m) cc_final: 0.8388 (m) REVERT: E 134 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7829 (mm-30) REVERT: E 138 GLU cc_start: 0.8238 (mp0) cc_final: 0.7833 (mm-30) REVERT: E 211 GLN cc_start: 0.7975 (tp40) cc_final: 0.7596 (mp10) REVERT: E 214 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7810 (tp30) REVERT: F 53 MET cc_start: 0.8128 (mtt) cc_final: 0.7900 (mmt) REVERT: F 73 ARG cc_start: 0.7619 (tpt-90) cc_final: 0.7339 (tpp-160) REVERT: F 149 GLN cc_start: 0.7441 (pt0) cc_final: 0.7150 (mm-40) REVERT: F 182 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7716 (mmt) REVERT: F 198 LYS cc_start: 0.8190 (mttt) cc_final: 0.7852 (mtpt) REVERT: F 235 LYS cc_start: 0.8559 (mmtp) cc_final: 0.8241 (tptp) REVERT: F 339 MET cc_start: 0.6410 (mmt) cc_final: 0.5736 (mmt) REVERT: G 53 MET cc_start: 0.7156 (ptm) cc_final: 0.6398 (ttp) REVERT: G 176 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7381 (ptt90) REVERT: G 182 MET cc_start: 0.7506 (mtp) cc_final: 0.6783 (mtp) REVERT: G 265 GLN cc_start: 0.7964 (mt0) cc_final: 0.7428 (mm-40) REVERT: G 298 GLU cc_start: 0.7004 (mp0) cc_final: 0.6666 (mt-10) REVERT: G 303 GLU cc_start: 0.7685 (tt0) cc_final: 0.7123 (tm-30) REVERT: G 326 ASP cc_start: 0.7769 (m-30) cc_final: 0.7398 (m-30) REVERT: G 332 LYS cc_start: 0.7045 (pttt) cc_final: 0.6713 (pptt) REVERT: G 350 GLU cc_start: 0.7672 (pt0) cc_final: 0.7319 (pm20) outliers start: 50 outliers final: 21 residues processed: 359 average time/residue: 0.7946 time to fit residues: 315.7253 Evaluate side-chains 351 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 318 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 176 ARG Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 227 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 179 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 156 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 248 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 51 optimal weight: 0.0670 chunk 128 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN B 330 GLN C 78 ASN C 160 GLN D 248 GLN F 221 ASN F 329 ASN G 143 GLN ** G 221 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 = 0.4232 r_free = 0.4232 target = 0.190759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.153733 restraints weight = 19715.321| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.41 r_work: 0.3671 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 21275 Z= 0.104 Angle : 0.487 6.859 29081 Z= 0.251 Chirality : 0.038 0.279 3349 Planarity : 0.004 0.051 3614 Dihedral : 13.911 159.211 3354 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.84 % Allowed : 14.24 % Favored : 83.92 % 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: 2.16 (0.17), residues: 2515 helix: 2.26 (0.15), residues: 1275 sheet: 0.98 (0.25), residues: 398 loop : 0.46 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 252 TYR 0.015 0.001 TYR G 284 PHE 0.015 0.001 PHE G 230 TRP 0.012 0.001 TRP C 10 HIS 0.003 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (21259) covalent geometry : angle 0.47235 / 0.25 (29057) hydrogen bonds : bond 0.02982 / 2.01 ( 1145) hydrogen bonds : angle 3.73151 / 2.73 ( 3225) metal coordination : bond 0.00210 / 0.14 ( 16) metal coordination : angle 4.17814 / 2.50 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 330 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ARG cc_start: 0.8106 (ttp-110) cc_final: 0.7529 (ttp-110) REVERT: B 176 LYS cc_start: 0.8746 (mtmt) cc_final: 0.8517 (mtpp) REVERT: B 208 ARG cc_start: 0.7950 (mmt180) cc_final: 0.7650 (ttp-110) REVERT: B 279 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7712 (tp30) REVERT: B 350 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8467 (mt-10) REVERT: C 145 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: C 148 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8181 (mm-30) REVERT: C 176 LYS cc_start: 0.8730 (mttt) cc_final: 0.8114 (mmtt) REVERT: C 216 ASP cc_start: 0.8175 (m-30) cc_final: 0.7957 (m-30) REVERT: D 2 SER cc_start: 0.6213 (m) cc_final: 0.5808 (t) REVERT: D 26 THR cc_start: 0.8183 (m) cc_final: 0.7946 (t) REVERT: D 65 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7317 (mt-10) REVERT: D 112 GLN cc_start: 0.8311 (pt0) cc_final: 0.7625 (mm-40) REVERT: D 145 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7677 (mt-10) REVERT: D 180 VAL cc_start: 0.8248 (t) cc_final: 0.7900 (m) REVERT: D 231 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7368 (mt0) REVERT: D 263 ARG cc_start: 0.7824 (ttt90) cc_final: 0.7154 (ttp-170) REVERT: D 277 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: E 56 HIS cc_start: 0.7261 (m-70) cc_final: 0.6734 (p-80) REVERT: E 97 THR cc_start: 0.8648 (m) cc_final: 0.8367 (m) REVERT: E 138 GLU cc_start: 0.8260 (mp0) cc_final: 0.7838 (mm-30) REVERT: E 211 GLN cc_start: 0.7969 (tp40) cc_final: 0.7609 (mp10) REVERT: E 309 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: F 53 MET cc_start: 0.8103 (mtt) cc_final: 0.7860 (mmt) REVERT: F 73 ARG cc_start: 0.7612 (tpt-90) cc_final: 0.7347 (tpp-160) REVERT: F 149 GLN cc_start: 0.7419 (pt0) cc_final: 0.7139 (mm-40) REVERT: F 198 LYS cc_start: 0.8181 (mttt) cc_final: 0.7856 (mtpt) REVERT: F 339 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.5702 (mmt) REVERT: G 53 MET cc_start: 0.7102 (ptm) cc_final: 0.6347 (ttp) REVERT: G 176 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7537 (ptt90) REVERT: G 182 MET cc_start: 0.7506 (mtp) cc_final: 0.6756 (mtp) REVERT: G 265 GLN cc_start: 0.7969 (mt0) cc_final: 0.7416 (mm-40) REVERT: G 298 GLU cc_start: 0.6943 (mp0) cc_final: 0.6647 (mt-10) REVERT: G 303 GLU cc_start: 0.7704 (tt0) cc_final: 0.7235 (tm-30) REVERT: G 326 ASP cc_start: 0.7782 (m-30) cc_final: 0.7447 (m-30) REVERT: G 332 LYS cc_start: 0.6962 (pttt) cc_final: 0.6663 (pptt) REVERT: G 350 GLU cc_start: 0.7650 (pt0) cc_final: 0.7304 (pm20) outliers start: 39 outliers final: 20 residues processed: 349 average time/residue: 0.7302 time to fit residues: 282.1826 Evaluate side-chains 351 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 323 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 176 ARG Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 227 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 30 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 chunk 213 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 140 optimal weight: 0.0050 chunk 52 optimal weight: 0.2980 chunk 143 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 330 GLN C 78 ASN C 160 GLN F 221 ASN F 329 ASN G 143 GLN ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.190908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.153674 restraints weight = 19787.231| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.42 r_work: 0.3674 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21275 Z= 0.103 Angle : 0.483 6.677 29081 Z= 0.249 Chirality : 0.037 0.280 3349 Planarity : 0.004 0.053 3614 Dihedral : 13.899 160.155 3354 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.75 % Allowed : 14.90 % Favored : 83.35 % 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: 2.20 (0.17), residues: 2515 helix: 2.30 (0.15), residues: 1275 sheet: 0.98 (0.25), residues: 398 loop : 0.48 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 252 TYR 0.014 0.001 TYR B 341 PHE 0.016 0.001 PHE G 230 TRP 0.013 0.001 TRP B 10 HIS 0.003 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (21259) covalent geometry : angle 0.46909 / 0.25 (29057) hydrogen bonds : bond 0.02909 / 1.96 ( 1145) hydrogen bonds : angle 3.67570 / 2.69 ( 3225) metal coordination : bond 0.00200 / 0.15 ( 16) metal coordination : angle 4.03883 / 2.42 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 337 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ARG cc_start: 0.8097 (ttp-110) cc_final: 0.7508 (ttp-110) REVERT: B 176 LYS cc_start: 0.8744 (mtmt) cc_final: 0.8517 (mtpp) REVERT: B 208 ARG cc_start: 0.7999 (mmt180) cc_final: 0.7672 (ttp-110) REVERT: B 279 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7702 (tp30) REVERT: B 311 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8262 (tp) REVERT: B 350 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8464 (mt-10) REVERT: C 148 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8179 (mm-30) REVERT: C 176 LYS cc_start: 0.8719 (mttt) cc_final: 0.8108 (mmtt) REVERT: C 181 GLU cc_start: 0.7985 (tp30) cc_final: 0.7607 (mp0) REVERT: C 216 ASP cc_start: 0.8098 (m-30) cc_final: 0.7868 (m-30) REVERT: C 345 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7770 (mtt-85) REVERT: D 26 THR cc_start: 0.8183 (m) cc_final: 0.7954 (t) REVERT: D 65 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7319 (mt-10) REVERT: D 112 GLN cc_start: 0.8299 (pt0) cc_final: 0.7631 (mm-40) REVERT: D 145 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: D 180 VAL cc_start: 0.8220 (t) cc_final: 0.7872 (m) REVERT: D 181 GLU cc_start: 0.7360 (tp30) cc_final: 0.6927 (tp30) REVERT: D 231 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7320 (mt0) REVERT: D 263 ARG cc_start: 0.7790 (ttt90) cc_final: 0.7105 (ttp-170) REVERT: D 277 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: E 22 ARG cc_start: 0.8209 (mmt180) cc_final: 0.7987 (mmp80) REVERT: E 56 HIS cc_start: 0.7225 (m-70) cc_final: 0.6700 (p-80) REVERT: E 97 THR cc_start: 0.8631 (m) cc_final: 0.8355 (m) REVERT: E 138 GLU cc_start: 0.8293 (mp0) cc_final: 0.7871 (mm-30) REVERT: E 211 GLN cc_start: 0.7963 (tp40) cc_final: 0.7603 (mp10) REVERT: E 228 ASP cc_start: 0.8509 (t0) cc_final: 0.8271 (t70) REVERT: E 309 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: F 53 MET cc_start: 0.8122 (mtt) cc_final: 0.7869 (mmt) REVERT: F 73 ARG cc_start: 0.7626 (tpt-90) cc_final: 0.7335 (tpp-160) REVERT: F 149 GLN cc_start: 0.7480 (pt0) cc_final: 0.7197 (mm-40) REVERT: F 198 LYS cc_start: 0.8194 (mttt) cc_final: 0.7855 (mtpt) REVERT: F 339 MET cc_start: 0.6437 (OUTLIER) cc_final: 0.5695 (mmt) REVERT: G 53 MET cc_start: 0.7054 (ptm) cc_final: 0.6368 (ttp) REVERT: G 176 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7704 (ptt90) REVERT: G 182 MET cc_start: 0.7531 (mtp) cc_final: 0.6774 (mtp) REVERT: G 265 GLN cc_start: 0.7962 (mt0) cc_final: 0.7419 (mm-40) REVERT: G 277 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.6952 (mttm) REVERT: G 298 GLU cc_start: 0.6860 (mp0) cc_final: 0.6596 (mt-10) REVERT: G 303 GLU cc_start: 0.7666 (tt0) cc_final: 0.7179 (tm-30) REVERT: G 326 ASP cc_start: 0.7755 (m-30) cc_final: 0.7390 (m-30) REVERT: G 332 LYS cc_start: 0.6955 (pttt) cc_final: 0.6651 (pptt) REVERT: G 350 GLU cc_start: 0.7604 (pt0) cc_final: 0.7247 (pm20) outliers start: 37 outliers final: 24 residues processed: 358 average time/residue: 0.7695 time to fit residues: 305.2185 Evaluate side-chains 356 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 322 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 176 ARG Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 277 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 135 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 250 optimal weight: 20.0000 chunk 139 optimal weight: 0.0570 chunk 140 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN B 330 GLN C 160 GLN D 248 GLN F 221 ASN F 329 ASN G 143 GLN ** G 221 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 = 0.4234 r_free = 0.4234 target = 0.196534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.153405 restraints weight = 20635.235| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.76 r_work: 0.3640 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21275 Z= 0.106 Angle : 0.491 8.793 29081 Z= 0.251 Chirality : 0.038 0.280 3349 Planarity : 0.004 0.059 3614 Dihedral : 13.935 159.038 3354 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.84 % Allowed : 15.33 % Favored : 82.83 % 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: 2.24 (0.17), residues: 2515 helix: 2.31 (0.15), residues: 1275 sheet: 1.16 (0.25), residues: 387 loop : 0.47 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 80 TYR 0.016 0.001 TYR G 284 PHE 0.016 0.001 PHE G 230 TRP 0.012 0.001 TRP B 10 HIS 0.004 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (21259) covalent geometry : angle 0.47660 / 0.25 (29057) hydrogen bonds : bond 0.02920 / 1.96 ( 1145) hydrogen bonds : angle 3.67300 / 2.69 ( 3225) metal coordination : bond 0.00199 / 0.15 ( 16) metal coordination : angle 4.08289 / 2.44 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 333 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ARG cc_start: 0.8159 (ttp-110) cc_final: 0.7531 (ttp-110) REVERT: A 286 MET cc_start: 0.8496 (mmm) cc_final: 0.8175 (tpt) REVERT: B 176 LYS cc_start: 0.8776 (mtmt) cc_final: 0.8538 (mtpp) REVERT: B 208 ARG cc_start: 0.8058 (mmt180) cc_final: 0.7640 (ttp-110) REVERT: B 279 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7787 (tp30) REVERT: B 311 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8248 (tp) REVERT: B 350 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8532 (mt-10) REVERT: C 148 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8209 (mm-30) REVERT: C 176 LYS cc_start: 0.8740 (mttt) cc_final: 0.8110 (mmtt) REVERT: C 181 GLU cc_start: 0.8069 (tp30) cc_final: 0.7642 (mp0) REVERT: C 216 ASP cc_start: 0.8161 (m-30) cc_final: 0.7910 (m-30) REVERT: C 345 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7788 (mtt-85) REVERT: D 26 THR cc_start: 0.8205 (m) cc_final: 0.7973 (t) REVERT: D 65 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7279 (mt-10) REVERT: D 112 GLN cc_start: 0.8328 (pt0) cc_final: 0.7620 (mm-40) REVERT: D 145 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: D 180 VAL cc_start: 0.8202 (t) cc_final: 0.7883 (m) REVERT: D 181 GLU cc_start: 0.7360 (tp30) cc_final: 0.6849 (tp30) REVERT: D 231 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7345 (mt0) REVERT: D 263 ARG cc_start: 0.7834 (ttt90) cc_final: 0.7114 (ttp-170) REVERT: D 277 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: E 22 ARG cc_start: 0.8204 (mmt180) cc_final: 0.7873 (mmp80) REVERT: E 56 HIS cc_start: 0.7292 (m-70) cc_final: 0.6714 (p-80) REVERT: E 97 THR cc_start: 0.8652 (m) cc_final: 0.8379 (m) REVERT: E 138 GLU cc_start: 0.8390 (mp0) cc_final: 0.7889 (mm-30) REVERT: E 211 GLN cc_start: 0.8069 (tp40) cc_final: 0.7636 (mp10) REVERT: E 214 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7806 (tp30) REVERT: E 228 ASP cc_start: 0.8550 (t0) cc_final: 0.8306 (t70) REVERT: E 309 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: F 53 MET cc_start: 0.8215 (mtt) cc_final: 0.7963 (mmt) REVERT: F 73 ARG cc_start: 0.7697 (tpt-90) cc_final: 0.7338 (tpp-160) REVERT: F 149 GLN cc_start: 0.7544 (pt0) cc_final: 0.7193 (mm-40) REVERT: F 198 LYS cc_start: 0.8238 (mttt) cc_final: 0.7899 (mtpt) REVERT: F 235 LYS cc_start: 0.8559 (mmtp) cc_final: 0.8224 (tptp) REVERT: G 1 MET cc_start: 0.3744 (mmm) cc_final: 0.0440 (mmm) REVERT: G 53 MET cc_start: 0.7150 (ptm) cc_final: 0.6441 (ttp) REVERT: G 176 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7781 (ptt90) REVERT: G 182 MET cc_start: 0.7553 (mtp) cc_final: 0.6787 (mtp) REVERT: G 265 GLN cc_start: 0.7970 (mt0) cc_final: 0.7412 (mm-40) REVERT: G 277 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6992 (mttm) REVERT: G 298 GLU cc_start: 0.6856 (mp0) cc_final: 0.6583 (mt-10) REVERT: G 303 GLU cc_start: 0.7767 (tt0) cc_final: 0.7206 (tm-30) REVERT: G 326 ASP cc_start: 0.7827 (m-30) cc_final: 0.7452 (m-30) REVERT: G 332 LYS cc_start: 0.6973 (pttt) cc_final: 0.6653 (pptt) REVERT: G 350 GLU cc_start: 0.7685 (pt0) cc_final: 0.7251 (pm20) outliers start: 39 outliers final: 23 residues processed: 357 average time/residue: 0.7736 time to fit residues: 305.4067 Evaluate side-chains 360 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 327 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 176 ARG Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 277 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 145 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 chunk 163 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 chunk 232 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 200 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 330 GLN C 78 ASN C 160 GLN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 GLN F 329 ASN G 143 GLN ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.196585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.153519 restraints weight = 20692.065| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.77 r_work: 0.3647 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21275 Z= 0.104 Angle : 0.488 6.862 29081 Z= 0.251 Chirality : 0.037 0.278 3349 Planarity : 0.004 0.056 3614 Dihedral : 13.945 159.686 3354 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.84 % Allowed : 15.52 % Favored : 82.64 % 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: 2.24 (0.17), residues: 2515 helix: 2.31 (0.15), residues: 1280 sheet: 1.10 (0.25), residues: 393 loop : 0.48 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 80 TYR 0.014 0.001 TYR B 341 PHE 0.016 0.001 PHE F 278 TRP 0.011 0.001 TRP C 10 HIS 0.005 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (21259) covalent geometry : angle 0.47439 / 0.25 (29057) hydrogen bonds : bond 0.02876 / 1.93 ( 1145) hydrogen bonds : angle 3.65102 / 2.67 ( 3225) metal coordination : bond 0.00208 / 0.15 ( 16) metal coordination : angle 4.03836 / 2.43 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 344 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.7742 (tt0) cc_final: 0.7363 (tp30) REVERT: A 149 ARG cc_start: 0.8167 (ttp-110) cc_final: 0.7548 (ttp-110) REVERT: A 286 MET cc_start: 0.8469 (mmm) cc_final: 0.8149 (tpt) REVERT: B 176 LYS cc_start: 0.8775 (mtmt) cc_final: 0.8534 (mtpp) REVERT: B 208 ARG cc_start: 0.8040 (mmt180) cc_final: 0.7638 (ttp-110) REVERT: B 279 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7785 (tp30) REVERT: B 311 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8259 (tp) REVERT: B 350 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8493 (mt-10) REVERT: C 80 ARG cc_start: 0.7667 (mtm110) cc_final: 0.7400 (mtm110) REVERT: C 148 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8193 (mm-30) REVERT: C 176 LYS cc_start: 0.8728 (mttt) cc_final: 0.8098 (mmtt) REVERT: C 181 GLU cc_start: 0.8008 (tp30) cc_final: 0.7633 (mp0) REVERT: C 216 ASP cc_start: 0.8146 (m-30) cc_final: 0.7916 (m-30) REVERT: D 26 THR cc_start: 0.8156 (m) cc_final: 0.7943 (t) REVERT: D 65 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7279 (mt-10) REVERT: D 112 GLN cc_start: 0.8283 (pt0) cc_final: 0.7606 (mm-40) REVERT: D 145 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: D 180 VAL cc_start: 0.8187 (t) cc_final: 0.7868 (m) REVERT: D 181 GLU cc_start: 0.7279 (tp30) cc_final: 0.6794 (tp30) REVERT: D 231 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7344 (mt0) REVERT: D 263 ARG cc_start: 0.7827 (ttt90) cc_final: 0.7110 (ttp-170) REVERT: D 277 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: E 22 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7958 (mmp80) REVERT: E 56 HIS cc_start: 0.7027 (m-70) cc_final: 0.6451 (p-80) REVERT: E 97 THR cc_start: 0.8640 (m) cc_final: 0.8368 (m) REVERT: E 138 GLU cc_start: 0.8379 (mp0) cc_final: 0.7887 (mm-30) REVERT: E 211 GLN cc_start: 0.8057 (tp40) cc_final: 0.7632 (mp10) REVERT: E 214 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7825 (tp30) REVERT: E 228 ASP cc_start: 0.8537 (t0) cc_final: 0.8293 (t70) REVERT: E 309 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: F 53 MET cc_start: 0.8200 (mtt) cc_final: 0.7947 (mmt) REVERT: F 73 ARG cc_start: 0.7689 (tpt-90) cc_final: 0.7347 (tpp-160) REVERT: F 149 GLN cc_start: 0.7531 (pt0) cc_final: 0.7204 (mm-40) REVERT: F 198 LYS cc_start: 0.8224 (mttt) cc_final: 0.7886 (mtpt) REVERT: F 339 MET cc_start: 0.6460 (mtt) cc_final: 0.6104 (mmt) REVERT: G 1 MET cc_start: 0.3691 (mmm) cc_final: 0.0559 (mmm) REVERT: G 53 MET cc_start: 0.7134 (ptm) cc_final: 0.6434 (ttp) REVERT: G 176 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7787 (ptt90) REVERT: G 265 GLN cc_start: 0.7993 (mt0) cc_final: 0.7438 (mm-40) REVERT: G 277 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.6966 (mttm) REVERT: G 298 GLU cc_start: 0.6780 (mp0) cc_final: 0.6511 (mt-10) REVERT: G 303 GLU cc_start: 0.7737 (tt0) cc_final: 0.7214 (tm-30) REVERT: G 326 ASP cc_start: 0.7812 (m-30) cc_final: 0.7480 (m-30) REVERT: G 350 GLU cc_start: 0.7693 (pt0) cc_final: 0.7336 (pm20) outliers start: 39 outliers final: 25 residues processed: 366 average time/residue: 0.7905 time to fit residues: 320.1371 Evaluate side-chains 364 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 329 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 176 ARG Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 277 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 203 optimal weight: 10.0000 chunk 50 optimal weight: 0.3980 chunk 201 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 220 optimal weight: 0.0050 chunk 219 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN B 330 GLN C 78 ASN C 110 ASN C 160 GLN C 192 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN G 143 GLN ** G 221 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 = 0.4236 r_free = 0.4236 target = 0.196722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.153574 restraints weight = 20857.208| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.81 r_work: 0.3646 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21275 Z= 0.101 Angle : 0.487 6.814 29081 Z= 0.251 Chirality : 0.037 0.279 3349 Planarity : 0.004 0.060 3614 Dihedral : 13.934 159.684 3354 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.80 % Allowed : 15.99 % Favored : 82.21 % 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: 2.26 (0.17), residues: 2515 helix: 2.33 (0.15), residues: 1280 sheet: 1.05 (0.25), residues: 405 loop : 0.51 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 80 TYR 0.014 0.001 TYR B 341 PHE 0.029 0.001 PHE A 65 TRP 0.013 0.001 TRP B 10 HIS 0.005 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (21259) covalent geometry : angle 0.47316 / 0.25 (29057) hydrogen bonds : bond 0.02819 / 1.88 ( 1145) hydrogen bonds : angle 3.63885 / 2.66 ( 3225) metal coordination : bond 0.00205 / 0.16 ( 16) metal coordination : angle 4.02716 / 2.42 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 339 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.7752 (tt0) cc_final: 0.7338 (tp30) REVERT: A 149 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.7544 (ttp-110) REVERT: A 286 MET cc_start: 0.8482 (mmm) cc_final: 0.8175 (tpt) REVERT: B 176 LYS cc_start: 0.8775 (mtmt) cc_final: 0.8535 (mtpp) REVERT: B 208 ARG cc_start: 0.8053 (mmt180) cc_final: 0.7644 (ttp-110) REVERT: B 279 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7785 (tp30) REVERT: B 311 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8245 (tp) REVERT: B 350 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8492 (mt-10) REVERT: C 80 ARG cc_start: 0.7737 (mtm110) cc_final: 0.7473 (mtm110) REVERT: C 148 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8201 (mm-30) REVERT: C 176 LYS cc_start: 0.8720 (mttt) cc_final: 0.8092 (mmtt) REVERT: C 181 GLU cc_start: 0.7980 (tp30) cc_final: 0.7621 (mp0) REVERT: C 216 ASP cc_start: 0.8060 (m-30) cc_final: 0.7823 (m-30) REVERT: D 2 SER cc_start: 0.6165 (m) cc_final: 0.5675 (t) REVERT: D 26 THR cc_start: 0.8165 (m) cc_final: 0.7950 (t) REVERT: D 65 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7264 (mt-10) REVERT: D 112 GLN cc_start: 0.8225 (pt0) cc_final: 0.7581 (mm-40) REVERT: D 145 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: D 180 VAL cc_start: 0.8174 (t) cc_final: 0.7849 (m) REVERT: D 181 GLU cc_start: 0.7240 (tp30) cc_final: 0.6761 (tp30) REVERT: D 231 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7339 (mt0) REVERT: D 263 ARG cc_start: 0.7818 (ttt90) cc_final: 0.7086 (ttp-170) REVERT: E 22 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7892 (mmp80) REVERT: E 56 HIS cc_start: 0.6635 (m-70) cc_final: 0.6238 (p-80) REVERT: E 97 THR cc_start: 0.8620 (m) cc_final: 0.8351 (m) REVERT: E 138 GLU cc_start: 0.8391 (mp0) cc_final: 0.7894 (mm-30) REVERT: E 211 GLN cc_start: 0.8067 (tp40) cc_final: 0.7618 (mp10) REVERT: E 214 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7793 (tp30) REVERT: E 228 ASP cc_start: 0.8530 (t0) cc_final: 0.8262 (t70) REVERT: E 309 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: F 53 MET cc_start: 0.8198 (mtt) cc_final: 0.7914 (mmt) REVERT: F 73 ARG cc_start: 0.7697 (tpt-90) cc_final: 0.7330 (tpp-160) REVERT: F 149 GLN cc_start: 0.7573 (pt0) cc_final: 0.7216 (mm-40) REVERT: F 198 LYS cc_start: 0.8191 (mttt) cc_final: 0.7849 (mtpt) REVERT: F 319 PHE cc_start: 0.6618 (m-80) cc_final: 0.6307 (m-80) REVERT: F 339 MET cc_start: 0.6478 (mtt) cc_final: 0.6145 (mmt) REVERT: G 1 MET cc_start: 0.3759 (mmm) cc_final: 0.0630 (mmm) REVERT: G 53 MET cc_start: 0.7163 (ptm) cc_final: 0.6464 (ttp) REVERT: G 176 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7937 (ptt180) REVERT: G 265 GLN cc_start: 0.7996 (mt0) cc_final: 0.7429 (mm-40) REVERT: G 303 GLU cc_start: 0.7714 (tt0) cc_final: 0.7167 (tm-30) REVERT: G 326 ASP cc_start: 0.7817 (m-30) cc_final: 0.7479 (m-30) REVERT: G 350 GLU cc_start: 0.7746 (pt0) cc_final: 0.7354 (pm20) outliers start: 38 outliers final: 24 residues processed: 359 average time/residue: 0.7336 time to fit residues: 291.6339 Evaluate side-chains 361 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 329 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 176 ARG Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 195 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 135 optimal weight: 0.0370 chunk 67 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 104 optimal weight: 0.0770 chunk 90 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 172 GLN B 330 GLN C 160 GLN C 192 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 GLN ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN G 143 GLN ** G 221 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 = 0.4241 r_free = 0.4241 target = 0.197208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.154222 restraints weight = 20820.626| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.79 r_work: 0.3649 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21275 Z= 0.098 Angle : 0.486 6.703 29081 Z= 0.250 Chirality : 0.037 0.280 3349 Planarity : 0.004 0.059 3614 Dihedral : 13.924 159.717 3354 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.75 % Allowed : 16.27 % Favored : 81.98 % 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: 2.31 (0.17), residues: 2515 helix: 2.38 (0.15), residues: 1280 sheet: 1.05 (0.25), residues: 405 loop : 0.52 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 80 TYR 0.014 0.001 TYR G 284 PHE 0.014 0.001 PHE G 230 TRP 0.012 0.001 TRP B 10 HIS 0.005 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (21259) covalent geometry : angle 0.47138 / 0.25 (29057) hydrogen bonds : bond 0.02767 / 1.85 ( 1145) hydrogen bonds : angle 3.61218 / 2.64 ( 3225) metal coordination : bond 0.00227 / 0.18 ( 16) metal coordination : angle 4.08454 / 2.43 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9713.59 seconds wall clock time: 165 minutes 25.73 seconds (9925.73 seconds total)