Starting phenix.real_space_refine on Fri Aug 7 09:41:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ukf_64237/08_2026/9ukf_64237.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ukf_64237/08_2026/9ukf_64237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ukf_64237/08_2026/9ukf_64237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ukf_64237/08_2026/9ukf_64237.map" model { file = "/net/cci-nas-00/data/ceres_data/9ukf_64237/08_2026/9ukf_64237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ukf_64237/08_2026/9ukf_64237.cif" } resolution = 3.3 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= 0.030 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: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 5 5.21 5 S 86 5.16 5 C 12737 2.51 5 N 3603 2.21 5 O 3853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20302 Number of models: 1 Model: "" Number of chains: 15 Chain: "E" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2519 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 12, 'TRANS': 307} Chain: "F" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2514 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 12, 'TRANS': 306} Chain: "G" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2423 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 10, 'TRANS': 293} Chain: "a" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1462 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 190} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 6, 'ASN:plan1': 1, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "c" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1475 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 192} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2390 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 12, 'TRANS': 289} Chain breaks: 1 Chain: "B" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2357 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 12, 'TRANS': 284} Chain breaks: 1 Chain: "C" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2457 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 12, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2514 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 12, 'TRANS': 306} Chain: "E" 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: "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} 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" 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: 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: 4.16, per 1000 atoms: 0.20 Number of scatterers: 20302 At special positions: 0 Unit cell: (117.962, 128.432, 150.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 86 16.00 P 18 15.00 Mg 5 11.99 O 3853 8.00 N 3603 7.00 C 12737 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 756.1 milliseconds 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4864 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 25 sheets defined 49.7% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'E' and resid 18 through 22 Processing helix chain 'E' and resid 50 through 64 Processing helix chain 'E' and resid 77 through 89 removed outlier: 3.713A pdb=" N ILE E 81 " --> pdb=" O LYS E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 126 through 133 Processing helix chain 'E' and resid 154 through 159 removed outlier: 3.734A pdb=" N GLU E 159 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 209 Processing helix chain 'E' and resid 221 through 233 Processing helix chain 'E' and resid 234 through 237 removed outlier: 3.609A pdb=" N GLN E 237 " --> pdb=" O LYS E 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 234 through 237' Processing helix chain 'E' and resid 238 through 262 removed outlier: 3.888A pdb=" N ARG E 242 " --> pdb=" O ASN E 238 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU E 243 " --> pdb=" O ALA E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 283 Processing helix chain 'E' and resid 285 through 294 Processing helix chain 'E' and resid 295 through 298 Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 302 through 315 removed outlier: 3.851A pdb=" N VAL E 306 " --> pdb=" O GLU E 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 removed outlier: 3.588A pdb=" N PHE F 22 " --> pdb=" O VAL F 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 18 through 22' Processing helix chain 'F' and resid 50 through 64 Processing helix chain 'F' and resid 77 through 88 Processing helix chain 'F' and resid 102 through 107 Processing helix chain 'F' and resid 127 through 134 removed outlier: 3.575A pdb=" N GLN F 133 " --> pdb=" O PRO F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 146 removed outlier: 3.757A pdb=" N GLY F 146 " --> pdb=" O TYR F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 143 through 146' Processing helix chain 'F' and resid 147 through 160 removed outlier: 3.730A pdb=" N VAL F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 210 removed outlier: 3.710A pdb=" N ASP F 209 " --> pdb=" O ALA F 206 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG F 210 " --> pdb=" O GLN F 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 206 through 210' Processing helix chain 'F' and resid 221 through 233 Processing helix chain 'F' and resid 238 through 262 removed outlier: 3.765A pdb=" N ARG F 242 " --> pdb=" O ASN F 238 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU F 243 " --> pdb=" O ALA F 239 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE F 244 " --> pdb=" O GLU F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 283 Processing helix chain 'F' and resid 285 through 294 Processing helix chain 'F' and resid 295 through 298 Processing helix chain 'F' and resid 302 through 315 removed outlier: 3.691A pdb=" N VAL F 306 " --> pdb=" O GLU F 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 354 removed outlier: 3.680A pdb=" N PHE G 346 " --> pdb=" O ARG G 342 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN G 350 " --> pdb=" O PHE G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 368 removed outlier: 4.195A pdb=" N ARG G 360 " --> pdb=" O GLY G 356 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN G 366 " --> pdb=" O ALA G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 390 No H-bonds generated for 'chain 'G' and resid 388 through 390' Processing helix chain 'G' and resid 391 through 397 removed outlier: 3.605A pdb=" N VAL G 395 " --> pdb=" O LEU G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 428 removed outlier: 3.977A pdb=" N ARG G 428 " --> pdb=" O GLY G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 447 removed outlier: 4.009A pdb=" N GLU G 447 " --> pdb=" O ALA G 443 " (cutoff:3.500A) Processing helix chain 'G' and resid 448 through 450 No H-bonds generated for 'chain 'G' and resid 448 through 450' Processing helix chain 'G' and resid 462 through 465 removed outlier: 3.569A pdb=" N GLY G 465 " --> pdb=" O ALA G 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 462 through 465' Processing helix chain 'G' and resid 466 through 475 removed outlier: 3.612A pdb=" N GLU G 470 " --> pdb=" O GLY G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 521 through 533 Processing helix chain 'G' and resid 551 through 557 removed outlier: 4.345A pdb=" N VAL G 557 " --> pdb=" O SER G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 577 removed outlier: 4.281A pdb=" N GLU G 564 " --> pdb=" O GLY G 560 " (cutoff:3.500A) Processing helix chain 'G' and resid 606 through 611 Processing helix chain 'G' and resid 611 through 618 removed outlier: 3.914A pdb=" N LEU G 618 " --> pdb=" O GLN G 614 " (cutoff:3.500A) Processing helix chain 'a' and resid 23 through 38 removed outlier: 3.709A pdb=" N ARG a 27 " --> pdb=" O GLU a 23 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 89 removed outlier: 3.549A pdb=" N GLY a 79 " --> pdb=" O THR a 75 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP a 80 " --> pdb=" O ARG a 76 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS a 89 " --> pdb=" O ARG a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 97 Processing helix chain 'a' and resid 103 through 124 removed outlier: 3.591A pdb=" N VAL a 116 " --> pdb=" O GLU a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 124 through 143 removed outlier: 3.855A pdb=" N ALA a 128 " --> pdb=" O MET a 124 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP a 129 " --> pdb=" O ALA a 125 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN a 130 " --> pdb=" O GLY a 126 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR a 133 " --> pdb=" O ASP a 129 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET a 134 " --> pdb=" O ASN a 130 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU a 135 " --> pdb=" O LEU a 131 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA a 136 " --> pdb=" O SER a 132 " (cutoff:3.500A) Processing helix chain 'a' and resid 154 through 169 Processing helix chain 'a' and resid 178 through 191 removed outlier: 5.046A pdb=" N ASP a 185 " --> pdb=" O GLU a 181 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TRP a 186 " --> pdb=" O LEU a 182 " (cutoff:3.500A) Processing helix chain 'a' and resid 193 through 201 removed outlier: 3.658A pdb=" N GLU a 200 " --> pdb=" O ALA a 196 " (cutoff:3.500A) Processing helix chain 'a' and resid 204 through 218 Processing helix chain 'c' and resid 22 through 36 Processing helix chain 'c' and resid 68 through 88 removed outlier: 4.276A pdb=" N ARG c 88 " --> pdb=" O LEU c 84 " (cutoff:3.500A) Processing helix chain 'c' and resid 101 through 124 removed outlier: 4.046A pdb=" N ARG c 105 " --> pdb=" O GLY c 101 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA c 106 " --> pdb=" O LYS c 102 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASP c 109 " --> pdb=" O ARG c 105 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA c 110 " --> pdb=" O ALA c 106 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY c 120 " --> pdb=" O VAL c 116 " (cutoff:3.500A) Processing helix chain 'c' and resid 125 through 142 Processing helix chain 'c' and resid 154 through 167 removed outlier: 3.894A pdb=" N ALA c 158 " --> pdb=" O PRO c 154 " (cutoff:3.500A) Processing helix chain 'c' and resid 178 through 191 removed outlier: 4.658A pdb=" N ASP c 185 " --> pdb=" O GLU c 181 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TRP c 186 " --> pdb=" O LEU c 182 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA c 191 " --> pdb=" O ILE c 187 " (cutoff:3.500A) Processing helix chain 'c' and resid 192 through 200 removed outlier: 4.057A pdb=" N ALA c 196 " --> pdb=" O SER c 192 " (cutoff:3.500A) Processing helix chain 'c' and resid 207 through 218 Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 50 through 64 Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.877A pdb=" N ILE A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 150 through 159 removed outlier: 3.547A pdb=" N ILE A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL A 157 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 221 through 232 removed outlier: 3.511A pdb=" N VAL A 226 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 261 Processing helix chain 'A' and resid 269 through 284 removed outlier: 3.702A pdb=" N VAL A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.783A pdb=" N ARG A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 removed outlier: 3.569A pdb=" N VAL A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 50 through 63 Processing helix chain 'B' and resid 76 through 89 Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 150 through 160 removed outlier: 4.065A pdb=" N ILE B 154 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 removed outlier: 3.774A pdb=" N ARG B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 224 through 231 removed outlier: 4.085A pdb=" N ILE B 228 " --> pdb=" O ASN B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 241 through 262 removed outlier: 3.522A pdb=" N ILE B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 284 removed outlier: 3.765A pdb=" N ILE B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.541A pdb=" N ARG B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 298 Processing helix chain 'B' and resid 299 through 314 removed outlier: 3.960A pdb=" N ALA B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N THR B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 56 through 64 Processing helix chain 'C' and resid 76 through 89 removed outlier: 3.655A pdb=" N ILE C 81 " --> pdb=" O LYS C 77 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.567A pdb=" N LEU C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 133 removed outlier: 3.581A pdb=" N GLN C 133 " --> pdb=" O PRO C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 159 removed outlier: 3.636A pdb=" N GLN C 155 " --> pdb=" O MET C 151 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL C 157 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU C 159 " --> pdb=" O GLN C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 151 through 159' Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 221 through 232 removed outlier: 3.957A pdb=" N ASN C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 261 removed outlier: 3.735A pdb=" N GLU C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS C 247 " --> pdb=" O GLU C 243 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 284 removed outlier: 3.871A pdb=" N THR C 272 " --> pdb=" O MET C 268 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 294 removed outlier: 3.564A pdb=" N LEU C 292 " --> pdb=" O PHE C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 298 Processing helix chain 'C' and resid 302 through 315 removed outlier: 3.633A pdb=" N VAL C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLU C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 22 Processing helix chain 'D' and resid 50 through 63 removed outlier: 3.550A pdb=" N TYR D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 88 Processing helix chain 'D' and resid 102 through 107 Processing helix chain 'D' and resid 126 through 133 removed outlier: 3.752A pdb=" N GLN D 133 " --> pdb=" O PRO D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 146 Processing helix chain 'D' and resid 150 through 155 removed outlier: 3.752A pdb=" N ILE D 154 " --> pdb=" O MET D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 160 removed outlier: 4.376A pdb=" N SER D 160 " --> pdb=" O VAL D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 210 removed outlier: 3.606A pdb=" N ARG D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 233 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 238 through 262 removed outlier: 3.581A pdb=" N ARG D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 284 removed outlier: 3.533A pdb=" N ALA D 281 " --> pdb=" O ALA D 277 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 295 through 298 Processing helix chain 'D' and resid 299 through 315 removed outlier: 4.450A pdb=" N ALA D 304 " --> pdb=" O GLU D 300 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 14 through 17 Processing sheet with id=AA2, first strand: chain 'E' and resid 92 through 96 removed outlier: 3.527A pdb=" N VAL E 67 " --> pdb=" O LEU E 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 108 through 113 Processing sheet with id=AA4, first strand: chain 'E' and resid 164 through 166 removed outlier: 3.507A pdb=" N LEU E 164 " --> pdb=" O ILE E 173 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG E 171 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 15 through 17 Processing sheet with id=AA6, first strand: chain 'F' and resid 92 through 96 removed outlier: 6.111A pdb=" N LEU F 138 " --> pdb=" O PHE F 182 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N THR F 184 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE F 140 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL F 67 " --> pdb=" O LEU F 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 108 through 113 Processing sheet with id=AA8, first strand: chain 'F' and resid 164 through 165 Processing sheet with id=AA9, first strand: chain 'G' and resid 327 through 330 removed outlier: 6.946A pdb=" N GLU G 327 " --> pdb=" O HIS G 489 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL G 491 " --> pdb=" O GLU G 327 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL G 329 " --> pdb=" O VAL G 491 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL G 417 " --> pdb=" O GLU G 454 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU G 456 " --> pdb=" O VAL G 417 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU G 419 " --> pdb=" O LEU G 456 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE G 458 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU G 421 " --> pdb=" O PHE G 458 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU G 541 " --> pdb=" O ILE G 583 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ILE G 585 " --> pdb=" O LEU G 541 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N MET G 543 " --> pdb=" O ILE G 585 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N ILE G 587 " --> pdb=" O MET G 543 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL G 599 " --> pdb=" O LEU G 582 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ALA G 584 " --> pdb=" O VAL G 599 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE G 601 " --> pdb=" O ALA G 584 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLY G 586 " --> pdb=" O ILE G 601 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 378 through 381 removed outlier: 3.566A pdb=" N ASP G 380 " --> pdb=" O TYR G 404 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TYR G 404 " --> pdb=" O ASP G 380 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 43 through 45 Processing sheet with id=AB3, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AB4, first strand: chain 'A' and resid 92 through 96 removed outlier: 6.059A pdb=" N LEU A 138 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N THR A 184 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE A 140 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N ASN A 186 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 67 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A 185 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N MET A 68 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 109 through 113 Processing sheet with id=AB6, first strand: chain 'B' and resid 14 through 17 Processing sheet with id=AB7, first strand: chain 'B' and resid 92 through 96 removed outlier: 5.831A pdb=" N LEU B 138 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR B 184 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE B 140 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N MET B 68 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 108 through 115 Processing sheet with id=AB9, first strand: chain 'C' and resid 14 through 17 removed outlier: 3.610A pdb=" N VAL C 30 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 92 through 96 removed outlier: 6.604A pdb=" N VAL C 67 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ALA C 185 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL C 69 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 108 through 115 Processing sheet with id=AC3, first strand: chain 'C' and resid 164 through 166 removed outlier: 4.170A pdb=" N ARG C 171 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 14 through 17 Processing sheet with id=AC5, first strand: chain 'D' and resid 92 through 96 removed outlier: 3.674A pdb=" N VAL D 67 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 108 through 115 Processing sheet with id=AC7, first strand: chain 'D' and resid 164 through 166 removed outlier: 3.902A pdb=" N ARG D 171 " --> pdb=" O LEU D 166 " (cutoff:3.500A) 870 hydrogen bonds defined for protein. 2517 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: 3.53 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5186 1.33 - 1.45: 3892 1.45 - 1.57: 11445 1.57 - 1.69: 25 1.69 - 1.81: 155 Bond restraints: 20703 Sorted by residual: bond pdb=" N GLU D 320 " pdb=" CA GLU D 320 " ideal model delta sigma weight residual 1.457 1.486 -0.030 6.40e-03 2.44e+04 2.15e+01 bond pdb=" N ASP D 110 " pdb=" CA ASP D 110 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.17e-02 7.31e+03 9.38e+00 bond pdb=" N VAL C 188 " pdb=" CA VAL C 188 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.12e+00 bond pdb=" N ILE F 325 " pdb=" CA ILE F 325 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.39e+00 bond pdb=" N GLU D 317 " pdb=" CA GLU D 317 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.27e+00 ... (remaining 20698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 27657 1.98 - 3.95: 470 3.95 - 5.93: 57 5.93 - 7.91: 8 7.91 - 9.89: 3 Bond angle restraints: 28195 Sorted by residual: angle pdb=" C GLU D 320 " pdb=" CA GLU D 320 " pdb=" CB GLU D 320 " ideal model delta sigma weight residual 117.07 110.74 6.33 1.44e+00 4.82e-01 1.93e+01 angle pdb=" C LEU A 318 " pdb=" N PRO A 319 " pdb=" CA PRO A 319 " ideal model delta sigma weight residual 119.82 124.00 -4.18 9.80e-01 1.04e+00 1.82e+01 angle pdb=" O GLU D 320 " pdb=" C GLU D 320 " pdb=" N SER D 321 " ideal model delta sigma weight residual 121.47 124.66 -3.19 7.50e-01 1.78e+00 1.81e+01 angle pdb=" C ASP G 440 " pdb=" CA ASP G 440 " pdb=" CB ASP G 440 " ideal model delta sigma weight residual 110.88 116.82 -5.94 1.57e+00 4.06e-01 1.43e+01 angle pdb=" N GLN E 207 " pdb=" CA GLN E 207 " pdb=" C GLN E 207 " ideal model delta sigma weight residual 113.55 109.09 4.46 1.26e+00 6.30e-01 1.25e+01 ... (remaining 28190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10330 17.95 - 35.91: 1497 35.91 - 53.86: 517 53.86 - 71.82: 121 71.82 - 89.77: 41 Dihedral angle restraints: 12506 sinusoidal: 5005 harmonic: 7501 Sorted by residual: dihedral pdb=" CA LEU A 318 " pdb=" C LEU A 318 " pdb=" N PRO A 319 " pdb=" CA PRO A 319 " ideal model delta harmonic sigma weight residual 180.00 -150.88 -29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA THR C 53 " pdb=" C THR C 53 " pdb=" N THR C 54 " pdb=" CA THR C 54 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PRO a 154 " pdb=" C PRO a 154 " pdb=" N LEU a 155 " pdb=" CA LEU a 155 " ideal model delta harmonic sigma weight residual -180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 12503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2443 0.047 - 0.094: 620 0.094 - 0.140: 134 0.140 - 0.187: 6 0.187 - 0.234: 4 Chirality restraints: 3207 Sorted by residual: chirality pdb=" CA VAL D 316 " pdb=" N VAL D 316 " pdb=" C VAL D 316 " pdb=" CB VAL D 316 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA VAL C 316 " pdb=" N VAL C 316 " pdb=" C VAL C 316 " pdb=" CB VAL C 316 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA VAL A 316 " pdb=" N VAL A 316 " pdb=" C VAL A 316 " pdb=" CB VAL A 316 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3204 not shown) Planarity restraints: 3669 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 269 " -0.061 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO A 270 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 269 " 0.058 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO B 270 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 176 " -0.044 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO A 177 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 177 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 177 " -0.038 5.00e-02 4.00e+02 ... (remaining 3666 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 133 2.50 - 3.10: 14506 3.10 - 3.70: 31676 3.70 - 4.30: 44621 4.30 - 4.90: 74280 Nonbonded interactions: 165216 Sorted by model distance: nonbonded pdb=" O2G ATP A 401 " pdb="MG MG A 402 " model vdw 1.895 2.170 nonbonded pdb=" O3B ATP C 401 " pdb="MG MG C 402 " model vdw 1.909 2.170 nonbonded pdb=" OG SER A 78 " pdb="MG MG A 402 " model vdw 1.913 2.170 nonbonded pdb=" O1B ATP E 401 " pdb="MG MG E 402 " model vdw 1.931 2.170 nonbonded pdb=" O3B ATP F 401 " pdb="MG MG F 402 " model vdw 1.942 2.170 ... (remaining 165211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 9 through 319) selection = (chain 'B' and resid 9 through 319) selection = (chain 'C' and (resid 9 through 188 or resid 203 through 319)) selection = (chain 'D' and (resid 9 through 188 or resid 203 through 319)) selection = (chain 'E' and (resid 9 through 188 or resid 203 through 319)) selection = (chain 'F' and (resid 9 through 188 or resid 203 through 319)) } ncs_group { reference = chain 'a' selection = (chain 'c' and resid 22 through 222) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.950 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.030 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 0.073 20703 Z= 0.212 Angle : 0.605 9.887 28195 Z= 0.339 Chirality : 0.042 0.234 3207 Planarity : 0.005 0.090 3669 Dihedral : 19.909 89.771 7642 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.52 % Favored : 92.24 % Rotamer: Outliers : 1.32 % Allowed : 37.82 % Favored : 60.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.17), residues: 2553 helix: 0.07 (0.16), residues: 1108 sheet: -1.10 (0.30), residues: 314 loop : -1.38 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG a 76 TYR 0.011 0.001 TYR D 219 PHE 0.011 0.001 PHE B 179 TRP 0.019 0.001 TRP a 183 HIS 0.014 0.001 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.21 (20703) covalent geometry : angle 0.60481 / 0.34 (28195) hydrogen bonds : bond 0.18258 / 12.61 ( 870) hydrogen bonds : angle 6.98589 / 4.92 ( 2517) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 489 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 51 ARG cc_start: 0.8249 (ttt90) cc_final: 0.7949 (ttt90) REVERT: E 112 ILE cc_start: 0.9077 (mm) cc_final: 0.8797 (mt) REVERT: F 163 ARG cc_start: 0.6964 (mtm110) cc_final: 0.6580 (mtm110) REVERT: G 364 ARG cc_start: 0.6297 (mmt90) cc_final: 0.5946 (mmt90) REVERT: G 447 GLU cc_start: 0.5640 (OUTLIER) cc_final: 0.4964 (mm-30) REVERT: a 76 ARG cc_start: 0.7613 (tpp80) cc_final: 0.7372 (tpp80) REVERT: A 225 GLU cc_start: 0.7754 (tt0) cc_final: 0.7460 (tt0) REVERT: C 119 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8285 (mt0) REVERT: C 251 VAL cc_start: 0.8263 (t) cc_final: 0.8047 (p) REVERT: C 320 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6131 (tt0) outliers start: 28 outliers final: 8 residues processed: 511 average time/residue: 0.1516 time to fit residues: 114.6671 Evaluate side-chains 494 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 484 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain G residue 351 LEU Chi-restraints excluded: chain G residue 447 GLU Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 320 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 247 optimal weight: 0.9980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 83 GLN E 119 GLN E 222 HIS E 296 ASN F 155 GLN ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 HIS c 113 GLN A 205 GLN A 207 GLN A 218 ASN A 296 ASN ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN B 218 ASN B 235 HIS B 238 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN C 296 ASN C 324 ASN D 52 GLN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.165377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.126022 restraints weight = 29424.228| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.51 r_work: 0.3338 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20703 Z= 0.237 Angle : 0.567 7.656 28195 Z= 0.301 Chirality : 0.043 0.151 3207 Planarity : 0.005 0.063 3669 Dihedral : 10.045 85.409 3051 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.40 % Favored : 92.56 % Rotamer: Outliers : 4.82 % Allowed : 33.66 % Favored : 61.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.17), residues: 2553 helix: 0.26 (0.16), residues: 1112 sheet: -1.24 (0.31), residues: 294 loop : -1.30 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 87 TYR 0.010 0.001 TYR G 404 PHE 0.016 0.002 PHE B 179 TRP 0.010 0.001 TRP D 90 HIS 0.010 0.001 HIS F 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.24 (20703) covalent geometry : angle 0.56718 / 0.30 (28195) hydrogen bonds : bond 0.04877 / 3.32 ( 870) hydrogen bonds : angle 5.25891 / 3.69 ( 2517) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 490 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 51 ARG cc_start: 0.8402 (ttt90) cc_final: 0.8159 (ttt90) REVERT: E 112 ILE cc_start: 0.9004 (mm) cc_final: 0.8745 (mm) REVERT: F 110 ASP cc_start: 0.7570 (p0) cc_final: 0.6938 (p0) REVERT: F 124 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7385 (tttt) REVERT: F 163 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6872 (mtm110) REVERT: F 300 GLU cc_start: 0.7358 (mp0) cc_final: 0.7048 (mp0) REVERT: G 364 ARG cc_start: 0.6371 (mmt90) cc_final: 0.6061 (mmt90) REVERT: G 407 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6928 (tm-30) REVERT: G 447 GLU cc_start: 0.5739 (OUTLIER) cc_final: 0.5129 (mm-30) REVERT: G 504 ARG cc_start: 0.6106 (mtm180) cc_final: 0.5489 (mtm-85) REVERT: a 46 PHE cc_start: 0.5615 (OUTLIER) cc_final: 0.5084 (m-10) REVERT: A 77 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7062 (mtmt) REVERT: A 141 ASP cc_start: 0.7569 (t0) cc_final: 0.7218 (t0) REVERT: A 292 LEU cc_start: 0.8376 (mt) cc_final: 0.8100 (mp) REVERT: A 300 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7405 (tm-30) REVERT: C 52 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7456 (tm-30) REVERT: C 94 ARG cc_start: 0.8238 (ttp-110) cc_final: 0.7937 (mtp-110) REVERT: C 119 GLN cc_start: 0.8383 (mm110) cc_final: 0.8155 (mm-40) REVERT: C 135 ASN cc_start: 0.8653 (p0) cc_final: 0.8385 (p0) REVERT: C 210 ARG cc_start: 0.8731 (mtp85) cc_final: 0.8516 (mtp85) REVERT: C 243 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7417 (tm-30) REVERT: D 46 ASP cc_start: 0.6729 (OUTLIER) cc_final: 0.6151 (p0) REVERT: D 65 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7451 (mmp80) REVERT: D 110 ASP cc_start: 0.7692 (m-30) cc_final: 0.7439 (m-30) REVERT: D 291 ARG cc_start: 0.8306 (mtp85) cc_final: 0.8079 (mtt-85) REVERT: D 300 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.6080 (mp0) outliers start: 102 outliers final: 57 residues processed: 556 average time/residue: 0.1474 time to fit residues: 121.7269 Evaluate side-chains 548 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 483 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 351 LEU Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 447 GLU Chi-restraints excluded: chain G residue 563 LEU Chi-restraints excluded: chain a residue 46 PHE Chi-restraints excluded: chain a residue 94 HIS Chi-restraints excluded: chain a residue 117 GLU Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain c residue 124 MET Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 320 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 188 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 236 optimal weight: 1.9990 chunk 189 optimal weight: 0.5980 chunk 202 optimal weight: 0.2980 chunk 102 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 31 optimal weight: 5.9990 chunk 216 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 83 GLN E 207 GLN E 222 HIS E 296 ASN F 261 ASN A 52 GLN A 224 ASN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN B 207 GLN B 227 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN D 73 HIS ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** 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 = 0.4041 r_free = 0.4041 target = 0.167405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.128116 restraints weight = 29332.527| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.55 r_work: 0.3359 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20703 Z= 0.130 Angle : 0.500 7.966 28195 Z= 0.263 Chirality : 0.040 0.177 3207 Planarity : 0.004 0.059 3669 Dihedral : 9.468 85.748 3040 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.58 % Favored : 93.38 % Rotamer: Outliers : 4.58 % Allowed : 33.38 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.17), residues: 2553 helix: 0.47 (0.16), residues: 1115 sheet: -1.11 (0.29), residues: 334 loop : -1.30 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 87 TYR 0.009 0.001 TYR C 72 PHE 0.013 0.001 PHE C 259 TRP 0.010 0.001 TRP a 183 HIS 0.010 0.001 HIS F 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (20703) covalent geometry : angle 0.50044 / 0.26 (28195) hydrogen bonds : bond 0.03824 / 2.61 ( 870) hydrogen bonds : angle 4.87110 / 3.41 ( 2517) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 483 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 112 ILE cc_start: 0.9004 (mm) cc_final: 0.8762 (mm) REVERT: E 165 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8151 (p) REVERT: F 110 ASP cc_start: 0.7512 (p0) cc_final: 0.6891 (p0) REVERT: F 124 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7602 (tttt) REVERT: F 163 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6926 (mtm110) REVERT: F 171 ARG cc_start: 0.6423 (OUTLIER) cc_final: 0.6149 (tpt-90) REVERT: F 300 GLU cc_start: 0.7344 (mp0) cc_final: 0.7024 (mp0) REVERT: G 364 ARG cc_start: 0.6389 (mmt90) cc_final: 0.6066 (mmt90) REVERT: G 407 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6901 (tm-30) REVERT: G 447 GLU cc_start: 0.5765 (OUTLIER) cc_final: 0.5153 (mm-30) REVERT: G 504 ARG cc_start: 0.6084 (mtm180) cc_final: 0.5536 (mtm-85) REVERT: a 46 PHE cc_start: 0.5652 (OUTLIER) cc_final: 0.4998 (m-80) REVERT: c 117 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.5891 (mp0) REVERT: A 141 ASP cc_start: 0.7402 (t0) cc_final: 0.7099 (t0) REVERT: A 292 LEU cc_start: 0.8301 (mt) cc_final: 0.8037 (mp) REVERT: B 308 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7248 (mm-30) REVERT: B 314 PHE cc_start: 0.7182 (t80) cc_final: 0.6866 (t80) REVERT: C 20 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: C 52 GLN cc_start: 0.8013 (tm-30) cc_final: 0.7381 (tm-30) REVERT: C 94 ARG cc_start: 0.8284 (ttp-110) cc_final: 0.7944 (mtp-110) REVERT: C 100 HIS cc_start: 0.6271 (OUTLIER) cc_final: 0.5932 (t70) REVERT: C 119 GLN cc_start: 0.8411 (mm110) cc_final: 0.7978 (mt0) REVERT: C 135 ASN cc_start: 0.8655 (p0) cc_final: 0.8367 (p0) REVERT: C 155 GLN cc_start: 0.7934 (tt0) cc_final: 0.7622 (tt0) REVERT: C 210 ARG cc_start: 0.8706 (mtp85) cc_final: 0.8454 (mtp85) REVERT: C 243 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7311 (tm-30) REVERT: D 65 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7449 (mmp80) REVERT: D 110 ASP cc_start: 0.7650 (m-30) cc_final: 0.7342 (m-30) outliers start: 97 outliers final: 56 residues processed: 549 average time/residue: 0.1480 time to fit residues: 119.4097 Evaluate side-chains 543 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 477 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 171 ARG Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 351 LEU Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 447 GLU Chi-restraints excluded: chain G residue 510 MET Chi-restraints excluded: chain G residue 526 TRP Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain G residue 563 LEU Chi-restraints excluded: chain a residue 46 PHE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 94 HIS Chi-restraints excluded: chain a residue 117 GLU Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain a residue 157 GLU Chi-restraints excluded: chain c residue 117 GLU Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 184 ARG Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 320 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 155 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 80 HIS E 83 GLN E 119 GLN E 207 GLN E 222 HIS E 296 ASN A 205 GLN A 224 ASN A 238 ASN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS B 155 GLN B 207 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** 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 = 0.4030 r_free = 0.4030 target = 0.166387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.127226 restraints weight = 29457.296| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.52 r_work: 0.3341 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20703 Z= 0.190 Angle : 0.527 9.863 28195 Z= 0.275 Chirality : 0.041 0.139 3207 Planarity : 0.004 0.055 3669 Dihedral : 9.362 89.163 3040 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.74 % Favored : 93.22 % Rotamer: Outliers : 6.47 % Allowed : 31.59 % Favored : 61.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.17), residues: 2553 helix: 0.42 (0.16), residues: 1124 sheet: -1.08 (0.30), residues: 314 loop : -1.28 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 103 TYR 0.011 0.001 TYR F 63 PHE 0.017 0.001 PHE B 259 TRP 0.012 0.001 TRP a 183 HIS 0.011 0.001 HIS F 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (20703) covalent geometry : angle 0.52742 / 0.27 (28195) hydrogen bonds : bond 0.04039 / 2.76 ( 870) hydrogen bonds : angle 4.84488 / 3.40 ( 2517) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 503 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 112 ILE cc_start: 0.9005 (mm) cc_final: 0.8780 (mm) REVERT: E 165 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8184 (p) REVERT: F 17 SER cc_start: 0.8259 (OUTLIER) cc_final: 0.7981 (p) REVERT: F 55 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7901 (mp) REVERT: F 110 ASP cc_start: 0.7442 (p0) cc_final: 0.6840 (p0) REVERT: F 124 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7409 (tttt) REVERT: F 163 ARG cc_start: 0.7288 (mtm110) cc_final: 0.6890 (mtm110) REVERT: F 171 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.6162 (tpt-90) REVERT: F 300 GLU cc_start: 0.7375 (mp0) cc_final: 0.7064 (mp0) REVERT: G 364 ARG cc_start: 0.6418 (mmt90) cc_final: 0.6068 (mmt90) REVERT: G 407 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6886 (tm-30) REVERT: G 447 GLU cc_start: 0.5810 (OUTLIER) cc_final: 0.5196 (mm-30) REVERT: G 504 ARG cc_start: 0.6161 (mtm180) cc_final: 0.5608 (mtm-85) REVERT: a 46 PHE cc_start: 0.5707 (OUTLIER) cc_final: 0.5026 (m-80) REVERT: a 216 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7514 (mp) REVERT: a 221 MET cc_start: 0.7443 (mpp) cc_final: 0.7219 (mpp) REVERT: c 116 VAL cc_start: 0.7543 (OUTLIER) cc_final: 0.7050 (p) REVERT: c 117 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.5967 (mp0) REVERT: c 124 MET cc_start: 0.6022 (mpp) cc_final: 0.5725 (ptp) REVERT: A 29 MET cc_start: 0.6480 (mmm) cc_final: 0.6044 (mmm) REVERT: A 77 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7067 (mtmt) REVERT: A 94 ARG cc_start: 0.8284 (mtp85) cc_final: 0.7805 (mtp85) REVERT: A 110 ASP cc_start: 0.6546 (OUTLIER) cc_final: 0.6173 (t0) REVERT: A 141 ASP cc_start: 0.7482 (t0) cc_final: 0.7048 (t0) REVERT: A 246 ASN cc_start: 0.8152 (m110) cc_final: 0.7886 (m110) REVERT: A 300 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7386 (tm-30) REVERT: A 308 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7673 (mm-30) REVERT: B 227 ASN cc_start: 0.7716 (m110) cc_final: 0.7445 (m-40) REVERT: B 278 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7392 (mt-10) REVERT: B 308 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7187 (mm-30) REVERT: B 314 PHE cc_start: 0.7359 (t80) cc_final: 0.6956 (t80) REVERT: C 20 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: C 52 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7361 (tm-30) REVERT: C 100 HIS cc_start: 0.6336 (OUTLIER) cc_final: 0.5969 (t70) REVERT: C 119 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7991 (mt0) REVERT: C 312 ARG cc_start: 0.8377 (ttm110) cc_final: 0.7998 (ttm-80) REVERT: D 65 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7427 (mmp80) REVERT: D 110 ASP cc_start: 0.7672 (m-30) cc_final: 0.7395 (m-30) REVERT: D 300 GLU cc_start: 0.6244 (OUTLIER) cc_final: 0.5823 (mp0) outliers start: 137 outliers final: 86 residues processed: 597 average time/residue: 0.1477 time to fit residues: 131.9221 Evaluate side-chains 606 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 503 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 171 ARG Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 351 LEU Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 447 GLU Chi-restraints excluded: chain G residue 508 LEU Chi-restraints excluded: chain G residue 510 MET Chi-restraints excluded: chain G residue 526 TRP Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain G residue 563 LEU Chi-restraints excluded: chain G residue 583 ILE Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain a residue 46 PHE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 94 HIS Chi-restraints excluded: chain a residue 117 GLU Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain a residue 157 GLU Chi-restraints excluded: chain a residue 179 VAL Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 117 GLU Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 147 VAL Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 184 ARG Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 320 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 82 optimal weight: 0.0270 chunk 229 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 33 optimal weight: 0.0070 chunk 243 optimal weight: 0.9980 chunk 230 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 238 optimal weight: 0.4980 chunk 215 optimal weight: 0.7980 chunk 172 optimal weight: 0.0770 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 83 GLN E 119 GLN E 207 GLN E 222 HIS E 296 ASN F 261 ASN A 224 ASN A 246 ASN A 311 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN C 237 GLN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.170006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.130487 restraints weight = 29168.963| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.56 r_work: 0.3381 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20703 Z= 0.099 Angle : 0.490 8.169 28195 Z= 0.254 Chirality : 0.039 0.137 3207 Planarity : 0.004 0.054 3669 Dihedral : 8.889 83.989 3040 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.15 % Favored : 93.81 % Rotamer: Outliers : 4.63 % Allowed : 33.33 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.17), residues: 2553 helix: 0.67 (0.16), residues: 1122 sheet: -1.04 (0.30), residues: 333 loop : -1.18 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 51 TYR 0.013 0.001 TYR F 63 PHE 0.014 0.001 PHE B 259 TRP 0.013 0.001 TRP a 183 HIS 0.019 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (20703) covalent geometry : angle 0.49025 / 0.25 (28195) hydrogen bonds : bond 0.03233 / 2.20 ( 870) hydrogen bonds : angle 4.60678 / 3.24 ( 2517) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 484 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 165 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8135 (p) REVERT: E 302 GLU cc_start: 0.7378 (mp0) cc_final: 0.7047 (mp0) REVERT: F 124 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7609 (tttt) REVERT: F 163 ARG cc_start: 0.7289 (mtm110) cc_final: 0.6895 (mtm110) REVERT: F 171 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.6132 (tpt-90) REVERT: F 300 GLU cc_start: 0.7327 (mp0) cc_final: 0.7036 (mp0) REVERT: G 364 ARG cc_start: 0.6308 (mmt90) cc_final: 0.5969 (mmt90) REVERT: G 407 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6887 (tm-30) REVERT: G 447 GLU cc_start: 0.5792 (OUTLIER) cc_final: 0.5158 (mm-30) REVERT: G 451 VAL cc_start: 0.7491 (t) cc_final: 0.6453 (t) REVERT: G 504 ARG cc_start: 0.6150 (mtm180) cc_final: 0.5630 (mtm-85) REVERT: a 46 PHE cc_start: 0.5644 (OUTLIER) cc_final: 0.4869 (m-80) REVERT: a 76 ARG cc_start: 0.7457 (ttm170) cc_final: 0.7133 (mmm-85) REVERT: a 216 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7450 (mp) REVERT: a 221 MET cc_start: 0.7325 (mpp) cc_final: 0.7099 (mpp) REVERT: c 117 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.5942 (mp0) REVERT: c 124 MET cc_start: 0.5841 (mpp) cc_final: 0.5586 (ptp) REVERT: A 110 ASP cc_start: 0.6561 (OUTLIER) cc_final: 0.6171 (t0) REVERT: A 141 ASP cc_start: 0.7259 (t0) cc_final: 0.6935 (t0) REVERT: A 246 ASN cc_start: 0.8050 (m-40) cc_final: 0.7707 (m110) REVERT: A 254 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.6798 (mpp) REVERT: A 292 LEU cc_start: 0.8327 (mt) cc_final: 0.8016 (mp) REVERT: B 80 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.7061 (t-90) REVERT: B 242 ARG cc_start: 0.7785 (ptm-80) cc_final: 0.7137 (tmt-80) REVERT: B 278 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7382 (mt-10) REVERT: B 308 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7157 (mm-30) REVERT: C 52 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7357 (tm-30) REVERT: C 100 HIS cc_start: 0.6280 (OUTLIER) cc_final: 0.5926 (t70) REVERT: C 119 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7774 (mt0) REVERT: C 135 ASN cc_start: 0.8578 (p0) cc_final: 0.8368 (p0) REVERT: C 285 ASP cc_start: 0.6951 (p0) cc_final: 0.6588 (p0) REVERT: D 65 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7413 (mmp80) REVERT: D 110 ASP cc_start: 0.7641 (m-30) cc_final: 0.7310 (m-30) outliers start: 98 outliers final: 66 residues processed: 549 average time/residue: 0.1518 time to fit residues: 121.9701 Evaluate side-chains 560 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 481 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 171 ARG Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 351 LEU Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 447 GLU Chi-restraints excluded: chain G residue 508 LEU Chi-restraints excluded: chain G residue 510 MET Chi-restraints excluded: chain G residue 514 LEU Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain G residue 563 LEU Chi-restraints excluded: chain G residue 583 ILE Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 618 LEU Chi-restraints excluded: chain a residue 46 PHE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 82 MET Chi-restraints excluded: chain a residue 94 HIS Chi-restraints excluded: chain a residue 117 GLU Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain a residue 157 GLU Chi-restraints excluded: chain a residue 179 VAL Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain c residue 42 MET Chi-restraints excluded: chain c residue 117 GLU Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 147 VAL Chi-restraints excluded: chain c residue 167 LEU Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 121 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 147 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 83 GLN E 207 GLN E 296 ASN F 261 ASN A 205 GLN A 224 ASN A 237 GLN A 261 ASN ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS B 227 ASN B 311 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN C 205 GLN C 237 GLN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.168227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.128906 restraints weight = 28945.588| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.53 r_work: 0.3325 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20703 Z= 0.240 Angle : 0.553 11.328 28195 Z= 0.288 Chirality : 0.042 0.146 3207 Planarity : 0.005 0.052 3669 Dihedral : 9.041 80.022 3037 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.01 % Favored : 92.95 % Rotamer: Outliers : 5.43 % Allowed : 33.29 % Favored : 61.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.17), residues: 2553 helix: 0.46 (0.16), residues: 1122 sheet: -1.04 (0.31), residues: 314 loop : -1.24 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 87 TYR 0.019 0.001 TYR F 63 PHE 0.016 0.002 PHE C 182 TRP 0.010 0.001 TRP A 90 HIS 0.013 0.001 HIS F 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.24 (20703) covalent geometry : angle 0.55250 / 0.29 (28195) hydrogen bonds : bond 0.04204 / 2.86 ( 870) hydrogen bonds : angle 4.79971 / 3.37 ( 2517) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 502 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 112 ILE cc_start: 0.8997 (mm) cc_final: 0.8797 (mm) REVERT: E 165 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8228 (p) REVERT: E 263 ASP cc_start: 0.7818 (t0) cc_final: 0.7576 (t0) REVERT: E 302 GLU cc_start: 0.7389 (mp0) cc_final: 0.7021 (mp0) REVERT: F 110 ASP cc_start: 0.7548 (p0) cc_final: 0.6947 (p0) REVERT: F 124 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7403 (tttt) REVERT: F 163 ARG cc_start: 0.7308 (mtm110) cc_final: 0.6910 (mtm110) REVERT: F 171 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.6155 (tpt-90) REVERT: F 227 ASN cc_start: 0.7758 (m110) cc_final: 0.7404 (m-40) REVERT: F 300 GLU cc_start: 0.7396 (mp0) cc_final: 0.7088 (mp0) REVERT: G 364 ARG cc_start: 0.6337 (mmt90) cc_final: 0.5963 (mmt90) REVERT: G 375 ARG cc_start: 0.6348 (tpp-160) cc_final: 0.5957 (tpp-160) REVERT: G 407 GLU cc_start: 0.7299 (tm-30) cc_final: 0.6830 (tm-30) REVERT: a 46 PHE cc_start: 0.5741 (OUTLIER) cc_final: 0.4984 (m-80) REVERT: a 76 ARG cc_start: 0.7497 (ttm170) cc_final: 0.7114 (ttt180) REVERT: a 216 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7397 (mp) REVERT: a 221 MET cc_start: 0.7323 (mpp) cc_final: 0.7059 (mpp) REVERT: c 116 VAL cc_start: 0.7520 (OUTLIER) cc_final: 0.7066 (p) REVERT: c 117 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6039 (mp0) REVERT: c 166 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7389 (mptm) REVERT: A 94 ARG cc_start: 0.8272 (mtp85) cc_final: 0.7796 (mtp85) REVERT: A 95 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8470 (m) REVERT: A 110 ASP cc_start: 0.6582 (OUTLIER) cc_final: 0.6195 (t0) REVERT: A 141 ASP cc_start: 0.7537 (t0) cc_final: 0.7090 (t0) REVERT: B 242 ARG cc_start: 0.7918 (ptm-80) cc_final: 0.7343 (tmt-80) REVERT: B 278 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7345 (mt-10) REVERT: C 52 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7341 (tm-30) REVERT: C 94 ARG cc_start: 0.8219 (ttp-110) cc_final: 0.7890 (mtp-110) REVERT: C 100 HIS cc_start: 0.6326 (OUTLIER) cc_final: 0.5967 (t70) REVERT: C 119 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7987 (mt0) REVERT: C 210 ARG cc_start: 0.8757 (mtp85) cc_final: 0.8204 (mtt90) REVERT: C 285 ASP cc_start: 0.6952 (p0) cc_final: 0.6560 (p0) REVERT: C 308 GLU cc_start: 0.7502 (pm20) cc_final: 0.7047 (pm20) REVERT: D 110 ASP cc_start: 0.7724 (m-30) cc_final: 0.7460 (m-30) REVERT: D 300 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5849 (mp0) outliers start: 115 outliers final: 81 residues processed: 581 average time/residue: 0.1626 time to fit residues: 140.5883 Evaluate side-chains 594 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 500 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 171 ARG Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 508 LEU Chi-restraints excluded: chain G residue 510 MET Chi-restraints excluded: chain G residue 514 LEU Chi-restraints excluded: chain G residue 526 TRP Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain G residue 563 LEU Chi-restraints excluded: chain G residue 583 ILE Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 618 LEU Chi-restraints excluded: chain a residue 46 PHE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 82 MET Chi-restraints excluded: chain a residue 94 HIS Chi-restraints excluded: chain a residue 117 GLU Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain a residue 157 GLU Chi-restraints excluded: chain a residue 179 VAL Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 117 GLU Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 147 VAL Chi-restraints excluded: chain c residue 166 LYS Chi-restraints excluded: chain c residue 167 LEU Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain D residue 271 ARG Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 317 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 109 optimal weight: 1.9990 chunk 130 optimal weight: 40.0000 chunk 86 optimal weight: 50.0000 chunk 162 optimal weight: 0.2980 chunk 245 optimal weight: 0.4980 chunk 46 optimal weight: 0.2980 chunk 95 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 204 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 83 GLN E 207 GLN E 222 HIS E 296 ASN A 142 GLN A 186 ASN A 224 ASN A 246 ASN A 311 GLN B 80 HIS ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.170852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.132030 restraints weight = 29186.117| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.53 r_work: 0.3370 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20703 Z= 0.112 Angle : 0.508 9.771 28195 Z= 0.262 Chirality : 0.040 0.143 3207 Planarity : 0.004 0.052 3669 Dihedral : 8.526 84.907 3032 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.31 % Favored : 93.65 % Rotamer: Outliers : 5.05 % Allowed : 33.47 % Favored : 61.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.17), residues: 2553 helix: 0.65 (0.16), residues: 1124 sheet: -1.05 (0.30), residues: 331 loop : -1.19 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 87 TYR 0.010 0.001 TYR F 63 PHE 0.013 0.001 PHE B 259 TRP 0.016 0.001 TRP a 183 HIS 0.013 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (20703) covalent geometry : angle 0.50752 / 0.26 (28195) hydrogen bonds : bond 0.03352 / 2.29 ( 870) hydrogen bonds : angle 4.59026 / 3.23 ( 2517) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 489 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 165 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8169 (p) REVERT: E 263 ASP cc_start: 0.7804 (t0) cc_final: 0.7583 (t0) REVERT: E 302 GLU cc_start: 0.7367 (mp0) cc_final: 0.6928 (mp0) REVERT: F 110 ASP cc_start: 0.7549 (p0) cc_final: 0.6917 (p0) REVERT: F 124 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7613 (tttt) REVERT: F 163 ARG cc_start: 0.7276 (mtm110) cc_final: 0.6881 (mtm110) REVERT: F 171 ARG cc_start: 0.6437 (OUTLIER) cc_final: 0.6133 (tpt-90) REVERT: F 227 ASN cc_start: 0.7745 (m110) cc_final: 0.7357 (m-40) REVERT: F 300 GLU cc_start: 0.7337 (mp0) cc_final: 0.7032 (mp0) REVERT: G 364 ARG cc_start: 0.6286 (mmt90) cc_final: 0.5904 (mmt90) REVERT: G 407 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6822 (tm-30) REVERT: a 46 PHE cc_start: 0.5674 (OUTLIER) cc_final: 0.4917 (m-80) REVERT: a 76 ARG cc_start: 0.7466 (ttm170) cc_final: 0.7105 (ttm170) REVERT: a 216 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7271 (mp) REVERT: a 221 MET cc_start: 0.7240 (mpp) cc_final: 0.6730 (mpp) REVERT: c 116 VAL cc_start: 0.7508 (OUTLIER) cc_final: 0.7074 (p) REVERT: c 117 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6043 (mp0) REVERT: c 166 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7382 (mptm) REVERT: A 29 MET cc_start: 0.6301 (mmm) cc_final: 0.5823 (mmm) REVERT: A 94 ARG cc_start: 0.8225 (mtp85) cc_final: 0.7719 (mtp85) REVERT: A 110 ASP cc_start: 0.6536 (OUTLIER) cc_final: 0.6156 (t0) REVERT: A 141 ASP cc_start: 0.7302 (t0) cc_final: 0.6840 (t0) REVERT: A 246 ASN cc_start: 0.8078 (m-40) cc_final: 0.7860 (m110) REVERT: A 292 LEU cc_start: 0.8338 (mt) cc_final: 0.8022 (mp) REVERT: B 242 ARG cc_start: 0.7823 (ptm-80) cc_final: 0.7246 (tmt-80) REVERT: B 248 MET cc_start: 0.7648 (mtm) cc_final: 0.7447 (mtt) REVERT: B 278 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7328 (mt-10) REVERT: B 308 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7099 (mm-30) REVERT: C 52 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7312 (tm-30) REVERT: C 100 HIS cc_start: 0.6275 (OUTLIER) cc_final: 0.5911 (t70) REVERT: C 119 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7840 (mt0) REVERT: C 135 ASN cc_start: 0.8601 (p0) cc_final: 0.8295 (p0) REVERT: C 155 GLN cc_start: 0.7966 (tt0) cc_final: 0.7630 (tt0) REVERT: C 210 ARG cc_start: 0.8721 (mtp85) cc_final: 0.8469 (mtt90) REVERT: C 234 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.7053 (tptp) REVERT: C 250 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6781 (mtm-85) REVERT: C 285 ASP cc_start: 0.6930 (p0) cc_final: 0.6536 (p0) REVERT: C 308 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7029 (pm20) REVERT: D 65 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7409 (mmp80) REVERT: D 110 ASP cc_start: 0.7668 (m-30) cc_final: 0.7347 (m-30) REVERT: D 300 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5763 (mp0) outliers start: 107 outliers final: 69 residues processed: 565 average time/residue: 0.1617 time to fit residues: 134.8105 Evaluate side-chains 570 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 485 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 171 ARG Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 510 MET Chi-restraints excluded: chain G residue 514 LEU Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain G residue 563 LEU Chi-restraints excluded: chain G residue 583 ILE Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain a residue 46 PHE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 82 MET Chi-restraints excluded: chain a residue 94 HIS Chi-restraints excluded: chain a residue 117 GLU Chi-restraints excluded: chain a residue 157 GLU Chi-restraints excluded: chain a residue 179 VAL Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 117 GLU Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 147 VAL Chi-restraints excluded: chain c residue 166 LYS Chi-restraints excluded: chain c residue 167 LEU Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 320 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 189 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 203 optimal weight: 0.0030 chunk 229 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 242 optimal weight: 0.7980 chunk 143 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 170 optimal weight: 0.5980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 80 HIS E 83 GLN E 207 GLN E 222 HIS E 296 ASN A 224 ASN B 80 HIS ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN D 119 GLN D 257 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.171837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.132338 restraints weight = 28753.222| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.52 r_work: 0.3407 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20703 Z= 0.136 Angle : 0.518 9.313 28195 Z= 0.267 Chirality : 0.040 0.142 3207 Planarity : 0.004 0.051 3669 Dihedral : 8.433 86.172 3031 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.27 % Favored : 93.69 % Rotamer: Outliers : 4.67 % Allowed : 33.99 % Favored : 61.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.17), residues: 2553 helix: 0.66 (0.16), residues: 1124 sheet: -0.95 (0.30), residues: 329 loop : -1.18 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 210 TYR 0.032 0.001 TYR F 63 PHE 0.011 0.001 PHE E 283 TRP 0.014 0.001 TRP a 183 HIS 0.013 0.001 HIS F 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (20703) covalent geometry : angle 0.51762 / 0.27 (28195) hydrogen bonds : bond 0.03421 / 2.34 ( 870) hydrogen bonds : angle 4.59093 / 3.23 ( 2517) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 490 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 165 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8173 (p) REVERT: E 263 ASP cc_start: 0.7847 (t0) cc_final: 0.7598 (t0) REVERT: E 302 GLU cc_start: 0.7358 (mp0) cc_final: 0.6876 (mp0) REVERT: F 17 SER cc_start: 0.8209 (OUTLIER) cc_final: 0.7919 (p) REVERT: F 110 ASP cc_start: 0.7534 (p0) cc_final: 0.6887 (p0) REVERT: F 124 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7520 (tttt) REVERT: F 163 ARG cc_start: 0.7317 (mtm110) cc_final: 0.6909 (mtm110) REVERT: F 171 ARG cc_start: 0.6507 (OUTLIER) cc_final: 0.6183 (tpt-90) REVERT: G 364 ARG cc_start: 0.6268 (mmt90) cc_final: 0.5863 (mmt90) REVERT: G 407 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6727 (tm-30) REVERT: a 46 PHE cc_start: 0.5638 (OUTLIER) cc_final: 0.4914 (m-80) REVERT: a 76 ARG cc_start: 0.7504 (ttm170) cc_final: 0.7163 (ttt180) REVERT: a 216 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7265 (mp) REVERT: a 221 MET cc_start: 0.7223 (mpp) cc_final: 0.6694 (mpp) REVERT: c 116 VAL cc_start: 0.7483 (OUTLIER) cc_final: 0.7064 (p) REVERT: c 117 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.6003 (mp0) REVERT: c 166 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7403 (mptm) REVERT: A 29 MET cc_start: 0.6301 (mmm) cc_final: 0.5794 (mmm) REVERT: A 110 ASP cc_start: 0.6519 (OUTLIER) cc_final: 0.6130 (t0) REVERT: A 141 ASP cc_start: 0.7408 (t0) cc_final: 0.7013 (t0) REVERT: A 292 LEU cc_start: 0.8278 (mt) cc_final: 0.7954 (mp) REVERT: B 242 ARG cc_start: 0.7805 (ptm-80) cc_final: 0.7244 (tmt-80) REVERT: B 278 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7344 (mt-10) REVERT: C 52 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7307 (tm-30) REVERT: C 100 HIS cc_start: 0.6302 (OUTLIER) cc_final: 0.5932 (t70) REVERT: C 119 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7808 (mt0) REVERT: C 155 GLN cc_start: 0.7965 (tt0) cc_final: 0.7603 (tt0) REVERT: C 210 ARG cc_start: 0.8752 (mtp85) cc_final: 0.8507 (mtt90) REVERT: C 250 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6741 (mtm-85) REVERT: C 285 ASP cc_start: 0.6897 (p0) cc_final: 0.6503 (p0) REVERT: C 308 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7006 (pm20) REVERT: D 65 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7387 (mmp80) REVERT: D 110 ASP cc_start: 0.7708 (m-30) cc_final: 0.7382 (m-30) REVERT: D 300 GLU cc_start: 0.6123 (OUTLIER) cc_final: 0.5708 (mp0) outliers start: 99 outliers final: 73 residues processed: 559 average time/residue: 0.1543 time to fit residues: 127.8525 Evaluate side-chains 578 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 489 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 171 ARG Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 510 MET Chi-restraints excluded: chain G residue 514 LEU Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain G residue 563 LEU Chi-restraints excluded: chain G residue 583 ILE Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain a residue 46 PHE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 82 MET Chi-restraints excluded: chain a residue 94 HIS Chi-restraints excluded: chain a residue 117 GLU Chi-restraints excluded: chain a residue 157 GLU Chi-restraints excluded: chain a residue 179 VAL Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 117 GLU Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 147 VAL Chi-restraints excluded: chain c residue 166 LYS Chi-restraints excluded: chain c residue 167 LEU Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 320 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 230 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 245 optimal weight: 0.8980 chunk 228 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 83 GLN E 207 GLN E 222 HIS F 261 ASN A 134 HIS A 224 ASN B 80 HIS ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.171602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.132125 restraints weight = 28670.441| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.52 r_work: 0.3380 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20703 Z= 0.155 Angle : 0.536 11.782 28195 Z= 0.276 Chirality : 0.041 0.142 3207 Planarity : 0.004 0.051 3669 Dihedral : 8.385 82.798 3028 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.58 % Favored : 93.38 % Rotamer: Outliers : 4.96 % Allowed : 33.81 % Favored : 61.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.17), residues: 2553 helix: 0.63 (0.16), residues: 1125 sheet: -0.98 (0.30), residues: 333 loop : -1.17 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 51 TYR 0.024 0.001 TYR F 63 PHE 0.012 0.001 PHE E 283 TRP 0.013 0.001 TRP a 183 HIS 0.016 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (20703) covalent geometry : angle 0.53613 / 0.28 (28195) hydrogen bonds : bond 0.03531 / 2.41 ( 870) hydrogen bonds : angle 4.63284 / 3.26 ( 2517) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 485 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 163 ARG cc_start: 0.8167 (mpt180) cc_final: 0.7852 (mpt180) REVERT: E 165 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8164 (p) REVERT: E 263 ASP cc_start: 0.7857 (t0) cc_final: 0.7618 (t0) REVERT: E 302 GLU cc_start: 0.7366 (mp0) cc_final: 0.6873 (mp0) REVERT: F 17 SER cc_start: 0.8200 (OUTLIER) cc_final: 0.7950 (p) REVERT: F 110 ASP cc_start: 0.7524 (p0) cc_final: 0.6871 (p0) REVERT: F 124 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7488 (tttt) REVERT: F 163 ARG cc_start: 0.7321 (mtm110) cc_final: 0.6906 (mtm110) REVERT: F 171 ARG cc_start: 0.6532 (OUTLIER) cc_final: 0.6186 (tpt-90) REVERT: G 364 ARG cc_start: 0.6258 (mmt90) cc_final: 0.5844 (mmt90) REVERT: G 407 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6739 (tm-30) REVERT: a 46 PHE cc_start: 0.5620 (OUTLIER) cc_final: 0.4915 (m-80) REVERT: a 76 ARG cc_start: 0.7521 (ttm170) cc_final: 0.7241 (ttm170) REVERT: a 216 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7257 (mp) REVERT: a 221 MET cc_start: 0.7254 (mpp) cc_final: 0.6709 (mpp) REVERT: c 116 VAL cc_start: 0.7478 (OUTLIER) cc_final: 0.7060 (p) REVERT: c 117 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6006 (mp0) REVERT: c 166 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7430 (mptm) REVERT: A 29 MET cc_start: 0.6326 (mmm) cc_final: 0.5807 (mmm) REVERT: A 94 ARG cc_start: 0.8216 (mtp85) cc_final: 0.7763 (mtp85) REVERT: A 110 ASP cc_start: 0.6533 (OUTLIER) cc_final: 0.6140 (t0) REVERT: A 141 ASP cc_start: 0.7474 (t0) cc_final: 0.7012 (t0) REVERT: B 242 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7279 (tmt-80) REVERT: B 248 MET cc_start: 0.7688 (mtm) cc_final: 0.7453 (mtt) REVERT: B 278 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7339 (mt-10) REVERT: C 52 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7326 (tm-30) REVERT: C 100 HIS cc_start: 0.6322 (OUTLIER) cc_final: 0.5948 (t70) REVERT: C 119 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7797 (mt0) REVERT: C 155 GLN cc_start: 0.7997 (tt0) cc_final: 0.7614 (tt0) REVERT: C 210 ARG cc_start: 0.8755 (mtp85) cc_final: 0.8505 (mtt90) REVERT: C 250 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6702 (mtm-85) REVERT: C 285 ASP cc_start: 0.6886 (p0) cc_final: 0.6493 (p0) REVERT: C 308 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7025 (pm20) REVERT: D 65 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7382 (mmp80) REVERT: D 110 ASP cc_start: 0.7707 (m-30) cc_final: 0.7384 (m-30) REVERT: D 300 GLU cc_start: 0.6158 (OUTLIER) cc_final: 0.5720 (mp0) outliers start: 105 outliers final: 79 residues processed: 552 average time/residue: 0.1479 time to fit residues: 120.8266 Evaluate side-chains 586 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 490 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 171 ARG Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 510 MET Chi-restraints excluded: chain G residue 514 LEU Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain G residue 563 LEU Chi-restraints excluded: chain G residue 583 ILE Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain a residue 46 PHE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 82 MET Chi-restraints excluded: chain a residue 94 HIS Chi-restraints excluded: chain a residue 117 GLU Chi-restraints excluded: chain a residue 157 GLU Chi-restraints excluded: chain a residue 179 VAL Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 117 GLU Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 147 VAL Chi-restraints excluded: chain c residue 166 LYS Chi-restraints excluded: chain c residue 167 LEU Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 317 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 48 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 180 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 248 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 chunk 120 optimal weight: 0.0000 chunk 79 optimal weight: 30.0000 overall best weight: 0.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 83 GLN E 207 GLN E 222 HIS E 296 ASN F 261 ASN ** c 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.172569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132951 restraints weight = 28879.360| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.56 r_work: 0.3416 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20703 Z= 0.114 Angle : 0.524 11.589 28195 Z= 0.269 Chirality : 0.040 0.141 3207 Planarity : 0.004 0.068 3669 Dihedral : 8.239 80.124 3028 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.91 % Favored : 94.05 % Rotamer: Outliers : 4.67 % Allowed : 34.37 % Favored : 60.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.17), residues: 2553 helix: 0.73 (0.16), residues: 1126 sheet: -0.95 (0.30), residues: 337 loop : -1.12 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 312 TYR 0.020 0.001 TYR F 63 PHE 0.019 0.001 PHE A 283 TRP 0.014 0.001 TRP a 183 HIS 0.020 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (20703) covalent geometry : angle 0.52369 / 0.27 (28195) hydrogen bonds : bond 0.03246 / 2.22 ( 870) hydrogen bonds : angle 4.57843 / 3.22 ( 2517) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 477 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 165 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8126 (p) REVERT: E 263 ASP cc_start: 0.7838 (t0) cc_final: 0.7624 (t0) REVERT: E 302 GLU cc_start: 0.7367 (mp0) cc_final: 0.6834 (mp0) REVERT: F 17 SER cc_start: 0.8214 (OUTLIER) cc_final: 0.7958 (p) REVERT: F 110 ASP cc_start: 0.7528 (p0) cc_final: 0.6878 (p0) REVERT: F 124 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7520 (tttt) REVERT: F 163 ARG cc_start: 0.7295 (mtm110) cc_final: 0.6891 (mtm110) REVERT: F 165 THR cc_start: 0.8020 (m) cc_final: 0.7599 (t) REVERT: F 171 ARG cc_start: 0.6529 (OUTLIER) cc_final: 0.6199 (tpt-90) REVERT: G 364 ARG cc_start: 0.6260 (mmt90) cc_final: 0.5839 (mmt90) REVERT: G 407 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6776 (tm-30) REVERT: a 46 PHE cc_start: 0.5577 (OUTLIER) cc_final: 0.4916 (m-80) REVERT: a 76 ARG cc_start: 0.7476 (ttm170) cc_final: 0.7120 (ttt180) REVERT: a 216 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7265 (mp) REVERT: a 221 MET cc_start: 0.7228 (mpp) cc_final: 0.6716 (mpp) REVERT: c 116 VAL cc_start: 0.7484 (OUTLIER) cc_final: 0.7082 (p) REVERT: c 117 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.5999 (mp0) REVERT: c 166 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7430 (mptm) REVERT: A 29 MET cc_start: 0.6279 (mmm) cc_final: 0.5759 (mmm) REVERT: A 94 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7745 (mtp85) REVERT: A 110 ASP cc_start: 0.6576 (OUTLIER) cc_final: 0.6183 (t0) REVERT: A 141 ASP cc_start: 0.7391 (t0) cc_final: 0.6988 (t0) REVERT: B 80 HIS cc_start: 0.7904 (OUTLIER) cc_final: 0.7023 (t-90) REVERT: B 242 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7285 (tmt-80) REVERT: B 278 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7326 (mt-10) REVERT: B 314 PHE cc_start: 0.7315 (t80) cc_final: 0.7078 (t80) REVERT: B 317 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5917 (tm-30) REVERT: C 51 ARG cc_start: 0.8361 (ttt90) cc_final: 0.8130 (ttt90) REVERT: C 52 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7343 (tm-30) REVERT: C 100 HIS cc_start: 0.6283 (OUTLIER) cc_final: 0.5915 (t70) REVERT: C 155 GLN cc_start: 0.7940 (tt0) cc_final: 0.7567 (tt0) REVERT: C 210 ARG cc_start: 0.8752 (mtp85) cc_final: 0.8505 (mtt90) REVERT: C 250 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6782 (mtm-85) REVERT: C 285 ASP cc_start: 0.6916 (p0) cc_final: 0.6526 (p0) REVERT: C 308 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7027 (pm20) REVERT: D 65 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7388 (mmp80) REVERT: D 110 ASP cc_start: 0.7669 (m-30) cc_final: 0.7333 (m-30) REVERT: D 300 GLU cc_start: 0.6069 (OUTLIER) cc_final: 0.5649 (mp0) outliers start: 99 outliers final: 75 residues processed: 542 average time/residue: 0.1525 time to fit residues: 121.5401 Evaluate side-chains 570 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 477 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 171 ARG Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 510 MET Chi-restraints excluded: chain G residue 514 LEU Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain G residue 563 LEU Chi-restraints excluded: chain G residue 583 ILE Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain a residue 46 PHE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 82 MET Chi-restraints excluded: chain a residue 94 HIS Chi-restraints excluded: chain a residue 117 GLU Chi-restraints excluded: chain a residue 157 GLU Chi-restraints excluded: chain a residue 179 VAL Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 117 GLU Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 147 VAL Chi-restraints excluded: chain c residue 166 LYS Chi-restraints excluded: chain c residue 167 LEU Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 317 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 201 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 82 optimal weight: 20.0000 chunk 233 optimal weight: 0.9990 chunk 243 optimal weight: 0.9980 chunk 245 optimal weight: 2.9990 chunk 236 optimal weight: 0.9990 chunk 250 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 83 GLN E 207 GLN E 296 ASN F 237 GLN F 261 ASN ** c 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN B 80 HIS ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.171000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.131408 restraints weight = 28885.366| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.53 r_work: 0.3376 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20703 Z= 0.169 Angle : 0.549 12.176 28195 Z= 0.283 Chirality : 0.041 0.144 3207 Planarity : 0.004 0.050 3669 Dihedral : 8.348 80.708 3028 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.82 % Allowed : 34.32 % Favored : 60.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.17), residues: 2553 helix: 0.65 (0.16), residues: 1126 sheet: -0.92 (0.30), residues: 331 loop : -1.17 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 312 TYR 0.020 0.001 TYR F 63 PHE 0.013 0.001 PHE A 259 TRP 0.022 0.001 TRP a 183 HIS 0.013 0.001 HIS F 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (20703) covalent geometry : angle 0.54865 / 0.28 (28195) hydrogen bonds : bond 0.03669 / 2.51 ( 870) hydrogen bonds : angle 4.65861 / 3.28 ( 2517) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4786.77 seconds wall clock time: 82 minutes 38.95 seconds (4958.95 seconds total)