Starting phenix.real_space_refine on Fri Jun 5 13:41:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyj_71023/06_2026/9oyj_71023.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyj_71023/06_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_71023/06_2026/9oyj_71023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyj_71023/06_2026/9oyj_71023.map" model { file = "/net/cci-nas-00/data/ceres_data/9oyj_71023/06_2026/9oyj_71023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyj_71023/06_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-6079/lib/python3.9/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: 5.40, per 1000 atoms: 0.26 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: 1.67 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.87 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: 4.51 Time building geometry restraints manager: 2.27 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=" N VAL C 101 " pdb=" CA VAL C 101 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.26e-02 6.30e+03 8.05e+00 bond pdb=" O3B AGS D 702 " pdb=" PG AGS D 702 " ideal model delta sigma weight residual 1.559 1.616 -0.057 2.00e-02 2.50e+03 8.04e+00 bond pdb=" O3B AGS B 702 " pdb=" PG AGS B 702 " ideal model delta sigma weight residual 1.559 1.614 -0.055 2.00e-02 2.50e+03 7.68e+00 bond pdb=" O3G AGS B 702 " pdb=" PG AGS B 702 " ideal model delta sigma weight residual 1.558 1.504 0.054 2.00e-02 2.50e+03 7.36e+00 bond pdb=" N LYS B 100 " pdb=" CA LYS B 100 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.27e-02 6.20e+03 7.08e+00 ... (remaining 21254 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 28882 2.97 - 5.94: 141 5.94 - 8.91: 29 8.91 - 11.88: 1 11.88 - 14.86: 4 Bond angle restraints: 29057 Sorted by residual: angle pdb=" PB AGS B 702 " pdb=" O3B AGS B 702 " pdb=" PG AGS B 702 " ideal model delta sigma weight residual 120.12 134.98 -14.86 3.00e+00 1.11e-01 2.45e+01 angle pdb=" PA AGS D 702 " pdb=" O3A AGS D 702 " pdb=" PB AGS D 702 " ideal model delta sigma weight residual 119.76 134.07 -14.31 3.00e+00 1.11e-01 2.27e+01 angle pdb=" PB AGS D 702 " pdb=" O3B AGS D 702 " pdb=" PG AGS D 702 " ideal model delta sigma weight residual 120.12 133.86 -13.74 3.00e+00 1.11e-01 2.10e+01 angle pdb=" PA AGS B 702 " pdb=" O3A AGS B 702 " pdb=" PB AGS B 702 " ideal model delta sigma weight residual 119.76 133.19 -13.43 3.00e+00 1.11e-01 2.00e+01 angle pdb=" CA ASP B 216 " pdb=" CB ASP B 216 " pdb=" CG ASP B 216 " ideal model delta sigma weight residual 112.60 116.11 -3.51 1.00e+00 1.00e+00 1.23e+01 ... (remaining 29052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.84: 12379 31.84 - 63.67: 440 63.67 - 95.51: 27 95.51 - 127.34: 1 127.34 - 159.18: 4 Dihedral angle restraints: 12851 sinusoidal: 5519 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=" O1A AGS C 702 " pdb=" O3A AGS C 702 " pdb=" PA AGS C 702 " pdb=" PB AGS C 702 " ideal model delta sinusoidal sigma weight residual -67.73 69.61 -137.34 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" O1A AGS D 702 " pdb=" O3A AGS D 702 " pdb=" PA AGS D 702 " pdb=" PB AGS D 702 " ideal model delta sinusoidal sigma weight residual -67.73 62.76 -130.49 1 3.00e+01 1.11e-03 1.76e+01 ... (remaining 12848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 3307 0.112 - 0.223: 36 0.223 - 0.335: 0 0.335 - 0.447: 0 0.447 - 0.558: 12 Chirality restraints: 3355 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 2.35 -2.90 -0.56 2.00e-01 2.50e+01 7.79e+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 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.69e+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 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.69e+00 ... (remaining 3352 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.800 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 0.057 21275 Z= 0.180 Angle : 0.636 14.856 29081 Z= 0.319 Chirality : 0.049 0.558 3355 Planarity : 0.005 0.115 3614 Dihedral : 15.662 159.180 8093 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 0.00366 / 0.18 (21259) covalent geometry : angle 0.62399 / 0.32 (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 : 0.782 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: 0.8027 time to fit residues: 477.7812 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 : 0.669 ------------------------------------------------------------------------------- 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: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 136 GLN A 144 GLN A 146 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 137 ASN 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 295 ASN G 348 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.187360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.148788 restraints weight = 19885.806| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.52 r_work: 0.3648 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21275 Z= 0.173 Angle : 0.577 8.893 29081 Z= 0.291 Chirality : 0.040 0.162 3355 Planarity : 0.005 0.064 3614 Dihedral : 14.584 158.592 3304 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.32 % Allowed : 10.26 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.17), residues: 2515 helix: 1.91 (0.15), residues: 1271 sheet: 1.18 (0.25), residues: 394 loop : 0.37 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 80 TYR 0.017 0.001 TYR G 284 PHE 0.017 0.002 PHE F 278 TRP 0.013 0.001 TRP C 10 HIS 0.009 0.001 HIS F 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (21259) covalent geometry : angle 0.56068 / 0.29 (29057) hydrogen bonds : bond 0.04149 / 2.78 ( 1145) hydrogen bonds : angle 4.28448 / 3.14 ( 3225) metal coordination : bond 0.00368 / 0.27 ( 16) metal coordination : angle 4.72395 / 2.84 ( 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 418 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 369 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ARG cc_start: 0.8031 (ttp-110) cc_final: 0.7527 (ttp80) REVERT: A 219 ASP cc_start: 0.8242 (m-30) cc_final: 0.8041 (m-30) REVERT: A 252 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7581 (mtt180) REVERT: B 176 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8483 (mtpp) REVERT: B 208 ARG cc_start: 0.8040 (mmt180) cc_final: 0.7633 (ttp-110) REVERT: B 274 ARG cc_start: 0.7272 (ttp80) cc_final: 0.6850 (ttt90) REVERT: B 279 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7898 (tp30) REVERT: B 311 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8180 (tp) REVERT: B 350 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8567 (mt-10) REVERT: C 102 GLU cc_start: 0.7854 (tp30) cc_final: 0.7259 (pm20) REVERT: C 126 ASP cc_start: 0.8120 (t0) cc_final: 0.7565 (m-30) REVERT: C 145 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: C 148 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8235 (mm-30) REVERT: C 176 LYS cc_start: 0.8782 (mttt) cc_final: 0.8185 (mmtt) REVERT: D 26 THR cc_start: 0.8189 (m) cc_final: 0.7933 (t) REVERT: D 65 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7456 (mt-10) REVERT: D 112 GLN cc_start: 0.8284 (pt0) cc_final: 0.7520 (mm-40) REVERT: D 141 LYS cc_start: 0.8467 (tptt) cc_final: 0.8152 (tmtt) REVERT: D 145 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: D 263 ARG cc_start: 0.7875 (ttt90) cc_final: 0.7163 (ttp-170) REVERT: D 277 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: E 8 ARG cc_start: 0.8090 (tpm170) cc_final: 0.7478 (ttp80) REVERT: E 56 HIS cc_start: 0.7359 (m-70) cc_final: 0.6748 (p-80) REVERT: E 97 THR cc_start: 0.8858 (m) cc_final: 0.8564 (m) REVERT: E 138 GLU cc_start: 0.8312 (mp0) cc_final: 0.7845 (mm-30) REVERT: E 149 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: E 211 GLN cc_start: 0.8100 (tp40) cc_final: 0.7699 (mp10) REVERT: E 274 VAL cc_start: 0.8200 (m) cc_final: 0.7952 (t) REVERT: E 308 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8142 (ttp80) REVERT: F 53 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.8003 (mmt) REVERT: F 64 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8195 (mt-10) REVERT: F 73 ARG cc_start: 0.7699 (tpt-90) cc_final: 0.7309 (tpp-160) REVERT: F 140 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6720 (tm-30) REVERT: F 149 GLN cc_start: 0.7583 (pt0) cc_final: 0.7144 (mm110) REVERT: F 198 LYS cc_start: 0.8190 (mttt) cc_final: 0.7842 (mtpt) REVERT: F 215 ARG cc_start: 0.7153 (ttt180) cc_final: 0.6656 (ttp-110) REVERT: F 339 MET cc_start: 0.5935 (mmt) cc_final: 0.5378 (mmt) REVERT: G 51 MET cc_start: 0.8179 (ptp) cc_final: 0.7971 (ptt) REVERT: G 53 MET cc_start: 0.7108 (ptm) cc_final: 0.6402 (ttp) REVERT: G 182 MET cc_start: 0.7509 (mtp) cc_final: 0.6806 (mtp) REVERT: G 265 GLN cc_start: 0.8002 (mt0) cc_final: 0.7431 (mm-40) REVERT: G 278 PHE cc_start: 0.7024 (m-80) cc_final: 0.6676 (m-10) REVERT: G 303 GLU cc_start: 0.7867 (tt0) cc_final: 0.7614 (tm-30) REVERT: G 326 ASP cc_start: 0.7889 (m-30) cc_final: 0.7530 (m-30) REVERT: G 350 GLU cc_start: 0.7814 (pt0) cc_final: 0.7375 (pm20) outliers start: 49 outliers final: 18 residues processed: 400 average time/residue: 0.8063 time to fit residues: 354.7114 Evaluate side-chains 360 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 333 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 B residue 311 LEU 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 277 GLU Chi-restraints excluded: chain E residue 149 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 53 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 203 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 203 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 233 optimal weight: 10.0000 chunk 131 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 191 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 234 GLN B 13 GLN B 330 GLN C 4 GLN C 160 GLN D 204 GLN D 248 GLN D 290 HIS E 51 GLN E 333 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.186638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.145059 restraints weight = 19797.211| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.67 r_work: 0.3587 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21275 Z= 0.171 Angle : 0.572 8.744 29081 Z= 0.286 Chirality : 0.040 0.185 3355 Planarity : 0.004 0.055 3614 Dihedral : 14.613 160.702 3300 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.93 % Allowed : 11.64 % Favored : 85.43 % 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: 1.78 (0.17), residues: 2515 helix: 1.84 (0.15), residues: 1273 sheet: 1.09 (0.25), residues: 396 loop : 0.31 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 56 TYR 0.017 0.002 TYR G 284 PHE 0.017 0.002 PHE A 65 TRP 0.014 0.001 TRP C 10 HIS 0.007 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (21259) covalent geometry : angle 0.55567 / 0.28 (29057) hydrogen bonds : bond 0.03855 / 2.59 ( 1145) hydrogen bonds : angle 4.02743 / 2.95 ( 3225) metal coordination : bond 0.00346 / 0.25 ( 16) metal coordination : angle 4.77223 / 2.88 ( 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 419 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 357 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7250 (tpp) cc_final: 0.7031 (ttm) REVERT: A 18 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7265 (mtt-85) REVERT: A 149 ARG cc_start: 0.8031 (ttp-110) cc_final: 0.7416 (ttp80) REVERT: A 158 LEU cc_start: 0.8044 (mt) cc_final: 0.7806 (mp) REVERT: B 13 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8532 (mp10) REVERT: B 176 LYS cc_start: 0.8783 (mtmt) cc_final: 0.8432 (mtpp) REVERT: B 208 ARG cc_start: 0.8019 (mmt180) cc_final: 0.7552 (ttp-110) REVERT: B 274 ARG cc_start: 0.7287 (ttp80) cc_final: 0.6815 (ttt90) REVERT: B 279 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: B 350 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8564 (mt-10) REVERT: C 102 GLU cc_start: 0.7770 (tp30) cc_final: 0.7145 (pm20) REVERT: C 148 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8194 (mm-30) REVERT: C 176 LYS cc_start: 0.8829 (mttt) cc_final: 0.8137 (mmtt) REVERT: C 345 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7751 (mtt-85) REVERT: D 26 THR cc_start: 0.8137 (m) cc_final: 0.7909 (t) REVERT: D 65 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7413 (mt-10) REVERT: D 112 GLN cc_start: 0.8284 (pt0) cc_final: 0.7538 (mm-40) REVERT: D 141 LYS cc_start: 0.8408 (tptt) cc_final: 0.8073 (tmtt) REVERT: D 145 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: D 231 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7417 (mt0) REVERT: D 263 ARG cc_start: 0.7846 (ttt90) cc_final: 0.7060 (ttp-170) REVERT: D 277 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7294 (tm-30) REVERT: E 56 HIS cc_start: 0.7386 (m-70) cc_final: 0.6617 (p90) REVERT: E 97 THR cc_start: 0.8726 (m) cc_final: 0.8445 (m) REVERT: E 138 GLU cc_start: 0.8294 (mp0) cc_final: 0.7782 (mm-30) REVERT: E 211 GLN cc_start: 0.8162 (tp40) cc_final: 0.7647 (mp10) REVERT: E 308 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8337 (ttp-110) REVERT: E 324 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.6990 (mp-120) REVERT: F 53 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8004 (mmt) REVERT: F 73 ARG cc_start: 0.7667 (tpt-90) cc_final: 0.7268 (tpp-160) REVERT: F 149 GLN cc_start: 0.7640 (pt0) cc_final: 0.7229 (mm-40) REVERT: F 198 LYS cc_start: 0.8139 (mttt) cc_final: 0.7771 (mtpt) REVERT: F 220 SER cc_start: 0.8492 (t) cc_final: 0.8205 (t) REVERT: F 339 MET cc_start: 0.6363 (mmt) cc_final: 0.5680 (mmt) REVERT: G 51 MET cc_start: 0.8126 (ptp) cc_final: 0.7890 (ptt) REVERT: G 53 MET cc_start: 0.7061 (ptm) cc_final: 0.6288 (ttp) REVERT: G 236 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8317 (mt) REVERT: G 253 ASP cc_start: 0.6418 (m-30) cc_final: 0.5585 (t0) REVERT: G 265 GLN cc_start: 0.7977 (mt0) cc_final: 0.7366 (mm-40) REVERT: G 278 PHE cc_start: 0.7019 (m-80) cc_final: 0.6596 (m-10) REVERT: G 303 GLU cc_start: 0.7839 (tt0) cc_final: 0.7473 (tm-30) REVERT: G 326 ASP cc_start: 0.7813 (m-30) cc_final: 0.7434 (m-30) REVERT: G 350 GLU cc_start: 0.7705 (pt0) cc_final: 0.7221 (pm20) outliers start: 62 outliers final: 22 residues processed: 389 average time/residue: 0.7979 time to fit residues: 341.3643 Evaluate side-chains 374 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 341 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 68 ILE 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 294 MET Chi-restraints excluded: chain C residue 184 ARG 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 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 E residue 324 GLN Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 115 ASP 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 236 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 142 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 212 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS B 39 HIS B 330 GLN C 78 ASN C 160 GLN C 192 ASN D 204 GLN D 248 GLN E 333 HIS 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 = 0.4145 r_free = 0.4145 target = 0.183985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.145485 restraints weight = 19959.285| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.58 r_work: 0.3596 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21275 Z= 0.157 Angle : 0.555 7.863 29081 Z= 0.279 Chirality : 0.039 0.163 3355 Planarity : 0.004 0.055 3614 Dihedral : 14.600 157.223 3300 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.79 % Allowed : 13.48 % Favored : 83.73 % 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: 1.77 (0.17), residues: 2515 helix: 1.86 (0.14), residues: 1273 sheet: 0.99 (0.25), residues: 396 loop : 0.32 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 80 TYR 0.015 0.001 TYR B 341 PHE 0.013 0.001 PHE G 230 TRP 0.014 0.001 TRP C 10 HIS 0.006 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (21259) covalent geometry : angle 0.53931 / 0.28 (29057) hydrogen bonds : bond 0.03571 / 2.40 ( 1145) hydrogen bonds : angle 3.94946 / 2.89 ( 3225) metal coordination : bond 0.00310 / 0.23 ( 16) metal coordination : angle 4.65328 / 2.81 ( 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 413 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 354 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7341 (tpp) cc_final: 0.7071 (ttm) REVERT: A 149 ARG cc_start: 0.8124 (ttp-110) cc_final: 0.7540 (ttp80) REVERT: A 158 LEU cc_start: 0.8101 (mt) cc_final: 0.7865 (mp) REVERT: B 13 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8495 (mp10) REVERT: B 176 LYS cc_start: 0.8837 (mtmt) cc_final: 0.8526 (mtpp) REVERT: B 208 ARG cc_start: 0.8047 (mmt180) cc_final: 0.7686 (ttp-110) REVERT: B 274 ARG cc_start: 0.7340 (ttp80) cc_final: 0.6914 (ttt90) REVERT: B 279 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7864 (tp30) REVERT: B 311 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8286 (tp) REVERT: B 350 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8656 (mt-10) REVERT: C 102 GLU cc_start: 0.7929 (tp30) cc_final: 0.7262 (pm20) REVERT: C 148 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8264 (mm-30) REVERT: C 176 LYS cc_start: 0.8832 (mttt) cc_final: 0.8209 (mmtt) REVERT: C 345 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7749 (mtt-85) REVERT: D 26 THR cc_start: 0.8158 (m) cc_final: 0.7880 (t) REVERT: D 65 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7438 (mt-10) REVERT: D 112 GLN cc_start: 0.8340 (pt0) cc_final: 0.7627 (mm-40) REVERT: D 141 LYS cc_start: 0.8480 (tptt) cc_final: 0.8174 (tmtt) REVERT: D 145 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: D 231 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7402 (mt0) REVERT: D 263 ARG cc_start: 0.7916 (ttt90) cc_final: 0.7186 (ttp-170) REVERT: D 274 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.7365 (mtt90) REVERT: D 277 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7471 (tm-30) REVERT: E 56 HIS cc_start: 0.7265 (m-70) cc_final: 0.6693 (p90) REVERT: E 97 THR cc_start: 0.8760 (m) cc_final: 0.8481 (m) REVERT: E 134 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7913 (mm-30) REVERT: E 138 GLU cc_start: 0.8376 (mp0) cc_final: 0.7866 (mm-30) REVERT: E 211 GLN cc_start: 0.8223 (tp40) cc_final: 0.7793 (mp10) REVERT: E 214 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7772 (tp30) REVERT: E 308 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8359 (ttp-110) REVERT: E 324 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.6984 (mp-120) REVERT: F 53 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8069 (mmt) REVERT: F 73 ARG cc_start: 0.7751 (tpt-90) cc_final: 0.7341 (tpp-160) REVERT: F 140 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6721 (tm-30) REVERT: F 149 GLN cc_start: 0.7661 (pt0) cc_final: 0.7340 (mm-40) REVERT: F 198 LYS cc_start: 0.8231 (mttt) cc_final: 0.7892 (mtpt) REVERT: F 220 SER cc_start: 0.8455 (t) cc_final: 0.8159 (t) REVERT: F 339 MET cc_start: 0.6531 (mmt) cc_final: 0.5797 (mmt) REVERT: G 50 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6717 (tm-30) REVERT: G 53 MET cc_start: 0.7209 (ptm) cc_final: 0.6410 (ttp) REVERT: G 176 ARG cc_start: 0.8235 (ptt-90) cc_final: 0.8029 (ptt180) REVERT: G 182 MET cc_start: 0.7620 (mtp) cc_final: 0.6940 (mtt) REVERT: G 218 ILE cc_start: 0.8093 (mt) cc_final: 0.7849 (mp) REVERT: G 236 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.7316 (mp) REVERT: G 253 ASP cc_start: 0.6399 (m-30) cc_final: 0.5575 (t0) REVERT: G 277 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.6843 (mttm) REVERT: G 303 GLU cc_start: 0.7922 (tt0) cc_final: 0.7612 (tm-30) REVERT: G 326 ASP cc_start: 0.7922 (m-30) cc_final: 0.7476 (m-30) REVERT: G 350 GLU cc_start: 0.7781 (pt0) cc_final: 0.7425 (pm20) outliers start: 59 outliers final: 24 residues processed: 388 average time/residue: 0.7468 time to fit residues: 319.7078 Evaluate side-chains 373 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 334 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 13 GLN 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 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 294 MET Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 184 ARG 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 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 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 E residue 324 GLN Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 169 THR 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 129 THR Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 277 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 103 optimal weight: 0.0980 chunk 127 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 185 optimal weight: 6.9990 chunk 159 optimal weight: 0.8980 chunk 201 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 251 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN B 13 GLN B 330 GLN C 160 GLN C 192 ASN D 204 GLN D 248 GLN E 333 HIS F 329 ASN ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.193498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.151756 restraints weight = 20697.931| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.79 r_work: 0.3604 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21275 Z= 0.135 Angle : 0.533 7.897 29081 Z= 0.268 Chirality : 0.038 0.162 3355 Planarity : 0.004 0.053 3614 Dihedral : 14.546 156.512 3300 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.07 % Allowed : 13.72 % Favored : 83.21 % 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: 1.85 (0.17), residues: 2515 helix: 1.95 (0.14), residues: 1276 sheet: 1.10 (0.25), residues: 378 loop : 0.30 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 80 TYR 0.014 0.001 TYR B 341 PHE 0.017 0.001 PHE F 278 TRP 0.014 0.001 TRP C 10 HIS 0.004 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (21259) covalent geometry : angle 0.51664 / 0.27 (29057) hydrogen bonds : bond 0.03320 / 2.22 ( 1145) hydrogen bonds : angle 3.83590 / 2.81 ( 3225) metal coordination : bond 0.00273 / 0.21 ( 16) metal coordination : angle 4.52774 / 2.74 ( 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 416 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 351 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7213 (mtt-85) REVERT: A 149 ARG cc_start: 0.8100 (ttp-110) cc_final: 0.7525 (ttp80) REVERT: A 158 LEU cc_start: 0.8106 (mt) cc_final: 0.7897 (mp) REVERT: B 13 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8492 (mp10) REVERT: B 176 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8506 (mtpp) REVERT: B 208 ARG cc_start: 0.8020 (mmt180) cc_final: 0.7650 (ttp-110) REVERT: B 274 ARG cc_start: 0.7300 (ttp80) cc_final: 0.6890 (ttt90) REVERT: B 279 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7843 (tp30) REVERT: B 311 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8302 (tp) REVERT: B 350 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8572 (mt-10) REVERT: C 102 GLU cc_start: 0.7946 (tp30) cc_final: 0.7235 (pm20) REVERT: C 148 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8289 (mm-30) REVERT: C 176 LYS cc_start: 0.8823 (mttt) cc_final: 0.8184 (mmtt) REVERT: C 181 GLU cc_start: 0.8055 (tp30) cc_final: 0.7617 (mp0) REVERT: C 184 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7394 (tmm160) REVERT: C 345 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7738 (mtt-85) REVERT: D 26 THR cc_start: 0.8055 (m) cc_final: 0.7774 (t) REVERT: D 112 GLN cc_start: 0.8282 (pt0) cc_final: 0.7617 (mm-40) REVERT: D 141 LYS cc_start: 0.8440 (tptt) cc_final: 0.8120 (tmtt) REVERT: D 145 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7866 (mt-10) REVERT: D 231 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7440 (mt0) REVERT: D 263 ARG cc_start: 0.7876 (ttt90) cc_final: 0.7140 (ttp-170) REVERT: D 274 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7447 (mtm-85) REVERT: D 277 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: E 56 HIS cc_start: 0.7239 (m-70) cc_final: 0.6692 (p90) REVERT: E 97 THR cc_start: 0.8718 (m) cc_final: 0.8444 (m) REVERT: E 98 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7403 (tm-30) REVERT: E 122 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8295 (m-30) REVERT: E 134 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7895 (mm-30) REVERT: E 138 GLU cc_start: 0.8385 (mp0) cc_final: 0.7859 (mm-30) REVERT: E 211 GLN cc_start: 0.8218 (tp40) cc_final: 0.7775 (mp10) REVERT: E 214 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7791 (tp30) REVERT: E 324 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.6945 (mp-120) REVERT: F 53 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8052 (mmt) REVERT: F 73 ARG cc_start: 0.7726 (tpt-90) cc_final: 0.7336 (tpp-160) REVERT: F 140 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6732 (tm-30) REVERT: F 149 GLN cc_start: 0.7631 (pt0) cc_final: 0.7336 (mm-40) REVERT: F 198 LYS cc_start: 0.8200 (mttt) cc_final: 0.7854 (mtpt) REVERT: F 220 SER cc_start: 0.8475 (t) cc_final: 0.8169 (t) REVERT: F 339 MET cc_start: 0.6601 (mmt) cc_final: 0.5939 (mmt) REVERT: G 50 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6661 (tm-30) REVERT: G 53 MET cc_start: 0.7189 (ptm) cc_final: 0.6378 (ttp) REVERT: G 165 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7133 (tp30) REVERT: G 218 ILE cc_start: 0.8095 (mt) cc_final: 0.7854 (mp) REVERT: G 236 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8337 (mt) REVERT: G 246 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6686 (mmp-170) REVERT: G 253 ASP cc_start: 0.6328 (m-30) cc_final: 0.5554 (t0) REVERT: G 277 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.6957 (mttm) REVERT: G 298 GLU cc_start: 0.6989 (mp0) cc_final: 0.6607 (mt-10) REVERT: G 303 GLU cc_start: 0.7942 (tt0) cc_final: 0.7664 (tm-30) REVERT: G 326 ASP cc_start: 0.7907 (m-30) cc_final: 0.7536 (m-30) REVERT: G 350 GLU cc_start: 0.7828 (pt0) cc_final: 0.7489 (pm20) outliers start: 65 outliers final: 25 residues processed: 385 average time/residue: 0.7599 time to fit residues: 321.7533 Evaluate side-chains 378 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 333 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain B residue 13 GLN 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 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 294 MET Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 184 ARG 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 240 MET Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 274 VAL 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 E residue 324 GLN Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 169 THR 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 165 GLU Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 246 ARG Chi-restraints excluded: chain G residue 277 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 179 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 24 optimal weight: 0.0010 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 198 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 78 ASN C 160 GLN C 192 ASN D 204 GLN D 248 GLN E 333 HIS F 329 ASN ** 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 = 0.4215 r_free = 0.4215 target = 0.194531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.151775 restraints weight = 20760.296| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.70 r_work: 0.3633 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21275 Z= 0.111 Angle : 0.504 7.771 29081 Z= 0.256 Chirality : 0.037 0.161 3355 Planarity : 0.004 0.052 3614 Dihedral : 14.475 155.967 3300 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.22 % Allowed : 13.95 % 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: 1.98 (0.17), residues: 2515 helix: 2.07 (0.15), residues: 1279 sheet: 1.07 (0.25), residues: 385 loop : 0.37 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 80 TYR 0.014 0.001 TYR B 341 PHE 0.015 0.001 PHE G 230 TRP 0.013 0.001 TRP C 10 HIS 0.003 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (21259) covalent geometry : angle 0.48858 / 0.26 (29057) hydrogen bonds : bond 0.03038 / 2.03 ( 1145) hydrogen bonds : angle 3.73990 / 2.73 ( 3225) metal coordination : bond 0.00239 / 0.18 ( 16) metal coordination : angle 4.37835 / 2.65 ( 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 411 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 343 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7208 (mtt-85) REVERT: A 149 ARG cc_start: 0.8072 (ttp-110) cc_final: 0.7505 (ttp80) REVERT: B 176 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8506 (mtpp) REVERT: B 208 ARG cc_start: 0.8037 (mmt180) cc_final: 0.7661 (ttp-110) REVERT: B 274 ARG cc_start: 0.7252 (ttp80) cc_final: 0.6878 (ttt90) REVERT: B 279 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7807 (tp30) REVERT: B 311 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8301 (tp) REVERT: B 350 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8517 (mt-10) REVERT: C 148 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8250 (mm-30) REVERT: C 176 LYS cc_start: 0.8758 (mttt) cc_final: 0.8131 (mmtt) REVERT: C 181 GLU cc_start: 0.7922 (tp30) cc_final: 0.7563 (mp0) REVERT: C 345 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7672 (mtt-85) REVERT: D 112 GLN cc_start: 0.8206 (pt0) cc_final: 0.7578 (mm-40) REVERT: D 141 LYS cc_start: 0.8378 (tptt) cc_final: 0.8052 (tmtt) REVERT: D 145 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7758 (mt-10) REVERT: D 180 VAL cc_start: 0.8230 (t) cc_final: 0.7867 (m) REVERT: D 231 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7374 (mt0) REVERT: D 263 ARG cc_start: 0.7849 (ttt90) cc_final: 0.7113 (ttp-170) REVERT: D 274 ARG cc_start: 0.7656 (mtm-85) cc_final: 0.7389 (mtt90) REVERT: D 277 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: E 56 HIS cc_start: 0.7202 (m-70) cc_final: 0.6652 (p90) REVERT: E 97 THR cc_start: 0.8685 (m) cc_final: 0.8398 (m) REVERT: E 98 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: E 122 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8273 (m-30) REVERT: E 134 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7821 (mm-30) REVERT: E 138 GLU cc_start: 0.8354 (mp0) cc_final: 0.7855 (mm-30) REVERT: E 211 GLN cc_start: 0.8189 (tp40) cc_final: 0.7757 (mp10) REVERT: E 214 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7705 (tp30) REVERT: E 324 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6926 (mp-120) REVERT: F 53 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7947 (mmt) REVERT: F 73 ARG cc_start: 0.7700 (tpt-90) cc_final: 0.7314 (tpp-160) REVERT: F 149 GLN cc_start: 0.7579 (pt0) cc_final: 0.7349 (mm-40) REVERT: F 198 LYS cc_start: 0.8183 (mttt) cc_final: 0.7849 (mtpt) REVERT: F 220 SER cc_start: 0.8448 (t) cc_final: 0.8174 (t) REVERT: F 339 MET cc_start: 0.6525 (mmt) cc_final: 0.5821 (mmt) REVERT: G 1 MET cc_start: 0.3653 (mmm) cc_final: 0.0719 (mmm) REVERT: G 50 GLU cc_start: 0.6923 (tm-30) cc_final: 0.6602 (tm-30) REVERT: G 53 MET cc_start: 0.7188 (ptm) cc_final: 0.6417 (ttt) REVERT: G 165 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7033 (tp30) REVERT: G 236 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8314 (mt) REVERT: G 246 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6689 (mmp-170) REVERT: G 253 ASP cc_start: 0.6284 (m-30) cc_final: 0.5530 (t0) REVERT: G 277 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6964 (mttm) REVERT: G 298 GLU cc_start: 0.6989 (mp0) cc_final: 0.6638 (mt-10) REVERT: G 303 GLU cc_start: 0.7873 (tt0) cc_final: 0.7588 (tm-30) REVERT: G 326 ASP cc_start: 0.7835 (m-30) cc_final: 0.7471 (m-30) REVERT: G 350 GLU cc_start: 0.7760 (pt0) cc_final: 0.7502 (pm20) outliers start: 68 outliers final: 28 residues processed: 381 average time/residue: 0.7723 time to fit residues: 324.3438 Evaluate side-chains 379 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 334 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain B residue 5 VAL 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 294 MET 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 240 MET Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 274 VAL 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 E residue 324 GLN Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 246 ARG Chi-restraints excluded: chain G residue 277 LYS 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: 6.9990 chunk 89 optimal weight: 0.9980 chunk 213 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN B 13 GLN B 330 GLN C 160 GLN C 192 ASN D 84 GLN D 204 GLN D 248 GLN E 333 HIS F 329 ASN ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.181869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.141563 restraints weight = 19953.955| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.56 r_work: 0.3568 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21275 Z= 0.211 Angle : 0.615 8.571 29081 Z= 0.305 Chirality : 0.041 0.187 3355 Planarity : 0.005 0.057 3614 Dihedral : 14.706 156.211 3300 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.12 % Allowed : 14.10 % Favored : 82.78 % 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: 1.64 (0.17), residues: 2515 helix: 1.75 (0.14), residues: 1281 sheet: 0.82 (0.24), residues: 413 loop : 0.31 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 80 TYR 0.018 0.002 TYR B 341 PHE 0.016 0.002 PHE G 230 TRP 0.013 0.002 TRP C 10 HIS 0.007 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (21259) covalent geometry : angle 0.60047 / 0.30 (29057) hydrogen bonds : bond 0.03954 / 2.65 ( 1145) hydrogen bonds : angle 3.93935 / 2.89 ( 3225) metal coordination : bond 0.00388 / 0.29 ( 16) metal coordination : angle 4.74183 / 2.88 ( 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 393 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 327 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.7205 (m-40) cc_final: 0.6628 (m-40) REVERT: A 149 ARG cc_start: 0.8129 (ttp-110) cc_final: 0.7584 (ttp80) REVERT: B 68 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7018 (tt) REVERT: B 176 LYS cc_start: 0.8894 (mtmt) cc_final: 0.8600 (mtpp) REVERT: B 208 ARG cc_start: 0.8085 (mmt180) cc_final: 0.7692 (ttp-110) REVERT: B 274 ARG cc_start: 0.7430 (ttp80) cc_final: 0.7007 (ttt90) REVERT: B 279 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: B 311 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8317 (tp) REVERT: B 350 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8626 (mt-10) REVERT: C 148 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8359 (mm-30) REVERT: C 345 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7750 (mtt-85) REVERT: D 112 GLN cc_start: 0.8174 (pt0) cc_final: 0.7593 (mm-40) REVERT: D 141 LYS cc_start: 0.8530 (tptt) cc_final: 0.8191 (tmtt) REVERT: D 145 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: D 231 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7395 (mt0) REVERT: D 263 ARG cc_start: 0.7970 (ttt90) cc_final: 0.7216 (ttp-170) REVERT: D 274 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7496 (mtm-85) REVERT: D 277 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7529 (tm-30) REVERT: E 56 HIS cc_start: 0.7350 (m-70) cc_final: 0.6670 (p90) REVERT: E 97 THR cc_start: 0.8801 (m) cc_final: 0.8558 (m) REVERT: E 98 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: E 134 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7833 (mm-30) REVERT: E 138 GLU cc_start: 0.8425 (mp0) cc_final: 0.7845 (mm-30) REVERT: E 211 GLN cc_start: 0.8272 (tp40) cc_final: 0.7864 (mp10) REVERT: E 214 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7750 (tp30) REVERT: E 324 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7039 (mp-120) REVERT: F 53 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8161 (mmt) REVERT: F 73 ARG cc_start: 0.7867 (tpt-90) cc_final: 0.7415 (tpp-160) REVERT: F 149 GLN cc_start: 0.7776 (pt0) cc_final: 0.7450 (mm-40) REVERT: F 198 LYS cc_start: 0.8226 (mttt) cc_final: 0.7881 (mtpt) REVERT: F 220 SER cc_start: 0.8482 (t) cc_final: 0.8191 (t) REVERT: G 1 MET cc_start: 0.3710 (tmm) cc_final: 0.0632 (mmm) REVERT: G 50 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6781 (tm-30) REVERT: G 53 MET cc_start: 0.7337 (ptm) cc_final: 0.6522 (ttp) REVERT: G 165 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7108 (tp30) REVERT: G 236 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8420 (mt) REVERT: G 253 ASP cc_start: 0.6440 (m-30) cc_final: 0.5628 (t0) REVERT: G 264 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7887 (ttpt) REVERT: G 265 GLN cc_start: 0.7980 (mt0) cc_final: 0.7477 (mm-40) REVERT: G 277 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.6993 (mttm) REVERT: G 303 GLU cc_start: 0.7924 (tt0) cc_final: 0.7720 (tm-30) REVERT: G 326 ASP cc_start: 0.8025 (m-30) cc_final: 0.7625 (m-30) REVERT: G 350 GLU cc_start: 0.7864 (pt0) cc_final: 0.7426 (pm20) REVERT: G 355 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6770 (pt0) outliers start: 66 outliers final: 32 residues processed: 364 average time/residue: 0.7634 time to fit residues: 306.9516 Evaluate side-chains 367 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 318 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 5 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 B residue 294 MET Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain D residue 26 THR 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 257 VAL Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 324 GLN Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 264 LYS Chi-restraints excluded: chain G residue 277 LYS Chi-restraints excluded: chain G residue 355 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 135 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 139 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 GLN C 160 GLN C 192 ASN D 204 GLN D 248 GLN E 333 HIS F 320 ASN F 329 ASN G 143 GLN ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.193540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.150581 restraints weight = 20605.809| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.71 r_work: 0.3628 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21275 Z= 0.120 Angle : 0.522 8.005 29081 Z= 0.263 Chirality : 0.038 0.160 3355 Planarity : 0.004 0.052 3614 Dihedral : 14.527 155.365 3300 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.65 % Allowed : 14.85 % Favored : 82.50 % 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: 1.85 (0.17), residues: 2515 helix: 1.99 (0.14), residues: 1279 sheet: 0.75 (0.24), residues: 416 loop : 0.39 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 80 TYR 0.015 0.001 TYR B 341 PHE 0.018 0.001 PHE G 319 TRP 0.015 0.001 TRP B 10 HIS 0.004 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (21259) covalent geometry : angle 0.50549 / 0.26 (29057) hydrogen bonds : bond 0.03129 / 2.09 ( 1145) hydrogen bonds : angle 3.75142 / 2.75 ( 3225) metal coordination : bond 0.00237 / 0.19 ( 16) metal coordination : angle 4.59161 / 2.79 ( 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 391 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 335 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.7101 (m-40) cc_final: 0.6584 (m-40) REVERT: A 149 ARG cc_start: 0.8095 (ttp-110) cc_final: 0.7582 (ttp80) REVERT: B 68 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7097 (tt) REVERT: B 133 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7265 (ttp-110) REVERT: B 176 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8544 (mtpp) REVERT: B 208 ARG cc_start: 0.7997 (mmt180) cc_final: 0.7684 (ttp-110) REVERT: B 274 ARG cc_start: 0.7325 (ttp80) cc_final: 0.6963 (ttt90) REVERT: B 279 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7810 (tp30) REVERT: B 311 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8310 (tp) REVERT: B 350 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8548 (mt-10) REVERT: C 80 ARG cc_start: 0.7691 (mtm110) cc_final: 0.7438 (mtm110) REVERT: C 148 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8287 (mm-30) REVERT: C 176 LYS cc_start: 0.8784 (mttt) cc_final: 0.8147 (mmtt) REVERT: C 216 ASP cc_start: 0.8172 (m-30) cc_final: 0.7936 (m-30) REVERT: C 345 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7699 (mtt-85) REVERT: D 112 GLN cc_start: 0.8152 (pt0) cc_final: 0.7589 (mm-40) REVERT: D 141 LYS cc_start: 0.8410 (tptt) cc_final: 0.8094 (tmtt) REVERT: D 145 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: D 231 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7343 (mt0) REVERT: D 263 ARG cc_start: 0.7866 (ttt90) cc_final: 0.7152 (ttp-170) REVERT: D 274 ARG cc_start: 0.7673 (mtm-85) cc_final: 0.7398 (mtt90) REVERT: D 277 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: E 56 HIS cc_start: 0.7273 (m-70) cc_final: 0.6651 (p90) REVERT: E 97 THR cc_start: 0.8724 (m) cc_final: 0.8444 (m) REVERT: E 122 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8226 (m-30) REVERT: E 134 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: E 138 GLU cc_start: 0.8352 (mp0) cc_final: 0.7821 (mm-30) REVERT: E 211 GLN cc_start: 0.8201 (tp40) cc_final: 0.7818 (mp10) REVERT: E 214 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7662 (tp30) REVERT: E 274 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7995 (t) REVERT: E 324 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.6963 (mp-120) REVERT: F 53 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8040 (mmt) REVERT: F 73 ARG cc_start: 0.7699 (tpt-90) cc_final: 0.7350 (tpp-160) REVERT: F 109 SER cc_start: 0.8782 (m) cc_final: 0.8581 (p) REVERT: F 149 GLN cc_start: 0.7625 (pt0) cc_final: 0.7391 (mm-40) REVERT: F 198 LYS cc_start: 0.8190 (mttt) cc_final: 0.7863 (mtpt) REVERT: F 220 SER cc_start: 0.8442 (t) cc_final: 0.8196 (t) REVERT: F 339 MET cc_start: 0.6827 (mtm) cc_final: 0.6515 (ttm) REVERT: G 1 MET cc_start: 0.3605 (tmm) cc_final: 0.0608 (mmm) REVERT: G 50 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6397 (tm-30) REVERT: G 53 MET cc_start: 0.7302 (ptm) cc_final: 0.6554 (ttt) REVERT: G 165 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7121 (tp30) REVERT: G 215 ARG cc_start: 0.7508 (ttt-90) cc_final: 0.7127 (ttt180) REVERT: G 236 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8371 (mt) REVERT: G 253 ASP cc_start: 0.6405 (m-30) cc_final: 0.5647 (t0) REVERT: G 265 GLN cc_start: 0.7955 (mt0) cc_final: 0.7431 (mm-40) REVERT: G 277 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6981 (mttm) REVERT: G 303 GLU cc_start: 0.7866 (tt0) cc_final: 0.7653 (tm-30) REVERT: G 315 MET cc_start: 0.7142 (ptm) cc_final: 0.6704 (ttm) REVERT: G 326 ASP cc_start: 0.7907 (m-30) cc_final: 0.7556 (m-30) REVERT: G 332 LYS cc_start: 0.6912 (pttt) cc_final: 0.6545 (pptt) REVERT: G 350 GLU cc_start: 0.7878 (pt0) cc_final: 0.7463 (pm20) outliers start: 56 outliers final: 26 residues processed: 366 average time/residue: 0.7968 time to fit residues: 320.9942 Evaluate side-chains 369 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 327 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 136 PHE 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 B residue 363 MET 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 257 VAL Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 324 GLN Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 236 LEU 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: 4.9990 chunk 39 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 232 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 GLN C 160 GLN C 192 ASN D 204 GLN D 248 GLN 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 = 0.4141 r_free = 0.4141 target = 0.183367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.143968 restraints weight = 19860.797| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.53 r_work: 0.3589 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21275 Z= 0.155 Angle : 0.562 8.694 29081 Z= 0.280 Chirality : 0.039 0.165 3355 Planarity : 0.004 0.055 3614 Dihedral : 14.523 155.336 3300 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.84 % Allowed : 14.85 % Favored : 82.31 % 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: 1.79 (0.17), residues: 2515 helix: 1.90 (0.14), residues: 1281 sheet: 0.74 (0.24), residues: 417 loop : 0.40 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 80 TYR 0.017 0.001 TYR B 341 PHE 0.018 0.001 PHE G 319 TRP 0.012 0.001 TRP C 10 HIS 0.005 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (21259) covalent geometry : angle 0.54700 / 0.28 (29057) hydrogen bonds : bond 0.03446 / 2.31 ( 1145) hydrogen bonds : angle 3.79942 / 2.78 ( 3225) metal coordination : bond 0.00311 / 0.24 ( 16) metal coordination : angle 4.51478 / 2.74 ( 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 396 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 336 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.7250 (m-40) cc_final: 0.6674 (m-40) REVERT: A 149 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7597 (ttp80) REVERT: B 68 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7176 (tt) REVERT: B 133 ARG cc_start: 0.8051 (ttm-80) cc_final: 0.7306 (ttp-110) REVERT: B 176 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8599 (mtpp) REVERT: B 208 ARG cc_start: 0.8065 (mmt180) cc_final: 0.7670 (ttp-110) REVERT: B 274 ARG cc_start: 0.7408 (ttp80) cc_final: 0.6938 (ttt90) REVERT: B 279 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: B 311 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8302 (tp) REVERT: B 350 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8597 (mt-10) REVERT: C 148 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8323 (mm-30) REVERT: C 345 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7732 (mtt-85) REVERT: D 60 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7996 (ttmm) REVERT: D 112 GLN cc_start: 0.8198 (pt0) cc_final: 0.7596 (mm-40) REVERT: D 141 LYS cc_start: 0.8484 (tptt) cc_final: 0.8158 (tmtt) REVERT: D 145 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7884 (mt-10) REVERT: D 231 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7361 (mt0) REVERT: D 263 ARG cc_start: 0.7904 (ttt90) cc_final: 0.7148 (ttp-170) REVERT: D 277 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: E 56 HIS cc_start: 0.7331 (m-70) cc_final: 0.6666 (p90) REVERT: E 97 THR cc_start: 0.8785 (m) cc_final: 0.8532 (m) REVERT: E 134 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7766 (mm-30) REVERT: E 138 GLU cc_start: 0.8408 (mp0) cc_final: 0.7829 (mm-30) REVERT: E 211 GLN cc_start: 0.8243 (tp40) cc_final: 0.7797 (mp10) REVERT: E 214 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7716 (tp30) REVERT: E 228 ASP cc_start: 0.8553 (t0) cc_final: 0.8337 (t70) REVERT: E 324 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.6984 (mp-120) REVERT: F 53 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8107 (mmt) REVERT: F 73 ARG cc_start: 0.7757 (tpt-90) cc_final: 0.7364 (tpp-160) REVERT: F 95 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7866 (tp30) REVERT: F 109 SER cc_start: 0.8816 (m) cc_final: 0.8608 (p) REVERT: F 136 LYS cc_start: 0.7359 (tttt) cc_final: 0.7152 (ttmt) REVERT: F 149 GLN cc_start: 0.7710 (pt0) cc_final: 0.7405 (mm-40) REVERT: F 198 LYS cc_start: 0.8216 (mttt) cc_final: 0.7875 (mtpt) REVERT: F 220 SER cc_start: 0.8474 (t) cc_final: 0.8195 (t) REVERT: F 339 MET cc_start: 0.6874 (mtm) cc_final: 0.6490 (mtm) REVERT: G 1 MET cc_start: 0.3662 (tmm) cc_final: 0.0517 (mmm) REVERT: G 50 GLU cc_start: 0.6963 (tm-30) cc_final: 0.6469 (tm-30) REVERT: G 53 MET cc_start: 0.7334 (ptm) cc_final: 0.6553 (ttp) REVERT: G 165 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7101 (tp30) REVERT: G 236 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8435 (mt) REVERT: G 253 ASP cc_start: 0.6429 (m-30) cc_final: 0.5608 (t0) REVERT: G 264 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.7846 (ttpt) REVERT: G 265 GLN cc_start: 0.7995 (mt0) cc_final: 0.7463 (mm-40) REVERT: G 277 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7016 (mttm) REVERT: G 303 GLU cc_start: 0.7935 (tt0) cc_final: 0.7709 (tm-30) REVERT: G 315 MET cc_start: 0.7234 (ptm) cc_final: 0.6759 (ttm) REVERT: G 326 ASP cc_start: 0.7996 (m-30) cc_final: 0.7624 (m-30) REVERT: G 350 GLU cc_start: 0.7897 (pt0) cc_final: 0.7472 (pm20) outliers start: 60 outliers final: 33 residues processed: 370 average time/residue: 0.7858 time to fit residues: 319.9473 Evaluate side-chains 376 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 327 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP 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 136 PHE Chi-restraints excluded: chain B residue 157 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 294 MET Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 363 MET 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 60 LYS Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 257 VAL 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 274 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 324 GLN Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 179 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 Chi-restraints excluded: chain G residue 264 LYS 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: 8.9990 chunk 50 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 219 optimal weight: 20.0000 chunk 7 optimal weight: 0.1980 chunk 147 optimal weight: 0.5980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 HIS B 330 GLN C 160 GLN C 192 ASN D 204 GLN E 333 HIS F 320 ASN F 329 ASN G 143 GLN ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.183640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.144200 restraints weight = 19992.847| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.56 r_work: 0.3562 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21275 Z= 0.144 Angle : 0.550 7.901 29081 Z= 0.275 Chirality : 0.039 0.163 3355 Planarity : 0.004 0.058 3614 Dihedral : 14.433 158.162 3300 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.55 % Allowed : 15.61 % Favored : 81.84 % 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: 1.79 (0.17), residues: 2515 helix: 1.92 (0.14), residues: 1279 sheet: 0.69 (0.24), residues: 417 loop : 0.40 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 80 TYR 0.018 0.001 TYR B 341 PHE 0.022 0.001 PHE G 319 TRP 0.014 0.001 TRP B 10 HIS 0.005 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (21259) covalent geometry : angle 0.53394 / 0.27 (29057) hydrogen bonds : bond 0.03334 / 2.23 ( 1145) hydrogen bonds : angle 3.78311 / 2.77 ( 3225) metal coordination : bond 0.00279 / 0.22 ( 16) metal coordination : angle 4.58475 / 2.78 ( 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 384 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 330 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.7247 (m-40) cc_final: 0.6679 (m-40) REVERT: A 149 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7639 (ttp80) REVERT: A 285 MET cc_start: 0.8483 (ptp) cc_final: 0.8271 (ptp) REVERT: B 68 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7221 (tt) REVERT: B 133 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7299 (ttp-110) REVERT: B 176 LYS cc_start: 0.8889 (mtmt) cc_final: 0.8571 (mtpp) REVERT: B 208 ARG cc_start: 0.8118 (mmt180) cc_final: 0.7689 (ttp-110) REVERT: B 274 ARG cc_start: 0.7452 (ttp80) cc_final: 0.7042 (ttt90) REVERT: B 279 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.7946 (tp30) REVERT: B 311 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8330 (tp) REVERT: B 350 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8639 (mt-10) REVERT: C 80 ARG cc_start: 0.7804 (mtm110) cc_final: 0.7563 (mtm110) REVERT: C 148 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8355 (mm-30) REVERT: C 305 ASP cc_start: 0.7053 (m-30) cc_final: 0.6825 (m-30) REVERT: C 345 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7772 (mtt-85) REVERT: D 60 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8033 (ttmm) REVERT: D 112 GLN cc_start: 0.8206 (pt0) cc_final: 0.7597 (mm-40) REVERT: D 141 LYS cc_start: 0.8490 (tptt) cc_final: 0.8167 (tmtt) REVERT: D 145 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7914 (mt-10) REVERT: D 231 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7347 (mt0) REVERT: D 263 ARG cc_start: 0.7926 (ttt90) cc_final: 0.7172 (ttp-170) REVERT: D 274 ARG cc_start: 0.7726 (mtm-85) cc_final: 0.7449 (mtm-85) REVERT: D 277 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: E 56 HIS cc_start: 0.7395 (m-70) cc_final: 0.6694 (p90) REVERT: E 97 THR cc_start: 0.8794 (m) cc_final: 0.8541 (m) REVERT: E 98 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: E 134 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7789 (mm-30) REVERT: E 138 GLU cc_start: 0.8479 (mp0) cc_final: 0.7874 (mm-30) REVERT: E 211 GLN cc_start: 0.8288 (tp40) cc_final: 0.7831 (mp10) REVERT: E 214 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7795 (tp30) REVERT: E 228 ASP cc_start: 0.8589 (t0) cc_final: 0.8373 (t70) REVERT: E 324 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.6946 (mp-120) REVERT: F 53 MET cc_start: 0.8483 (mtt) cc_final: 0.8217 (mmt) REVERT: F 73 ARG cc_start: 0.7937 (tpt-90) cc_final: 0.7444 (tpp-160) REVERT: F 95 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7882 (tp30) REVERT: F 109 SER cc_start: 0.8830 (m) cc_final: 0.8625 (p) REVERT: F 136 LYS cc_start: 0.7351 (tttt) cc_final: 0.7130 (ttmt) REVERT: F 149 GLN cc_start: 0.7649 (pt0) cc_final: 0.7386 (mm-40) REVERT: F 198 LYS cc_start: 0.8242 (mttt) cc_final: 0.7911 (mtpt) REVERT: F 220 SER cc_start: 0.8484 (t) cc_final: 0.8195 (t) REVERT: F 291 LYS cc_start: 0.6386 (mttp) cc_final: 0.5941 (ptmt) REVERT: F 339 MET cc_start: 0.6881 (mtm) cc_final: 0.6522 (mtm) REVERT: G 1 MET cc_start: 0.3643 (tmm) cc_final: 0.0565 (mmm) REVERT: G 50 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6603 (tm-30) REVERT: G 53 MET cc_start: 0.7384 (ptm) cc_final: 0.6547 (ttp) REVERT: G 97 MET cc_start: 0.4319 (ttm) cc_final: 0.3728 (tpt) REVERT: G 165 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7076 (tp30) REVERT: G 236 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8470 (mt) REVERT: G 253 ASP cc_start: 0.6425 (m-30) cc_final: 0.5592 (t0) REVERT: G 265 GLN cc_start: 0.8024 (mt0) cc_final: 0.7477 (mm-40) REVERT: G 277 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.6996 (mttm) REVERT: G 303 GLU cc_start: 0.8005 (tt0) cc_final: 0.7763 (tm-30) REVERT: G 314 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6044 (tp30) REVERT: G 315 MET cc_start: 0.7281 (ptm) cc_final: 0.6526 (ttm) REVERT: G 326 ASP cc_start: 0.8086 (m-30) cc_final: 0.7664 (m-30) REVERT: G 350 GLU cc_start: 0.7952 (pt0) cc_final: 0.7605 (pm20) outliers start: 54 outliers final: 35 residues processed: 363 average time/residue: 0.8054 time to fit residues: 322.3941 Evaluate side-chains 373 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 323 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 156 LYS 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 136 PHE 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 294 MET Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 363 MET 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 26 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 324 GLN Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 179 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 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 195 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 chunk 104 optimal weight: 0.3980 chunk 90 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 125 optimal weight: 0.4980 chunk 80 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 GLN C 160 GLN C 192 ASN D 204 GLN F 329 ASN G 15 GLN 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 = 0.4154 r_free = 0.4154 target = 0.184748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.144496 restraints weight = 19957.064| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.59 r_work: 0.3623 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21275 Z= 0.119 Angle : 0.526 7.759 29081 Z= 0.266 Chirality : 0.038 0.160 3355 Planarity : 0.004 0.059 3614 Dihedral : 14.359 160.682 3300 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.37 % Allowed : 15.94 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.90 (0.17), residues: 2515 helix: 2.04 (0.15), residues: 1278 sheet: 0.73 (0.24), residues: 415 loop : 0.44 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 80 TYR 0.017 0.001 TYR B 341 PHE 0.013 0.001 PHE G 76 TRP 0.015 0.001 TRP B 10 HIS 0.004 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (21259) covalent geometry : angle 0.51088 / 0.26 (29057) hydrogen bonds : bond 0.03101 / 2.07 ( 1145) hydrogen bonds : angle 3.72575 / 2.73 ( 3225) metal coordination : bond 0.00238 / 0.18 ( 16) metal coordination : angle 4.43457 / 2.68 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9597.93 seconds wall clock time: 163 minutes 20.14 seconds (9800.14 seconds total)