Starting phenix.real_space_refine on Sat Jul 4 14:03:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyn_71027/07_2026/9oyn_71027.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyn_71027/07_2026/9oyn_71027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oyn_71027/07_2026/9oyn_71027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyn_71027/07_2026/9oyn_71027.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oyn_71027/07_2026/9oyn_71027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyn_71027/07_2026/9oyn_71027.map" } resolution = 2.7 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 55 5.49 5 Mg 3 5.21 5 S 112 5.16 5 C 12929 2.51 5 N 3720 2.21 5 O 3979 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20802 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: 2807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2807 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 14, 'TRANS': 346} Chain: "E" Number of atoms: 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 80.088 85.072 113.725 1.00 72.80 S ATOM 3269 SG CYS B 73 83.828 84.555 113.863 1.00 93.59 S ATOM 3286 SG CYS B 76 81.675 81.528 114.518 1.00101.98 S ATOM 3308 SG CYS B 79 81.673 82.918 111.096 1.00 85.36 S ATOM 6049 SG CYS C 64 102.760 55.670 85.128 1.00 67.86 S ATOM 6109 SG CYS C 73 104.509 52.987 83.176 1.00 79.70 S ATOM 6126 SG CYS C 76 101.688 51.881 85.365 1.00 96.09 S ATOM 6148 SG CYS C 79 100.802 53.846 82.403 1.00 76.58 S ATOM 8922 SG CYS D 64 80.623 28.795 54.106 1.00 93.02 S ATOM 8982 SG CYS D 73 78.881 26.292 51.932 1.00120.44 S ATOM 8999 SG CYS D 76 77.594 26.750 55.469 1.00112.48 S ATOM 9021 SG CYS D 79 77.020 29.460 52.964 1.00106.32 S ATOM 11645 SG CYS E 50 34.516 34.275 48.863 1.00 93.31 S ATOM 11714 SG CYS E 59 31.047 33.214 49.714 1.00 90.71 S ATOM 11734 SG CYS E 62 33.405 33.609 52.561 1.00 98.56 S ATOM 11755 SG CYS E 65 32.312 36.710 50.773 1.00 99.59 S Time building chain proxies: 4.12, per 1000 atoms: 0.20 Number of scatterers: 20802 At special positions: 0 Unit cell: (115.092, 123.372, 148.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 112 16.00 P 55 15.00 Mg 3 11.99 O 3979 8.00 N 3720 7.00 C 12929 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 622.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 79 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 64 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 76 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 79 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 73 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 76 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 64 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 73 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 79 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 76 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 64 " pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 62 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 59 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 65 " Number of angles added : 24 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 13 sheets defined 55.6% alpha, 14.8% beta 15 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'A' and resid 5 through 7 No H-bonds generated for 'chain 'A' and resid 5 through 7' Processing helix chain 'A' and resid 8 through 15 Processing helix chain 'A' and resid 27 through 46 Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.941A pdb=" N GLU A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.564A 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 204 removed outlier: 3.628A pdb=" N GLN A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 225 through 240 Processing helix chain 'A' and resid 242 through 264 removed outlier: 3.760A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 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 removed outlier: 3.518A pdb=" N GLU A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 21 through 34 removed outlier: 4.257A 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: 4.027A 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 removed outlier: 3.582A pdb=" N ASP B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) 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 128 through 131 Processing helix chain 'B' and resid 132 through 145 removed outlier: 4.054A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 removed outlier: 3.930A pdb=" N LYS B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 179 through 195 Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.842A pdb=" N GLU B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 229 removed outlier: 3.579A pdb=" N ALA B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 247 through 258 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 277 through 296 Processing helix chain 'B' and resid 298 through 302 removed outlier: 3.779A pdb=" N LEU B 302 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.701A pdb=" N MET B 306 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.604A 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 21 through 35 Processing helix chain 'C' and resid 50 through 64 Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 100 through 110 removed outlier: 3.699A pdb=" N ASN C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 131 Processing helix chain 'C' and resid 132 through 139 Processing helix chain 'C' and resid 139 through 145 Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 163 through 169 removed outlier: 3.609A pdb=" N ARG C 169 " --> pdb=" O THR C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 195 Processing helix chain 'C' and resid 199 through 211 removed outlier: 4.124A pdb=" N GLU C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.721A pdb=" N ALA C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 245 through 259 removed outlier: 3.597A pdb=" N LEU C 252 " --> pdb=" O GLN C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 274 removed outlier: 3.543A pdb=" N VAL C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 298 Processing helix chain 'C' and resid 299 through 302 removed outlier: 4.272A 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: 4.551A 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: 3.741A pdb=" N VAL D 18 " --> pdb=" O PHE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 34 removed outlier: 3.986A pdb=" N ALA D 27 " --> pdb=" O HIS D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 64 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 100 through 110 removed outlier: 3.619A pdb=" N ASN D 110 " --> pdb=" O ASP D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'D' and resid 132 through 139 removed outlier: 3.584A pdb=" N LEU D 139 " --> pdb=" O SER D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 163 through 168 Processing helix chain 'D' and resid 179 through 195 Processing helix chain 'D' and resid 199 through 210 Processing helix chain 'D' and resid 213 through 228 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 247 through 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: 3.986A pdb=" N LEU D 302 " --> pdb=" O PRO D 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 299 through 302' Processing helix chain 'D' and resid 303 through 307 Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 321 through 338 removed outlier: 3.644A pdb=" N GLN D 326 " --> pdb=" O PRO D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 342 Processing helix chain 'D' and resid 344 through 357 Processing helix chain 'E' and resid 6 through 20 removed outlier: 4.698A pdb=" N ASP E 10 " --> pdb=" O TRP E 6 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER E 17 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA E 20 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 50 Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 89 through 102 removed outlier: 3.832A pdb=" N VAL E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU E 102 " --> pdb=" O GLU E 98 " (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 180 removed outlier: 3.706A pdb=" N ARG E 178 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU E 179 " --> pdb=" O TRP E 175 " (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 removed outlier: 3.586A pdb=" N SER E 231 " --> pdb=" O ASP E 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 228 through 231' Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 240 through 260 Processing helix chain 'E' and resid 270 through 281 Processing helix chain 'E' and resid 282 through 303 Processing helix chain 'E' and resid 307 through 323 Processing helix chain 'F' and resid 7 through 19 removed outlier: 4.548A 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 72 through 82 Processing helix chain 'F' and resid 112 through 116 Processing helix chain 'F' and resid 131 through 141 Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'F' and resid 152 through 155 Processing helix chain 'F' and resid 197 through 207 removed outlier: 3.638A pdb=" N LEU F 207 " --> pdb=" O LEU F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 247 Processing helix chain 'F' and resid 260 through 273 removed outlier: 3.737A pdb=" N ILE F 272 " --> pdb=" O ALA F 268 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 332 removed outlier: 3.714A pdb=" N LYS F 332 " --> pdb=" O LEU F 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 18 removed outlier: 4.717A 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 82 removed outlier: 3.501A pdb=" N LEU G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 141 removed outlier: 4.071A pdb=" N MET G 135 " --> pdb=" O PRO G 131 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS G 136 " --> pdb=" O GLN G 132 " (cutoff:3.500A) 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: 4.082A 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 removed outlier: 3.505A pdb=" N LYS G 332 " --> pdb=" O LEU G 328 " (cutoff:3.500A) 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 3 through 4 removed outlier: 7.230A pdb=" N LEU A 4 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU A 49 " --> pdb=" O THR A 79 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N LEU A 81 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N HIS A 51 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU A 83 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 7.130A 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: 6.766A pdb=" N GLU A 161 " --> pdb=" O LEU A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.036A pdb=" N LYS B 121 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU B 153 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR B 123 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ALA B 155 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE B 125 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N TYR B 41 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA B 40 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N PHE B 173 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.460A 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 91 through 94 removed outlier: 6.343A pdb=" N LYS C 121 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU C 153 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ALA C 155 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE C 125 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 90 through 94 Processing sheet with id=AA7, first strand: chain 'E' and resid 76 through 79 removed outlier: 6.262A pdb=" N VAL E 112 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ALA E 144 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL E 114 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 2 through 6 removed outlier: 3.521A pdb=" N ARG F 96 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU G 301 " --> pdb=" O SER F 107 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASN G 295 " --> pdb=" O GLY G 280 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLY G 280 " --> pdb=" O ASN G 295 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 66 through 71 removed outlier: 3.598A pdb=" N GLY F 66 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASN F 32 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N THR F 47 " --> pdb=" O ASN F 32 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR F 41 " --> pdb=" O ALA F 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 309 through 310 removed outlier: 4.343A pdb=" N ASP F 351 " --> pdb=" O ALA F 357 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ALA F 357 " --> pdb=" O ASP F 351 " (cutoff:3.500A) removed outlier: 12.282A pdb=" N CYS F 180 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 11.325A pdb=" N THR F 172 " --> pdb=" O CYS F 180 " (cutoff:3.500A) removed outlier: 12.314A pdb=" N MET F 182 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 11.319A pdb=" N VAL F 170 " --> pdb=" O MET F 182 " (cutoff:3.500A) removed outlier: 11.454A pdb=" N ILE F 184 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 11.594A pdb=" N ARG F 168 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N GLN F 186 " --> pdb=" O GLU F 166 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLU F 166 " --> pdb=" O GLN F 186 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY F 164 " --> pdb=" O LEU F 188 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER F 190 " --> pdb=" O THR F 162 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR F 162 " --> pdb=" O SER F 190 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER F 192 " --> pdb=" O PHE F 160 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE F 160 " --> pdb=" O SER F 192 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE F 194 " --> pdb=" O MET F 158 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N MET F 158 " --> pdb=" O ILE F 194 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 315 through 320 removed outlier: 6.550A pdb=" N GLY F 280 " --> pdb=" O ASN F 295 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASN F 295 " --> pdb=" O GLY F 280 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 67 through 68 removed outlier: 3.803A pdb=" N ASN G 222 " --> pdb=" O GLY G 219 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU G 130 " --> pdb=" O LEU G 214 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 309 through 310 removed outlier: 3.956A pdb=" N ASP G 351 " --> pdb=" O ALA G 357 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA G 357 " --> pdb=" O ASP G 351 " (cutoff:3.500A) removed outlier: 15.865A pdb=" N SER G 181 " --> pdb=" O THR G 172 " (cutoff:3.500A) removed outlier: 15.940A pdb=" N THR G 172 " --> pdb=" O SER G 181 " (cutoff:3.500A) removed outlier: 14.556A pdb=" N VAL G 170 " --> pdb=" O PRO G 183 " (cutoff:3.500A) removed outlier: 13.907A pdb=" N GLY G 185 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 13.988A pdb=" N ARG G 168 " --> pdb=" O GLY G 185 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N SER G 187 " --> pdb=" O GLU G 166 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N GLU G 166 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLY G 164 " --> pdb=" O PRO G 189 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS G 191 " --> pdb=" O THR G 162 " (cutoff:3.500A) 1089 hydrogen bonds defined for protein. 3099 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 4.25 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7126 1.36 - 1.51: 5938 1.51 - 1.65: 8017 1.65 - 1.80: 136 1.80 - 1.95: 50 Bond restraints: 21267 Sorted by residual: bond pdb=" O3B AGS D 702 " pdb=" PB AGS D 702 " ideal model delta sigma weight residual 1.673 1.577 0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" O3B AGS C 702 " pdb=" PB AGS C 702 " ideal model delta sigma weight residual 1.673 1.579 0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" O3A AGS B 702 " pdb=" PA AGS B 702 " ideal model delta sigma weight residual 1.664 1.573 0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" O3B AGS B 702 " pdb=" PB AGS B 702 " ideal model delta sigma weight residual 1.673 1.582 0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" O3A AGS C 702 " pdb=" PA AGS C 702 " ideal model delta sigma weight residual 1.664 1.574 0.090 2.00e-02 2.50e+03 2.01e+01 ... (remaining 21262 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 28550 2.11 - 4.21: 443 4.21 - 6.32: 53 6.32 - 8.42: 13 8.42 - 10.53: 8 Bond angle restraints: 29067 Sorted by residual: angle pdb=" N3 DT I 14 " pdb=" C4 DT I 14 " pdb=" O4 DT I 14 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT I 8 " pdb=" C4 DT I 8 " pdb=" O4 DT I 8 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT H 27 " pdb=" C4 DT H 27 " pdb=" O4 DT H 27 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT H 29 " pdb=" C4 DT H 29 " pdb=" O4 DT H 29 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT H 30 " pdb=" C4 DT H 30 " pdb=" O4 DT H 30 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 ... (remaining 29062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.25: 12400 32.25 - 64.50: 476 64.50 - 96.76: 33 96.76 - 129.01: 0 129.01 - 161.26: 2 Dihedral angle restraints: 12911 sinusoidal: 5576 harmonic: 7335 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 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA VAL C 19 " pdb=" C VAL C 19 " pdb=" N GLY C 20 " pdb=" CA GLY C 20 " ideal model delta harmonic sigma weight residual 180.00 158.56 21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" C4' DT H 26 " pdb=" C3' DT H 26 " pdb=" O3' DT H 26 " pdb=" P DT H 27 " ideal model delta sinusoidal sigma weight residual 220.00 58.74 161.26 1 3.50e+01 8.16e-04 1.53e+01 ... (remaining 12908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 3332 0.129 - 0.258: 13 0.258 - 0.387: 3 0.387 - 0.516: 0 0.516 - 0.645: 2 Chirality restraints: 3350 Sorted by residual: chirality pdb=" P DT H 25 " pdb=" OP1 DT H 25 " pdb=" OP2 DT H 25 " pdb=" O5' DT H 25 " both_signs ideal model delta sigma weight residual True 2.34 2.98 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P DT H 26 " pdb=" OP1 DT H 26 " pdb=" OP2 DT H 26 " pdb=" O5' DT H 26 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" C3' AGS C 702 " pdb=" C2' AGS C 702 " pdb=" C4' AGS C 702 " pdb=" O3' AGS C 702 " both_signs ideal model delta sigma weight residual False -2.37 -2.66 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 3347 not shown) Planarity restraints: 3615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 56 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO A 57 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 136 " 0.014 2.00e-02 2.50e+03 1.25e-02 2.73e+00 pdb=" CG PHE D 136 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE D 136 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 136 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE D 136 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 136 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 136 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 136 " 0.011 2.00e-02 2.50e+03 1.15e-02 2.32e+00 pdb=" CG PHE B 136 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE B 136 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 136 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 136 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 136 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 136 " 0.001 2.00e-02 2.50e+03 ... (remaining 3612 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 86 2.48 - 3.09: 13920 3.09 - 3.69: 31676 3.69 - 4.30: 47088 4.30 - 4.90: 79166 Nonbonded interactions: 171936 Sorted by model distance: nonbonded pdb=" OG1 THR C 52 " pdb="MG MG C 703 " model vdw 1.880 2.170 nonbonded pdb=" O2G AGS D 702 " pdb="MG MG D 703 " model vdw 1.938 2.170 nonbonded pdb=" OG1 THR D 52 " pdb="MG MG D 703 " model vdw 1.938 2.170 nonbonded pdb=" OG1 THR B 52 " pdb="MG MG B 703 " model vdw 1.945 2.170 nonbonded pdb=" O2B AGS B 702 " pdb="MG MG B 703 " model vdw 2.061 2.170 ... (remaining 171931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 2 through 361 or resid 701 through 703)) selection = (chain 'C' and (resid 2 through 361 or resid 701 through 703)) selection = (chain 'D' and resid 2 through 703) } ncs_group { reference = chain 'F' selection = (chain 'G' 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 23.200 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 : 0.008 0.858 21284 Z= 0.655 Angle : 0.653 10.530 29091 Z= 0.347 Chirality : 0.045 0.645 3350 Planarity : 0.004 0.044 3615 Dihedral : 15.730 161.262 8151 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: 1.26 (0.17), residues: 2516 helix: 1.27 (0.15), residues: 1261 sheet: 1.08 (0.26), residues: 415 loop : 0.21 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 47 TYR 0.009 0.001 TYR E 47 PHE 0.029 0.002 PHE D 136 TRP 0.010 0.001 TRP B 10 HIS 0.005 0.001 HIS C 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.29 (21267) covalent geometry : angle 0.64622 / 0.35 (29067) hydrogen bonds : bond 0.15759 / 10.68 ( 1127) hydrogen bonds : angle 5.74616 / 4.19 ( 3171) metal coordination : bond 0.00359 / 0.16 ( 16) metal coordination : angle 3.40882 / 2.03 ( 24) Misc. bond : bond 0.85821 / 45.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 584 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7466 (mmt180) cc_final: 0.7191 (mmt180) REVERT: A 49 GLU cc_start: 0.6947 (tt0) cc_final: 0.6665 (mm-30) REVERT: A 86 GLU cc_start: 0.7400 (mp0) cc_final: 0.7034 (mm-30) REVERT: A 156 LYS cc_start: 0.7719 (mmtp) cc_final: 0.7065 (mmpt) REVERT: A 277 ARG cc_start: 0.6323 (ptm-80) cc_final: 0.5865 (ptm-80) REVERT: B 38 HIS cc_start: 0.7479 (m90) cc_final: 0.6210 (t-90) REVERT: B 77 ASP cc_start: 0.6727 (m-30) cc_final: 0.6482 (m-30) REVERT: B 127 GLU cc_start: 0.6235 (mm-30) cc_final: 0.6006 (mp0) REVERT: B 130 MET cc_start: 0.7413 (mmp) cc_final: 0.7174 (mmp) REVERT: B 133 ARG cc_start: 0.7450 (tpp80) cc_final: 0.7016 (mmm160) REVERT: B 188 GLU cc_start: 0.8127 (tt0) cc_final: 0.7812 (tt0) REVERT: B 262 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7275 (pm20) REVERT: B 294 MET cc_start: 0.7146 (mtm) cc_final: 0.6743 (mpm) REVERT: B 337 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7646 (mppt) REVERT: C 66 THR cc_start: 0.8184 (p) cc_final: 0.7957 (p) REVERT: C 98 ARG cc_start: 0.7513 (mtp-110) cc_final: 0.7189 (mtp-110) REVERT: C 109 ASP cc_start: 0.7525 (m-30) cc_final: 0.7202 (m-30) REVERT: C 110 ASN cc_start: 0.7583 (m-40) cc_final: 0.6673 (p0) REVERT: C 112 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7435 (mp10) REVERT: C 126 ASP cc_start: 0.8349 (m-30) cc_final: 0.8079 (m-30) REVERT: C 141 LYS cc_start: 0.7786 (tppt) cc_final: 0.7424 (tmtt) REVERT: C 145 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7795 (mt-10) REVERT: C 148 GLU cc_start: 0.7636 (mp0) cc_final: 0.7139 (tp30) REVERT: C 176 LYS cc_start: 0.8459 (mtpp) cc_final: 0.7890 (mmtt) REVERT: C 181 GLU cc_start: 0.7447 (pt0) cc_final: 0.7017 (tp30) REVERT: C 211 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7674 (mt-10) REVERT: C 262 GLU cc_start: 0.7435 (pt0) cc_final: 0.7145 (mm-30) REVERT: C 274 ARG cc_start: 0.7300 (mtm-85) cc_final: 0.6945 (mtm-85) REVERT: C 315 GLU cc_start: 0.7597 (tp30) cc_final: 0.7304 (mm-30) REVERT: C 318 ARG cc_start: 0.7566 (ptm-80) cc_final: 0.7096 (ptp-110) REVERT: C 347 MET cc_start: 0.8417 (mtt) cc_final: 0.8118 (mtt) REVERT: C 363 MET cc_start: 0.8140 (ptp) cc_final: 0.7859 (ptt) REVERT: D 1 MET cc_start: 0.3663 (tmm) cc_final: 0.3095 (tpt) REVERT: D 80 ARG cc_start: 0.7218 (mmt-90) cc_final: 0.6817 (mtm-85) REVERT: D 102 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6328 (pm20) REVERT: D 127 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7582 (mp0) REVERT: D 148 GLU cc_start: 0.7925 (mp0) cc_final: 0.7587 (tp30) REVERT: D 176 LYS cc_start: 0.8496 (mttm) cc_final: 0.8210 (mppt) REVERT: D 263 ARG cc_start: 0.7442 (tpp-160) cc_final: 0.7128 (ttt90) REVERT: D 279 GLU cc_start: 0.7923 (tt0) cc_final: 0.7696 (tt0) REVERT: D 284 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7462 (mm-30) REVERT: D 315 GLU cc_start: 0.7734 (tp30) cc_final: 0.6973 (mp0) REVERT: E 13 LYS cc_start: 0.8050 (ptmt) cc_final: 0.7818 (ttmm) REVERT: E 15 VAL cc_start: 0.8323 (t) cc_final: 0.7805 (m) REVERT: E 134 GLU cc_start: 0.7063 (tt0) cc_final: 0.6325 (pp20) REVERT: E 178 ARG cc_start: 0.7740 (mtm110) cc_final: 0.7096 (mtt180) REVERT: E 206 GLN cc_start: 0.7391 (pt0) cc_final: 0.6674 (pp30) REVERT: E 211 GLN cc_start: 0.7768 (tp40) cc_final: 0.6732 (mm110) REVERT: E 214 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7333 (mm-30) REVERT: E 292 ASP cc_start: 0.7751 (m-30) cc_final: 0.7433 (m-30) REVERT: F 36 GLN cc_start: 0.7560 (mt0) cc_final: 0.7084 (mt0) REVERT: F 50 GLU cc_start: 0.7465 (pt0) cc_final: 0.7035 (pt0) REVERT: F 64 GLU cc_start: 0.7513 (tt0) cc_final: 0.6440 (mm-30) REVERT: F 98 LEU cc_start: 0.7573 (mm) cc_final: 0.6769 (tp) REVERT: F 105 ARG cc_start: 0.7040 (ttt180) cc_final: 0.6780 (tmt-80) REVERT: F 125 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6994 (tp30) REVERT: F 150 ASP cc_start: 0.6767 (t0) cc_final: 0.6301 (t70) REVERT: F 181 SER cc_start: 0.8234 (p) cc_final: 0.7943 (m) REVERT: F 198 LYS cc_start: 0.7783 (mttm) cc_final: 0.7039 (mppt) REVERT: F 202 GLU cc_start: 0.7576 (tp30) cc_final: 0.7103 (mm-30) REVERT: F 235 LYS cc_start: 0.8227 (mtmt) cc_final: 0.7936 (mtmm) REVERT: F 306 LEU cc_start: 0.8006 (mt) cc_final: 0.7634 (mp) REVERT: F 338 MET cc_start: 0.6673 (ptp) cc_final: 0.6350 (ptm) REVERT: G 136 LYS cc_start: 0.6050 (tttm) cc_final: 0.5465 (ttmm) REVERT: G 137 ARG cc_start: 0.5962 (tpt90) cc_final: 0.4707 (mmp80) REVERT: G 150 ASP cc_start: 0.6305 (m-30) cc_final: 0.5730 (m-30) REVERT: G 206 MET cc_start: 0.5601 (mtp) cc_final: 0.5185 (mtp) REVERT: G 246 ARG cc_start: 0.6164 (ttt180) cc_final: 0.5507 (ttp80) REVERT: G 261 ASP cc_start: 0.5564 (m-30) cc_final: 0.4948 (t0) REVERT: G 282 ARG cc_start: 0.6325 (mtt180) cc_final: 0.6058 (mmt-90) REVERT: G 285 VAL cc_start: 0.4151 (t) cc_final: 0.3832 (m) REVERT: G 289 GLN cc_start: 0.5105 (tt0) cc_final: 0.4351 (mm110) REVERT: G 295 ASN cc_start: 0.7601 (m-40) cc_final: 0.7282 (t0) REVERT: G 300 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6673 (mp0) REVERT: G 304 GLU cc_start: 0.7089 (mp0) cc_final: 0.6542 (tp30) REVERT: G 350 GLU cc_start: 0.6109 (pt0) cc_final: 0.5529 (pt0) REVERT: J 10 GLN cc_start: 0.7653 (tt0) cc_final: 0.7136 (mt0) outliers start: 0 outliers final: 0 residues processed: 584 average time/residue: 0.7560 time to fit residues: 489.0368 Evaluate side-chains 373 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN A 69 GLN A 280 GLN A 291 ASN B 4 GLN B 39 HIS B 84 GLN B 192 ASN C 4 GLN C 198 HIS E 19 GLN E 54 GLN E 56 HIS E 103 HIS E 218 GLN E 279 ASN E 280 HIS F 91 GLN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 GLN G 275 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.198632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.152457 restraints weight = 21199.041| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.82 r_work: 0.3707 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21284 Z= 0.155 Angle : 0.590 9.492 29091 Z= 0.298 Chirality : 0.040 0.305 3350 Planarity : 0.004 0.053 3615 Dihedral : 14.193 165.004 3355 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.15 % Favored : 97.81 % Rotamer: Outliers : 2.88 % Allowed : 11.63 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.17), residues: 2516 helix: 1.54 (0.15), residues: 1269 sheet: 1.11 (0.25), residues: 397 loop : 0.24 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 197 TYR 0.015 0.001 TYR E 47 PHE 0.016 0.002 PHE D 136 TRP 0.015 0.001 TRP B 10 HIS 0.011 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (21267) covalent geometry : angle 0.57379 / 0.30 (29067) hydrogen bonds : bond 0.04441 / 3.00 ( 1127) hydrogen bonds : angle 4.34743 / 3.17 ( 3171) metal coordination : bond 0.00290 / 0.16 ( 16) metal coordination : angle 4.83310 / 2.90 ( 24) Misc. bond : bond 0.01614 / 0.85 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 414 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.7010 (mp10) REVERT: A 18 ARG cc_start: 0.7590 (mmt180) cc_final: 0.7231 (mmt180) REVERT: A 39 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6471 (mtm180) REVERT: A 49 GLU cc_start: 0.7057 (tt0) cc_final: 0.6667 (mm-30) REVERT: A 86 GLU cc_start: 0.7172 (mp0) cc_final: 0.6836 (mm-30) REVERT: A 277 ARG cc_start: 0.6250 (ptm-80) cc_final: 0.5979 (ptm-80) REVERT: A 320 VAL cc_start: 0.8380 (p) cc_final: 0.8131 (t) REVERT: B 38 HIS cc_start: 0.7606 (m90) cc_final: 0.6249 (t-90) REVERT: B 80 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7219 (ttp80) REVERT: B 127 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6373 (mp0) REVERT: B 130 MET cc_start: 0.7443 (mmp) cc_final: 0.7210 (mmp) REVERT: B 188 GLU cc_start: 0.8143 (tt0) cc_final: 0.7730 (tt0) REVERT: B 222 ASP cc_start: 0.7446 (t0) cc_final: 0.7031 (m-30) REVERT: B 229 ASP cc_start: 0.7872 (t0) cc_final: 0.7607 (t0) REVERT: B 262 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7307 (pm20) REVERT: B 294 MET cc_start: 0.7442 (mtm) cc_final: 0.7082 (mpm) REVERT: B 337 LYS cc_start: 0.7986 (mtmt) cc_final: 0.7419 (mppt) REVERT: C 66 THR cc_start: 0.8295 (p) cc_final: 0.8087 (p) REVERT: C 98 ARG cc_start: 0.7711 (mtp-110) cc_final: 0.7424 (mtp-110) REVERT: C 109 ASP cc_start: 0.7666 (m-30) cc_final: 0.7344 (m-30) REVERT: C 110 ASN cc_start: 0.7611 (m-40) cc_final: 0.6871 (p0) REVERT: C 112 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7619 (mp10) REVERT: C 117 ARG cc_start: 0.7991 (mtm110) cc_final: 0.7467 (ttm170) REVERT: C 126 ASP cc_start: 0.8317 (m-30) cc_final: 0.8038 (m-30) REVERT: C 141 LYS cc_start: 0.7732 (tppt) cc_final: 0.7507 (tmtt) REVERT: C 145 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7820 (mt-10) REVERT: C 148 GLU cc_start: 0.7581 (mp0) cc_final: 0.7228 (tp30) REVERT: C 176 LYS cc_start: 0.8388 (mtpp) cc_final: 0.7928 (mmtt) REVERT: C 181 GLU cc_start: 0.7369 (pt0) cc_final: 0.7117 (tp30) REVERT: C 211 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7651 (mt-10) REVERT: C 274 ARG cc_start: 0.7238 (mtm-85) cc_final: 0.6926 (mtm-85) REVERT: C 288 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7952 (mp) REVERT: C 315 GLU cc_start: 0.7659 (tp30) cc_final: 0.7300 (mm-30) REVERT: C 363 MET cc_start: 0.7952 (ptp) cc_final: 0.7687 (ptt) REVERT: D 1 MET cc_start: 0.3125 (tmm) cc_final: 0.2270 (tpt) REVERT: D 80 ARG cc_start: 0.7338 (mmt-90) cc_final: 0.6948 (mtm-85) REVERT: D 102 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6510 (mp0) REVERT: D 112 GLN cc_start: 0.6918 (pm20) cc_final: 0.6472 (pm20) REVERT: D 127 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7425 (mp0) REVERT: D 145 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: D 176 LYS cc_start: 0.8504 (mttm) cc_final: 0.8232 (mppt) REVERT: D 204 GLN cc_start: 0.7339 (tt0) cc_final: 0.6764 (mt0) REVERT: D 208 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6761 (ttm170) REVERT: D 222 ASP cc_start: 0.7580 (t70) cc_final: 0.7229 (t0) REVERT: D 248 GLN cc_start: 0.7292 (tt0) cc_final: 0.6856 (pt0) REVERT: D 263 ARG cc_start: 0.7457 (tpp-160) cc_final: 0.7109 (ttt90) REVERT: D 274 ARG cc_start: 0.7259 (mtm180) cc_final: 0.7009 (mtm180) REVERT: D 277 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.6060 (tm-30) REVERT: D 279 GLU cc_start: 0.7779 (tt0) cc_final: 0.7377 (tt0) REVERT: D 284 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7175 (mm-30) REVERT: D 315 GLU cc_start: 0.7557 (tp30) cc_final: 0.6707 (mp0) REVERT: D 351 MET cc_start: 0.8230 (mtp) cc_final: 0.7904 (mtm) REVERT: E 15 VAL cc_start: 0.8254 (t) cc_final: 0.7865 (m) REVERT: E 22 ARG cc_start: 0.6984 (mmp-170) cc_final: 0.6752 (mmt90) REVERT: E 134 GLU cc_start: 0.7101 (tt0) cc_final: 0.6421 (pp20) REVERT: E 149 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7304 (mp0) REVERT: E 178 ARG cc_start: 0.7541 (mtm110) cc_final: 0.6877 (mtt180) REVERT: E 206 GLN cc_start: 0.7389 (pt0) cc_final: 0.6651 (pp30) REVERT: E 211 GLN cc_start: 0.7730 (tp40) cc_final: 0.6743 (mm110) REVERT: E 214 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7036 (mm-30) REVERT: E 279 ASN cc_start: 0.8136 (m-40) cc_final: 0.7877 (m-40) REVERT: E 292 ASP cc_start: 0.7816 (m-30) cc_final: 0.7489 (m-30) REVERT: F 1 MET cc_start: 0.7003 (ptt) cc_final: 0.6783 (ptt) REVERT: F 64 GLU cc_start: 0.7374 (tt0) cc_final: 0.6344 (mm-30) REVERT: F 98 LEU cc_start: 0.7561 (mm) cc_final: 0.6685 (tp) REVERT: F 105 ARG cc_start: 0.7021 (ttt180) cc_final: 0.6805 (tmt-80) REVERT: F 125 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7074 (tp30) REVERT: F 150 ASP cc_start: 0.6855 (t0) cc_final: 0.6509 (t70) REVERT: F 154 TYR cc_start: 0.7948 (p90) cc_final: 0.7702 (p90) REVERT: F 198 LYS cc_start: 0.7577 (mttm) cc_final: 0.6791 (mppt) REVERT: F 202 GLU cc_start: 0.7555 (tp30) cc_final: 0.7139 (mm-30) REVERT: F 303 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6292 (pp20) REVERT: F 306 LEU cc_start: 0.7749 (mt) cc_final: 0.7460 (mp) REVERT: F 338 MET cc_start: 0.6528 (ptp) cc_final: 0.6231 (ptp) REVERT: G 1 MET cc_start: 0.4283 (tpp) cc_final: 0.4028 (tpt) REVERT: G 61 GLN cc_start: 0.6521 (OUTLIER) cc_final: 0.6062 (tp-100) REVERT: G 64 GLU cc_start: 0.5886 (mt-10) cc_final: 0.5083 (tm-30) REVERT: G 115 ASP cc_start: 0.6857 (m-30) cc_final: 0.6476 (t70) REVERT: G 128 PHE cc_start: 0.6011 (p90) cc_final: 0.5588 (p90) REVERT: G 136 LYS cc_start: 0.6044 (tttm) cc_final: 0.5382 (ttmm) REVERT: G 137 ARG cc_start: 0.5560 (tpt90) cc_final: 0.4541 (mmp80) REVERT: G 158 MET cc_start: 0.4397 (ttm) cc_final: 0.3861 (ttm) REVERT: G 182 MET cc_start: 0.4612 (ttt) cc_final: 0.4344 (ttm) REVERT: G 246 ARG cc_start: 0.6219 (ttt180) cc_final: 0.5576 (ttp80) REVERT: G 289 GLN cc_start: 0.5112 (tt0) cc_final: 0.4348 (mm110) REVERT: G 291 LYS cc_start: 0.6508 (tttt) cc_final: 0.5972 (ttmt) REVERT: G 300 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6842 (mp0) REVERT: G 304 GLU cc_start: 0.6836 (mp0) cc_final: 0.6512 (tp30) REVERT: G 355 GLN cc_start: 0.5884 (mp10) cc_final: 0.5525 (mm-40) REVERT: G 364 MET cc_start: 0.5445 (ttm) cc_final: 0.5240 (mtp) outliers start: 61 outliers final: 22 residues processed: 447 average time/residue: 0.7399 time to fit residues: 366.1870 Evaluate side-chains 393 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 363 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain J residue 15 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 102 optimal weight: 0.7980 chunk 168 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 178 optimal weight: 7.9990 chunk 195 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 GLN B 13 GLN B 23 HIS B 39 HIS B 84 GLN C 4 GLN D 231 GLN E 54 GLN ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 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 = 0.4256 r_free = 0.4256 target = 0.194896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.146702 restraints weight = 20794.592| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.63 r_work: 0.3612 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 21284 Z= 0.252 Angle : 0.704 13.374 29091 Z= 0.345 Chirality : 0.045 0.282 3350 Planarity : 0.006 0.076 3615 Dihedral : 14.526 166.748 3355 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.54 % Favored : 97.42 % Rotamer: Outliers : 4.63 % Allowed : 13.52 % 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: 1.10 (0.17), residues: 2516 helix: 1.18 (0.15), residues: 1282 sheet: 0.90 (0.25), residues: 405 loop : 0.10 (0.23), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 318 TYR 0.021 0.002 TYR E 47 PHE 0.023 0.002 PHE G 160 TRP 0.017 0.002 TRP B 10 HIS 0.013 0.002 HIS D 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.25 (21267) covalent geometry : angle 0.68460 / 0.34 (29067) hydrogen bonds : bond 0.04762 / 3.25 ( 1127) hydrogen bonds : angle 4.25656 / 3.12 ( 3171) metal coordination : bond 0.00445 / 0.23 ( 16) metal coordination : angle 5.68564 / 3.53 ( 24) Misc. bond : bond 0.00073 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 389 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.6640 (mpp-170) REVERT: A 18 ARG cc_start: 0.7678 (mmt180) cc_final: 0.7392 (mmt180) REVERT: A 39 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6727 (mtm180) REVERT: A 86 GLU cc_start: 0.7287 (mp0) cc_final: 0.6985 (mm-30) REVERT: A 113 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7616 (ttp-170) REVERT: A 156 LYS cc_start: 0.7848 (mmtm) cc_final: 0.7270 (mmpt) REVERT: A 175 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: A 277 ARG cc_start: 0.6427 (ptm-80) cc_final: 0.6068 (ptm-80) REVERT: B 126 ASP cc_start: 0.8709 (m-30) cc_final: 0.8278 (m-30) REVERT: B 127 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6452 (mp0) REVERT: B 169 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7048 (mmm160) REVERT: B 188 GLU cc_start: 0.8347 (tt0) cc_final: 0.7964 (tt0) REVERT: B 284 GLU cc_start: 0.8013 (tt0) cc_final: 0.7291 (mt-10) REVERT: B 294 MET cc_start: 0.7805 (mtm) cc_final: 0.7253 (mmp) REVERT: B 311 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7532 (mm) REVERT: B 337 LYS cc_start: 0.7958 (mtmt) cc_final: 0.7429 (mppt) REVERT: C 84 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7301 (mt0) REVERT: C 98 ARG cc_start: 0.7904 (mtp-110) cc_final: 0.7632 (mtp-110) REVERT: C 109 ASP cc_start: 0.7759 (m-30) cc_final: 0.7492 (m-30) REVERT: C 110 ASN cc_start: 0.7702 (m-40) cc_final: 0.7174 (p0) REVERT: C 112 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7708 (mp10) REVERT: C 126 ASP cc_start: 0.8392 (m-30) cc_final: 0.8084 (m-30) REVERT: C 141 LYS cc_start: 0.7927 (tppt) cc_final: 0.7621 (tmtt) REVERT: C 145 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7896 (mt-10) REVERT: C 148 GLU cc_start: 0.8170 (mp0) cc_final: 0.7527 (tm-30) REVERT: C 176 LYS cc_start: 0.8627 (mtpp) cc_final: 0.8045 (mmtt) REVERT: C 208 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7407 (mtp85) REVERT: C 274 ARG cc_start: 0.7391 (mtm-85) cc_final: 0.6962 (mtm-85) REVERT: C 288 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8214 (mp) REVERT: C 315 GLU cc_start: 0.7886 (tp30) cc_final: 0.7278 (mm-30) REVERT: C 319 THR cc_start: 0.8824 (m) cc_final: 0.8441 (p) REVERT: C 362 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7041 (mtp85) REVERT: C 363 MET cc_start: 0.8047 (ptp) cc_final: 0.7781 (ptt) REVERT: D 1 MET cc_start: 0.3393 (tmm) cc_final: 0.2593 (tpt) REVERT: D 56 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7681 (mtt-85) REVERT: D 102 GLU cc_start: 0.7402 (mm-30) cc_final: 0.6607 (mp0) REVERT: D 112 GLN cc_start: 0.6954 (pm20) cc_final: 0.6491 (pm20) REVERT: D 127 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7372 (mp0) REVERT: D 145 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8289 (mt-10) REVERT: D 204 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.6953 (mt0) REVERT: D 222 ASP cc_start: 0.7716 (t70) cc_final: 0.7422 (t0) REVERT: D 263 ARG cc_start: 0.7791 (tpp-160) cc_final: 0.7437 (ttt90) REVERT: D 277 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.6437 (tm-30) REVERT: D 284 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7317 (mp0) REVERT: D 315 GLU cc_start: 0.7743 (tp30) cc_final: 0.6837 (mp0) REVERT: D 351 MET cc_start: 0.8596 (mtp) cc_final: 0.8300 (mtm) REVERT: E 22 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6675 (mmt90) REVERT: E 134 GLU cc_start: 0.7264 (tt0) cc_final: 0.6625 (pp20) REVERT: E 178 ARG cc_start: 0.7695 (mtm110) cc_final: 0.7063 (mtt180) REVERT: E 211 GLN cc_start: 0.7790 (tp40) cc_final: 0.6853 (mm110) REVERT: E 214 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7141 (mm-30) REVERT: E 239 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: E 258 ARG cc_start: 0.8068 (ttt180) cc_final: 0.7692 (ttt90) REVERT: E 279 ASN cc_start: 0.8108 (m-40) cc_final: 0.7870 (m110) REVERT: E 292 ASP cc_start: 0.8118 (m-30) cc_final: 0.7776 (m-30) REVERT: F 1 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6853 (ptt) REVERT: F 8 GLU cc_start: 0.5981 (mm-30) cc_final: 0.5360 (mp0) REVERT: F 12 LYS cc_start: 0.6794 (ttpt) cc_final: 0.6436 (mmmm) REVERT: F 64 GLU cc_start: 0.7528 (tt0) cc_final: 0.6415 (mm-30) REVERT: F 98 LEU cc_start: 0.7776 (mm) cc_final: 0.6798 (tp) REVERT: F 105 ARG cc_start: 0.7050 (ttt180) cc_final: 0.6783 (tmt-80) REVERT: F 125 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7051 (tp30) REVERT: F 136 LYS cc_start: 0.7570 (tttt) cc_final: 0.7075 (ttmt) REVERT: F 150 ASP cc_start: 0.7296 (t0) cc_final: 0.7036 (t70) REVERT: F 198 LYS cc_start: 0.7631 (mttm) cc_final: 0.6924 (mppt) REVERT: F 202 GLU cc_start: 0.7707 (tp30) cc_final: 0.7220 (tp30) REVERT: F 265 GLN cc_start: 0.6292 (mt0) cc_final: 0.6070 (mm-40) REVERT: F 303 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6383 (pp20) REVERT: F 306 LEU cc_start: 0.8172 (mt) cc_final: 0.7831 (mp) REVERT: F 315 MET cc_start: 0.7167 (ttm) cc_final: 0.6952 (ttm) REVERT: G 1 MET cc_start: 0.4468 (tpp) cc_final: 0.4137 (tpp) REVERT: G 50 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6312 (tt0) REVERT: G 61 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.6200 (tp-100) REVERT: G 64 GLU cc_start: 0.5955 (mt-10) cc_final: 0.5188 (tm-30) REVERT: G 97 MET cc_start: 0.6323 (ttm) cc_final: 0.6017 (ttm) REVERT: G 115 ASP cc_start: 0.6934 (m-30) cc_final: 0.6544 (t70) REVERT: G 128 PHE cc_start: 0.5995 (p90) cc_final: 0.5506 (p90) REVERT: G 136 LYS cc_start: 0.6010 (tttm) cc_final: 0.5425 (ttmt) REVERT: G 137 ARG cc_start: 0.5702 (tpt90) cc_final: 0.4564 (mmp80) REVERT: G 160 PHE cc_start: 0.4072 (m-80) cc_final: 0.3797 (m-80) REVERT: G 182 MET cc_start: 0.4516 (ttt) cc_final: 0.4311 (ttm) REVERT: G 246 ARG cc_start: 0.6391 (ttt180) cc_final: 0.5665 (ttp80) REVERT: G 289 GLN cc_start: 0.5087 (tt0) cc_final: 0.4234 (mm110) REVERT: G 291 LYS cc_start: 0.6263 (tttt) cc_final: 0.6052 (tmtt) REVERT: G 300 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6986 (mp0) REVERT: G 304 GLU cc_start: 0.7028 (mp0) cc_final: 0.6613 (tp30) REVERT: G 342 ASP cc_start: 0.6397 (m-30) cc_final: 0.5073 (p0) REVERT: G 355 GLN cc_start: 0.5832 (mp10) cc_final: 0.5503 (mm-40) outliers start: 98 outliers final: 32 residues processed: 449 average time/residue: 0.7571 time to fit residues: 376.8379 Evaluate side-chains 402 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 351 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 285 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 22 optimal weight: 0.7980 chunk 180 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 158 optimal weight: 0.0030 chunk 2 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 171 optimal weight: 0.5980 chunk 225 optimal weight: 5.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 4 GLN B 13 GLN B 39 HIS C 231 GLN D 231 GLN E 54 GLN ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 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 = 0.4285 r_free = 0.4285 target = 0.197834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.153266 restraints weight = 21118.174| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.53 r_work: 0.3802 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21284 Z= 0.115 Angle : 0.540 9.733 29091 Z= 0.271 Chirality : 0.038 0.297 3350 Planarity : 0.004 0.061 3615 Dihedral : 14.369 164.891 3355 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.79 % Favored : 98.17 % Rotamer: Outliers : 3.03 % Allowed : 16.60 % Favored : 80.38 % 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: 1.57 (0.17), residues: 2516 helix: 1.66 (0.15), residues: 1275 sheet: 1.02 (0.25), residues: 395 loop : 0.22 (0.23), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 279 TYR 0.018 0.001 TYR E 47 PHE 0.016 0.001 PHE F 230 TRP 0.014 0.001 TRP B 10 HIS 0.006 0.001 HIS G 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (21267) covalent geometry : angle 0.52085 / 0.27 (29067) hydrogen bonds : bond 0.03676 / 2.51 ( 1127) hydrogen bonds : angle 3.92341 / 2.86 ( 3171) metal coordination : bond 0.00147 / 0.08 ( 16) metal coordination : angle 5.03106 / 2.99 ( 24) Misc. bond : bond 0.00203 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 384 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7610 (mmt180) cc_final: 0.7386 (mmt180) REVERT: A 113 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7512 (ttp-170) REVERT: A 168 GLN cc_start: 0.7080 (mt0) cc_final: 0.6873 (mt0) REVERT: A 189 SER cc_start: 0.8236 (OUTLIER) cc_final: 0.7894 (p) REVERT: A 234 GLN cc_start: 0.7763 (mt0) cc_final: 0.7450 (mt0) REVERT: A 277 ARG cc_start: 0.6287 (ptm-80) cc_final: 0.6072 (ptm-80) REVERT: B 80 ARG cc_start: 0.7644 (ttp80) cc_final: 0.7383 (ttp80) REVERT: B 84 GLN cc_start: 0.8226 (mt0) cc_final: 0.7966 (pt0) REVERT: B 108 LEU cc_start: 0.7940 (mp) cc_final: 0.7637 (mp) REVERT: B 126 ASP cc_start: 0.8501 (m-30) cc_final: 0.8025 (m-30) REVERT: B 169 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7449 (mmm160) REVERT: B 188 GLU cc_start: 0.8384 (tt0) cc_final: 0.7956 (tt0) REVERT: B 284 GLU cc_start: 0.7955 (tt0) cc_final: 0.7439 (mt-10) REVERT: B 294 MET cc_start: 0.7842 (mtm) cc_final: 0.7357 (mmp) REVERT: B 337 LYS cc_start: 0.7932 (mtmt) cc_final: 0.7542 (mppt) REVERT: C 109 ASP cc_start: 0.7771 (m-30) cc_final: 0.7542 (m-30) REVERT: C 110 ASN cc_start: 0.7767 (m-40) cc_final: 0.7335 (p0) REVERT: C 112 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7805 (mp10) REVERT: C 126 ASP cc_start: 0.8205 (m-30) cc_final: 0.7933 (m-30) REVERT: C 133 ARG cc_start: 0.7984 (ttm110) cc_final: 0.7646 (mtm-85) REVERT: C 141 LYS cc_start: 0.7871 (tppt) cc_final: 0.7590 (tmtt) REVERT: C 145 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7984 (mt-10) REVERT: C 148 GLU cc_start: 0.8050 (mp0) cc_final: 0.7589 (tm-30) REVERT: C 176 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8215 (mmtm) REVERT: C 274 ARG cc_start: 0.7432 (mtm-85) cc_final: 0.7040 (mtm-85) REVERT: C 288 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8323 (mp) REVERT: C 315 GLU cc_start: 0.7814 (tp30) cc_final: 0.7394 (mm-30) REVERT: C 363 MET cc_start: 0.7873 (ptp) cc_final: 0.7648 (ptt) REVERT: D 1 MET cc_start: 0.3520 (tmm) cc_final: 0.2685 (tpt) REVERT: D 56 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7695 (mtt-85) REVERT: D 80 ARG cc_start: 0.7309 (mmt-90) cc_final: 0.7044 (mtm-85) REVERT: D 102 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6851 (mp0) REVERT: D 112 GLN cc_start: 0.7118 (pm20) cc_final: 0.6780 (pm20) REVERT: D 145 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8281 (mt-10) REVERT: D 204 GLN cc_start: 0.7578 (tt0) cc_final: 0.7046 (mt0) REVERT: D 222 ASP cc_start: 0.7781 (t70) cc_final: 0.7444 (t0) REVERT: D 276 ILE cc_start: 0.7929 (tp) cc_final: 0.7577 (pt) REVERT: D 277 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.6460 (tm-30) REVERT: D 284 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7242 (mm-30) REVERT: D 315 GLU cc_start: 0.7811 (tp30) cc_final: 0.6980 (mp0) REVERT: D 351 MET cc_start: 0.8673 (mtp) cc_final: 0.8372 (mtm) REVERT: E 22 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6845 (mmt90) REVERT: E 134 GLU cc_start: 0.7108 (tt0) cc_final: 0.6525 (pp20) REVERT: E 178 ARG cc_start: 0.7738 (mtm110) cc_final: 0.7264 (mtt180) REVERT: E 211 GLN cc_start: 0.7844 (tp40) cc_final: 0.7123 (mm110) REVERT: E 214 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7387 (mm-30) REVERT: E 239 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7410 (tm-30) REVERT: F 1 MET cc_start: 0.7363 (ptt) cc_final: 0.6945 (ptt) REVERT: F 8 GLU cc_start: 0.6197 (mm-30) cc_final: 0.5690 (mp0) REVERT: F 12 LYS cc_start: 0.6867 (ttpt) cc_final: 0.6545 (mmtm) REVERT: F 64 GLU cc_start: 0.7544 (tt0) cc_final: 0.6538 (mm-30) REVERT: F 98 LEU cc_start: 0.7787 (mm) cc_final: 0.6899 (tp) REVERT: F 125 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7132 (tp30) REVERT: F 198 LYS cc_start: 0.7725 (mttm) cc_final: 0.7135 (mppt) REVERT: F 202 GLU cc_start: 0.7684 (tp30) cc_final: 0.7285 (mm-30) REVERT: F 246 ARG cc_start: 0.7397 (ptt-90) cc_final: 0.7124 (ptt-90) REVERT: F 275 ASN cc_start: 0.7426 (OUTLIER) cc_final: 0.6828 (t0) REVERT: F 288 ASN cc_start: 0.6975 (OUTLIER) cc_final: 0.6528 (t0) REVERT: F 303 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6476 (pp20) REVERT: F 306 LEU cc_start: 0.8086 (mt) cc_final: 0.7795 (mp) REVERT: F 326 ASP cc_start: 0.7075 (m-30) cc_final: 0.6740 (m-30) REVERT: G 1 MET cc_start: 0.4336 (tpp) cc_final: 0.3990 (tpp) REVERT: G 34 LEU cc_start: 0.5359 (tm) cc_final: 0.4509 (mm) REVERT: G 50 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.6219 (tt0) REVERT: G 61 GLN cc_start: 0.6698 (OUTLIER) cc_final: 0.6182 (tp-100) REVERT: G 64 GLU cc_start: 0.6020 (mt-10) cc_final: 0.5199 (tm-30) REVERT: G 97 MET cc_start: 0.6433 (OUTLIER) cc_final: 0.6072 (ttm) REVERT: G 115 ASP cc_start: 0.6863 (m-30) cc_final: 0.6506 (t70) REVERT: G 128 PHE cc_start: 0.6003 (p90) cc_final: 0.5562 (p90) REVERT: G 136 LYS cc_start: 0.5967 (tttm) cc_final: 0.5473 (ttmt) REVERT: G 137 ARG cc_start: 0.5581 (tpt90) cc_final: 0.4508 (mmp80) REVERT: G 182 MET cc_start: 0.4398 (ttt) cc_final: 0.4171 (ttm) REVERT: G 246 ARG cc_start: 0.6426 (ttt180) cc_final: 0.5703 (ttp80) REVERT: G 289 GLN cc_start: 0.5165 (tt0) cc_final: 0.4276 (mm110) REVERT: G 291 LYS cc_start: 0.6515 (tttt) cc_final: 0.6054 (ttmp) REVERT: G 300 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6977 (mp0) REVERT: G 304 GLU cc_start: 0.7033 (mp0) cc_final: 0.6728 (tp30) REVERT: G 342 ASP cc_start: 0.6378 (OUTLIER) cc_final: 0.5202 (p0) outliers start: 64 outliers final: 19 residues processed: 425 average time/residue: 0.7375 time to fit residues: 347.5626 Evaluate side-chains 386 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 352 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 342 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 144 optimal weight: 8.9990 chunk 22 optimal weight: 0.0670 chunk 154 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 237 optimal weight: 3.9990 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 GLN A 276 HIS A 297 GLN A 333 HIS B 13 GLN B 112 GLN C 231 GLN D 231 GLN E 54 GLN E 279 ASN ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 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 = 0.4271 r_free = 0.4271 target = 0.196294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.152430 restraints weight = 20987.036| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.04 r_work: 0.3754 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21284 Z= 0.144 Angle : 0.560 10.900 29091 Z= 0.279 Chirality : 0.039 0.284 3350 Planarity : 0.004 0.066 3615 Dihedral : 14.418 165.438 3355 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.23 % Favored : 97.73 % Rotamer: Outliers : 3.50 % Allowed : 17.26 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.17), residues: 2516 helix: 1.70 (0.15), residues: 1275 sheet: 0.99 (0.25), residues: 403 loop : 0.18 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 98 TYR 0.011 0.001 TYR B 341 PHE 0.018 0.001 PHE F 230 TRP 0.015 0.001 TRP B 10 HIS 0.017 0.001 HIS E 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (21267) covalent geometry : angle 0.54225 / 0.28 (29067) hydrogen bonds : bond 0.03780 / 2.58 ( 1127) hydrogen bonds : angle 3.88666 / 2.85 ( 3171) metal coordination : bond 0.00246 / 0.13 ( 16) metal coordination : angle 4.89176 / 3.01 ( 24) Misc. bond : bond 0.00065 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 355 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6372 (mpp-170) REVERT: A 18 ARG cc_start: 0.7565 (mmt180) cc_final: 0.7326 (mmt180) REVERT: A 113 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7545 (ttp-170) REVERT: A 189 SER cc_start: 0.8254 (OUTLIER) cc_final: 0.7915 (p) REVERT: A 234 GLN cc_start: 0.7788 (mt0) cc_final: 0.7456 (mt0) REVERT: A 275 LYS cc_start: 0.8045 (ttpp) cc_final: 0.7823 (ttpp) REVERT: A 277 ARG cc_start: 0.6408 (ptm-80) cc_final: 0.6107 (ptm-80) REVERT: B 84 GLN cc_start: 0.8128 (mt0) cc_final: 0.7898 (pt0) REVERT: B 99 THR cc_start: 0.8381 (m) cc_final: 0.8129 (p) REVERT: B 108 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7736 (mp) REVERT: B 126 ASP cc_start: 0.8539 (m-30) cc_final: 0.8031 (m-30) REVERT: B 169 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7095 (mmm160) REVERT: B 188 GLU cc_start: 0.8408 (tt0) cc_final: 0.8024 (tt0) REVERT: B 284 GLU cc_start: 0.8038 (tt0) cc_final: 0.7499 (mt-10) REVERT: B 294 MET cc_start: 0.7948 (mtm) cc_final: 0.7374 (mmp) REVERT: B 337 LYS cc_start: 0.7924 (mtmt) cc_final: 0.7546 (mppt) REVERT: C 109 ASP cc_start: 0.7803 (m-30) cc_final: 0.7547 (m-30) REVERT: C 110 ASN cc_start: 0.7889 (m-40) cc_final: 0.7292 (p0) REVERT: C 112 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7744 (mp10) REVERT: C 126 ASP cc_start: 0.8231 (m-30) cc_final: 0.7939 (m-30) REVERT: C 133 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7754 (mtm-85) REVERT: C 141 LYS cc_start: 0.7903 (tppt) cc_final: 0.7640 (tmtt) REVERT: C 145 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7926 (mt-10) REVERT: C 148 GLU cc_start: 0.8153 (mp0) cc_final: 0.7632 (tm-30) REVERT: C 176 LYS cc_start: 0.8635 (mtpp) cc_final: 0.8198 (mmtm) REVERT: C 274 ARG cc_start: 0.7451 (mtm-85) cc_final: 0.7038 (mtm-85) REVERT: C 288 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8330 (mp) REVERT: C 315 GLU cc_start: 0.7862 (tp30) cc_final: 0.7385 (mm-30) REVERT: C 319 THR cc_start: 0.8852 (m) cc_final: 0.8497 (p) REVERT: C 362 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7109 (mtp85) REVERT: D 1 MET cc_start: 0.3506 (tmm) cc_final: 0.2708 (tpt) REVERT: D 56 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7666 (mtt-85) REVERT: D 80 ARG cc_start: 0.7297 (mmt-90) cc_final: 0.7023 (mtm-85) REVERT: D 83 GLU cc_start: 0.7360 (tt0) cc_final: 0.7092 (tt0) REVERT: D 102 GLU cc_start: 0.7493 (mm-30) cc_final: 0.6828 (mp0) REVERT: D 112 GLN cc_start: 0.7066 (pm20) cc_final: 0.6695 (pm20) REVERT: D 145 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8267 (mt-10) REVERT: D 204 GLN cc_start: 0.7581 (tt0) cc_final: 0.6997 (mt0) REVERT: D 222 ASP cc_start: 0.7767 (t70) cc_final: 0.7427 (t0) REVERT: D 274 ARG cc_start: 0.7427 (mtm-85) cc_final: 0.7136 (mtm-85) REVERT: D 277 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.6412 (tm-30) REVERT: D 315 GLU cc_start: 0.7856 (tp30) cc_final: 0.7017 (mp0) REVERT: D 351 MET cc_start: 0.8655 (mtp) cc_final: 0.8336 (mtm) REVERT: E 22 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6850 (mmt90) REVERT: E 134 GLU cc_start: 0.7132 (tt0) cc_final: 0.6512 (pp20) REVERT: E 178 ARG cc_start: 0.7788 (mtm110) cc_final: 0.7273 (mtt180) REVERT: E 211 GLN cc_start: 0.7904 (tp40) cc_final: 0.7152 (mm110) REVERT: E 214 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7400 (mm-30) REVERT: E 239 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: E 258 ARG cc_start: 0.7901 (ttt180) cc_final: 0.7502 (mtp-110) REVERT: F 8 GLU cc_start: 0.6174 (mm-30) cc_final: 0.5616 (mp0) REVERT: F 12 LYS cc_start: 0.6889 (ttpt) cc_final: 0.6520 (mmtm) REVERT: F 64 GLU cc_start: 0.7613 (tt0) cc_final: 0.6573 (mm-30) REVERT: F 97 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7417 (ttm) REVERT: F 105 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6946 (tmt170) REVERT: F 125 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7170 (tp30) REVERT: F 198 LYS cc_start: 0.7790 (mttm) cc_final: 0.7117 (mppt) REVERT: F 202 GLU cc_start: 0.7671 (tp30) cc_final: 0.7263 (mm-30) REVERT: F 303 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6623 (tm-30) REVERT: F 326 ASP cc_start: 0.7113 (m-30) cc_final: 0.6805 (m-30) REVERT: G 1 MET cc_start: 0.4218 (tpp) cc_final: 0.4018 (tpp) REVERT: G 34 LEU cc_start: 0.5309 (tm) cc_final: 0.4498 (mm) REVERT: G 50 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6358 (tt0) REVERT: G 61 GLN cc_start: 0.6657 (OUTLIER) cc_final: 0.6117 (tp-100) REVERT: G 115 ASP cc_start: 0.6925 (m-30) cc_final: 0.6569 (t70) REVERT: G 128 PHE cc_start: 0.5897 (p90) cc_final: 0.5471 (p90) REVERT: G 136 LYS cc_start: 0.6019 (tttm) cc_final: 0.5432 (ttmt) REVERT: G 137 ARG cc_start: 0.5646 (tpt90) cc_final: 0.4535 (mmp80) REVERT: G 160 PHE cc_start: 0.4948 (m-80) cc_final: 0.4660 (m-80) REVERT: G 182 MET cc_start: 0.4459 (ttt) cc_final: 0.4189 (ttm) REVERT: G 246 ARG cc_start: 0.6451 (ttt180) cc_final: 0.5687 (ttp80) REVERT: G 289 GLN cc_start: 0.5160 (tt0) cc_final: 0.4317 (mm110) REVERT: G 291 LYS cc_start: 0.6373 (tttt) cc_final: 0.5934 (ttmp) REVERT: G 300 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6894 (mp0) REVERT: G 342 ASP cc_start: 0.6324 (OUTLIER) cc_final: 0.5158 (p0) outliers start: 74 outliers final: 24 residues processed: 399 average time/residue: 0.6849 time to fit residues: 303.1545 Evaluate side-chains 388 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 347 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 342 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 211 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 233 optimal weight: 20.0000 chunk 242 optimal weight: 0.9980 chunk 217 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 GLN D 231 GLN E 54 GLN E 259 HIS E 279 ASN ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 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 = 0.4271 r_free = 0.4271 target = 0.196271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.151343 restraints weight = 20958.691| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.86 r_work: 0.3655 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21284 Z= 0.145 Angle : 0.557 10.405 29091 Z= 0.277 Chirality : 0.039 0.285 3350 Planarity : 0.004 0.068 3615 Dihedral : 14.434 165.100 3355 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.93 % Rotamer: Outliers : 3.88 % Allowed : 17.73 % Favored : 78.39 % 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: 1.61 (0.17), residues: 2516 helix: 1.71 (0.15), residues: 1275 sheet: 1.04 (0.25), residues: 396 loop : 0.22 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 208 TYR 0.016 0.001 TYR E 47 PHE 0.011 0.001 PHE G 128 TRP 0.014 0.001 TRP B 10 HIS 0.004 0.001 HIS E 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (21267) covalent geometry : angle 0.53940 / 0.28 (29067) hydrogen bonds : bond 0.03728 / 2.55 ( 1127) hydrogen bonds : angle 3.84579 / 2.82 ( 3171) metal coordination : bond 0.00224 / 0.11 ( 16) metal coordination : angle 4.80678 / 2.93 ( 24) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 371 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.6410 (mpp-170) REVERT: A 18 ARG cc_start: 0.7628 (mmt180) cc_final: 0.7388 (mmt180) REVERT: A 113 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7636 (ttp-170) REVERT: A 175 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: A 189 SER cc_start: 0.8333 (OUTLIER) cc_final: 0.8004 (p) REVERT: A 204 GLN cc_start: 0.8101 (mt0) cc_final: 0.7522 (pt0) REVERT: A 234 GLN cc_start: 0.7817 (mt0) cc_final: 0.7536 (mt0) REVERT: A 277 ARG cc_start: 0.6494 (ptm-80) cc_final: 0.6130 (ptm-80) REVERT: B 108 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7705 (mp) REVERT: B 126 ASP cc_start: 0.8578 (m-30) cc_final: 0.8084 (m-30) REVERT: B 169 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7116 (mmm160) REVERT: B 188 GLU cc_start: 0.8460 (tt0) cc_final: 0.8101 (tt0) REVERT: B 284 GLU cc_start: 0.8141 (tt0) cc_final: 0.7664 (mt-10) REVERT: B 294 MET cc_start: 0.8025 (mtm) cc_final: 0.7458 (mmp) REVERT: B 337 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7637 (mppt) REVERT: C 109 ASP cc_start: 0.7873 (m-30) cc_final: 0.7624 (m-30) REVERT: C 110 ASN cc_start: 0.7932 (m-40) cc_final: 0.7393 (p0) REVERT: C 112 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7772 (mp10) REVERT: C 126 ASP cc_start: 0.8263 (m-30) cc_final: 0.7969 (m-30) REVERT: C 133 ARG cc_start: 0.8128 (ttm110) cc_final: 0.7857 (mtm-85) REVERT: C 141 LYS cc_start: 0.7947 (tppt) cc_final: 0.7691 (tmtt) REVERT: C 145 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7902 (mt-10) REVERT: C 148 GLU cc_start: 0.8227 (mp0) cc_final: 0.7702 (tm-30) REVERT: C 158 ASP cc_start: 0.7496 (t0) cc_final: 0.7185 (t0) REVERT: C 160 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7290 (mp10) REVERT: C 176 LYS cc_start: 0.8675 (mtpp) cc_final: 0.8221 (mmtm) REVERT: C 193 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8128 (mm-30) REVERT: C 208 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7577 (mtp85) REVERT: C 274 ARG cc_start: 0.7522 (mtm-85) cc_final: 0.7107 (mtp85) REVERT: C 288 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8398 (mp) REVERT: C 315 GLU cc_start: 0.7876 (tp30) cc_final: 0.7475 (mm-30) REVERT: C 362 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7054 (mtp85) REVERT: D 1 MET cc_start: 0.3631 (tmm) cc_final: 0.2785 (tpt) REVERT: D 83 GLU cc_start: 0.7371 (tt0) cc_final: 0.7098 (tt0) REVERT: D 102 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6937 (mp0) REVERT: D 112 GLN cc_start: 0.7122 (pm20) cc_final: 0.6821 (pm20) REVERT: D 145 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8294 (mt-10) REVERT: D 204 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7140 (mt0) REVERT: D 222 ASP cc_start: 0.7881 (t70) cc_final: 0.7532 (t0) REVERT: D 274 ARG cc_start: 0.7529 (mtm-85) cc_final: 0.7084 (mtm180) REVERT: D 277 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.6537 (tm-30) REVERT: D 315 GLU cc_start: 0.7903 (tp30) cc_final: 0.7134 (mp0) REVERT: D 351 MET cc_start: 0.8702 (mtp) cc_final: 0.8393 (mtm) REVERT: E 22 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6877 (mmt90) REVERT: E 134 GLU cc_start: 0.7180 (tt0) cc_final: 0.6589 (pp20) REVERT: E 178 ARG cc_start: 0.7818 (mtm110) cc_final: 0.7338 (mtt180) REVERT: E 211 GLN cc_start: 0.7979 (tp40) cc_final: 0.7237 (mm110) REVERT: E 214 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7510 (mm-30) REVERT: E 239 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: E 258 ARG cc_start: 0.8123 (ttt180) cc_final: 0.7756 (mtp-110) REVERT: F 1 MET cc_start: 0.7116 (ptt) cc_final: 0.6794 (ptt) REVERT: F 8 GLU cc_start: 0.6233 (mm-30) cc_final: 0.5705 (mp0) REVERT: F 12 LYS cc_start: 0.6968 (ttpt) cc_final: 0.6656 (mmtm) REVERT: F 105 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.7093 (tmt170) REVERT: F 198 LYS cc_start: 0.7910 (mttm) cc_final: 0.7247 (mppt) REVERT: F 202 GLU cc_start: 0.7738 (tp30) cc_final: 0.7314 (mm-30) REVERT: F 303 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6673 (tm-30) REVERT: F 326 ASP cc_start: 0.7208 (m-30) cc_final: 0.6909 (m-30) REVERT: G 1 MET cc_start: 0.4247 (tpp) cc_final: 0.3948 (tpp) REVERT: G 50 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6432 (tt0) REVERT: G 61 GLN cc_start: 0.6565 (OUTLIER) cc_final: 0.6073 (tp-100) REVERT: G 64 GLU cc_start: 0.6114 (mt-10) cc_final: 0.5257 (tm-30) REVERT: G 115 ASP cc_start: 0.6903 (m-30) cc_final: 0.6658 (t70) REVERT: G 128 PHE cc_start: 0.5913 (p90) cc_final: 0.5419 (p90) REVERT: G 136 LYS cc_start: 0.5961 (tttm) cc_final: 0.5308 (ttmm) REVERT: G 137 ARG cc_start: 0.5668 (tpt90) cc_final: 0.4610 (mmp80) REVERT: G 160 PHE cc_start: 0.4998 (m-80) cc_final: 0.4697 (m-80) REVERT: G 182 MET cc_start: 0.4366 (ttt) cc_final: 0.4109 (ttm) REVERT: G 205 ARG cc_start: 0.6392 (OUTLIER) cc_final: 0.5807 (ttt90) REVERT: G 246 ARG cc_start: 0.6537 (ttt180) cc_final: 0.5762 (ttp80) REVERT: G 262 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7543 (mp) REVERT: G 289 GLN cc_start: 0.5391 (tt0) cc_final: 0.4311 (mm110) REVERT: G 291 LYS cc_start: 0.6469 (tttt) cc_final: 0.6043 (ttmt) REVERT: G 300 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6954 (mp0) REVERT: G 342 ASP cc_start: 0.6292 (OUTLIER) cc_final: 0.5159 (p0) REVERT: G 364 MET cc_start: 0.5617 (mtp) cc_final: 0.5386 (ptp) outliers start: 82 outliers final: 27 residues processed: 417 average time/residue: 0.7257 time to fit residues: 335.3415 Evaluate side-chains 386 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 339 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 204 MET Chi-restraints excluded: chain G residue 205 ARG Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 342 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 42 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 250 optimal weight: 20.0000 chunk 203 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 226 optimal weight: 10.0000 chunk 76 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 225 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS B 13 GLN B 78 ASN C 231 GLN E 54 GLN E 279 ASN ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 HIS F 295 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.195952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.152600 restraints weight = 21071.703| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.87 r_work: 0.3749 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21284 Z= 0.141 Angle : 0.558 10.075 29091 Z= 0.278 Chirality : 0.039 0.281 3350 Planarity : 0.004 0.074 3615 Dihedral : 14.442 165.193 3355 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.34 % Favored : 97.62 % Rotamer: Outliers : 3.69 % Allowed : 17.73 % Favored : 78.58 % 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: 2516 helix: 1.76 (0.15), residues: 1274 sheet: 0.90 (0.25), residues: 410 loop : 0.25 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 119 TYR 0.016 0.001 TYR E 47 PHE 0.011 0.001 PHE G 128 TRP 0.014 0.001 TRP B 10 HIS 0.005 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (21267) covalent geometry : angle 0.54097 / 0.28 (29067) hydrogen bonds : bond 0.03678 / 2.51 ( 1127) hydrogen bonds : angle 3.84518 / 2.82 ( 3171) metal coordination : bond 0.00198 / 0.10 ( 16) metal coordination : angle 4.77232 / 2.88 ( 24) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 349 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6584 (mpp-170) REVERT: A 18 ARG cc_start: 0.7607 (mmt180) cc_final: 0.7355 (mmt180) REVERT: A 39 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7135 (mtm180) REVERT: A 113 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7584 (ttp-170) REVERT: A 175 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: A 189 SER cc_start: 0.8315 (OUTLIER) cc_final: 0.7984 (p) REVERT: A 204 GLN cc_start: 0.8077 (mt0) cc_final: 0.7536 (pt0) REVERT: A 234 GLN cc_start: 0.7763 (mt0) cc_final: 0.7458 (mt0) REVERT: A 277 ARG cc_start: 0.6422 (ptm-80) cc_final: 0.6116 (ptm-80) REVERT: B 108 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7671 (mp) REVERT: B 124 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7663 (tt) REVERT: B 126 ASP cc_start: 0.8548 (m-30) cc_final: 0.8059 (m-30) REVERT: B 169 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7078 (mmm160) REVERT: B 188 GLU cc_start: 0.8410 (tt0) cc_final: 0.8028 (tt0) REVERT: B 193 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: B 284 GLU cc_start: 0.8124 (tt0) cc_final: 0.7614 (mt-10) REVERT: B 294 MET cc_start: 0.7917 (mtm) cc_final: 0.7420 (mmp) REVERT: B 337 LYS cc_start: 0.7936 (mtmt) cc_final: 0.7630 (mppt) REVERT: C 110 ASN cc_start: 0.7908 (m-40) cc_final: 0.7396 (p0) REVERT: C 112 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7760 (mp10) REVERT: C 126 ASP cc_start: 0.8228 (m-30) cc_final: 0.7935 (m-30) REVERT: C 133 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7806 (mtm-85) REVERT: C 141 LYS cc_start: 0.7902 (tppt) cc_final: 0.7663 (tmtt) REVERT: C 145 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7870 (mt-10) REVERT: C 148 GLU cc_start: 0.8194 (mp0) cc_final: 0.7695 (tm-30) REVERT: C 176 LYS cc_start: 0.8667 (mtpp) cc_final: 0.8194 (mmtm) REVERT: C 193 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8125 (mm-30) REVERT: C 208 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7523 (mtp85) REVERT: C 274 ARG cc_start: 0.7486 (mtm-85) cc_final: 0.7079 (mtp85) REVERT: C 288 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8389 (mp) REVERT: C 315 GLU cc_start: 0.7916 (tp30) cc_final: 0.7397 (mm-30) REVERT: C 318 ARG cc_start: 0.8119 (mtm110) cc_final: 0.7817 (mtm110) REVERT: C 319 THR cc_start: 0.8833 (m) cc_final: 0.8568 (p) REVERT: C 362 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7016 (mtp85) REVERT: D 1 MET cc_start: 0.3533 (tmm) cc_final: 0.2756 (tpt) REVERT: D 83 GLU cc_start: 0.7359 (tt0) cc_final: 0.7107 (tt0) REVERT: D 102 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6888 (mp0) REVERT: D 112 GLN cc_start: 0.7084 (pm20) cc_final: 0.6778 (pm20) REVERT: D 145 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8274 (mt-10) REVERT: D 148 GLU cc_start: 0.8124 (mp0) cc_final: 0.7868 (tp30) REVERT: D 204 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7090 (mt0) REVERT: D 222 ASP cc_start: 0.7823 (t70) cc_final: 0.7465 (t0) REVERT: D 274 ARG cc_start: 0.7501 (mtm-85) cc_final: 0.7062 (mtm180) REVERT: D 277 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.6453 (tm-30) REVERT: D 315 GLU cc_start: 0.7917 (tp30) cc_final: 0.7154 (mp0) REVERT: D 351 MET cc_start: 0.8702 (mtp) cc_final: 0.8387 (mtm) REVERT: E 15 VAL cc_start: 0.8128 (t) cc_final: 0.7862 (m) REVERT: E 22 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6890 (mmt90) REVERT: E 134 GLU cc_start: 0.7122 (tt0) cc_final: 0.6585 (pp20) REVERT: E 178 ARG cc_start: 0.7817 (mtm110) cc_final: 0.7338 (mtt180) REVERT: E 211 GLN cc_start: 0.7950 (tp40) cc_final: 0.7226 (mm110) REVERT: E 214 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7435 (mm-30) REVERT: E 239 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: E 258 ARG cc_start: 0.8156 (ttt180) cc_final: 0.7775 (mtp-110) REVERT: F 1 MET cc_start: 0.7202 (ptt) cc_final: 0.6769 (ptt) REVERT: F 8 GLU cc_start: 0.6229 (mm-30) cc_final: 0.5691 (mp0) REVERT: F 12 LYS cc_start: 0.6958 (ttpt) cc_final: 0.6633 (mmtm) REVERT: F 105 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.7009 (tmt170) REVERT: F 198 LYS cc_start: 0.7893 (mttm) cc_final: 0.7271 (mppt) REVERT: F 202 GLU cc_start: 0.7757 (tp30) cc_final: 0.7357 (mm-30) REVERT: F 282 ARG cc_start: 0.7361 (mtm-85) cc_final: 0.6930 (mtt180) REVERT: F 288 ASN cc_start: 0.7055 (OUTLIER) cc_final: 0.6687 (t0) REVERT: F 303 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6633 (tm-30) REVERT: F 326 ASP cc_start: 0.7067 (m-30) cc_final: 0.6774 (m-30) REVERT: G 50 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6501 (tt0) REVERT: G 61 GLN cc_start: 0.6587 (OUTLIER) cc_final: 0.6096 (tp-100) REVERT: G 115 ASP cc_start: 0.6911 (m-30) cc_final: 0.6575 (t70) REVERT: G 128 PHE cc_start: 0.5817 (p90) cc_final: 0.5501 (p90) REVERT: G 136 LYS cc_start: 0.6045 (tttm) cc_final: 0.5354 (ttmm) REVERT: G 137 ARG cc_start: 0.5675 (tpt90) cc_final: 0.4608 (mmp80) REVERT: G 160 PHE cc_start: 0.5001 (m-80) cc_final: 0.4694 (m-80) REVERT: G 205 ARG cc_start: 0.6360 (OUTLIER) cc_final: 0.5794 (ttt90) REVERT: G 246 ARG cc_start: 0.6534 (ttt180) cc_final: 0.5750 (ttp80) REVERT: G 262 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7534 (mp) REVERT: G 289 GLN cc_start: 0.5349 (tt0) cc_final: 0.4259 (mm110) REVERT: G 291 LYS cc_start: 0.6396 (tttt) cc_final: 0.5987 (ttmt) REVERT: G 300 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6890 (mp0) REVERT: G 342 ASP cc_start: 0.6237 (OUTLIER) cc_final: 0.5185 (p0) outliers start: 78 outliers final: 29 residues processed: 390 average time/residue: 0.7117 time to fit residues: 306.9707 Evaluate side-chains 389 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 335 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 205 ARG Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 317 ILE Chi-restraints excluded: chain G residue 342 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 81 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 22 optimal weight: 0.0770 chunk 147 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS B 13 GLN C 231 GLN E 54 GLN ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.196242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.151782 restraints weight = 21038.351| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.82 r_work: 0.3748 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21284 Z= 0.130 Angle : 0.550 9.634 29091 Z= 0.274 Chirality : 0.039 0.281 3350 Planarity : 0.004 0.076 3615 Dihedral : 14.437 165.185 3355 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.11 % Favored : 97.85 % Rotamer: Outliers : 3.26 % Allowed : 18.49 % Favored : 78.25 % 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: 1.69 (0.17), residues: 2516 helix: 1.82 (0.15), residues: 1274 sheet: 0.83 (0.25), residues: 419 loop : 0.30 (0.23), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 98 TYR 0.012 0.001 TYR F 154 PHE 0.010 0.001 PHE G 128 TRP 0.015 0.001 TRP B 10 HIS 0.004 0.001 HIS C 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (21267) covalent geometry : angle 0.53417 / 0.27 (29067) hydrogen bonds : bond 0.03585 / 2.44 ( 1127) hydrogen bonds : angle 3.80460 / 2.79 ( 3171) metal coordination : bond 0.00200 / 0.10 ( 16) metal coordination : angle 4.60717 / 2.80 ( 24) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 357 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6567 (mpp-170) REVERT: A 18 ARG cc_start: 0.7594 (mmt180) cc_final: 0.7341 (mmt180) REVERT: A 39 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7127 (mtm180) REVERT: A 113 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7593 (ttp-170) REVERT: A 175 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: A 189 SER cc_start: 0.8342 (OUTLIER) cc_final: 0.8012 (p) REVERT: A 198 THR cc_start: 0.8515 (m) cc_final: 0.8253 (m) REVERT: A 204 GLN cc_start: 0.8076 (mt0) cc_final: 0.7548 (pt0) REVERT: A 234 GLN cc_start: 0.7766 (mt0) cc_final: 0.7472 (mt0) REVERT: A 275 LYS cc_start: 0.8134 (ttpp) cc_final: 0.7913 (ttpp) REVERT: A 277 ARG cc_start: 0.6401 (ptm-80) cc_final: 0.6088 (ptm-80) REVERT: B 124 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7699 (tt) REVERT: B 126 ASP cc_start: 0.8550 (m-30) cc_final: 0.8180 (m-30) REVERT: B 169 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7082 (mmm160) REVERT: B 188 GLU cc_start: 0.8415 (tt0) cc_final: 0.8041 (tt0) REVERT: B 193 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.6714 (mp0) REVERT: B 284 GLU cc_start: 0.8119 (tt0) cc_final: 0.7613 (mt-10) REVERT: B 294 MET cc_start: 0.7932 (mtm) cc_final: 0.7447 (mmp) REVERT: B 337 LYS cc_start: 0.7904 (mtmt) cc_final: 0.7616 (mppt) REVERT: C 110 ASN cc_start: 0.7922 (m-40) cc_final: 0.7409 (p0) REVERT: C 112 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7786 (mp10) REVERT: C 126 ASP cc_start: 0.8267 (m-30) cc_final: 0.7972 (m-30) REVERT: C 133 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7814 (mtm-85) REVERT: C 141 LYS cc_start: 0.7893 (tppt) cc_final: 0.7669 (tmtt) REVERT: C 145 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7845 (mt-10) REVERT: C 148 GLU cc_start: 0.8201 (mp0) cc_final: 0.7685 (tm-30) REVERT: C 176 LYS cc_start: 0.8663 (mtpp) cc_final: 0.8179 (mmtm) REVERT: C 208 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7533 (mtp85) REVERT: C 274 ARG cc_start: 0.7477 (mtm-85) cc_final: 0.7070 (mtp85) REVERT: C 288 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8386 (mp) REVERT: C 315 GLU cc_start: 0.7890 (tp30) cc_final: 0.7379 (mm-30) REVERT: C 318 ARG cc_start: 0.8167 (mtm110) cc_final: 0.7956 (mtm110) REVERT: C 319 THR cc_start: 0.8820 (m) cc_final: 0.8555 (p) REVERT: C 362 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.6990 (mtp85) REVERT: D 1 MET cc_start: 0.3565 (tmm) cc_final: 0.2780 (tpt) REVERT: D 83 GLU cc_start: 0.7345 (tt0) cc_final: 0.7078 (tt0) REVERT: D 102 GLU cc_start: 0.7516 (mm-30) cc_final: 0.6909 (mp0) REVERT: D 112 GLN cc_start: 0.7101 (pm20) cc_final: 0.6790 (pm20) REVERT: D 145 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8271 (mt-10) REVERT: D 148 GLU cc_start: 0.8184 (mp0) cc_final: 0.7856 (tp30) REVERT: D 204 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7097 (mt0) REVERT: D 222 ASP cc_start: 0.7839 (t70) cc_final: 0.7503 (t0) REVERT: D 274 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.7072 (mtm180) REVERT: D 277 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.6543 (tm-30) REVERT: D 315 GLU cc_start: 0.7916 (tp30) cc_final: 0.7170 (mp0) REVERT: D 351 MET cc_start: 0.8693 (mtp) cc_final: 0.8364 (mtm) REVERT: E 22 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6887 (mmt90) REVERT: E 134 GLU cc_start: 0.7106 (tt0) cc_final: 0.6563 (pp20) REVERT: E 178 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7346 (mtt180) REVERT: E 211 GLN cc_start: 0.7984 (tp40) cc_final: 0.7249 (mm110) REVERT: E 214 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7471 (mm-30) REVERT: E 239 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: E 258 ARG cc_start: 0.8165 (ttt180) cc_final: 0.7769 (mtp-110) REVERT: F 1 MET cc_start: 0.7241 (ptt) cc_final: 0.6996 (ptt) REVERT: F 8 GLU cc_start: 0.6255 (mm-30) cc_final: 0.5737 (mp0) REVERT: F 12 LYS cc_start: 0.6966 (ttpt) cc_final: 0.6648 (mmtm) REVERT: F 51 MET cc_start: 0.7383 (ttp) cc_final: 0.6927 (ttp) REVERT: F 105 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.7043 (tmt170) REVERT: F 198 LYS cc_start: 0.7888 (mttm) cc_final: 0.7232 (mppt) REVERT: F 202 GLU cc_start: 0.7732 (tp30) cc_final: 0.7366 (mm-30) REVERT: F 246 ARG cc_start: 0.7556 (ptt-90) cc_final: 0.7179 (ptt-90) REVERT: F 288 ASN cc_start: 0.6992 (OUTLIER) cc_final: 0.6601 (m110) REVERT: F 295 ASN cc_start: 0.6952 (p0) cc_final: 0.6332 (t0) REVERT: F 303 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6553 (tm-30) REVERT: F 326 ASP cc_start: 0.7061 (m-30) cc_final: 0.6785 (m-30) REVERT: G 41 THR cc_start: 0.5544 (OUTLIER) cc_final: 0.5242 (t) REVERT: G 50 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6673 (tt0) REVERT: G 61 GLN cc_start: 0.6503 (OUTLIER) cc_final: 0.6067 (tp-100) REVERT: G 64 GLU cc_start: 0.6147 (mt-10) cc_final: 0.5358 (tm-30) REVERT: G 128 PHE cc_start: 0.5792 (p90) cc_final: 0.5518 (p90) REVERT: G 137 ARG cc_start: 0.5465 (tpt90) cc_final: 0.4436 (mmp80) REVERT: G 160 PHE cc_start: 0.5007 (m-80) cc_final: 0.4697 (m-80) REVERT: G 205 ARG cc_start: 0.6405 (OUTLIER) cc_final: 0.5806 (ttt90) REVERT: G 246 ARG cc_start: 0.6582 (ttt180) cc_final: 0.5805 (ttp80) REVERT: G 262 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7550 (mp) REVERT: G 289 GLN cc_start: 0.5357 (tt0) cc_final: 0.4289 (mm110) REVERT: G 291 LYS cc_start: 0.6364 (tttt) cc_final: 0.5959 (ttmt) REVERT: G 300 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6960 (mp0) REVERT: G 342 ASP cc_start: 0.6273 (OUTLIER) cc_final: 0.5213 (p0) REVERT: G 364 MET cc_start: 0.5818 (mtp) cc_final: 0.5492 (ptp) outliers start: 69 outliers final: 27 residues processed: 396 average time/residue: 0.7249 time to fit residues: 318.0323 Evaluate side-chains 392 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 340 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 205 ARG Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 317 ILE Chi-restraints excluded: chain G residue 342 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 128 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 188 optimal weight: 0.3980 chunk 246 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 chunk 226 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS B 78 ASN C 231 GLN D 231 GLN E 54 GLN ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.195833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.151324 restraints weight = 21035.452| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 1.45 r_work: 0.3792 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21284 Z= 0.145 Angle : 0.566 9.632 29091 Z= 0.282 Chirality : 0.039 0.280 3350 Planarity : 0.005 0.102 3615 Dihedral : 14.448 165.402 3355 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.23 % Favored : 97.73 % Rotamer: Outliers : 3.26 % Allowed : 19.01 % Favored : 77.73 % 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: 1.68 (0.17), residues: 2516 helix: 1.81 (0.15), residues: 1270 sheet: 0.86 (0.25), residues: 418 loop : 0.28 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 98 TYR 0.015 0.001 TYR B 341 PHE 0.011 0.001 PHE G 128 TRP 0.014 0.001 TRP B 10 HIS 0.005 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (21267) covalent geometry : angle 0.55023 / 0.28 (29067) hydrogen bonds : bond 0.03662 / 2.49 ( 1127) hydrogen bonds : angle 3.81682 / 2.81 ( 3171) metal coordination : bond 0.00215 / 0.11 ( 16) metal coordination : angle 4.60543 / 2.78 ( 24) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 341 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.6571 (mpp-170) REVERT: A 18 ARG cc_start: 0.7533 (mmt180) cc_final: 0.7269 (mmt180) REVERT: A 39 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7127 (mtm180) REVERT: A 113 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7582 (ttp-170) REVERT: A 175 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: A 189 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.8057 (p) REVERT: A 204 GLN cc_start: 0.8056 (mt0) cc_final: 0.7547 (pt0) REVERT: A 234 GLN cc_start: 0.7721 (mt0) cc_final: 0.7410 (mt0) REVERT: A 275 LYS cc_start: 0.8142 (ttpp) cc_final: 0.7739 (ttpp) REVERT: A 277 ARG cc_start: 0.6411 (ptm-80) cc_final: 0.6108 (ptm-80) REVERT: B 124 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7708 (tt) REVERT: B 126 ASP cc_start: 0.8471 (m-30) cc_final: 0.8128 (m-30) REVERT: B 169 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7084 (mmm160) REVERT: B 188 GLU cc_start: 0.8323 (tt0) cc_final: 0.7985 (tt0) REVERT: B 193 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: B 284 GLU cc_start: 0.8018 (tt0) cc_final: 0.7545 (mt-10) REVERT: B 294 MET cc_start: 0.7866 (mtm) cc_final: 0.7411 (mmp) REVERT: B 337 LYS cc_start: 0.7876 (mtmt) cc_final: 0.7584 (mppt) REVERT: C 110 ASN cc_start: 0.7901 (m-40) cc_final: 0.7441 (p0) REVERT: C 112 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7798 (mp10) REVERT: C 126 ASP cc_start: 0.8211 (m-30) cc_final: 0.7904 (m-30) REVERT: C 133 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7777 (mtm-85) REVERT: C 148 GLU cc_start: 0.8145 (mp0) cc_final: 0.7678 (tm-30) REVERT: C 176 LYS cc_start: 0.8626 (mtpp) cc_final: 0.8157 (mmtm) REVERT: C 208 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7471 (mtp85) REVERT: C 274 ARG cc_start: 0.7474 (mtm-85) cc_final: 0.7106 (mtp85) REVERT: C 288 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8356 (mp) REVERT: C 315 GLU cc_start: 0.7863 (tp30) cc_final: 0.7384 (mm-30) REVERT: C 319 THR cc_start: 0.8809 (m) cc_final: 0.8547 (p) REVERT: C 362 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.6989 (mtp85) REVERT: D 1 MET cc_start: 0.3499 (tmm) cc_final: 0.2720 (tpt) REVERT: D 83 GLU cc_start: 0.7311 (tt0) cc_final: 0.7039 (tt0) REVERT: D 102 GLU cc_start: 0.7452 (mm-30) cc_final: 0.6954 (mp0) REVERT: D 112 GLN cc_start: 0.7114 (pm20) cc_final: 0.6813 (pm20) REVERT: D 145 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8246 (mt-10) REVERT: D 148 GLU cc_start: 0.8160 (mp0) cc_final: 0.7849 (tp30) REVERT: D 204 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7118 (mt0) REVERT: D 222 ASP cc_start: 0.7784 (t70) cc_final: 0.7434 (t0) REVERT: D 274 ARG cc_start: 0.7499 (mtm-85) cc_final: 0.7140 (mtm-85) REVERT: D 277 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.6492 (tm-30) REVERT: D 315 GLU cc_start: 0.7856 (tp30) cc_final: 0.7199 (mp0) REVERT: D 351 MET cc_start: 0.8676 (mtp) cc_final: 0.8396 (mtm) REVERT: E 15 VAL cc_start: 0.8233 (t) cc_final: 0.7938 (m) REVERT: E 134 GLU cc_start: 0.7141 (tt0) cc_final: 0.6662 (pp20) REVERT: E 178 ARG cc_start: 0.7795 (mtm110) cc_final: 0.7352 (mtt180) REVERT: E 211 GLN cc_start: 0.7931 (tp40) cc_final: 0.7227 (mm110) REVERT: E 214 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7436 (mm-30) REVERT: E 239 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: E 258 ARG cc_start: 0.8111 (ttt180) cc_final: 0.7787 (mtp-110) REVERT: F 8 GLU cc_start: 0.6247 (mm-30) cc_final: 0.5762 (mp0) REVERT: F 12 LYS cc_start: 0.6952 (ttpt) cc_final: 0.6642 (mmtm) REVERT: F 198 LYS cc_start: 0.7858 (mttm) cc_final: 0.7244 (mppt) REVERT: F 202 GLU cc_start: 0.7710 (tp30) cc_final: 0.7340 (mm-30) REVERT: F 295 ASN cc_start: 0.6937 (p0) cc_final: 0.6352 (t0) REVERT: F 303 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6589 (tm-30) REVERT: F 326 ASP cc_start: 0.7051 (m-30) cc_final: 0.6775 (m-30) REVERT: F 338 MET cc_start: 0.6650 (ptp) cc_final: 0.6007 (ttp) REVERT: G 41 THR cc_start: 0.5721 (OUTLIER) cc_final: 0.5461 (t) REVERT: G 50 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6647 (tt0) REVERT: G 61 GLN cc_start: 0.6505 (OUTLIER) cc_final: 0.6113 (tp-100) REVERT: G 64 GLU cc_start: 0.6122 (mt-10) cc_final: 0.5453 (tm-30) REVERT: G 128 PHE cc_start: 0.5785 (p90) cc_final: 0.5515 (p90) REVERT: G 137 ARG cc_start: 0.5405 (tpt90) cc_final: 0.4412 (mmp80) REVERT: G 160 PHE cc_start: 0.4901 (m-80) cc_final: 0.4616 (m-80) REVERT: G 205 ARG cc_start: 0.6609 (OUTLIER) cc_final: 0.5879 (ttt90) REVERT: G 246 ARG cc_start: 0.6576 (ttt180) cc_final: 0.5801 (ttp80) REVERT: G 262 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7619 (mp) REVERT: G 289 GLN cc_start: 0.5401 (tt0) cc_final: 0.4275 (mm110) REVERT: G 291 LYS cc_start: 0.6386 (tttt) cc_final: 0.5985 (ttmt) REVERT: G 300 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6980 (mp0) REVERT: G 342 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.5241 (p0) outliers start: 69 outliers final: 29 residues processed: 378 average time/residue: 0.6936 time to fit residues: 291.0698 Evaluate side-chains 387 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 336 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 205 ARG Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 317 ILE Chi-restraints excluded: chain G residue 342 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 214 optimal weight: 8.9990 chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 14 optimal weight: 0.0470 chunk 233 optimal weight: 20.0000 chunk 139 optimal weight: 0.5980 chunk 209 optimal weight: 0.2980 chunk 226 optimal weight: 9.9990 chunk 181 optimal weight: 0.9990 chunk 234 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS B 13 GLN C 231 GLN E 54 GLN E 66 GLN ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.197793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.154490 restraints weight = 21142.368| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.85 r_work: 0.3769 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21284 Z= 0.107 Angle : 0.536 9.180 29091 Z= 0.269 Chirality : 0.038 0.277 3350 Planarity : 0.004 0.077 3615 Dihedral : 14.361 165.430 3355 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.79 % Favored : 98.17 % Rotamer: Outliers : 2.27 % Allowed : 20.24 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2516 helix: 1.99 (0.15), residues: 1272 sheet: 0.95 (0.25), residues: 397 loop : 0.28 (0.23), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 98 TYR 0.014 0.001 TYR F 154 PHE 0.009 0.001 PHE G 319 TRP 0.017 0.001 TRP B 10 HIS 0.004 0.001 HIS G 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (21267) covalent geometry : angle 0.52054 / 0.27 (29067) hydrogen bonds : bond 0.03332 / 2.26 ( 1127) hydrogen bonds : angle 3.73144 / 2.74 ( 3171) metal coordination : bond 0.00184 / 0.09 ( 16) metal coordination : angle 4.45274 / 2.70 ( 24) Misc. bond : bond 0.00027 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 347 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.6428 (mpp-170) REVERT: A 18 ARG cc_start: 0.7542 (mmt180) cc_final: 0.7281 (mmt180) REVERT: A 39 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7100 (mtm180) REVERT: A 113 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7575 (ttp-170) REVERT: A 175 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: A 189 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.8028 (p) REVERT: A 204 GLN cc_start: 0.8038 (mt0) cc_final: 0.7571 (pt0) REVERT: A 234 GLN cc_start: 0.7751 (mt0) cc_final: 0.7448 (mt0) REVERT: A 275 LYS cc_start: 0.8076 (ttpp) cc_final: 0.7862 (ttpp) REVERT: A 277 ARG cc_start: 0.6385 (ptm-80) cc_final: 0.6006 (ptm-80) REVERT: B 124 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7698 (tt) REVERT: B 126 ASP cc_start: 0.8400 (m-30) cc_final: 0.8137 (m-30) REVERT: B 169 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7093 (mmm160) REVERT: B 188 GLU cc_start: 0.8384 (tt0) cc_final: 0.8028 (tt0) REVERT: B 284 GLU cc_start: 0.8035 (tt0) cc_final: 0.7547 (mt-10) REVERT: B 294 MET cc_start: 0.7920 (mtm) cc_final: 0.7440 (mmp) REVERT: B 337 LYS cc_start: 0.7835 (mtmt) cc_final: 0.7533 (mppt) REVERT: C 110 ASN cc_start: 0.7902 (m-40) cc_final: 0.7393 (p0) REVERT: C 112 GLN cc_start: 0.8107 (mm-40) cc_final: 0.7769 (mp10) REVERT: C 126 ASP cc_start: 0.8229 (m-30) cc_final: 0.7921 (m-30) REVERT: C 133 ARG cc_start: 0.8048 (ttm110) cc_final: 0.7824 (mtm-85) REVERT: C 148 GLU cc_start: 0.8188 (mp0) cc_final: 0.7675 (tm-30) REVERT: C 176 LYS cc_start: 0.8618 (mtpp) cc_final: 0.8133 (mmtm) REVERT: C 208 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7698 (mtp180) REVERT: C 274 ARG cc_start: 0.7493 (mtm-85) cc_final: 0.7111 (mtp85) REVERT: C 288 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8338 (mp) REVERT: C 315 GLU cc_start: 0.7862 (tp30) cc_final: 0.7359 (mm-30) REVERT: C 319 THR cc_start: 0.8783 (m) cc_final: 0.8524 (p) REVERT: C 362 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7614 (mmt180) REVERT: D 83 GLU cc_start: 0.7319 (tt0) cc_final: 0.7049 (tt0) REVERT: D 102 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6977 (mp0) REVERT: D 112 GLN cc_start: 0.7060 (pm20) cc_final: 0.6733 (pm20) REVERT: D 145 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8210 (mt-10) REVERT: D 148 GLU cc_start: 0.8154 (mp0) cc_final: 0.7801 (tp30) REVERT: D 204 GLN cc_start: 0.7611 (tt0) cc_final: 0.7054 (mt0) REVERT: D 222 ASP cc_start: 0.7808 (t70) cc_final: 0.7464 (t0) REVERT: D 274 ARG cc_start: 0.7451 (mtm-85) cc_final: 0.7118 (mtm180) REVERT: D 277 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.6572 (tm-30) REVERT: D 315 GLU cc_start: 0.7921 (tp30) cc_final: 0.7216 (mp0) REVERT: D 351 MET cc_start: 0.8723 (mtp) cc_final: 0.8432 (mtm) REVERT: E 15 VAL cc_start: 0.8130 (t) cc_final: 0.7867 (m) REVERT: E 134 GLU cc_start: 0.7193 (tt0) cc_final: 0.6624 (pp20) REVERT: E 178 ARG cc_start: 0.7796 (mtm110) cc_final: 0.7338 (mtt180) REVERT: E 211 GLN cc_start: 0.7950 (tp40) cc_final: 0.7213 (mm110) REVERT: E 214 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7453 (mm-30) REVERT: E 239 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: E 258 ARG cc_start: 0.8151 (ttt180) cc_final: 0.7802 (mtp-110) REVERT: F 8 GLU cc_start: 0.6253 (mm-30) cc_final: 0.5759 (mp0) REVERT: F 12 LYS cc_start: 0.6986 (ttpt) cc_final: 0.6683 (mmtm) REVERT: F 198 LYS cc_start: 0.7871 (mttm) cc_final: 0.7193 (mppt) REVERT: F 202 GLU cc_start: 0.7660 (tp30) cc_final: 0.7331 (mm-30) REVERT: F 288 ASN cc_start: 0.6976 (m-40) cc_final: 0.6594 (m110) REVERT: F 295 ASN cc_start: 0.6937 (p0) cc_final: 0.6339 (t0) REVERT: F 303 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6563 (tm-30) REVERT: F 326 ASP cc_start: 0.6932 (m-30) cc_final: 0.6660 (m-30) REVERT: F 338 MET cc_start: 0.6569 (ptp) cc_final: 0.6209 (ttp) REVERT: G 41 THR cc_start: 0.5607 (OUTLIER) cc_final: 0.5388 (t) REVERT: G 50 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6694 (tt0) REVERT: G 61 GLN cc_start: 0.6480 (OUTLIER) cc_final: 0.6132 (tp-100) REVERT: G 64 GLU cc_start: 0.6129 (mt-10) cc_final: 0.5422 (tm-30) REVERT: G 128 PHE cc_start: 0.5774 (p90) cc_final: 0.5504 (p90) REVERT: G 137 ARG cc_start: 0.5378 (tpt90) cc_final: 0.4383 (mmp80) REVERT: G 160 PHE cc_start: 0.4865 (m-80) cc_final: 0.4581 (m-80) REVERT: G 246 ARG cc_start: 0.6597 (ttt180) cc_final: 0.5772 (ttp80) REVERT: G 289 GLN cc_start: 0.5427 (tt0) cc_final: 0.4283 (mm110) REVERT: G 291 LYS cc_start: 0.6402 (tttt) cc_final: 0.6017 (ttmt) REVERT: G 300 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6806 (mp0) outliers start: 48 outliers final: 29 residues processed: 374 average time/residue: 0.7290 time to fit residues: 302.4125 Evaluate side-chains 370 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 325 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 317 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 172 optimal weight: 0.7980 chunk 167 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 92 optimal weight: 0.0020 chunk 132 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 189 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS B 129 HIS C 231 GLN E 54 GLN ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.197605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.150503 restraints weight = 21069.336| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.71 r_work: 0.3696 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21284 Z= 0.112 Angle : 0.542 9.153 29091 Z= 0.272 Chirality : 0.038 0.275 3350 Planarity : 0.004 0.080 3615 Dihedral : 14.317 165.734 3355 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.95 % Favored : 98.01 % Rotamer: Outliers : 2.51 % Allowed : 20.57 % Favored : 76.93 % 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: 2516 helix: 2.01 (0.15), residues: 1273 sheet: 0.87 (0.25), residues: 414 loop : 0.29 (0.23), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 98 TYR 0.012 0.001 TYR B 341 PHE 0.009 0.001 PHE G 128 TRP 0.016 0.001 TRP C 10 HIS 0.004 0.001 HIS C 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (21267) covalent geometry : angle 0.52720 / 0.27 (29067) hydrogen bonds : bond 0.03346 / 2.27 ( 1127) hydrogen bonds : angle 3.71437 / 2.73 ( 3171) metal coordination : bond 0.00201 / 0.10 ( 16) metal coordination : angle 4.37976 / 2.67 ( 24) Misc. bond : bond 0.00020 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8975.68 seconds wall clock time: 152 minutes 48.66 seconds (9168.66 seconds total)