Starting phenix.real_space_refine on Sat Feb 7 14:31:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pdl_71537/02_2026/9pdl_71537.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pdl_71537/02_2026/9pdl_71537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pdl_71537/02_2026/9pdl_71537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pdl_71537/02_2026/9pdl_71537.map" model { file = "/net/cci-nas-00/data/ceres_data/9pdl_71537/02_2026/9pdl_71537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pdl_71537/02_2026/9pdl_71537.cif" } resolution = 2.76 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= 0.002 sd= 0.039 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 1 6.06 5 P 15 5.49 5 Mg 5 5.21 5 S 181 5.16 5 C 20952 2.51 5 N 5761 2.21 5 O 6354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 246 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33269 Number of models: 1 Model: "" Number of chains: 22 Chain: "C" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3051 Classifications: {'peptide': 386} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 369} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1831 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 230} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1813 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain: "I" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1908 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 242} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "J" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1813 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "L" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1845 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 226} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1856 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2264 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "v" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3163 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 23, 'TRANS': 377} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3104 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 373} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3018 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 359} Chain breaks: 1 Chain: "E" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2750 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 15, 'TRANS': 331} Chain breaks: 2 Chain: "F" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2850 Classifications: {'peptide': 364} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1763 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.33, per 1000 atoms: 0.22 Number of scatterers: 33269 At special positions: 0 Unit cell: (126.808, 192.832, 162.44, 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 1 29.99 S 181 16.00 P 15 15.00 Mg 5 11.99 O 6354 8.00 N 5761 7.00 C 20952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 154 " distance=2.05 Simple disulfide: pdb=" SG CYS H 137 " - pdb=" SG CYS H 213 " distance=2.03 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 501 " pdb="ZN ZN c 501 " - pdb=" NE2 HIS c 115 " pdb="ZN ZN c 501 " - pdb=" NE2 HIS c 113 " 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7926 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 24 sheets defined 47.2% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'C' and resid 21 through 68 removed outlier: 3.604A pdb=" N GLU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.586A pdb=" N LEU C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 155 through 166 removed outlier: 3.709A pdb=" N VAL C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 172 through 179 Processing helix chain 'C' and resid 195 through 207 Processing helix chain 'C' and resid 225 through 241 Processing helix chain 'C' and resid 251 through 256 removed outlier: 3.609A pdb=" N SER C 256 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 281 Processing helix chain 'C' and resid 302 through 307 Processing helix chain 'C' and resid 321 through 333 Processing helix chain 'C' and resid 343 through 350 removed outlier: 3.606A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 373 Processing helix chain 'C' and resid 379 through 391 Processing helix chain 'C' and resid 398 through 403 Processing helix chain 'G' and resid 6 through 10 removed outlier: 3.911A pdb=" N PHE G 9 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP G 10 " --> pdb=" O ALA G 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 6 through 10' Processing helix chain 'G' and resid 22 through 32 Processing helix chain 'G' and resid 33 through 36 Processing helix chain 'G' and resid 62 through 66 Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 128 Processing helix chain 'G' and resid 172 through 183 Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 231 through 244 Processing helix chain 'H' and resid 3 through 7 removed outlier: 3.559A pdb=" N SER H 7 " --> pdb=" O ARG H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 31 removed outlier: 3.641A pdb=" N GLU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 102 removed outlier: 3.510A pdb=" N VAL H 85 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 121 removed outlier: 3.823A pdb=" N TYR H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 174 Processing helix chain 'H' and resid 183 through 197 Processing helix chain 'H' and resid 222 through 234 Processing helix chain 'I' and resid 18 through 27 Processing helix chain 'I' and resid 28 through 31 Processing helix chain 'I' and resid 80 through 102 Processing helix chain 'I' and resid 107 through 124 Processing helix chain 'I' and resid 167 through 179 Processing helix chain 'I' and resid 185 through 201 removed outlier: 3.924A pdb=" N LYS I 199 " --> pdb=" O LYS I 195 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET I 201 " --> pdb=" O LEU I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 209 No H-bonds generated for 'chain 'I' and resid 207 through 209' Processing helix chain 'I' and resid 229 through 250 removed outlier: 4.032A pdb=" N GLU I 250 " --> pdb=" O LYS I 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 removed outlier: 3.688A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS J 27 " --> pdb=" O GLN J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 59 Processing helix chain 'J' and resid 76 through 98 removed outlier: 3.519A pdb=" N ILE J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 119 Processing helix chain 'J' and resid 164 through 176 Processing helix chain 'J' and resid 183 through 199 removed outlier: 3.931A pdb=" N GLU J 197 " --> pdb=" O LYS J 193 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL J 198 " --> pdb=" O ALA J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 240 Processing helix chain 'L' and resid 19 through 29 removed outlier: 3.831A pdb=" N VAL L 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 77 through 100 Processing helix chain 'L' and resid 104 through 118 removed outlier: 3.777A pdb=" N ILE L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 121 No H-bonds generated for 'chain 'L' and resid 119 through 121' Processing helix chain 'L' and resid 165 through 175 Processing helix chain 'L' and resid 175 through 181 removed outlier: 3.825A pdb=" N PHE L 179 " --> pdb=" O HIS L 175 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET L 180 " --> pdb=" O MET L 176 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU L 181 " --> pdb=" O SER L 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 175 through 181' Processing helix chain 'L' and resid 183 through 199 removed outlier: 3.648A pdb=" N THR L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU L 199 " --> pdb=" O LEU L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 229 through 234 Processing helix chain 'M' and resid 20 through 32 removed outlier: 3.642A pdb=" N GLU M 24 " --> pdb=" O VAL M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 103 Processing helix chain 'M' and resid 107 through 121 Processing helix chain 'M' and resid 122 through 124 No H-bonds generated for 'chain 'M' and resid 122 through 124' Processing helix chain 'M' and resid 168 through 178 removed outlier: 4.093A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 200 removed outlier: 4.049A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 242 removed outlier: 5.000A pdb=" N GLU M 234 " --> pdb=" O ASP M 230 " (cutoff:3.500A) Processing helix chain 'c' and resid 35 through 49 Processing helix chain 'c' and resid 83 through 87 Processing helix chain 'c' and resid 88 through 103 Processing helix chain 'c' and resid 123 through 137 removed outlier: 4.027A pdb=" N LEU c 136 " --> pdb=" O SER c 132 " (cutoff:3.500A) Processing helix chain 'c' and resid 166 through 171 Processing helix chain 'c' and resid 188 through 195 Processing helix chain 'c' and resid 216 through 220 removed outlier: 3.718A pdb=" N LEU c 220 " --> pdb=" O LEU c 217 " (cutoff:3.500A) Processing helix chain 'c' and resid 233 through 262 removed outlier: 3.973A pdb=" N GLU c 262 " --> pdb=" O ALA c 258 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 274 removed outlier: 3.746A pdb=" N ILE c 272 " --> pdb=" O GLU c 268 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN c 274 " --> pdb=" O LEU c 270 " (cutoff:3.500A) Processing helix chain 'c' and resid 285 through 309 Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 41 through 64 Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.534A pdb=" N TRP A 78 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 90 removed outlier: 4.020A pdb=" N GLN A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 164 Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 251 through 267 Processing helix chain 'A' and resid 277 through 280 Processing helix chain 'A' and resid 293 through 307 Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 347 through 359 Processing helix chain 'A' and resid 369 through 376 Processing helix chain 'A' and resid 381 through 399 removed outlier: 3.574A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 427 through 431 removed outlier: 3.970A pdb=" N THR A 431 " --> pdb=" O PRO A 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 427 through 431' Processing helix chain 'B' and resid 58 through 86 removed outlier: 4.737A pdb=" N GLU B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 104 Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.505A pdb=" N VAL B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.526A pdb=" N TYR B 211 " --> pdb=" O HIS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 Processing helix chain 'B' and resid 261 through 277 Processing helix chain 'B' and resid 287 through 292 removed outlier: 3.762A pdb=" N THR B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 317 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 357 through 369 Processing helix chain 'B' and resid 380 through 386 removed outlier: 4.466A pdb=" N ALA B 386 " --> pdb=" O ASP B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 409 Processing helix chain 'B' and resid 415 through 427 Processing helix chain 'D' and resid 40 through 83 removed outlier: 4.036A pdb=" N GLN D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 155 through 159 removed outlier: 3.684A pdb=" N LYS D 159 " --> pdb=" O SER D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 182 removed outlier: 3.834A pdb=" N ALA D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 187 through 195 removed outlier: 4.195A pdb=" N TYR D 191 " --> pdb=" O HIS D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 223 Processing helix chain 'D' and resid 232 through 236 removed outlier: 3.942A pdb=" N VAL D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 232 through 236' Processing helix chain 'D' and resid 242 through 257 Processing helix chain 'D' and resid 268 through 272 removed outlier: 3.679A pdb=" N ALA D 271 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR D 272 " --> pdb=" O ALA D 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 268 through 272' Processing helix chain 'D' and resid 279 through 297 removed outlier: 3.747A pdb=" N VAL D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 351 removed outlier: 4.516A pdb=" N LYS D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 removed outlier: 3.966A pdb=" N TYR D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 389 removed outlier: 3.527A pdb=" N GLU D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'D' and resid 412 through 416 removed outlier: 4.019A pdb=" N GLU D 415 " --> pdb=" O GLN D 412 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE D 416 " --> pdb=" O GLU D 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 412 through 416' Processing helix chain 'E' and resid 16 through 51 removed outlier: 3.958A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 138 through 155 removed outlier: 4.372A pdb=" N LEU E 151 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 155 through 163 removed outlier: 4.260A pdb=" N PHE E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 187 removed outlier: 3.629A pdb=" N ALA E 184 " --> pdb=" O LYS E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 190 No H-bonds generated for 'chain 'E' and resid 188 through 190' Processing helix chain 'E' and resid 216 through 224 Processing helix chain 'E' and resid 234 through 238 Processing helix chain 'E' and resid 254 through 262 Processing helix chain 'E' and resid 264 through 269 removed outlier: 3.564A pdb=" N ASP E 268 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR E 269 " --> pdb=" O ASP E 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 264 through 269' Processing helix chain 'E' and resid 305 through 317 removed outlier: 4.197A pdb=" N ASP E 311 " --> pdb=" O GLN E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 335 Processing helix chain 'E' and resid 339 through 356 removed outlier: 4.037A pdb=" N ARG E 356 " --> pdb=" O MET E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 378 removed outlier: 4.171A pdb=" N ASP E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 84 Processing helix chain 'F' and resid 169 through 176 removed outlier: 3.619A pdb=" N GLU F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 188 Processing helix chain 'F' and resid 192 through 203 Processing helix chain 'F' and resid 203 through 208 Processing helix chain 'F' and resid 209 through 215 Processing helix chain 'F' and resid 232 through 243 Processing helix chain 'F' and resid 254 through 257 Processing helix chain 'F' and resid 262 through 278 Processing helix chain 'F' and resid 287 through 291 Processing helix chain 'F' and resid 302 through 320 removed outlier: 3.607A pdb=" N PHE F 320 " --> pdb=" O GLN F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 344 removed outlier: 4.171A pdb=" N LEU F 343 " --> pdb=" O ASP F 339 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG F 344 " --> pdb=" O PRO F 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 339 through 344' Processing helix chain 'F' and resid 358 through 370 Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 392 through 410 Processing helix chain 'F' and resid 416 through 428 removed outlier: 3.784A pdb=" N GLN F 428 " --> pdb=" O ILE F 424 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 32 removed outlier: 3.540A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 104 Processing helix chain 'K' and resid 108 through 122 removed outlier: 3.763A pdb=" N GLN K 122 " --> pdb=" O ASN K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 185 Processing helix chain 'K' and resid 190 through 206 Processing helix chain 'K' and resid 230 through 239 Processing sheet with id=AA1, first strand: chain 'C' and resid 71 through 79 removed outlier: 7.050A pdb=" N LEU C 86 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ALA C 79 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LYS C 84 " --> pdb=" O ALA C 79 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 93 through 98 current: chain 'C' and resid 123 through 125 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 123 through 125 current: chain 'A' and resid 110 through 115 removed outlier: 3.655A pdb=" N ALA A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 119 through 123 current: chain 'A' and resid 149 through 152 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 149 through 152 current: chain 'B' and resid 120 through 124 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 130 through 134 current: chain 'B' and resid 159 through 162 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 159 through 162 current: chain 'D' and resid 100 through 105 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 110 through 113 current: chain 'D' and resid 139 through 142 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 139 through 142 current: chain 'E' and resid 69 through 73 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 78 through 81 current: chain 'E' and resid 107 through 111 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 107 through 111 current: chain 'F' and resid 121 through 126 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 131 through 134 current: chain 'F' and resid 160 through 163 Processing sheet with id=AA2, first strand: chain 'C' and resid 210 through 213 removed outlier: 6.729A pdb=" N GLY C 185 " --> pdb=" O ARG C 313 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE C 315 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU C 187 " --> pdb=" O ILE C 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 337 through 338 removed outlier: 6.598A pdb=" N ASN C 337 " --> pdb=" O VAL C 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 405 through 406 removed outlier: 4.336A pdb=" N GLY I 78 " --> pdb=" O LYS C 406 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.980A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL G 217 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 69 through 71 removed outlier: 4.422A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS G 153 " --> pdb=" O CYS G 161 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLY G 162 " --> pdb=" O ASP H 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 160 through 163 removed outlier: 3.908A pdb=" N VAL H 44 " --> pdb=" O CYS H 213 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN H 214 " --> pdb=" O GLY H 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 66 through 69 removed outlier: 6.438A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY H 73 " --> pdb=" O CYS H 137 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS H 137 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER H 133 " --> pdb=" O SER H 77 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 161 through 164 Processing sheet with id=AB1, first strand: chain 'I' and resid 65 through 69 removed outlier: 6.530A pdb=" N MET I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU I 147 " --> pdb=" O TRP I 159 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY I 158 " --> pdb=" O ASP J 55 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 158 through 161 Processing sheet with id=AB3, first strand: chain 'J' and resid 62 through 64 Processing sheet with id=AB4, first strand: chain 'L' and resid 158 through 161 Processing sheet with id=AB5, first strand: chain 'L' and resid 63 through 67 removed outlier: 6.101A pdb=" N ILE L 63 " --> pdb=" O ILE L 74 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE L 74 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N HIS L 65 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE L 72 " --> pdb=" O HIS L 65 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE L 70 " --> pdb=" O ASP L 67 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP L 138 " --> pdb=" O GLY L 141 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 162 through 165 removed outlier: 3.750A pdb=" N GLU M 212 " --> pdb=" O VAL M 49 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS M 51 " --> pdb=" O GLU M 210 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP M 215 " --> pdb=" O GLU M 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 66 through 68 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 74 through 76 current: chain 'M' and resid 133 through 141 removed outlier: 3.634A pdb=" N MET M 150 " --> pdb=" O TYR M 158 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR M 158 " --> pdb=" O MET M 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'c' and resid 25 through 26 removed outlier: 6.812A pdb=" N VAL c 25 " --> pdb=" O GLN c 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'c' and resid 30 through 34 removed outlier: 6.196A pdb=" N GLN c 30 " --> pdb=" O VAL c 67 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL c 69 " --> pdb=" O GLN c 30 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR c 32 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASP c 71 " --> pdb=" O TYR c 32 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N SER c 34 " --> pdb=" O ASP c 71 " (cutoff:3.500A) removed outlier: 10.978A pdb=" N PHE c 73 " --> pdb=" O SER c 34 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR c 66 " --> pdb=" O VAL c 62 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL c 62 " --> pdb=" O THR c 66 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU c 58 " --> pdb=" O ILE c 70 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL c 72 " --> pdb=" O LEU c 56 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU c 56 " --> pdb=" O VAL c 72 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ALA c 74 " --> pdb=" O MET c 54 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N MET c 54 " --> pdb=" O ALA c 74 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY c 110 " --> pdb=" O MET c 57 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLY c 59 " --> pdb=" O VAL c 108 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL c 108 " --> pdb=" O GLY c 59 " (cutoff:3.500A) removed outlier: 9.791A pdb=" N VAL c 141 " --> pdb=" O MET c 107 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL c 109 " --> pdb=" O VAL c 141 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL c 143 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP c 111 " --> pdb=" O VAL c 143 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL c 145 " --> pdb=" O TRP c 111 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N HIS c 113 " --> pdb=" O VAL c 145 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N ILE c 157 " --> pdb=" O ILE c 205 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE c 205 " --> pdb=" O ILE c 157 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA c 159 " --> pdb=" O ILE c 203 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 236 through 240 removed outlier: 4.611A pdb=" N ASP A 275 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY A 211 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE A 341 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU A 213 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 246 through 250 removed outlier: 6.351A pdb=" N THR B 246 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N PHE B 283 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 248 " --> pdb=" O PHE B 283 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 226 through 231 removed outlier: 6.419A pdb=" N ALA D 226 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N PHE D 263 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE D 228 " --> pdb=" O PHE D 263 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ASP D 265 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL D 230 " --> pdb=" O ASP D 265 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA D 260 " --> pdb=" O LYS D 306 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE D 308 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE D 262 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ALA D 310 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE D 264 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 247 through 252 removed outlier: 6.793A pdb=" N SER F 281 " --> pdb=" O LYS F 327 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ILE F 329 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE F 283 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ALA F 331 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE F 285 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG F 350 " --> pdb=" O GLY F 222 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 167 through 170 removed outlier: 3.813A pdb=" N GLU K 216 " --> pdb=" O VAL K 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 67 through 71 removed outlier: 6.458A pdb=" N ILE K 67 " --> pdb=" O MET K 78 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N MET K 78 " --> pdb=" O ILE K 67 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU K 69 " --> pdb=" O CYS K 76 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N CYS K 76 " --> pdb=" O GLU K 69 " (cutoff:3.500A) 1626 hydrogen bonds defined for protein. 4698 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.49 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6832 1.33 - 1.45: 7206 1.45 - 1.57: 19433 1.57 - 1.70: 25 1.70 - 1.82: 304 Bond restraints: 33800 Sorted by residual: bond pdb=" CA ILE E 276 " pdb=" C ILE E 276 " ideal model delta sigma weight residual 1.523 1.580 -0.057 1.27e-02 6.20e+03 2.03e+01 bond pdb=" N TYR E 221 " pdb=" CA TYR E 221 " ideal model delta sigma weight residual 1.457 1.500 -0.042 1.35e-02 5.49e+03 9.90e+00 bond pdb=" N VAL E 115 " pdb=" CA VAL E 115 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.25e-02 6.40e+03 8.81e+00 bond pdb=" N PRO E 117 " pdb=" CA PRO E 117 " ideal model delta sigma weight residual 1.469 1.505 -0.037 1.28e-02 6.10e+03 8.14e+00 bond pdb=" N GLU E 234 " pdb=" CA GLU E 234 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.90e+00 ... (remaining 33795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 44948 2.59 - 5.18: 622 5.18 - 7.77: 80 7.77 - 10.35: 13 10.35 - 12.94: 5 Bond angle restraints: 45668 Sorted by residual: angle pdb=" C LEU G 114 " pdb=" N CYS G 115 " pdb=" CA CYS G 115 " ideal model delta sigma weight residual 122.56 109.62 12.94 1.72e+00 3.38e-01 5.66e+01 angle pdb=" N PRO c 23 " pdb=" CA PRO c 23 " pdb=" CB PRO c 23 " ideal model delta sigma weight residual 103.00 110.39 -7.39 1.10e+00 8.26e-01 4.51e+01 angle pdb=" CA GLY C 262 " pdb=" C GLY C 262 " pdb=" O GLY C 262 " ideal model delta sigma weight residual 122.16 117.51 4.65 8.20e-01 1.49e+00 3.21e+01 angle pdb=" N VAL M 204 " pdb=" CA VAL M 204 " pdb=" C VAL M 204 " ideal model delta sigma weight residual 113.53 108.20 5.33 9.80e-01 1.04e+00 2.96e+01 angle pdb=" N LYS G 184 " pdb=" CA LYS G 184 " pdb=" C LYS G 184 " ideal model delta sigma weight residual 114.75 108.01 6.74 1.26e+00 6.30e-01 2.86e+01 ... (remaining 45663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.86: 17577 18.86 - 37.71: 2439 37.71 - 56.57: 654 56.57 - 75.43: 125 75.43 - 94.28: 57 Dihedral angle restraints: 20852 sinusoidal: 8580 harmonic: 12272 Sorted by residual: dihedral pdb=" CD ARG E 113 " pdb=" NE ARG E 113 " pdb=" CZ ARG E 113 " pdb=" NH1 ARG E 113 " ideal model delta sinusoidal sigma weight residual 0.00 86.51 -86.51 1 1.00e+01 1.00e-02 9.02e+01 dihedral pdb=" CB CYS G 115 " pdb=" SG CYS G 115 " pdb=" SG CYS G 154 " pdb=" CB CYS G 154 " ideal model delta sinusoidal sigma weight residual -86.00 -163.38 77.38 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CA CYS G 154 " pdb=" C CYS G 154 " pdb=" N ASP G 155 " pdb=" CA ASP G 155 " ideal model delta harmonic sigma weight residual -180.00 -149.09 -30.91 0 5.00e+00 4.00e-02 3.82e+01 ... (remaining 20849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4638 0.073 - 0.146: 544 0.146 - 0.219: 20 0.219 - 0.292: 3 0.292 - 0.366: 2 Chirality restraints: 5207 Sorted by residual: chirality pdb=" CG LEU I 114 " pdb=" CB LEU I 114 " pdb=" CD1 LEU I 114 " pdb=" CD2 LEU I 114 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CB ILE E 22 " pdb=" CA ILE E 22 " pdb=" CG1 ILE E 22 " pdb=" CG2 ILE E 22 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA PRO c 23 " pdb=" N PRO c 23 " pdb=" C PRO c 23 " pdb=" CB PRO c 23 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 5204 not shown) Planarity restraints: 5894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 113 " -1.097 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG E 113 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG E 113 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG E 113 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG E 113 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 271 " 0.032 2.00e-02 2.50e+03 2.70e-02 1.09e+01 pdb=" CG HIS E 271 " -0.056 2.00e-02 2.50e+03 pdb=" ND1 HIS E 271 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS E 271 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS E 271 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS E 271 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN G 224 " 0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO G 225 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO G 225 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 225 " 0.034 5.00e-02 4.00e+02 ... (remaining 5891 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 277 2.53 - 3.12: 25591 3.12 - 3.71: 54515 3.71 - 4.31: 74470 4.31 - 4.90: 124864 Nonbonded interactions: 279717 Sorted by model distance: nonbonded pdb=" OG1 THR A 223 " pdb="MG MG A 502 " model vdw 1.935 2.170 nonbonded pdb=" OG1 THR F 234 " pdb="MG MG F 502 " model vdw 1.942 2.170 nonbonded pdb=" O2B ADP C 501 " pdb="MG MG C 502 " model vdw 1.953 2.170 nonbonded pdb=" O2G ATP A 501 " pdb="MG MG A 502 " model vdw 1.958 2.170 nonbonded pdb=" O2G ATP B 501 " pdb="MG MG B 502 " model vdw 1.981 2.170 ... (remaining 279712 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.580 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 31.910 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33805 Z= 0.189 Angle : 0.746 12.942 45674 Z= 0.412 Chirality : 0.045 0.366 5207 Planarity : 0.008 0.492 5894 Dihedral : 18.931 94.284 12917 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.67 % Favored : 94.97 % Rotamer: Outliers : 3.27 % Allowed : 35.21 % Favored : 61.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.35 (0.13), residues: 4174 helix: 1.27 (0.12), residues: 1810 sheet: -0.40 (0.19), residues: 716 loop : -0.54 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 213 TYR 0.026 0.002 TYR E 40 PHE 0.032 0.002 PHE c 73 TRP 0.019 0.002 TRP H 158 HIS 0.020 0.001 HIS E 271 Details of bonding type rmsd covalent geometry : bond 0.00391 (33800) covalent geometry : angle 0.74509 (45668) SS BOND : bond 0.01124 ( 3) SS BOND : angle 2.99145 ( 6) hydrogen bonds : bond 0.16702 ( 1626) hydrogen bonds : angle 6.49798 ( 4698) metal coordination : bond 0.00286 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 555 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 TYR cc_start: 0.3041 (OUTLIER) cc_final: 0.1362 (t80) REVERT: C 60 ARG cc_start: 0.8649 (mmt90) cc_final: 0.8224 (mmt180) REVERT: C 82 LYS cc_start: 0.8741 (mttt) cc_final: 0.8210 (mmtm) REVERT: C 88 LYS cc_start: 0.8819 (tttt) cc_final: 0.8341 (ttpp) REVERT: C 90 HIS cc_start: 0.8588 (t-90) cc_final: 0.7686 (p90) REVERT: C 149 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: C 230 MET cc_start: 0.9316 (mtp) cc_final: 0.9112 (mtp) REVERT: C 284 GLU cc_start: 0.9101 (tp30) cc_final: 0.8859 (tp30) REVERT: C 297 ARG cc_start: 0.8128 (mmm160) cc_final: 0.7862 (mmm-85) REVERT: G 30 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8510 (mtpt) REVERT: G 62 ASP cc_start: 0.8053 (t0) cc_final: 0.7486 (t0) REVERT: G 88 ARG cc_start: 0.8996 (tpp80) cc_final: 0.8684 (mmt90) REVERT: G 153 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7387 (ttmt) REVERT: H 23 GLU cc_start: 0.8922 (mp0) cc_final: 0.8255 (mp0) REVERT: H 49 GLU cc_start: 0.8847 (pp20) cc_final: 0.8458 (pp20) REVERT: H 51 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8085 (mtmm) REVERT: H 58 ASP cc_start: 0.8411 (t0) cc_final: 0.7960 (t0) REVERT: H 200 GLU cc_start: 0.8595 (mp0) cc_final: 0.8305 (mp0) REVERT: I 64 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7764 (tttm) REVERT: I 76 VAL cc_start: 0.8109 (OUTLIER) cc_final: 0.7585 (t) REVERT: I 88 ASN cc_start: 0.8612 (t0) cc_final: 0.8365 (t0) REVERT: I 156 TYR cc_start: 0.8687 (p90) cc_final: 0.8273 (p90) REVERT: J 43 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8414 (mp) REVERT: J 46 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7735 (pt0) REVERT: J 52 LYS cc_start: 0.8737 (ttpm) cc_final: 0.8318 (ttpt) REVERT: J 136 PHE cc_start: 0.8000 (m-80) cc_final: 0.7444 (m-80) REVERT: J 146 GLN cc_start: 0.9182 (tt0) cc_final: 0.8882 (tt0) REVERT: L 9 ASP cc_start: 0.8422 (t0) cc_final: 0.8185 (t70) REVERT: L 110 SER cc_start: 0.8981 (OUTLIER) cc_final: 0.8577 (m) REVERT: L 173 GLU cc_start: 0.8757 (tt0) cc_final: 0.8395 (mt-10) REVERT: L 186 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: M 27 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.7415 (mpp) REVERT: M 139 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8142 (t) REVERT: M 150 MET cc_start: 0.9025 (ttp) cc_final: 0.8693 (ttp) REVERT: A 50 ASP cc_start: 0.8589 (m-30) cc_final: 0.8176 (m-30) REVERT: A 164 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8464 (mtt) REVERT: A 210 LYS cc_start: 0.8389 (mmtp) cc_final: 0.8084 (mtmt) REVERT: A 259 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8822 (mm-30) REVERT: A 319 MET cc_start: 0.9184 (mtt) cc_final: 0.8819 (mtt) REVERT: A 407 LYS cc_start: 0.8872 (mppt) cc_final: 0.8537 (mmmm) REVERT: A 411 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8787 (mt-10) REVERT: B 62 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8874 (tp) REVERT: B 75 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7049 (tt0) REVERT: B 98 LYS cc_start: 0.8890 (mmtp) cc_final: 0.8273 (tttt) REVERT: B 217 LYS cc_start: 0.9133 (mmmm) cc_final: 0.8843 (mppt) REVERT: B 242 GLN cc_start: 0.8938 (tp40) cc_final: 0.8234 (tm-30) REVERT: B 371 ARG cc_start: 0.8911 (mtt-85) cc_final: 0.8552 (mmt180) REVERT: D 114 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.8008 (tpp80) REVERT: D 246 MET cc_start: 0.8822 (ttm) cc_final: 0.8503 (ttt) REVERT: D 276 ASP cc_start: 0.8050 (p0) cc_final: 0.7414 (p0) REVERT: E 114 GLU cc_start: 0.7067 (tt0) cc_final: 0.6786 (tm-30) REVERT: E 230 ILE cc_start: 0.8425 (mm) cc_final: 0.7842 (pt) REVERT: E 233 ASP cc_start: 0.6654 (OUTLIER) cc_final: 0.6199 (m-30) REVERT: E 264 MET cc_start: 0.7234 (ppp) cc_final: 0.6476 (tmm) REVERT: E 274 LYS cc_start: 0.6130 (mptt) cc_final: 0.4948 (tptp) REVERT: F 320 PHE cc_start: 0.8607 (m-10) cc_final: 0.8403 (m-10) REVERT: K 9 ASP cc_start: 0.8861 (p0) cc_final: 0.8510 (p0) REVERT: K 71 ASP cc_start: 0.8839 (t0) cc_final: 0.8564 (t0) REVERT: K 239 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8663 (mttm) outliers start: 117 outliers final: 76 residues processed: 642 average time/residue: 0.6927 time to fit residues: 529.8466 Evaluate side-chains 608 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 516 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain L residue 110 SER Chi-restraints excluded: chain L residue 167 SER Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 144 ASP Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 288 VAL Chi-restraints excluded: chain c residue 294 SER Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 87 PRO Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 83 LYS Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 239 LYS Chi-restraints excluded: chain K residue 241 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 179 ASN H 214 ASN I 100 GLN I 155 ASN ** I 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 GLN J 68 ASN J 120 GLN J 200 GLN ** L 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 176 GLN B 82 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN E 121 ASN ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN E 345 ASN ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN F 333 ASN K 225 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.119953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.088000 restraints weight = 58179.731| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.48 r_work: 0.3077 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33805 Z= 0.171 Angle : 0.641 11.650 45674 Z= 0.329 Chirality : 0.045 0.194 5207 Planarity : 0.005 0.055 5894 Dihedral : 8.906 93.866 4887 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.50 % Favored : 95.16 % Rotamer: Outliers : 5.59 % Allowed : 29.87 % Favored : 64.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.48 (0.13), residues: 4174 helix: 1.36 (0.12), residues: 1843 sheet: -0.38 (0.19), residues: 729 loop : -0.48 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 113 TYR 0.017 0.002 TYR M 25 PHE 0.018 0.001 PHE E 367 TRP 0.014 0.001 TRP A 78 HIS 0.007 0.001 HIS c 221 Details of bonding type rmsd covalent geometry : bond 0.00392 (33800) covalent geometry : angle 0.64118 (45668) SS BOND : bond 0.00919 ( 3) SS BOND : angle 1.66259 ( 6) hydrogen bonds : bond 0.04349 ( 1626) hydrogen bonds : angle 5.09699 ( 4698) metal coordination : bond 0.00367 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 591 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 TYR cc_start: 0.3483 (OUTLIER) cc_final: 0.1712 (t80) REVERT: C 60 ARG cc_start: 0.8682 (mmt90) cc_final: 0.8272 (mmt180) REVERT: C 82 LYS cc_start: 0.8747 (mttt) cc_final: 0.8185 (mmtm) REVERT: C 88 LYS cc_start: 0.8763 (tttt) cc_final: 0.8343 (ttpp) REVERT: C 149 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: C 302 ASP cc_start: 0.8030 (t0) cc_final: 0.7747 (t0) REVERT: C 335 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8938 (mtpp) REVERT: C 372 ARG cc_start: 0.8747 (ttt90) cc_final: 0.8164 (ttt90) REVERT: G 21 ARG cc_start: 0.8659 (mtp180) cc_final: 0.8446 (ptm160) REVERT: G 30 LYS cc_start: 0.8849 (ttmm) cc_final: 0.8468 (mtpt) REVERT: G 62 ASP cc_start: 0.8108 (t0) cc_final: 0.7558 (t0) REVERT: G 73 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.7922 (p) REVERT: G 88 ARG cc_start: 0.9026 (tpp80) cc_final: 0.8675 (mmt90) REVERT: G 117 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6609 (tpp-160) REVERT: G 153 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7746 (ttmm) REVERT: H 49 GLU cc_start: 0.8855 (pp20) cc_final: 0.8360 (pp20) REVERT: H 50 LYS cc_start: 0.8346 (ttmm) cc_final: 0.8094 (ttmm) REVERT: H 51 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.7919 (mtmm) REVERT: H 58 ASP cc_start: 0.8667 (t0) cc_final: 0.8184 (t0) REVERT: H 82 ASP cc_start: 0.9422 (m-30) cc_final: 0.9176 (m-30) REVERT: H 185 GLU cc_start: 0.9193 (mp0) cc_final: 0.8945 (mp0) REVERT: H 205 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6783 (pp20) REVERT: H 225 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8393 (mt-10) REVERT: I 88 ASN cc_start: 0.8583 (t0) cc_final: 0.8304 (t0) REVERT: J 136 PHE cc_start: 0.8029 (m-80) cc_final: 0.7435 (m-80) REVERT: J 146 GLN cc_start: 0.9230 (tt0) cc_final: 0.8971 (tt0) REVERT: L 9 ASP cc_start: 0.8522 (t0) cc_final: 0.8201 (t70) REVERT: L 56 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8205 (pt) REVERT: L 110 SER cc_start: 0.9017 (p) cc_final: 0.8695 (m) REVERT: L 173 GLU cc_start: 0.8756 (tt0) cc_final: 0.8446 (mt-10) REVERT: L 186 GLU cc_start: 0.8447 (mp0) cc_final: 0.7788 (mp0) REVERT: L 234 GLU cc_start: 0.8161 (mp0) cc_final: 0.7771 (mp0) REVERT: M 27 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.7618 (mpp) REVERT: M 150 MET cc_start: 0.8821 (ttp) cc_final: 0.8449 (ttp) REVERT: c 107 MET cc_start: 0.8145 (mpt) cc_final: 0.7885 (pmm) REVERT: c 233 ASP cc_start: 0.7377 (t0) cc_final: 0.6914 (t0) REVERT: c 238 CYS cc_start: 0.8355 (t) cc_final: 0.8017 (t) REVERT: c 286 GLU cc_start: 0.8549 (tt0) cc_final: 0.8095 (tm-30) REVERT: A 46 LYS cc_start: 0.8526 (tppp) cc_final: 0.8258 (ttmm) REVERT: A 50 ASP cc_start: 0.8648 (m-30) cc_final: 0.8270 (m-30) REVERT: A 210 LYS cc_start: 0.8567 (mmtp) cc_final: 0.8155 (mtmt) REVERT: A 293 ASN cc_start: 0.7944 (m-40) cc_final: 0.7502 (m-40) REVERT: A 319 MET cc_start: 0.9426 (mtt) cc_final: 0.8975 (mtt) REVERT: A 407 LYS cc_start: 0.8834 (mppt) cc_final: 0.8621 (mmmm) REVERT: B 62 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8862 (tp) REVERT: B 75 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6569 (tt0) REVERT: B 98 LYS cc_start: 0.8905 (mmtp) cc_final: 0.8293 (tttt) REVERT: B 132 TYR cc_start: 0.9401 (t80) cc_final: 0.9100 (t80) REVERT: B 217 LYS cc_start: 0.9083 (mmmm) cc_final: 0.8845 (mmtm) REVERT: B 230 THR cc_start: 0.9167 (m) cc_final: 0.8840 (p) REVERT: B 242 GLN cc_start: 0.8922 (tp40) cc_final: 0.8200 (tm-30) REVERT: B 352 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8576 (tt0) REVERT: B 371 ARG cc_start: 0.8958 (mtt-85) cc_final: 0.8578 (mtt180) REVERT: D 114 ARG cc_start: 0.8231 (ttm-80) cc_final: 0.7887 (ttm110) REVERT: D 172 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8866 (mp) REVERT: D 246 MET cc_start: 0.8810 (ttm) cc_final: 0.8479 (ttt) REVERT: D 276 ASP cc_start: 0.8117 (p0) cc_final: 0.7480 (p0) REVERT: E 114 GLU cc_start: 0.7412 (tt0) cc_final: 0.6940 (tm-30) REVERT: E 122 MET cc_start: 0.3173 (mpt) cc_final: 0.2836 (mpp) REVERT: E 198 VAL cc_start: 0.4722 (m) cc_final: 0.4102 (p) REVERT: E 230 ILE cc_start: 0.8303 (mm) cc_final: 0.7971 (pp) REVERT: E 233 ASP cc_start: 0.5839 (OUTLIER) cc_final: 0.5381 (m-30) REVERT: E 264 MET cc_start: 0.7245 (ppp) cc_final: 0.6638 (tmm) REVERT: E 274 LYS cc_start: 0.6003 (mptt) cc_final: 0.4903 (tptp) REVERT: E 277 MET cc_start: 0.8060 (tmt) cc_final: 0.7704 (tmt) REVERT: F 132 TYR cc_start: 0.8416 (m-80) cc_final: 0.8196 (m-80) REVERT: F 304 ARG cc_start: 0.8506 (mtt180) cc_final: 0.8013 (mpt180) REVERT: K 9 ASP cc_start: 0.8942 (p0) cc_final: 0.8611 (p0) REVERT: K 54 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8707 (pp) REVERT: K 71 ASP cc_start: 0.8642 (t0) cc_final: 0.8393 (t0) REVERT: K 221 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8953 (pt0) REVERT: K 239 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8567 (mttp) outliers start: 200 outliers final: 71 residues processed: 742 average time/residue: 0.6837 time to fit residues: 604.3925 Evaluate side-chains 600 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 512 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 117 ARG Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 207 SER Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 100 ASP Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 178 THR Chi-restraints excluded: chain c residue 260 GLU Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 288 VAL Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 83 LYS Chi-restraints excluded: chain K residue 221 GLN Chi-restraints excluded: chain K residue 239 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 21 optimal weight: 1.9990 chunk 362 optimal weight: 0.9990 chunk 308 optimal weight: 0.0030 chunk 334 optimal weight: 40.0000 chunk 354 optimal weight: 5.9990 chunk 188 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 276 optimal weight: 0.0570 chunk 39 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 overall best weight: 0.5110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 392 GLN G 172 GLN H 214 ASN I 100 GLN I 240 HIS J 23 GLN J 120 GLN J 200 GLN M 63 ASN c 44 HIS ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN E 75 ASN ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN F 307 GLN K 225 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.121861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.090005 restraints weight = 58068.072| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.50 r_work: 0.3115 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33805 Z= 0.122 Angle : 0.600 11.468 45674 Z= 0.306 Chirality : 0.043 0.184 5207 Planarity : 0.004 0.054 5894 Dihedral : 8.136 90.579 4807 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.36 % Favored : 95.33 % Rotamer: Outliers : 5.34 % Allowed : 29.61 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.61 (0.13), residues: 4174 helix: 1.51 (0.12), residues: 1838 sheet: -0.48 (0.19), residues: 723 loop : -0.36 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 43 TYR 0.022 0.001 TYR D 392 PHE 0.018 0.001 PHE H 173 TRP 0.009 0.001 TRP A 78 HIS 0.005 0.001 HIS c 221 Details of bonding type rmsd covalent geometry : bond 0.00267 (33800) covalent geometry : angle 0.59935 (45668) SS BOND : bond 0.02288 ( 3) SS BOND : angle 1.77321 ( 6) hydrogen bonds : bond 0.03911 ( 1626) hydrogen bonds : angle 4.82437 ( 4698) metal coordination : bond 0.00125 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 613 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 ARG cc_start: 0.5292 (tpp-160) cc_final: 0.4234 (mtt90) REVERT: C 23 TYR cc_start: 0.3457 (OUTLIER) cc_final: 0.1488 (t80) REVERT: C 82 LYS cc_start: 0.8693 (mttt) cc_final: 0.8117 (mmtm) REVERT: C 88 LYS cc_start: 0.8693 (tttt) cc_final: 0.8274 (ttpp) REVERT: C 149 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8248 (mp0) REVERT: C 160 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8719 (mt-10) REVERT: C 392 GLN cc_start: 0.8444 (tp40) cc_final: 0.7887 (pp30) REVERT: G 30 LYS cc_start: 0.8828 (ttmm) cc_final: 0.8458 (mtpt) REVERT: G 62 ASP cc_start: 0.8083 (t0) cc_final: 0.7535 (t0) REVERT: G 73 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.7964 (p) REVERT: G 88 ARG cc_start: 0.8996 (tpp80) cc_final: 0.8618 (mmt90) REVERT: G 117 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.6520 (tpp-160) REVERT: G 153 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7817 (tttp) REVERT: H 23 GLU cc_start: 0.9158 (mp0) cc_final: 0.8931 (mp0) REVERT: H 49 GLU cc_start: 0.8814 (pp20) cc_final: 0.8241 (pp20) REVERT: H 50 LYS cc_start: 0.8283 (ttmm) cc_final: 0.8010 (ttmm) REVERT: H 51 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.7967 (mtmm) REVERT: H 58 ASP cc_start: 0.8736 (t0) cc_final: 0.8206 (t0) REVERT: H 139 TRP cc_start: 0.8759 (t-100) cc_final: 0.7200 (t-100) REVERT: H 205 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6661 (pp20) REVERT: H 225 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8058 (mm-30) REVERT: I 63 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7279 (tm-30) REVERT: I 88 ASN cc_start: 0.8547 (t0) cc_final: 0.8282 (t0) REVERT: I 124 PHE cc_start: 0.8185 (m-10) cc_final: 0.7977 (m-10) REVERT: I 156 TYR cc_start: 0.8859 (p90) cc_final: 0.8559 (p90) REVERT: I 177 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8431 (tm-30) REVERT: I 226 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6333 (mmm-85) REVERT: J 68 ASN cc_start: 0.7879 (p0) cc_final: 0.7475 (p0) REVERT: J 136 PHE cc_start: 0.7986 (m-80) cc_final: 0.7273 (m-80) REVERT: J 146 GLN cc_start: 0.9271 (tt0) cc_final: 0.8959 (tt0) REVERT: L 9 ASP cc_start: 0.8494 (t0) cc_final: 0.8192 (t70) REVERT: L 110 SER cc_start: 0.8982 (p) cc_final: 0.8675 (m) REVERT: L 173 GLU cc_start: 0.8733 (tt0) cc_final: 0.8374 (mt-10) REVERT: L 186 GLU cc_start: 0.8458 (mp0) cc_final: 0.8032 (mp0) REVERT: L 189 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8452 (mptt) REVERT: L 233 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8680 (mp) REVERT: L 234 GLU cc_start: 0.8142 (mp0) cc_final: 0.7839 (mp0) REVERT: M 27 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.7409 (mpp) REVERT: M 150 MET cc_start: 0.8715 (ttp) cc_final: 0.8263 (tmm) REVERT: M 175 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7535 (tm-30) REVERT: M 231 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8340 (pt) REVERT: c 107 MET cc_start: 0.8225 (mpt) cc_final: 0.7962 (pmm) REVERT: c 131 GLN cc_start: 0.8989 (tp-100) cc_final: 0.8721 (tp-100) REVERT: c 194 HIS cc_start: 0.7877 (m90) cc_final: 0.7634 (m-70) REVERT: c 233 ASP cc_start: 0.7204 (t0) cc_final: 0.6675 (t0) REVERT: c 238 CYS cc_start: 0.8385 (t) cc_final: 0.8061 (t) REVERT: c 286 GLU cc_start: 0.8469 (tt0) cc_final: 0.8082 (tm-30) REVERT: A 50 ASP cc_start: 0.8659 (m-30) cc_final: 0.8194 (m-30) REVERT: A 210 LYS cc_start: 0.8574 (mmtp) cc_final: 0.8275 (mtmt) REVERT: A 293 ASN cc_start: 0.7731 (m-40) cc_final: 0.7360 (m-40) REVERT: A 319 MET cc_start: 0.9413 (mtt) cc_final: 0.9002 (mtt) REVERT: A 342 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8962 (tt0) REVERT: A 430 MET cc_start: 0.7870 (tpp) cc_final: 0.7653 (mmm) REVERT: B 75 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6650 (tt0) REVERT: B 98 LYS cc_start: 0.8939 (mmtp) cc_final: 0.8351 (tttt) REVERT: B 132 TYR cc_start: 0.9362 (t80) cc_final: 0.9041 (t80) REVERT: B 217 LYS cc_start: 0.9071 (mmmm) cc_final: 0.8852 (mmtm) REVERT: B 230 THR cc_start: 0.9203 (m) cc_final: 0.8877 (p) REVERT: B 371 ARG cc_start: 0.8992 (mtt-85) cc_final: 0.8503 (mtp85) REVERT: D 91 GLN cc_start: 0.7980 (mp10) cc_final: 0.7382 (mp10) REVERT: D 114 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7915 (ttm110) REVERT: D 122 GLU cc_start: 0.8539 (mp0) cc_final: 0.8272 (mp0) REVERT: D 246 MET cc_start: 0.8750 (ttm) cc_final: 0.8411 (ttt) REVERT: D 276 ASP cc_start: 0.7946 (p0) cc_final: 0.7289 (p0) REVERT: D 296 MET cc_start: 0.8792 (mtp) cc_final: 0.8497 (mtp) REVERT: D 408 LYS cc_start: 0.8686 (tppt) cc_final: 0.8408 (tppt) REVERT: E 114 GLU cc_start: 0.7302 (tt0) cc_final: 0.6908 (tm-30) REVERT: E 198 VAL cc_start: 0.4947 (m) cc_final: 0.4353 (p) REVERT: E 230 ILE cc_start: 0.8470 (mm) cc_final: 0.8149 (pp) REVERT: E 232 MET cc_start: 0.8100 (mmm) cc_final: 0.7373 (mmp) REVERT: E 233 ASP cc_start: 0.5598 (OUTLIER) cc_final: 0.4691 (m-30) REVERT: E 264 MET cc_start: 0.7144 (ppp) cc_final: 0.6711 (tmm) REVERT: E 274 LYS cc_start: 0.5945 (mptt) cc_final: 0.4876 (tptp) REVERT: E 276 ILE cc_start: 0.7987 (mt) cc_final: 0.7161 (tp) REVERT: F 304 ARG cc_start: 0.8484 (mtt180) cc_final: 0.7991 (mpt180) REVERT: F 307 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8227 (tp40) REVERT: F 320 PHE cc_start: 0.8630 (m-10) cc_final: 0.8416 (m-10) REVERT: K 6 SER cc_start: 0.8380 (m) cc_final: 0.8070 (t) REVERT: K 9 ASP cc_start: 0.8834 (p0) cc_final: 0.8495 (p0) REVERT: K 54 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8691 (pp) REVERT: K 71 ASP cc_start: 0.8616 (t0) cc_final: 0.8401 (t0) outliers start: 191 outliers final: 70 residues processed: 753 average time/residue: 0.6946 time to fit residues: 624.0534 Evaluate side-chains 613 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 527 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 117 ARG Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 207 SER Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 226 ARG Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 189 LYS Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 231 ILE Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 178 THR Chi-restraints excluded: chain c residue 260 GLU Chi-restraints excluded: chain c residue 279 ASP Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 288 VAL Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain K residue 54 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 78 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 chunk 313 optimal weight: 10.0000 chunk 303 optimal weight: 2.9990 chunk 319 optimal weight: 0.8980 chunk 229 optimal weight: 5.9990 chunk 328 optimal weight: 4.9990 chunk 336 optimal weight: 4.9990 chunk 274 optimal weight: 0.6980 chunk 285 optimal weight: 6.9990 chunk 338 optimal weight: 30.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 214 ASN J 23 GLN J 120 GLN L 143 HIS M 101 ASN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 199 HIS A 247 GLN D 65 GLN E 75 ASN E 155 ASN E 280 ASN E 345 ASN ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN K 225 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.120683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.089630 restraints weight = 57939.437| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.42 r_work: 0.3088 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33805 Z= 0.143 Angle : 0.597 11.309 45674 Z= 0.304 Chirality : 0.043 0.195 5207 Planarity : 0.004 0.053 5894 Dihedral : 7.991 90.524 4783 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.46 % Favored : 95.26 % Rotamer: Outliers : 4.95 % Allowed : 30.51 % Favored : 64.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.60 (0.13), residues: 4174 helix: 1.48 (0.12), residues: 1849 sheet: -0.49 (0.18), residues: 732 loop : -0.33 (0.17), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 43 TYR 0.018 0.001 TYR D 392 PHE 0.018 0.001 PHE H 173 TRP 0.010 0.001 TRP A 78 HIS 0.004 0.001 HIS c 221 Details of bonding type rmsd covalent geometry : bond 0.00332 (33800) covalent geometry : angle 0.59622 (45668) SS BOND : bond 0.00927 ( 3) SS BOND : angle 1.88729 ( 6) hydrogen bonds : bond 0.03774 ( 1626) hydrogen bonds : angle 4.71891 ( 4698) metal coordination : bond 0.00327 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 557 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 ARG cc_start: 0.5119 (tpp-160) cc_final: 0.4217 (mtt90) REVERT: C 23 TYR cc_start: 0.3406 (OUTLIER) cc_final: 0.1387 (t80) REVERT: C 60 ARG cc_start: 0.8606 (mmt90) cc_final: 0.8195 (mmt180) REVERT: C 88 LYS cc_start: 0.8725 (tttt) cc_final: 0.8330 (ttpp) REVERT: C 149 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8253 (mp0) REVERT: C 160 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8748 (mt-10) REVERT: C 297 ARG cc_start: 0.8094 (mmm160) cc_final: 0.7710 (mmm160) REVERT: C 392 GLN cc_start: 0.8460 (tp40) cc_final: 0.7893 (pp30) REVERT: G 30 LYS cc_start: 0.8838 (ttmm) cc_final: 0.8473 (mtpt) REVERT: G 62 ASP cc_start: 0.8066 (t0) cc_final: 0.7591 (t0) REVERT: G 73 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8044 (p) REVERT: G 88 ARG cc_start: 0.9021 (tpp80) cc_final: 0.8659 (mmt90) REVERT: G 117 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6653 (tpp-160) REVERT: G 153 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7782 (tttp) REVERT: H 49 GLU cc_start: 0.8794 (pp20) cc_final: 0.8204 (pp20) REVERT: H 50 LYS cc_start: 0.8327 (ttmm) cc_final: 0.8027 (ttmm) REVERT: H 51 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8013 (mtmm) REVERT: H 58 ASP cc_start: 0.8764 (t0) cc_final: 0.8243 (t0) REVERT: H 139 TRP cc_start: 0.8743 (t-100) cc_final: 0.7010 (t-100) REVERT: H 177 ARG cc_start: 0.4513 (OUTLIER) cc_final: 0.4095 (mmt180) REVERT: H 205 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6686 (pp20) REVERT: H 225 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8036 (mm-30) REVERT: H 228 ASP cc_start: 0.9178 (p0) cc_final: 0.8582 (p0) REVERT: I 63 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7264 (tm-30) REVERT: I 88 ASN cc_start: 0.8550 (t0) cc_final: 0.8286 (t0) REVERT: J 68 ASN cc_start: 0.8184 (p0) cc_final: 0.7820 (p0) REVERT: J 99 GLU cc_start: 0.5391 (mp0) cc_final: 0.5190 (mp0) REVERT: J 146 GLN cc_start: 0.9288 (tt0) cc_final: 0.8979 (tt0) REVERT: L 9 ASP cc_start: 0.8617 (t0) cc_final: 0.8298 (t70) REVERT: L 51 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.6934 (mtp180) REVERT: L 110 SER cc_start: 0.8999 (p) cc_final: 0.8689 (m) REVERT: L 173 GLU cc_start: 0.8742 (tt0) cc_final: 0.8422 (mt-10) REVERT: L 186 GLU cc_start: 0.8467 (mp0) cc_final: 0.8040 (mp0) REVERT: L 189 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8489 (mptt) REVERT: L 220 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7823 (pm20) REVERT: L 233 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8711 (mp) REVERT: L 234 GLU cc_start: 0.8187 (mp0) cc_final: 0.7816 (mp0) REVERT: M 27 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.7548 (mpp) REVERT: M 81 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8805 (tp) REVERT: M 231 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8401 (pt) REVERT: c 107 MET cc_start: 0.8282 (mpt) cc_final: 0.8031 (pmm) REVERT: c 131 GLN cc_start: 0.9022 (tp-100) cc_final: 0.8766 (tp-100) REVERT: c 194 HIS cc_start: 0.7929 (m90) cc_final: 0.7695 (m-70) REVERT: c 233 ASP cc_start: 0.7282 (t0) cc_final: 0.6873 (t0) REVERT: c 238 CYS cc_start: 0.8429 (t) cc_final: 0.8170 (t) REVERT: c 286 GLU cc_start: 0.8459 (tt0) cc_final: 0.8088 (tm-30) REVERT: A 50 ASP cc_start: 0.8671 (m-30) cc_final: 0.8199 (m-30) REVERT: A 210 LYS cc_start: 0.8608 (mmtp) cc_final: 0.8356 (mtmt) REVERT: A 293 ASN cc_start: 0.7711 (m-40) cc_final: 0.7310 (m-40) REVERT: A 319 MET cc_start: 0.9429 (mtt) cc_final: 0.9018 (mtt) REVERT: A 342 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8998 (tt0) REVERT: A 429 TYR cc_start: 0.5276 (OUTLIER) cc_final: 0.4945 (t80) REVERT: A 430 MET cc_start: 0.7984 (tpp) cc_final: 0.7778 (mmm) REVERT: B 62 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8838 (tp) REVERT: B 75 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6600 (tt0) REVERT: B 98 LYS cc_start: 0.8924 (mmtp) cc_final: 0.8356 (tttt) REVERT: B 132 TYR cc_start: 0.9373 (t80) cc_final: 0.9085 (t80) REVERT: B 217 LYS cc_start: 0.9070 (mmmm) cc_final: 0.8869 (mppt) REVERT: B 230 THR cc_start: 0.9224 (m) cc_final: 0.8924 (p) REVERT: B 371 ARG cc_start: 0.8843 (mtt-85) cc_final: 0.8606 (tpp80) REVERT: D 91 GLN cc_start: 0.7978 (mp10) cc_final: 0.7433 (mp10) REVERT: D 114 ARG cc_start: 0.8189 (ttm-80) cc_final: 0.7931 (ttm110) REVERT: D 122 GLU cc_start: 0.8679 (mp0) cc_final: 0.8322 (mp0) REVERT: D 229 ARG cc_start: 0.9012 (ttp80) cc_final: 0.8603 (tpt90) REVERT: D 246 MET cc_start: 0.8773 (ttm) cc_final: 0.8423 (ttt) REVERT: D 276 ASP cc_start: 0.7967 (p0) cc_final: 0.7308 (p0) REVERT: E 30 ARG cc_start: 0.7773 (mmp-170) cc_final: 0.7479 (mtt180) REVERT: E 114 GLU cc_start: 0.7323 (tt0) cc_final: 0.6889 (tm-30) REVERT: E 155 ASN cc_start: 0.8463 (t0) cc_final: 0.8228 (t0) REVERT: E 230 ILE cc_start: 0.8335 (mm) cc_final: 0.8102 (pp) REVERT: E 232 MET cc_start: 0.8110 (mmm) cc_final: 0.7250 (mmp) REVERT: E 233 ASP cc_start: 0.5908 (OUTLIER) cc_final: 0.5250 (m-30) REVERT: E 264 MET cc_start: 0.7221 (ppp) cc_final: 0.6767 (tmm) REVERT: E 276 ILE cc_start: 0.7959 (mt) cc_final: 0.7275 (tp) REVERT: E 280 ASN cc_start: 0.6946 (t0) cc_final: 0.6235 (t0) REVERT: F 132 TYR cc_start: 0.8465 (m-80) cc_final: 0.8248 (m-80) REVERT: F 304 ARG cc_start: 0.8466 (mtt180) cc_final: 0.8034 (mpt180) REVERT: F 307 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8432 (tp40) REVERT: F 320 PHE cc_start: 0.8658 (m-10) cc_final: 0.8436 (m-10) REVERT: K 5 ARG cc_start: 0.7081 (ttm170) cc_final: 0.6343 (ttm170) REVERT: K 6 SER cc_start: 0.8424 (m) cc_final: 0.8078 (t) REVERT: K 9 ASP cc_start: 0.8924 (p0) cc_final: 0.8619 (p0) REVERT: K 54 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8734 (pp) REVERT: K 71 ASP cc_start: 0.8634 (t0) cc_final: 0.8426 (t0) REVERT: K 224 GLN cc_start: 0.8211 (mp10) cc_final: 0.7707 (mp10) outliers start: 177 outliers final: 81 residues processed: 691 average time/residue: 0.6473 time to fit residues: 536.5225 Evaluate side-chains 622 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 521 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 117 ARG Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 207 SER Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 51 ARG Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain L residue 189 LYS Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 197 ILE Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 231 ILE Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 260 GLU Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 288 VAL Chi-restraints excluded: chain c residue 291 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 83 LYS Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 228 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 220 optimal weight: 9.9990 chunk 262 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 chunk 357 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 300 optimal weight: 0.3980 chunk 191 optimal weight: 7.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 198 ASN J 23 GLN J 120 GLN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 199 HIS D 65 GLN E 345 ASN ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN K 225 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.120522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.088611 restraints weight = 57780.789| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.48 r_work: 0.3089 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33805 Z= 0.141 Angle : 0.602 11.310 45674 Z= 0.306 Chirality : 0.043 0.209 5207 Planarity : 0.004 0.053 5894 Dihedral : 7.896 89.579 4775 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.74 % Favored : 94.99 % Rotamer: Outliers : 5.20 % Allowed : 30.12 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.65 (0.13), residues: 4174 helix: 1.53 (0.12), residues: 1840 sheet: -0.46 (0.18), residues: 730 loop : -0.32 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 80 TYR 0.032 0.001 TYR E 221 PHE 0.021 0.001 PHE H 173 TRP 0.010 0.001 TRP A 78 HIS 0.003 0.001 HIS c 194 Details of bonding type rmsd covalent geometry : bond 0.00326 (33800) covalent geometry : angle 0.60170 (45668) SS BOND : bond 0.01394 ( 3) SS BOND : angle 2.00682 ( 6) hydrogen bonds : bond 0.03702 ( 1626) hydrogen bonds : angle 4.66623 ( 4698) metal coordination : bond 0.00294 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 557 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 TYR cc_start: 0.3128 (OUTLIER) cc_final: 0.1113 (t80) REVERT: C 60 ARG cc_start: 0.8608 (mmt90) cc_final: 0.8212 (mmt180) REVERT: C 81 ASP cc_start: 0.7944 (t0) cc_final: 0.7709 (t0) REVERT: C 88 LYS cc_start: 0.8716 (tttt) cc_final: 0.8320 (ttpp) REVERT: C 149 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: C 160 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8718 (mt-10) REVERT: C 213 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.6809 (ptp90) REVERT: C 392 GLN cc_start: 0.8463 (tp40) cc_final: 0.7880 (pp30) REVERT: C 396 GLU cc_start: 0.8238 (tp30) cc_final: 0.7983 (tp30) REVERT: G 30 LYS cc_start: 0.8821 (ttmm) cc_final: 0.8440 (mtpt) REVERT: G 62 ASP cc_start: 0.8165 (t0) cc_final: 0.7659 (t0) REVERT: G 73 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8110 (p) REVERT: G 88 ARG cc_start: 0.9050 (tpp80) cc_final: 0.8700 (mmt90) REVERT: G 117 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6651 (tpp-160) REVERT: G 153 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7736 (tttp) REVERT: H 23 GLU cc_start: 0.9121 (mp0) cc_final: 0.8901 (mp0) REVERT: H 49 GLU cc_start: 0.8799 (pp20) cc_final: 0.8183 (pp20) REVERT: H 50 LYS cc_start: 0.8303 (ttmm) cc_final: 0.7969 (ttmm) REVERT: H 51 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.7987 (mtmm) REVERT: H 58 ASP cc_start: 0.8761 (t0) cc_final: 0.8127 (t0) REVERT: H 139 TRP cc_start: 0.8735 (t-100) cc_final: 0.6992 (t-100) REVERT: H 177 ARG cc_start: 0.4474 (OUTLIER) cc_final: 0.4133 (mmt180) REVERT: H 205 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6688 (pp20) REVERT: H 225 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8033 (mm-30) REVERT: H 228 ASP cc_start: 0.9170 (p0) cc_final: 0.8542 (p0) REVERT: I 63 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7075 (tm-30) REVERT: I 88 ASN cc_start: 0.8494 (t0) cc_final: 0.8219 (t160) REVERT: I 162 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8476 (p) REVERT: I 212 GLU cc_start: 0.7344 (mt-10) cc_final: 0.7010 (mp0) REVERT: I 226 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6307 (mmm-85) REVERT: J 4 ASP cc_start: 0.8985 (p0) cc_final: 0.8271 (p0) REVERT: J 52 LYS cc_start: 0.8888 (ptmt) cc_final: 0.8285 (ptpp) REVERT: J 68 ASN cc_start: 0.8139 (p0) cc_final: 0.7794 (p0) REVERT: J 146 GLN cc_start: 0.9299 (tt0) cc_final: 0.8962 (tt0) REVERT: J 159 ASN cc_start: 0.8475 (t0) cc_final: 0.7998 (t160) REVERT: L 9 ASP cc_start: 0.8620 (t0) cc_final: 0.8283 (t70) REVERT: L 51 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.6931 (mtp180) REVERT: L 110 SER cc_start: 0.8990 (p) cc_final: 0.8690 (m) REVERT: L 173 GLU cc_start: 0.8767 (tt0) cc_final: 0.8420 (mt-10) REVERT: L 186 GLU cc_start: 0.8465 (mp0) cc_final: 0.8123 (mp0) REVERT: L 189 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8464 (mptt) REVERT: L 220 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7822 (pm20) REVERT: L 233 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8738 (mp) REVERT: L 234 GLU cc_start: 0.8187 (mp0) cc_final: 0.7848 (mp0) REVERT: M 27 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.7514 (mpp) REVERT: M 243 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5635 (mm) REVERT: c 104 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.5271 (tpp-160) REVERT: c 107 MET cc_start: 0.8370 (mpt) cc_final: 0.8114 (pmm) REVERT: c 131 GLN cc_start: 0.9018 (tp-100) cc_final: 0.8709 (tp-100) REVERT: c 194 HIS cc_start: 0.7961 (m90) cc_final: 0.7660 (m-70) REVERT: c 226 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8029 (mpt) REVERT: c 233 ASP cc_start: 0.7298 (t0) cc_final: 0.6897 (t0) REVERT: c 238 CYS cc_start: 0.8422 (t) cc_final: 0.8180 (t) REVERT: c 283 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.7841 (m170) REVERT: c 286 GLU cc_start: 0.8473 (tt0) cc_final: 0.8112 (tm-30) REVERT: A 50 ASP cc_start: 0.8642 (m-30) cc_final: 0.8157 (m-30) REVERT: A 55 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8239 (mp) REVERT: A 210 LYS cc_start: 0.8611 (mmtp) cc_final: 0.8335 (mtmt) REVERT: A 293 ASN cc_start: 0.7629 (m-40) cc_final: 0.7189 (m-40) REVERT: A 319 MET cc_start: 0.9428 (mtt) cc_final: 0.9019 (mtt) REVERT: A 342 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8995 (tt0) REVERT: A 429 TYR cc_start: 0.5355 (OUTLIER) cc_final: 0.4991 (t80) REVERT: A 430 MET cc_start: 0.7988 (tpp) cc_final: 0.7774 (mmm) REVERT: B 62 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8802 (tp) REVERT: B 75 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6479 (tt0) REVERT: B 98 LYS cc_start: 0.8902 (mmtp) cc_final: 0.8370 (tttt) REVERT: B 217 LYS cc_start: 0.9052 (mmmm) cc_final: 0.8845 (mppt) REVERT: B 230 THR cc_start: 0.9221 (m) cc_final: 0.8931 (p) REVERT: D 91 GLN cc_start: 0.7959 (mp10) cc_final: 0.7485 (mp10) REVERT: D 114 ARG cc_start: 0.8161 (ttm-80) cc_final: 0.7930 (ttm110) REVERT: D 122 GLU cc_start: 0.8676 (mp0) cc_final: 0.8298 (mp0) REVERT: D 229 ARG cc_start: 0.9029 (ttp80) cc_final: 0.8516 (tpt90) REVERT: D 246 MET cc_start: 0.8779 (ttm) cc_final: 0.8431 (ttt) REVERT: D 270 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8717 (pp) REVERT: D 276 ASP cc_start: 0.7936 (p0) cc_final: 0.7276 (p0) REVERT: D 415 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8249 (mt-10) REVERT: E 30 ARG cc_start: 0.7727 (mmp-170) cc_final: 0.7491 (mtt180) REVERT: E 114 GLU cc_start: 0.7384 (tt0) cc_final: 0.6948 (tm-30) REVERT: E 230 ILE cc_start: 0.8347 (mm) cc_final: 0.8089 (pp) REVERT: E 232 MET cc_start: 0.7902 (mmm) cc_final: 0.7435 (mmp) REVERT: E 233 ASP cc_start: 0.5970 (OUTLIER) cc_final: 0.5439 (m-30) REVERT: E 264 MET cc_start: 0.7239 (ppp) cc_final: 0.6800 (tmm) REVERT: E 274 LYS cc_start: 0.6566 (mptt) cc_final: 0.5064 (tptm) REVERT: E 276 ILE cc_start: 0.7824 (mt) cc_final: 0.7014 (tp) REVERT: E 280 ASN cc_start: 0.6839 (t0) cc_final: 0.6208 (t0) REVERT: F 132 TYR cc_start: 0.8497 (m-80) cc_final: 0.8260 (m-80) REVERT: F 304 ARG cc_start: 0.8456 (mtt180) cc_final: 0.8028 (mpt180) REVERT: F 320 PHE cc_start: 0.8658 (m-10) cc_final: 0.8426 (m-10) REVERT: K 5 ARG cc_start: 0.7110 (ttm170) cc_final: 0.6376 (ttm170) REVERT: K 6 SER cc_start: 0.8464 (m) cc_final: 0.8124 (t) REVERT: K 9 ASP cc_start: 0.8929 (p0) cc_final: 0.8632 (p0) REVERT: K 54 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8774 (pp) REVERT: K 71 ASP cc_start: 0.8651 (t0) cc_final: 0.8451 (t0) REVERT: K 224 GLN cc_start: 0.8219 (mp10) cc_final: 0.7689 (mp10) outliers start: 186 outliers final: 90 residues processed: 692 average time/residue: 0.6443 time to fit residues: 532.3606 Evaluate side-chains 647 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 531 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 117 ARG Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 207 SER Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 226 ARG Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 205 ASN Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 51 ARG Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain L residue 189 LYS Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 181 MET Chi-restraints excluded: chain M residue 227 VAL Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain c residue 104 ARG Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 178 THR Chi-restraints excluded: chain c residue 226 MET Chi-restraints excluded: chain c residue 260 GLU Chi-restraints excluded: chain c residue 279 ASP Chi-restraints excluded: chain c residue 283 HIS Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 288 VAL Chi-restraints excluded: chain c residue 291 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 316 HIS Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 83 LYS Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 228 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 79 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 295 optimal weight: 5.9990 chunk 284 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 272 optimal weight: 6.9990 chunk 389 optimal weight: 0.6980 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 GLN J 23 GLN J 120 GLN J 154 HIS L 5 GLN M 22 GLN M 101 ASN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 HIS D 257 ASN D 312 ASN E 75 ASN ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 HIS E 345 ASN ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN F 321 GLN K 225 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.116551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.084045 restraints weight = 58343.198| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.53 r_work: 0.3002 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 33805 Z= 0.293 Angle : 0.701 10.664 45674 Z= 0.358 Chirality : 0.047 0.271 5207 Planarity : 0.005 0.056 5894 Dihedral : 8.330 96.439 4774 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.01 % Favored : 94.73 % Rotamer: Outliers : 6.26 % Allowed : 29.61 % Favored : 64.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.46 (0.13), residues: 4174 helix: 1.32 (0.12), residues: 1851 sheet: -0.53 (0.18), residues: 735 loop : -0.38 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 80 TYR 0.022 0.002 TYR M 25 PHE 0.028 0.002 PHE K 123 TRP 0.015 0.002 TRP A 78 HIS 0.006 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00692 (33800) covalent geometry : angle 0.70086 (45668) SS BOND : bond 0.02341 ( 3) SS BOND : angle 2.46245 ( 6) hydrogen bonds : bond 0.04338 ( 1626) hydrogen bonds : angle 4.82632 ( 4698) metal coordination : bond 0.00940 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 528 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 TYR cc_start: 0.3109 (OUTLIER) cc_final: 0.0907 (t80) REVERT: C 88 LYS cc_start: 0.8748 (tttt) cc_final: 0.8363 (ttpp) REVERT: C 149 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: C 160 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8762 (mt-10) REVERT: C 213 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.6970 (ptp90) REVERT: C 302 ASP cc_start: 0.8711 (t0) cc_final: 0.8386 (t0) REVERT: C 335 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8940 (mtpp) REVERT: G 62 ASP cc_start: 0.8425 (t0) cc_final: 0.8036 (t0) REVERT: G 73 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8173 (p) REVERT: G 88 ARG cc_start: 0.9185 (tpp80) cc_final: 0.8791 (mmt90) REVERT: G 108 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: G 117 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6783 (tpp-160) REVERT: G 153 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8266 (tttt) REVERT: H 49 GLU cc_start: 0.8848 (pp20) cc_final: 0.8424 (pp20) REVERT: H 51 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.7949 (mtmm) REVERT: H 58 ASP cc_start: 0.8756 (t0) cc_final: 0.8194 (t0) REVERT: H 177 ARG cc_start: 0.4813 (OUTLIER) cc_final: 0.3730 (mmt180) REVERT: H 181 ASP cc_start: 0.8639 (m-30) cc_final: 0.8329 (m-30) REVERT: H 205 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7044 (pp20) REVERT: H 225 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8127 (mm-30) REVERT: H 228 ASP cc_start: 0.9232 (p0) cc_final: 0.8699 (p0) REVERT: I 63 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7400 (tm-30) REVERT: I 71 ASP cc_start: 0.8369 (p0) cc_final: 0.8164 (p0) REVERT: I 88 ASN cc_start: 0.8519 (t0) cc_final: 0.8242 (t0) REVERT: J 52 LYS cc_start: 0.8913 (ptmt) cc_final: 0.8275 (ptpp) REVERT: J 68 ASN cc_start: 0.8517 (p0) cc_final: 0.8293 (p0) REVERT: J 146 GLN cc_start: 0.9333 (tt0) cc_final: 0.9003 (tt0) REVERT: J 197 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7186 (pt0) REVERT: L 9 ASP cc_start: 0.8757 (t0) cc_final: 0.8405 (t70) REVERT: L 51 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7100 (mtp180) REVERT: L 110 SER cc_start: 0.9041 (p) cc_final: 0.8823 (m) REVERT: L 186 GLU cc_start: 0.8498 (mp0) cc_final: 0.8151 (mp0) REVERT: L 220 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7854 (pm20) REVERT: L 233 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8854 (mp) REVERT: M 27 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.7972 (mpp) REVERT: M 75 MET cc_start: 0.9289 (ttm) cc_final: 0.8974 (ttm) REVERT: M 81 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8849 (tp) REVERT: M 150 MET cc_start: 0.8861 (ttp) cc_final: 0.8657 (ttp) REVERT: M 158 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: M 175 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7930 (mm-30) REVERT: M 243 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5728 (mm) REVERT: c 104 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6148 (tpp-160) REVERT: c 131 GLN cc_start: 0.8947 (tp-100) cc_final: 0.8683 (tp-100) REVERT: c 233 ASP cc_start: 0.7259 (t0) cc_final: 0.6591 (t0) REVERT: c 238 CYS cc_start: 0.8621 (t) cc_final: 0.8361 (t) REVERT: c 279 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8155 (t0) REVERT: c 283 HIS cc_start: 0.8398 (OUTLIER) cc_final: 0.7918 (m170) REVERT: c 286 GLU cc_start: 0.8647 (tt0) cc_final: 0.8242 (tm-30) REVERT: A 50 ASP cc_start: 0.8727 (m-30) cc_final: 0.8229 (m-30) REVERT: A 55 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8183 (mp) REVERT: A 116 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7958 (mmpt) REVERT: A 210 LYS cc_start: 0.8688 (mmtp) cc_final: 0.8427 (mtmt) REVERT: A 293 ASN cc_start: 0.7899 (m-40) cc_final: 0.7457 (m-40) REVERT: A 319 MET cc_start: 0.9491 (mtt) cc_final: 0.9115 (mtt) REVERT: A 429 TYR cc_start: 0.5576 (OUTLIER) cc_final: 0.5257 (t80) REVERT: B 62 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8943 (tp) REVERT: B 75 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6541 (tt0) REVERT: B 85 MET cc_start: 0.7389 (tmm) cc_final: 0.7189 (tmm) REVERT: B 98 LYS cc_start: 0.8926 (mmtp) cc_final: 0.8410 (tttt) REVERT: B 181 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8403 (pp30) REVERT: B 217 LYS cc_start: 0.9077 (mmmm) cc_final: 0.8818 (mmtm) REVERT: B 230 THR cc_start: 0.9220 (m) cc_final: 0.8968 (p) REVERT: D 70 LYS cc_start: 0.8670 (mttm) cc_final: 0.8303 (mtpt) REVERT: D 91 GLN cc_start: 0.8113 (mp10) cc_final: 0.7655 (mp10) REVERT: D 114 ARG cc_start: 0.8270 (ttm-80) cc_final: 0.7937 (ttm110) REVERT: D 122 GLU cc_start: 0.8784 (mp0) cc_final: 0.8423 (mp0) REVERT: D 171 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8562 (p0) REVERT: D 246 MET cc_start: 0.8928 (ttm) cc_final: 0.8614 (ttt) REVERT: D 276 ASP cc_start: 0.8150 (p0) cc_final: 0.7462 (p0) REVERT: D 408 LYS cc_start: 0.8879 (tppt) cc_final: 0.8652 (tppt) REVERT: E 114 GLU cc_start: 0.7642 (tt0) cc_final: 0.6953 (tm-30) REVERT: E 230 ILE cc_start: 0.8128 (mm) cc_final: 0.7880 (pp) REVERT: E 260 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.5983 (mm) REVERT: E 264 MET cc_start: 0.7402 (ppp) cc_final: 0.6910 (tmm) REVERT: E 280 ASN cc_start: 0.6786 (t0) cc_final: 0.6135 (t0) REVERT: F 179 GLU cc_start: 0.8192 (tp30) cc_final: 0.7532 (tt0) REVERT: F 304 ARG cc_start: 0.8500 (mtt180) cc_final: 0.7973 (mpt180) REVERT: F 321 GLN cc_start: 0.5806 (OUTLIER) cc_final: 0.5587 (pp30) REVERT: F 353 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8335 (tp30) REVERT: K 6 SER cc_start: 0.8462 (m) cc_final: 0.8183 (t) REVERT: K 9 ASP cc_start: 0.9205 (p0) cc_final: 0.8860 (p0) REVERT: K 71 ASP cc_start: 0.8761 (t0) cc_final: 0.8526 (t0) REVERT: K 148 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8792 (pm20) REVERT: K 221 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8912 (pt0) outliers start: 224 outliers final: 97 residues processed: 698 average time/residue: 0.6735 time to fit residues: 562.1961 Evaluate side-chains 617 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 488 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 117 ARG Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 207 SER Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 51 ARG Chi-restraints excluded: chain L residue 182 CYS Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain c residue 35 SER Chi-restraints excluded: chain c residue 72 VAL Chi-restraints excluded: chain c residue 104 ARG Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 177 THR Chi-restraints excluded: chain c residue 186 LYS Chi-restraints excluded: chain c residue 260 GLU Chi-restraints excluded: chain c residue 279 ASP Chi-restraints excluded: chain c residue 283 HIS Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 288 VAL Chi-restraints excluded: chain c residue 292 MET Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 321 GLN Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 83 LYS Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 221 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 305 optimal weight: 0.1980 chunk 233 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 254 optimal weight: 10.0000 chunk 198 optimal weight: 0.0000 chunk 112 optimal weight: 10.0000 chunk 320 optimal weight: 5.9990 chunk 256 optimal weight: 0.8980 chunk 409 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 392 GLN G 75 ASN I 167 ASN I 198 ASN J 23 GLN ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 154 HIS L 5 GLN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 HIS E 75 ASN E 121 ASN ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.118802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.087530 restraints weight = 57556.390| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.45 r_work: 0.3054 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33805 Z= 0.130 Angle : 0.630 11.956 45674 Z= 0.319 Chirality : 0.043 0.203 5207 Planarity : 0.004 0.053 5894 Dihedral : 7.964 90.453 4770 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.55 % Favored : 95.21 % Rotamer: Outliers : 4.31 % Allowed : 32.02 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.56 (0.13), residues: 4174 helix: 1.47 (0.12), residues: 1849 sheet: -0.59 (0.18), residues: 735 loop : -0.36 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 43 TYR 0.033 0.001 TYR E 221 PHE 0.027 0.001 PHE H 173 TRP 0.014 0.001 TRP H 158 HIS 0.008 0.001 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00290 (33800) covalent geometry : angle 0.62995 (45668) SS BOND : bond 0.01122 ( 3) SS BOND : angle 2.21503 ( 6) hydrogen bonds : bond 0.03699 ( 1626) hydrogen bonds : angle 4.67732 ( 4698) metal coordination : bond 0.00144 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 570 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 TYR cc_start: 0.3186 (OUTLIER) cc_final: 0.1153 (t80) REVERT: C 60 ARG cc_start: 0.8589 (mmt90) cc_final: 0.8173 (mmt180) REVERT: C 88 LYS cc_start: 0.8583 (tttt) cc_final: 0.8170 (ttpp) REVERT: C 149 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: C 160 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8672 (mt-10) REVERT: C 213 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.6647 (ptp90) REVERT: C 297 ARG cc_start: 0.8071 (mmm160) cc_final: 0.7771 (mmm160) REVERT: C 372 ARG cc_start: 0.8409 (ttt90) cc_final: 0.8204 (ttt90) REVERT: G 30 LYS cc_start: 0.8781 (ttmm) cc_final: 0.8354 (mtpt) REVERT: G 58 ASP cc_start: 0.8302 (t0) cc_final: 0.8079 (t0) REVERT: G 62 ASP cc_start: 0.8250 (t0) cc_final: 0.7884 (t0) REVERT: G 73 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8100 (p) REVERT: G 88 ARG cc_start: 0.9084 (tpp80) cc_final: 0.8657 (mmt90) REVERT: G 108 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7902 (tm-30) REVERT: G 153 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7850 (tttp) REVERT: H 23 GLU cc_start: 0.9189 (mp0) cc_final: 0.8901 (mp0) REVERT: H 49 GLU cc_start: 0.8846 (pp20) cc_final: 0.8190 (pp20) REVERT: H 51 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.7960 (mtmm) REVERT: H 58 ASP cc_start: 0.8712 (t0) cc_final: 0.8160 (t0) REVERT: H 177 ARG cc_start: 0.4465 (OUTLIER) cc_final: 0.4164 (mmt180) REVERT: H 181 ASP cc_start: 0.8539 (m-30) cc_final: 0.8229 (m-30) REVERT: H 205 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6782 (pp20) REVERT: H 225 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8066 (mm-30) REVERT: H 228 ASP cc_start: 0.9188 (p0) cc_final: 0.8592 (p0) REVERT: I 26 GLU cc_start: 0.9056 (tt0) cc_final: 0.8762 (tt0) REVERT: I 63 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7194 (tm-30) REVERT: I 88 ASN cc_start: 0.8473 (t0) cc_final: 0.8199 (t160) REVERT: I 156 TYR cc_start: 0.8810 (p90) cc_final: 0.8576 (p90) REVERT: I 212 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7040 (mp0) REVERT: J 52 LYS cc_start: 0.8868 (ptmt) cc_final: 0.8216 (ptpp) REVERT: J 56 GLU cc_start: 0.8396 (mp0) cc_final: 0.7876 (tm-30) REVERT: J 120 GLN cc_start: 0.8484 (tt0) cc_final: 0.8253 (tp40) REVERT: J 146 GLN cc_start: 0.9303 (tt0) cc_final: 0.8953 (tt0) REVERT: J 212 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7795 (mtt180) REVERT: L 9 ASP cc_start: 0.8631 (t0) cc_final: 0.8269 (t70) REVERT: L 30 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9070 (mtpt) REVERT: L 51 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.6951 (mtp180) REVERT: L 110 SER cc_start: 0.8955 (p) cc_final: 0.8739 (m) REVERT: L 173 GLU cc_start: 0.8703 (tt0) cc_final: 0.8172 (mt-10) REVERT: M 27 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.7655 (mpp) REVERT: M 75 MET cc_start: 0.9215 (ttm) cc_final: 0.8892 (ttm) REVERT: M 81 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8687 (tp) REVERT: M 158 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7650 (m-80) REVERT: M 175 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7801 (mm-30) REVERT: M 243 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5676 (mm) REVERT: c 104 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.5447 (tpp-160) REVERT: c 107 MET cc_start: 0.8451 (ptt) cc_final: 0.8136 (pmm) REVERT: c 131 GLN cc_start: 0.8927 (tp-100) cc_final: 0.8637 (tp-100) REVERT: c 132 SER cc_start: 0.9155 (OUTLIER) cc_final: 0.8733 (p) REVERT: c 233 ASP cc_start: 0.7219 (t0) cc_final: 0.6731 (t0) REVERT: c 238 CYS cc_start: 0.8440 (t) cc_final: 0.8222 (t) REVERT: c 286 GLU cc_start: 0.8549 (tt0) cc_final: 0.8087 (tm-30) REVERT: A 50 ASP cc_start: 0.8661 (m-30) cc_final: 0.8156 (m-30) REVERT: A 55 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8098 (mp) REVERT: A 210 LYS cc_start: 0.8523 (mmtp) cc_final: 0.8285 (mtmt) REVERT: A 293 ASN cc_start: 0.7576 (m-40) cc_final: 0.7190 (m-40) REVERT: A 319 MET cc_start: 0.9403 (mtt) cc_final: 0.8980 (mtt) REVERT: A 429 TYR cc_start: 0.5313 (OUTLIER) cc_final: 0.4954 (t80) REVERT: B 62 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8753 (tp) REVERT: B 75 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6381 (tt0) REVERT: B 98 LYS cc_start: 0.8933 (mmtp) cc_final: 0.8383 (tttt) REVERT: B 217 LYS cc_start: 0.9032 (mmmm) cc_final: 0.8754 (mmtm) REVERT: B 230 THR cc_start: 0.9181 (m) cc_final: 0.8941 (p) REVERT: D 70 LYS cc_start: 0.8621 (mttm) cc_final: 0.8238 (mtpp) REVERT: D 91 GLN cc_start: 0.7979 (mp10) cc_final: 0.7494 (mp10) REVERT: D 114 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7849 (ttm110) REVERT: D 122 GLU cc_start: 0.8834 (mp0) cc_final: 0.8468 (mp0) REVERT: D 170 MET cc_start: 0.8763 (ttp) cc_final: 0.8459 (ttm) REVERT: D 171 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8388 (p0) REVERT: D 246 MET cc_start: 0.8856 (ttm) cc_final: 0.8497 (ttt) REVERT: D 276 ASP cc_start: 0.8048 (p0) cc_final: 0.7336 (p0) REVERT: D 408 LYS cc_start: 0.8891 (tppt) cc_final: 0.8529 (tptt) REVERT: E 30 ARG cc_start: 0.7758 (mmp-170) cc_final: 0.7421 (mtt180) REVERT: E 114 GLU cc_start: 0.7607 (tt0) cc_final: 0.6907 (tm-30) REVERT: E 218 MET cc_start: 0.8345 (mpt) cc_final: 0.8110 (pmm) REVERT: E 264 MET cc_start: 0.7261 (ppp) cc_final: 0.6833 (tmm) REVERT: E 274 LYS cc_start: 0.6666 (mptt) cc_final: 0.4822 (tmtm) REVERT: E 280 ASN cc_start: 0.6670 (t0) cc_final: 0.6167 (t0) REVERT: E 361 PHE cc_start: 0.7914 (p90) cc_final: 0.7525 (p90) REVERT: F 155 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8435 (ttpp) REVERT: F 226 TYR cc_start: 0.8910 (p90) cc_final: 0.8581 (p90) REVERT: F 304 ARG cc_start: 0.8455 (mtt180) cc_final: 0.7946 (mpt180) REVERT: F 353 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8306 (tp30) REVERT: K 5 ARG cc_start: 0.6950 (ttm170) cc_final: 0.6248 (ttm170) REVERT: K 6 SER cc_start: 0.8514 (m) cc_final: 0.8280 (t) REVERT: K 9 ASP cc_start: 0.8923 (p0) cc_final: 0.8606 (p0) REVERT: K 71 ASP cc_start: 0.8667 (t0) cc_final: 0.8458 (t70) REVERT: K 146 VAL cc_start: 0.9295 (m) cc_final: 0.9074 (t) REVERT: K 148 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8692 (pm20) outliers start: 154 outliers final: 60 residues processed: 685 average time/residue: 0.7166 time to fit residues: 585.3707 Evaluate side-chains 593 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 508 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 207 SER Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 212 ARG Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 51 ARG Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 242 SER Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain c residue 104 ARG Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 260 GLU Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 288 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 83 LYS Chi-restraints excluded: chain K residue 148 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 85 optimal weight: 0.3980 chunk 5 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 182 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 379 optimal weight: 9.9990 chunk 232 optimal weight: 0.9980 chunk 309 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 212 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 167 ASN J 23 GLN ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 GLN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 HIS ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN F 333 ASN K 225 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.117398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.086208 restraints weight = 57489.818| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.43 r_work: 0.3035 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33805 Z= 0.168 Angle : 0.639 11.454 45674 Z= 0.323 Chirality : 0.044 0.239 5207 Planarity : 0.004 0.053 5894 Dihedral : 7.943 89.871 4765 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.84 % Favored : 94.90 % Rotamer: Outliers : 3.97 % Allowed : 32.97 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.59 (0.13), residues: 4174 helix: 1.47 (0.12), residues: 1849 sheet: -0.52 (0.18), residues: 739 loop : -0.33 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 43 TYR 0.019 0.001 TYR J 110 PHE 0.030 0.001 PHE H 173 TRP 0.012 0.001 TRP A 78 HIS 0.010 0.001 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00395 (33800) covalent geometry : angle 0.63898 (45668) SS BOND : bond 0.01609 ( 3) SS BOND : angle 2.04288 ( 6) hydrogen bonds : bond 0.03759 ( 1626) hydrogen bonds : angle 4.67381 ( 4698) metal coordination : bond 0.00410 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 534 time to evaluate : 1.132 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: C 23 TYR cc_start: 0.3414 (OUTLIER) cc_final: 0.1169 (t80) REVERT: C 60 ARG cc_start: 0.8596 (mmt90) cc_final: 0.8181 (mmt180) REVERT: C 88 LYS cc_start: 0.8592 (tttt) cc_final: 0.8175 (ttpp) REVERT: C 139 MET cc_start: 0.9244 (ttm) cc_final: 0.8221 (ttm) REVERT: C 149 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8151 (mp0) REVERT: C 160 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8689 (mt-10) REVERT: C 213 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.6657 (ptp90) REVERT: C 297 ARG cc_start: 0.8166 (mmm160) cc_final: 0.7679 (mmm-85) REVERT: C 372 ARG cc_start: 0.8439 (ttt90) cc_final: 0.8215 (ttt90) REVERT: G 58 ASP cc_start: 0.8448 (t0) cc_final: 0.8190 (t0) REVERT: G 62 ASP cc_start: 0.8263 (t0) cc_final: 0.7893 (t0) REVERT: G 73 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8118 (p) REVERT: G 88 ARG cc_start: 0.9077 (tpp80) cc_final: 0.8650 (mmt90) REVERT: G 108 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: G 153 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7933 (tttp) REVERT: H 23 GLU cc_start: 0.9205 (mp0) cc_final: 0.8911 (mp0) REVERT: H 49 GLU cc_start: 0.8846 (pp20) cc_final: 0.8201 (pp20) REVERT: H 51 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.7989 (mtmm) REVERT: H 58 ASP cc_start: 0.8720 (t0) cc_final: 0.8156 (t0) REVERT: H 177 ARG cc_start: 0.4546 (OUTLIER) cc_final: 0.4170 (mmt180) REVERT: H 181 ASP cc_start: 0.8581 (m-30) cc_final: 0.8273 (m-30) REVERT: H 205 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6966 (pp20) REVERT: H 225 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8076 (mm-30) REVERT: H 228 ASP cc_start: 0.9184 (p0) cc_final: 0.8622 (p0) REVERT: I 26 GLU cc_start: 0.9049 (tt0) cc_final: 0.8739 (tt0) REVERT: I 63 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7185 (tm-30) REVERT: I 88 ASN cc_start: 0.8473 (t0) cc_final: 0.8190 (t160) REVERT: I 156 TYR cc_start: 0.8830 (p90) cc_final: 0.8611 (p90) REVERT: I 212 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7040 (mp0) REVERT: J 52 LYS cc_start: 0.8847 (ptmt) cc_final: 0.8196 (ptpp) REVERT: J 56 GLU cc_start: 0.8422 (mp0) cc_final: 0.7892 (tm-30) REVERT: J 68 ASN cc_start: 0.8300 (p0) cc_final: 0.7946 (p0) REVERT: J 120 GLN cc_start: 0.8491 (tt0) cc_final: 0.8234 (tp40) REVERT: J 146 GLN cc_start: 0.9352 (tt0) cc_final: 0.9006 (tt0) REVERT: J 212 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7724 (mtt180) REVERT: L 9 ASP cc_start: 0.8652 (t0) cc_final: 0.8294 (t70) REVERT: L 51 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.6945 (mtp180) REVERT: L 110 SER cc_start: 0.8964 (p) cc_final: 0.8748 (m) REVERT: L 173 GLU cc_start: 0.8678 (tt0) cc_final: 0.8173 (mt-10) REVERT: L 186 GLU cc_start: 0.8442 (mp0) cc_final: 0.8049 (mp0) REVERT: L 220 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7777 (pm20) REVERT: M 27 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.7617 (mpp) REVERT: M 75 MET cc_start: 0.9244 (ttm) cc_final: 0.8992 (ttm) REVERT: M 81 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8703 (tp) REVERT: M 158 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.7704 (m-80) REVERT: M 175 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7806 (mm-30) REVERT: M 243 LEU cc_start: 0.6135 (OUTLIER) cc_final: 0.5737 (mm) REVERT: c 88 ASP cc_start: 0.9190 (t0) cc_final: 0.8864 (t0) REVERT: c 104 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.5524 (tpp-160) REVERT: c 107 MET cc_start: 0.8637 (ptt) cc_final: 0.8275 (pmm) REVERT: c 131 GLN cc_start: 0.8950 (tp-100) cc_final: 0.8649 (tp-100) REVERT: c 146 ASP cc_start: 0.8062 (t0) cc_final: 0.7857 (t70) REVERT: c 233 ASP cc_start: 0.7215 (t0) cc_final: 0.6752 (t0) REVERT: c 238 CYS cc_start: 0.8490 (t) cc_final: 0.8280 (t) REVERT: c 286 GLU cc_start: 0.8528 (tt0) cc_final: 0.8179 (tm-30) REVERT: A 50 ASP cc_start: 0.8677 (m-30) cc_final: 0.8169 (m-30) REVERT: A 55 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8120 (mp) REVERT: A 146 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8812 (mtpp) REVERT: A 210 LYS cc_start: 0.8534 (mmtp) cc_final: 0.8303 (mtmt) REVERT: A 293 ASN cc_start: 0.7600 (m-40) cc_final: 0.7218 (m-40) REVERT: A 319 MET cc_start: 0.9431 (mtt) cc_final: 0.8977 (mtt) REVERT: A 429 TYR cc_start: 0.5310 (OUTLIER) cc_final: 0.4954 (t80) REVERT: B 62 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8755 (tp) REVERT: B 75 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6464 (tt0) REVERT: B 98 LYS cc_start: 0.8924 (mmtp) cc_final: 0.8380 (tttt) REVERT: B 217 LYS cc_start: 0.9045 (mmmm) cc_final: 0.8768 (mmtm) REVERT: B 230 THR cc_start: 0.9125 (m) cc_final: 0.8894 (p) REVERT: D 70 LYS cc_start: 0.8618 (mttm) cc_final: 0.8252 (mtpt) REVERT: D 91 GLN cc_start: 0.7970 (mp10) cc_final: 0.7544 (mp10) REVERT: D 114 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7839 (ttm110) REVERT: D 122 GLU cc_start: 0.8831 (mp0) cc_final: 0.8473 (mp0) REVERT: D 170 MET cc_start: 0.8879 (ttp) cc_final: 0.8579 (ttm) REVERT: D 171 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8420 (p0) REVERT: D 246 MET cc_start: 0.8869 (ttm) cc_final: 0.8517 (ttt) REVERT: D 276 ASP cc_start: 0.8051 (p0) cc_final: 0.7350 (p0) REVERT: D 408 LYS cc_start: 0.8954 (tppt) cc_final: 0.8580 (tptt) REVERT: D 415 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8300 (mt-10) REVERT: E 30 ARG cc_start: 0.7775 (mmp-170) cc_final: 0.7484 (mtt180) REVERT: E 37 THR cc_start: 0.8257 (m) cc_final: 0.7832 (p) REVERT: E 114 GLU cc_start: 0.7578 (tt0) cc_final: 0.6957 (tm-30) REVERT: E 218 MET cc_start: 0.8326 (mpt) cc_final: 0.8115 (pmm) REVERT: E 264 MET cc_start: 0.7332 (ppp) cc_final: 0.6905 (tmm) REVERT: E 274 LYS cc_start: 0.6425 (mptt) cc_final: 0.4812 (tmtm) REVERT: E 280 ASN cc_start: 0.6616 (t0) cc_final: 0.6122 (t0) REVERT: E 361 PHE cc_start: 0.7993 (p90) cc_final: 0.7575 (p90) REVERT: F 155 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8486 (ttpp) REVERT: F 179 GLU cc_start: 0.8212 (tp30) cc_final: 0.7420 (tt0) REVERT: F 304 ARG cc_start: 0.8465 (mtt180) cc_final: 0.7947 (mpt180) REVERT: F 305 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: F 353 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8386 (tp30) REVERT: K 5 ARG cc_start: 0.6991 (ttm170) cc_final: 0.6271 (ttm170) REVERT: K 9 ASP cc_start: 0.9002 (p0) cc_final: 0.8704 (p0) REVERT: K 146 VAL cc_start: 0.9283 (m) cc_final: 0.9060 (t) REVERT: K 148 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8727 (pm20) outliers start: 142 outliers final: 74 residues processed: 643 average time/residue: 0.7344 time to fit residues: 560.3036 Evaluate side-chains 613 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 514 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 207 SER Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 212 ARG Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 51 ARG Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 197 ILE Chi-restraints excluded: chain M residue 242 SER Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain c residue 104 ARG Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 260 GLU Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 288 VAL Chi-restraints excluded: chain c residue 292 MET Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 83 LYS Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 228 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 246 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 279 optimal weight: 1.9990 chunk 243 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 151 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 251 optimal weight: 0.0770 chunk 25 optimal weight: 3.9990 chunk 300 optimal weight: 0.7980 chunk 179 optimal weight: 8.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 75 ASN I 167 ASN I 198 ASN J 23 GLN ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 GLN L 43 HIS ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 149 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 HIS D 175 GLN E 75 ASN ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN F 333 ASN K 225 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.119249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.086988 restraints weight = 57724.538| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.51 r_work: 0.3059 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33805 Z= 0.135 Angle : 0.635 12.300 45674 Z= 0.320 Chirality : 0.043 0.233 5207 Planarity : 0.004 0.052 5894 Dihedral : 7.851 87.903 4763 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.70 % Favored : 95.06 % Rotamer: Outliers : 3.55 % Allowed : 33.39 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.66 (0.13), residues: 4174 helix: 1.53 (0.12), residues: 1843 sheet: -0.46 (0.19), residues: 732 loop : -0.30 (0.17), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 43 TYR 0.043 0.001 TYR E 221 PHE 0.028 0.001 PHE H 173 TRP 0.015 0.001 TRP H 158 HIS 0.010 0.001 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00311 (33800) covalent geometry : angle 0.63448 (45668) SS BOND : bond 0.01451 ( 3) SS BOND : angle 2.20920 ( 6) hydrogen bonds : bond 0.03634 ( 1626) hydrogen bonds : angle 4.63335 ( 4698) metal coordination : bond 0.00219 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 551 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 TYR cc_start: 0.3460 (OUTLIER) cc_final: 0.1101 (t80) REVERT: C 60 ARG cc_start: 0.8566 (mmt90) cc_final: 0.8139 (mmt180) REVERT: C 88 LYS cc_start: 0.8650 (tttt) cc_final: 0.8226 (ttpp) REVERT: C 149 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8167 (mp0) REVERT: C 160 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8718 (mt-10) REVERT: C 297 ARG cc_start: 0.8198 (mmm160) cc_final: 0.7749 (mmm-85) REVERT: G 30 LYS cc_start: 0.8811 (ttmm) cc_final: 0.8400 (mtpt) REVERT: G 58 ASP cc_start: 0.8489 (t0) cc_final: 0.8238 (t0) REVERT: G 62 ASP cc_start: 0.8194 (t0) cc_final: 0.7821 (t0) REVERT: G 73 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8150 (p) REVERT: G 88 ARG cc_start: 0.9085 (tpp80) cc_final: 0.8653 (mmt90) REVERT: G 107 TYR cc_start: 0.8720 (p90) cc_final: 0.8461 (p90) REVERT: G 108 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8048 (tm-30) REVERT: G 153 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7732 (tttp) REVERT: H 23 GLU cc_start: 0.9263 (mp0) cc_final: 0.8850 (mp0) REVERT: H 49 GLU cc_start: 0.8789 (pp20) cc_final: 0.8143 (pp20) REVERT: H 51 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.7889 (mtmm) REVERT: H 58 ASP cc_start: 0.8718 (t0) cc_final: 0.8138 (t0) REVERT: H 177 ARG cc_start: 0.4592 (OUTLIER) cc_final: 0.4291 (mmt180) REVERT: H 181 ASP cc_start: 0.8609 (m-30) cc_final: 0.8324 (m-30) REVERT: H 205 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6875 (pp20) REVERT: H 225 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8068 (mm-30) REVERT: H 228 ASP cc_start: 0.9176 (p0) cc_final: 0.8507 (p0) REVERT: I 26 GLU cc_start: 0.9020 (tt0) cc_final: 0.8697 (tt0) REVERT: I 63 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7226 (tm-30) REVERT: I 88 ASN cc_start: 0.8427 (t0) cc_final: 0.8154 (t160) REVERT: I 156 TYR cc_start: 0.8693 (p90) cc_final: 0.8472 (p90) REVERT: I 186 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8426 (tt) REVERT: I 212 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7048 (mp0) REVERT: J 4 ASP cc_start: 0.8961 (p0) cc_final: 0.8207 (p0) REVERT: J 52 LYS cc_start: 0.8792 (ptmt) cc_final: 0.8131 (ptpp) REVERT: J 55 ASP cc_start: 0.8129 (t0) cc_final: 0.7912 (t0) REVERT: J 56 GLU cc_start: 0.8436 (mp0) cc_final: 0.7935 (tm-30) REVERT: J 68 ASN cc_start: 0.8404 (p0) cc_final: 0.7954 (p0) REVERT: J 146 GLN cc_start: 0.9354 (tt0) cc_final: 0.9023 (tt0) REVERT: J 212 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7715 (mmt180) REVERT: L 9 ASP cc_start: 0.8698 (t0) cc_final: 0.8340 (t70) REVERT: L 51 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.6974 (mtp180) REVERT: L 110 SER cc_start: 0.8978 (p) cc_final: 0.8756 (m) REVERT: L 173 GLU cc_start: 0.8707 (tt0) cc_final: 0.8175 (mt-10) REVERT: L 234 GLU cc_start: 0.8189 (mp0) cc_final: 0.7899 (mp0) REVERT: M 27 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.7549 (mpp) REVERT: M 75 MET cc_start: 0.9241 (ttm) cc_final: 0.8975 (ttm) REVERT: M 81 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8713 (tp) REVERT: M 158 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7780 (m-80) REVERT: M 175 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7760 (mm-30) REVERT: M 221 ASN cc_start: 0.8694 (p0) cc_final: 0.8129 (p0) REVERT: c 104 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.5280 (tpp-160) REVERT: c 107 MET cc_start: 0.8680 (ptt) cc_final: 0.8311 (pmm) REVERT: c 131 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8625 (tp-100) REVERT: c 132 SER cc_start: 0.9029 (OUTLIER) cc_final: 0.8563 (p) REVERT: c 194 HIS cc_start: 0.8106 (m90) cc_final: 0.7815 (m-70) REVERT: c 233 ASP cc_start: 0.7193 (t0) cc_final: 0.6726 (t0) REVERT: c 262 GLU cc_start: 0.6407 (tp30) cc_final: 0.6169 (tp30) REVERT: c 286 GLU cc_start: 0.8533 (tt0) cc_final: 0.8209 (tm-30) REVERT: A 50 ASP cc_start: 0.8678 (m-30) cc_final: 0.8193 (m-30) REVERT: A 55 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8134 (mp) REVERT: A 146 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8774 (mtpp) REVERT: A 158 ASP cc_start: 0.8714 (t0) cc_final: 0.8191 (t0) REVERT: A 210 LYS cc_start: 0.8511 (mmtp) cc_final: 0.8283 (mtmt) REVERT: A 293 ASN cc_start: 0.7599 (m-40) cc_final: 0.7197 (m-40) REVERT: A 319 MET cc_start: 0.9451 (mtt) cc_final: 0.9018 (mtt) REVERT: A 429 TYR cc_start: 0.5296 (OUTLIER) cc_final: 0.4949 (t80) REVERT: B 62 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8769 (tp) REVERT: B 75 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6432 (tt0) REVERT: B 80 ARG cc_start: 0.8765 (ttm-80) cc_final: 0.8450 (tpp80) REVERT: B 98 LYS cc_start: 0.8915 (mmtp) cc_final: 0.7921 (tttt) REVERT: B 217 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8772 (mmtm) REVERT: B 230 THR cc_start: 0.9125 (m) cc_final: 0.8914 (p) REVERT: D 70 LYS cc_start: 0.8637 (mttm) cc_final: 0.8261 (mtpt) REVERT: D 91 GLN cc_start: 0.7934 (mp10) cc_final: 0.7432 (mp10) REVERT: D 114 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7810 (ttm110) REVERT: D 122 GLU cc_start: 0.8830 (mp0) cc_final: 0.8516 (mp0) REVERT: D 170 MET cc_start: 0.8831 (ttp) cc_final: 0.8590 (ttm) REVERT: D 171 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8542 (p0) REVERT: D 197 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8467 (m-30) REVERT: D 229 ARG cc_start: 0.9043 (ttp80) cc_final: 0.8542 (tmt170) REVERT: D 246 MET cc_start: 0.8814 (ttm) cc_final: 0.8467 (ttt) REVERT: D 276 ASP cc_start: 0.8005 (p0) cc_final: 0.7316 (p0) REVERT: D 408 LYS cc_start: 0.8920 (tppt) cc_final: 0.8498 (tptt) REVERT: D 415 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8193 (mt-10) REVERT: E 30 ARG cc_start: 0.7778 (mmp-170) cc_final: 0.7481 (mtt180) REVERT: E 37 THR cc_start: 0.8244 (m) cc_final: 0.7825 (p) REVERT: E 114 GLU cc_start: 0.7644 (tt0) cc_final: 0.6998 (tm-30) REVERT: E 218 MET cc_start: 0.8273 (mpt) cc_final: 0.8069 (pmm) REVERT: E 264 MET cc_start: 0.7355 (ppp) cc_final: 0.6908 (tmm) REVERT: E 274 LYS cc_start: 0.6338 (mptt) cc_final: 0.6021 (mmtm) REVERT: E 280 ASN cc_start: 0.6592 (t0) cc_final: 0.6133 (t0) REVERT: E 361 PHE cc_start: 0.7947 (p90) cc_final: 0.7486 (p90) REVERT: E 368 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6936 (mmt) REVERT: F 132 TYR cc_start: 0.8695 (m-80) cc_final: 0.8415 (m-80) REVERT: F 155 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8524 (ttpp) REVERT: F 304 ARG cc_start: 0.8428 (mtt180) cc_final: 0.7910 (mpt180) REVERT: F 305 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7420 (tm-30) REVERT: F 324 THR cc_start: 0.7271 (t) cc_final: 0.6963 (t) REVERT: F 353 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8355 (tp30) REVERT: K 5 ARG cc_start: 0.7086 (ttm170) cc_final: 0.6375 (ttm170) REVERT: K 9 ASP cc_start: 0.8943 (p0) cc_final: 0.8675 (p0) REVERT: K 71 ASP cc_start: 0.8702 (t0) cc_final: 0.8346 (t70) REVERT: K 148 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8678 (pm20) outliers start: 127 outliers final: 69 residues processed: 645 average time/residue: 0.7224 time to fit residues: 554.6627 Evaluate side-chains 614 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 518 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 212 ARG Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 51 ARG Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 242 SER Chi-restraints excluded: chain c residue 104 ARG Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 260 GLU Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 288 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 368 MET Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 83 LYS Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 228 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 381 optimal weight: 8.9990 chunk 382 optimal weight: 5.9990 chunk 143 optimal weight: 0.4980 chunk 284 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 384 optimal weight: 1.9990 chunk 405 optimal weight: 4.9990 chunk 386 optimal weight: 2.9990 chunk 38 optimal weight: 0.0070 chunk 274 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 392 GLN I 167 ASN J 23 GLN ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 159 ASN L 5 GLN M 101 ASN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN E 75 ASN ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN K 225 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.119879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.087646 restraints weight = 57968.287| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.52 r_work: 0.3076 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33805 Z= 0.131 Angle : 0.641 12.225 45674 Z= 0.322 Chirality : 0.043 0.266 5207 Planarity : 0.004 0.073 5894 Dihedral : 7.788 86.976 4763 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.86 % Favored : 94.90 % Rotamer: Outliers : 3.36 % Allowed : 33.86 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.70 (0.13), residues: 4174 helix: 1.56 (0.12), residues: 1840 sheet: -0.42 (0.19), residues: 733 loop : -0.27 (0.17), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 43 TYR 0.025 0.001 TYR G 27 PHE 0.018 0.001 PHE J 73 TRP 0.019 0.002 TRP J 156 HIS 0.010 0.001 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00303 (33800) covalent geometry : angle 0.64021 (45668) SS BOND : bond 0.01264 ( 3) SS BOND : angle 2.07231 ( 6) hydrogen bonds : bond 0.03577 ( 1626) hydrogen bonds : angle 4.60494 ( 4698) metal coordination : bond 0.00226 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8348 Ramachandran restraints generated. 4174 Oldfield, 0 Emsley, 4174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 557 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 TYR cc_start: 0.3786 (OUTLIER) cc_final: 0.1338 (t80) REVERT: C 60 ARG cc_start: 0.8531 (mmt90) cc_final: 0.8089 (mmt180) REVERT: C 88 LYS cc_start: 0.8614 (tttt) cc_final: 0.8196 (ttpp) REVERT: C 90 HIS cc_start: 0.8657 (t-90) cc_final: 0.7655 (p-80) REVERT: C 149 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8164 (mp0) REVERT: C 160 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8720 (mt-10) REVERT: G 30 LYS cc_start: 0.8806 (ttmm) cc_final: 0.8396 (mtpt) REVERT: G 58 ASP cc_start: 0.8484 (t0) cc_final: 0.8248 (t0) REVERT: G 62 ASP cc_start: 0.8171 (t0) cc_final: 0.7806 (t0) REVERT: G 73 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8154 (p) REVERT: G 88 ARG cc_start: 0.9096 (tpp80) cc_final: 0.8705 (mmt90) REVERT: G 108 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8156 (tm-30) REVERT: G 153 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7674 (tttp) REVERT: H 23 GLU cc_start: 0.9250 (mp0) cc_final: 0.8856 (mp0) REVERT: H 49 GLU cc_start: 0.8780 (pp20) cc_final: 0.8128 (pp20) REVERT: H 51 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7892 (mtmm) REVERT: H 58 ASP cc_start: 0.8684 (t0) cc_final: 0.8101 (t0) REVERT: H 177 ARG cc_start: 0.4538 (OUTLIER) cc_final: 0.4266 (mmt180) REVERT: H 181 ASP cc_start: 0.8621 (m-30) cc_final: 0.8335 (m-30) REVERT: H 205 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6808 (pp20) REVERT: H 225 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8066 (mm-30) REVERT: H 228 ASP cc_start: 0.9170 (p0) cc_final: 0.8492 (p0) REVERT: I 26 GLU cc_start: 0.9058 (tt0) cc_final: 0.8733 (tt0) REVERT: I 57 ASP cc_start: 0.8169 (t0) cc_final: 0.7834 (t0) REVERT: I 63 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7242 (tm-30) REVERT: I 88 ASN cc_start: 0.8408 (t0) cc_final: 0.8132 (t160) REVERT: I 156 TYR cc_start: 0.8677 (p90) cc_final: 0.8431 (p90) REVERT: J 52 LYS cc_start: 0.8793 (ptmt) cc_final: 0.8129 (ptpp) REVERT: J 56 GLU cc_start: 0.8391 (mp0) cc_final: 0.7791 (tm-30) REVERT: J 68 ASN cc_start: 0.8462 (p0) cc_final: 0.8044 (p0) REVERT: J 146 GLN cc_start: 0.9341 (tt0) cc_final: 0.8971 (tt0) REVERT: J 212 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7641 (mmt180) REVERT: L 9 ASP cc_start: 0.8691 (t0) cc_final: 0.8321 (t70) REVERT: L 51 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.6972 (mtp180) REVERT: L 110 SER cc_start: 0.8967 (p) cc_final: 0.8722 (m) REVERT: L 173 GLU cc_start: 0.8705 (tt0) cc_final: 0.8188 (mt-10) REVERT: L 186 GLU cc_start: 0.8469 (mp0) cc_final: 0.8120 (mp0) REVERT: L 220 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7749 (pm20) REVERT: L 234 GLU cc_start: 0.8129 (mp0) cc_final: 0.7877 (mp0) REVERT: M 27 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.7374 (mpp) REVERT: M 75 MET cc_start: 0.9238 (ttm) cc_final: 0.8964 (ttm) REVERT: M 81 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8626 (tp) REVERT: M 175 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7737 (mm-30) REVERT: M 221 ASN cc_start: 0.8678 (p0) cc_final: 0.8124 (p0) REVERT: c 71 ASP cc_start: 0.8014 (t70) cc_final: 0.6735 (m-30) REVERT: c 88 ASP cc_start: 0.9185 (t0) cc_final: 0.8886 (t0) REVERT: c 104 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.5133 (tpp-160) REVERT: c 107 MET cc_start: 0.8692 (ptt) cc_final: 0.8289 (pmm) REVERT: c 131 GLN cc_start: 0.8889 (tp-100) cc_final: 0.8614 (tp-100) REVERT: c 132 SER cc_start: 0.9014 (OUTLIER) cc_final: 0.8541 (p) REVERT: c 146 ASP cc_start: 0.7994 (t0) cc_final: 0.7508 (t0) REVERT: c 194 HIS cc_start: 0.8045 (m90) cc_final: 0.7767 (m-70) REVERT: c 233 ASP cc_start: 0.7176 (t0) cc_final: 0.6714 (t0) REVERT: c 262 GLU cc_start: 0.6337 (tp30) cc_final: 0.6108 (tp30) REVERT: c 284 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6645 (mm) REVERT: c 286 GLU cc_start: 0.8501 (tt0) cc_final: 0.8185 (tm-30) REVERT: A 50 ASP cc_start: 0.8674 (m-30) cc_final: 0.8181 (m-30) REVERT: A 55 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8148 (mp) REVERT: A 66 LYS cc_start: 0.8635 (mptt) cc_final: 0.7628 (mtpp) REVERT: A 146 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8777 (mtpp) REVERT: A 158 ASP cc_start: 0.8728 (t0) cc_final: 0.8194 (t0) REVERT: A 210 LYS cc_start: 0.8507 (mmtp) cc_final: 0.8279 (mtmt) REVERT: A 293 ASN cc_start: 0.7514 (m-40) cc_final: 0.7134 (m-40) REVERT: A 319 MET cc_start: 0.9444 (mtt) cc_final: 0.9020 (mtt) REVERT: A 429 TYR cc_start: 0.5297 (OUTLIER) cc_final: 0.4943 (t80) REVERT: B 62 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8743 (tp) REVERT: B 75 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6452 (tt0) REVERT: B 80 ARG cc_start: 0.8770 (ttm-80) cc_final: 0.8372 (tpp80) REVERT: B 82 GLN cc_start: 0.6336 (tt0) cc_final: 0.6018 (tm-30) REVERT: B 98 LYS cc_start: 0.8641 (mmtp) cc_final: 0.8110 (tttt) REVERT: B 217 LYS cc_start: 0.9033 (mmmm) cc_final: 0.8770 (mmtm) REVERT: B 230 THR cc_start: 0.9111 (m) cc_final: 0.8908 (p) REVERT: D 70 LYS cc_start: 0.8628 (mttm) cc_final: 0.8251 (mtpt) REVERT: D 91 GLN cc_start: 0.7892 (mp10) cc_final: 0.6979 (mp10) REVERT: D 114 ARG cc_start: 0.8041 (ttm-80) cc_final: 0.7812 (ttm110) REVERT: D 120 ASP cc_start: 0.8948 (t0) cc_final: 0.8710 (t0) REVERT: D 122 GLU cc_start: 0.8817 (mp0) cc_final: 0.8571 (mp0) REVERT: D 141 ASP cc_start: 0.8959 (t0) cc_final: 0.8685 (t0) REVERT: D 170 MET cc_start: 0.8888 (ttp) cc_final: 0.8611 (ttm) REVERT: D 171 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8550 (p0) REVERT: D 246 MET cc_start: 0.8798 (ttm) cc_final: 0.8457 (ttt) REVERT: D 276 ASP cc_start: 0.7981 (p0) cc_final: 0.7288 (p0) REVERT: D 408 LYS cc_start: 0.8980 (tppt) cc_final: 0.8574 (tptt) REVERT: D 415 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8180 (mt-10) REVERT: E 30 ARG cc_start: 0.7768 (mmp-170) cc_final: 0.7496 (mtt180) REVERT: E 37 THR cc_start: 0.8227 (m) cc_final: 0.7813 (p) REVERT: E 66 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8309 (tp30) REVERT: E 114 GLU cc_start: 0.7576 (tt0) cc_final: 0.6909 (tm-30) REVERT: E 218 MET cc_start: 0.8272 (mpt) cc_final: 0.8007 (pmm) REVERT: E 264 MET cc_start: 0.7349 (ppp) cc_final: 0.6903 (tmm) REVERT: E 280 ASN cc_start: 0.6635 (t0) cc_final: 0.6232 (t0) REVERT: E 361 PHE cc_start: 0.7942 (p90) cc_final: 0.7463 (p90) REVERT: F 132 TYR cc_start: 0.8590 (m-80) cc_final: 0.8370 (m-80) REVERT: F 155 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8523 (ttpp) REVERT: F 179 GLU cc_start: 0.8198 (tp30) cc_final: 0.7418 (tt0) REVERT: F 304 ARG cc_start: 0.8435 (mtt180) cc_final: 0.7910 (mpt180) REVERT: F 305 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: F 321 GLN cc_start: 0.5972 (pp30) cc_final: 0.5766 (pp30) REVERT: F 324 THR cc_start: 0.7209 (t) cc_final: 0.6820 (t) REVERT: F 353 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8369 (tp30) REVERT: K 5 ARG cc_start: 0.7071 (ttm170) cc_final: 0.6319 (ttm170) REVERT: K 9 ASP cc_start: 0.8912 (p0) cc_final: 0.8640 (p0) REVERT: K 52 LYS cc_start: 0.8654 (mmtp) cc_final: 0.8351 (mmtt) REVERT: K 71 ASP cc_start: 0.8696 (t0) cc_final: 0.8331 (t70) REVERT: K 148 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8695 (pm20) outliers start: 120 outliers final: 78 residues processed: 644 average time/residue: 0.6969 time to fit residues: 532.5935 Evaluate side-chains 624 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 521 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 159 ASN Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 212 ARG Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 51 ARG Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 101 ASN Chi-restraints excluded: chain M residue 242 SER Chi-restraints excluded: chain c residue 104 ARG Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 145 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 260 GLU Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 288 VAL Chi-restraints excluded: chain c residue 291 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 83 LYS Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 228 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 377 optimal weight: 0.7980 chunk 337 optimal weight: 7.9990 chunk 359 optimal weight: 8.9990 chunk 154 optimal weight: 0.4980 chunk 131 optimal weight: 0.0060 chunk 187 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 182 optimal weight: 0.0470 chunk 24 optimal weight: 0.3980 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 167 ASN I 198 ASN J 23 GLN ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 159 ASN L 5 GLN M 101 ASN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN F 333 ASN K 225 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.120795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.088831 restraints weight = 57833.502| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.52 r_work: 0.3091 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33805 Z= 0.124 Angle : 0.651 11.442 45674 Z= 0.327 Chirality : 0.044 0.270 5207 Planarity : 0.005 0.117 5894 Dihedral : 7.718 88.641 4760 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.79 % Favored : 94.99 % Rotamer: Outliers : 3.22 % Allowed : 34.31 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.73 (0.13), residues: 4174 helix: 1.58 (0.12), residues: 1841 sheet: -0.37 (0.19), residues: 722 loop : -0.30 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 43 TYR 0.043 0.001 TYR E 221 PHE 0.021 0.001 PHE M 102 TRP 0.020 0.002 TRP H 158 HIS 0.010 0.001 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00277 (33800) covalent geometry : angle 0.65046 (45668) SS BOND : bond 0.01294 ( 3) SS BOND : angle 2.02647 ( 6) hydrogen bonds : bond 0.03522 ( 1626) hydrogen bonds : angle 4.58771 ( 4698) metal coordination : bond 0.00099 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16422.78 seconds wall clock time: 279 minutes 24.99 seconds (16764.99 seconds total)