Starting phenix.real_space_refine on Mon Sep 14 03:07:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vok_21267/09_2026/6vok_21267.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vok_21267/09_2026/6vok_21267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6vok_21267/09_2026/6vok_21267.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vok_21267/09_2026/6vok_21267.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vok_21267/09_2026/6vok_21267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vok_21267/09_2026/6vok_21267.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vok_21267/09_2026/6vok_21267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vok_21267/09_2026/6vok_21267.map" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 103 5.16 5 C 17274 2.51 5 N 4747 2.21 5 O 5372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27512 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3827 Classifications: {'peptide': 498} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 479} Chain: "B" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3851 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3849 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "D" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 453} Chain: "E" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Chain: "F" Number of atoms: 3627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3627 Classifications: {'peptide': 479} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "d" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1383 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "g" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2502 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'ATP': 1, 'TTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.25, per 1000 atoms: 0.23 Number of scatterers: 27512 At special positions: 0 Unit cell: (129.519, 127.413, 161.109, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 103 16.00 P 16 15.00 O 5372 8.00 N 4747 7.00 C 17274 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: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6560 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 28 sheets defined 46.0% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 151 through 157 Processing helix chain 'A' and resid 175 through 187 removed outlier: 3.724A pdb=" N ILE A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.816A pdb=" N TYR A 221 " --> pdb=" O ALA A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 253 removed outlier: 3.504A pdb=" N GLN A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.654A pdb=" N GLN A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.536A pdb=" N ALA A 286 " --> pdb=" O GLY A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.035A pdb=" N ALA A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 392 removed outlier: 4.240A pdb=" N LYS A 378 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 422 Processing helix chain 'A' and resid 430 through 443 Processing helix chain 'A' and resid 453 through 468 Processing helix chain 'A' and resid 470 through 480 removed outlier: 3.547A pdb=" N GLU A 474 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 504 removed outlier: 3.816A pdb=" N LEU A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 19 removed outlier: 4.361A pdb=" N GLY B 19 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 175 through 186 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 232 through 253 Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 288 through 289 No H-bonds generated for 'chain 'B' and resid 288 through 289' Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.992A pdb=" N ALA B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 380 Processing helix chain 'B' and resid 382 through 397 Processing helix chain 'B' and resid 404 through 420 Processing helix chain 'B' and resid 430 through 443 removed outlier: 3.756A pdb=" N ASN B 443 " --> pdb=" O TYR B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 469 removed outlier: 4.372A pdb=" N LYS B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU B 460 " --> pdb=" O LYS B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 479 removed outlier: 3.897A pdb=" N GLN B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 479 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 503 Processing helix chain 'C' and resid 5 through 16 removed outlier: 3.941A pdb=" N SER C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS C 11 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ARG C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG C 16 " --> pdb=" O ILE C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 105 removed outlier: 3.991A pdb=" N TYR C 104 " --> pdb=" O SER C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 158 Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.654A pdb=" N GLN C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.570A pdb=" N TYR C 221 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR C 222 " --> pdb=" O MET C 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 218 through 222' Processing helix chain 'C' and resid 232 through 253 Proline residue: C 240 - end of helix removed outlier: 3.882A pdb=" N PHE C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG C 253 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 278 Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.545A pdb=" N TYR C 287 " --> pdb=" O ARG C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 289 No H-bonds generated for 'chain 'C' and resid 288 through 289' Processing helix chain 'C' and resid 290 through 300 removed outlier: 4.232A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 373 through 395 removed outlier: 5.187A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU C 383 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 413 Processing helix chain 'C' and resid 414 through 422 removed outlier: 3.699A pdb=" N ARG C 418 " --> pdb=" O GLY C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 444 removed outlier: 4.027A pdb=" N GLY C 441 " --> pdb=" O THR C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 468 Processing helix chain 'C' and resid 471 through 480 Processing helix chain 'C' and resid 483 through 503 removed outlier: 3.501A pdb=" N LEU C 503 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 142 removed outlier: 4.090A pdb=" N LEU D 142 " --> pdb=" O PHE D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 177 through 190 Processing helix chain 'D' and resid 191 through 193 No H-bonds generated for 'chain 'D' and resid 191 through 193' Processing helix chain 'D' and resid 205 through 218 Processing helix chain 'D' and resid 242 through 263 removed outlier: 3.696A pdb=" N ARG D 246 " --> pdb=" O PRO D 242 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 287 removed outlier: 3.599A pdb=" N PHE D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 311 Processing helix chain 'D' and resid 330 through 333 Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.532A pdb=" N GLY D 381 " --> pdb=" O PRO D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 406 removed outlier: 4.739A pdb=" N ASP D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 431 removed outlier: 4.001A pdb=" N ARG D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.795A pdb=" N GLY D 464 " --> pdb=" O LEU D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 496 Processing helix chain 'E' and resid 138 through 142 removed outlier: 3.684A pdb=" N LEU E 142 " --> pdb=" O PHE E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 159 Processing helix chain 'E' and resid 177 through 190 Processing helix chain 'E' and resid 205 through 220 removed outlier: 3.750A pdb=" N TYR E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 264 removed outlier: 5.136A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE E 260 " --> pdb=" O MET E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 286 removed outlier: 3.715A pdb=" N GLY E 282 " --> pdb=" O PHE E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 311 removed outlier: 3.722A pdb=" N LEU E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 314 No H-bonds generated for 'chain 'E' and resid 312 through 314' Processing helix chain 'E' and resid 330 through 333 Processing helix chain 'E' and resid 336 through 343 Processing helix chain 'E' and resid 344 through 346 No H-bonds generated for 'chain 'E' and resid 344 through 346' Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 376 through 408 removed outlier: 7.467A pdb=" N GLU E 382 " --> pdb=" O ARG E 378 " (cutoff:3.500A) removed outlier: 9.153A pdb=" N GLU E 383 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N HIS E 384 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR E 385 " --> pdb=" O GLY E 381 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 431 removed outlier: 3.803A pdb=" N THR E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 450 through 464 removed outlier: 3.866A pdb=" N ARG E 456 " --> pdb=" O ALA E 452 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY E 464 " --> pdb=" O LEU E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 490 removed outlier: 3.631A pdb=" N ALA E 483 " --> pdb=" O ASN E 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 159 Processing helix chain 'F' and resid 177 through 193 removed outlier: 3.675A pdb=" N LEU F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 219 Processing helix chain 'F' and resid 244 through 265 removed outlier: 5.219A pdb=" N GLY F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU F 251 " --> pdb=" O MET F 247 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE F 260 " --> pdb=" O MET F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 289 removed outlier: 3.710A pdb=" N PHE F 278 " --> pdb=" O ASN F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 311 removed outlier: 3.687A pdb=" N GLU F 305 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 333 Processing helix chain 'F' and resid 336 through 343 Processing helix chain 'F' and resid 354 through 360 Processing helix chain 'F' and resid 376 through 381 removed outlier: 3.506A pdb=" N VAL F 380 " --> pdb=" O GLN F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 405 removed outlier: 3.629A pdb=" N GLU F 400 " --> pdb=" O GLN F 396 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 431 removed outlier: 4.016A pdb=" N THR F 420 " --> pdb=" O GLU F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 437 No H-bonds generated for 'chain 'F' and resid 435 through 437' Processing helix chain 'F' and resid 438 through 443 Processing helix chain 'F' and resid 450 through 463 Processing helix chain 'F' and resid 470 through 474 removed outlier: 3.803A pdb=" N PHE F 474 " --> pdb=" O GLU F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 495 Processing helix chain 'd' and resid 75 through 90 Processing helix chain 'd' and resid 91 through 107 removed outlier: 3.606A pdb=" N THR d 95 " --> pdb=" O THR d 91 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER d 97 " --> pdb=" O GLU d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 117 Processing helix chain 'd' and resid 121 through 137 removed outlier: 3.599A pdb=" N LYS d 125 " --> pdb=" O SER d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 152 removed outlier: 4.999A pdb=" N PHE d 145 " --> pdb=" O HIS d 141 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE d 146 " --> pdb=" O THR d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 156 No H-bonds generated for 'chain 'd' and resid 154 through 156' Processing helix chain 'd' and resid 157 through 174 removed outlier: 4.386A pdb=" N GLU d 166 " --> pdb=" O LEU d 162 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP d 167 " --> pdb=" O ASN d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 203 removed outlier: 3.874A pdb=" N LEU d 191 " --> pdb=" O GLU d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 237 through 249 removed outlier: 4.682A pdb=" N LEU d 248 " --> pdb=" O ILE d 244 " (cutoff:3.500A) Processing helix chain 'e' and resid 88 through 104 removed outlier: 4.470A pdb=" N ARG e 104 " --> pdb=" O GLU e 100 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 113 Processing helix chain 'e' and resid 115 through 130 removed outlier: 3.882A pdb=" N ALA e 128 " --> pdb=" O THR e 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 81 removed outlier: 3.612A pdb=" N VAL g 80 " --> pdb=" O GLN g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 82 through 96 Processing helix chain 'g' and resid 131 through 151 removed outlier: 4.443A pdb=" N ASN g 135 " --> pdb=" O GLY g 131 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS g 149 " --> pdb=" O ILE g 145 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS g 150 " --> pdb=" O ALA g 146 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 161 through 170 removed outlier: 4.397A pdb=" N TYR g 167 " --> pdb=" O LYS g 163 " (cutoff:3.500A) Processing helix chain 'g' and resid 188 through 204 removed outlier: 3.975A pdb=" N SER g 204 " --> pdb=" O SER g 200 " (cutoff:3.500A) Processing helix chain 'g' and resid 247 through 251 removed outlier: 3.701A pdb=" N ALA g 250 " --> pdb=" O VAL g 247 " (cutoff:3.500A) Processing helix chain 'g' and resid 287 through 363 Proline residue: g 297 - end of helix Processing sheet with id=AA1, first strand: chain 'F' and resid 91 through 93 removed outlier: 5.687A pdb=" N VAL F 65 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL F 77 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN F 67 " --> pdb=" O ARG F 75 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 89 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.059A pdb=" N GLU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 319 through 321 removed outlier: 8.080A pdb=" N VAL A 320 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE A 168 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU A 167 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU A 345 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 169 " --> pdb=" O LEU A 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 227 removed outlier: 5.652A pdb=" N TYR A 196 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLU A 227 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA A 198 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 55 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 21 through 27 current: chain 'B' and resid 39 through 44 removed outlier: 6.608A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG B 41 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 30 " --> pdb=" O VAL B 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 55 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 61 through 67 current: chain 'D' and resid 46 through 52 removed outlier: 3.563A pdb=" N VAL D 49 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 61 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL D 65 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN D 67 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASP D 32 " --> pdb=" O ALA D 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 21 through 27 current: chain 'B' and resid 39 through 44 removed outlier: 6.608A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG B 41 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 30 " --> pdb=" O VAL B 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 109 removed outlier: 7.922A pdb=" N VAL B 225 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLU B 227 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA B 198 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 319 through 321 removed outlier: 6.397A pdb=" N LEU B 167 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 27 through 28 Processing sheet with id=AB2, first strand: chain 'C' and resid 32 through 36 removed outlier: 6.580A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLU C 52 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 53 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 92 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.718A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 108 through 109 removed outlier: 6.087A pdb=" N ILE C 109 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N THR C 228 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 319 through 321 Processing sheet with id=AB6, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AB7, first strand: chain 'D' and resid 110 through 111 removed outlier: 6.218A pdb=" N PHE D 111 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N SER D 197 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N VAL D 235 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE D 199 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL D 268 " --> pdb=" O THR D 322 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ILE D 324 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU D 270 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ALA D 326 " --> pdb=" O LEU D 270 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE D 272 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N TYR D 328 " --> pdb=" O ILE D 272 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE D 168 " --> pdb=" O GLN D 325 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL D 327 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU D 170 " --> pdb=" O VAL D 327 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 20 through 27 removed outlier: 5.036A pdb=" N ILE E 23 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ALA E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG E 73 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU E 68 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG E 75 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN E 45 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ALA E 96 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ILE E 48 " --> pdb=" O THR E 94 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR E 94 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AC1, first strand: chain 'E' and resid 110 through 111 removed outlier: 3.550A pdb=" N TYR E 236 " --> pdb=" O PHE E 111 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N SER E 197 " --> pdb=" O ALA E 233 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL E 235 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE E 199 " --> pdb=" O VAL E 235 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY E 237 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY E 201 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE E 168 " --> pdb=" O GLN E 325 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL E 327 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU E 170 " --> pdb=" O VAL E 327 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE E 171 " --> pdb=" O THR E 350 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AC3, first strand: chain 'F' and resid 110 through 111 removed outlier: 8.435A pdb=" N ALA F 233 " --> pdb=" O GLY F 195 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N SER F 197 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL F 235 " --> pdb=" O SER F 197 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE F 199 " --> pdb=" O VAL F 235 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLY F 237 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY F 201 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL F 196 " --> pdb=" O ASP F 267 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE F 272 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE F 168 " --> pdb=" O GLN F 325 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS F 167 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N THR F 350 " --> pdb=" O LYS F 167 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY F 169 " --> pdb=" O THR F 350 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'd' and resid 175 through 182 removed outlier: 5.817A pdb=" N GLU d 176 " --> pdb=" O ARG d 208 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LYS d 210 " --> pdb=" O GLU d 176 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ALA d 178 " --> pdb=" O LYS d 210 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL d 212 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL d 180 " --> pdb=" O VAL d 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'e' and resid 13 through 15 removed outlier: 3.719A pdb=" N TRP e 15 " --> pdb=" O VAL e 7 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN e 4 " --> pdb=" O ILE e 74 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE e 76 " --> pdb=" O ASN e 4 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N CYS e 6 " --> pdb=" O ILE e 76 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'e' and resid 30 through 33 removed outlier: 3.704A pdb=" N ILE e 22 " --> pdb=" O VAL e 33 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE e 51 " --> pdb=" O LEU e 58 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU e 58 " --> pdb=" O ILE e 51 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'e' and resid 30 through 33 removed outlier: 3.704A pdb=" N ILE e 22 " --> pdb=" O VAL e 33 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE e 51 " --> pdb=" O LEU e 58 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU e 58 " --> pdb=" O ILE e 51 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'e' and resid 41 through 42 Processing sheet with id=AC9, first strand: chain 'g' and resid 176 through 179 removed outlier: 8.521A pdb=" N ILE g 157 " --> pdb=" O ASP g 177 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N TYR g 179 " --> pdb=" O ILE g 157 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER g 159 " --> pdb=" O TYR g 179 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE g 158 " --> pdb=" O VAL g 118 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU g 120 " --> pdb=" O ILE g 158 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA g 119 " --> pdb=" O GLU g 211 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU g 213 " --> pdb=" O ALA g 119 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET g 121 " --> pdb=" O LEU g 213 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'g' and resid 258 through 259 1251 hydrogen bonds defined for protein. 3657 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: 5.30 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9163 1.34 - 1.46: 4451 1.46 - 1.58: 14062 1.58 - 1.70: 26 1.70 - 1.82: 195 Bond restraints: 27897 Sorted by residual: bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.59e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.49e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.11e+01 bond pdb=" C4 ATP E 601 " pdb=" C5 ATP E 601 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 4.99e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.64e+01 ... (remaining 27892 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.78: 37634 4.78 - 9.56: 167 9.56 - 14.33: 7 14.33 - 19.11: 2 19.11 - 23.89: 5 Bond angle restraints: 37815 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 115.98 23.89 1.00e+00 1.00e+00 5.71e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 119.85 20.02 1.00e+00 1.00e+00 4.01e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 120.56 19.31 1.00e+00 1.00e+00 3.73e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 117.61 19.22 1.00e+00 1.00e+00 3.70e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 117.69 19.14 1.00e+00 1.00e+00 3.66e+02 ... (remaining 37810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.79: 16395 31.79 - 63.59: 587 63.59 - 95.38: 53 95.38 - 127.18: 2 127.18 - 158.97: 1 Dihedral angle restraints: 17038 sinusoidal: 6817 harmonic: 10221 Sorted by residual: dihedral pdb=" CA ALA E 295 " pdb=" C ALA E 295 " pdb=" N VAL E 296 " pdb=" CA VAL E 296 " ideal model delta harmonic sigma weight residual -180.00 -132.18 -47.82 0 5.00e+00 4.00e-02 9.15e+01 dihedral pdb=" CA ALA D 295 " pdb=" C ALA D 295 " pdb=" N VAL D 296 " pdb=" CA VAL D 296 " ideal model delta harmonic sigma weight residual -180.00 -135.24 -44.76 0 5.00e+00 4.00e-02 8.01e+01 dihedral pdb=" O1B ADP F 601 " pdb=" O3A ADP F 601 " pdb=" PB ADP F 601 " pdb=" PA ADP F 601 " ideal model delta sinusoidal sigma weight residual 300.00 141.03 158.97 1 2.00e+01 2.50e-03 4.64e+01 ... (remaining 17035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3572 0.068 - 0.136: 803 0.136 - 0.203: 61 0.203 - 0.271: 8 0.271 - 0.339: 4 Chirality restraints: 4448 Sorted by residual: chirality pdb=" CB ILE g 227 " pdb=" CA ILE g 227 " pdb=" CG1 ILE g 227 " pdb=" CG2 ILE g 227 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C9 TTX C 602 " pdb=" C10 TTX C 602 " pdb=" C8 TTX C 602 " pdb=" N3 TTX C 602 " both_signs ideal model delta sigma weight residual False -2.28 -2.62 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CG LEU C 65 " pdb=" CB LEU C 65 " pdb=" CD1 LEU C 65 " pdb=" CD2 LEU C 65 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 4445 not shown) Planarity restraints: 4910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 TTX C 602 " 0.416 2.00e-02 2.50e+03 3.60e-01 1.94e+03 pdb=" C12 TTX C 602 " 0.052 2.00e-02 2.50e+03 pdb=" C13 TTX C 602 " -0.474 2.00e-02 2.50e+03 pdb=" C9 TTX C 602 " -0.440 2.00e-02 2.50e+03 pdb=" N3 TTX C 602 " 0.021 2.00e-02 2.50e+03 pdb=" O3 TTX C 602 " 0.425 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 TTX C 602 " -0.219 2.00e-02 2.50e+03 2.00e-01 5.99e+02 pdb=" C5 TTX C 602 " 0.255 2.00e-02 2.50e+03 pdb=" C6 TTX C 602 " -0.042 2.00e-02 2.50e+03 pdb=" C7 TTX C 602 " 0.265 2.00e-02 2.50e+03 pdb=" N1 TTX C 602 " -0.028 2.00e-02 2.50e+03 pdb=" O1 TTX C 602 " -0.232 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 TTX C 602 " -0.152 2.00e-02 2.50e+03 1.25e-01 1.95e+02 pdb=" C8 TTX C 602 " 0.058 2.00e-02 2.50e+03 pdb=" C9 TTX C 602 " -0.117 2.00e-02 2.50e+03 pdb=" N2 TTX C 602 " 0.194 2.00e-02 2.50e+03 pdb=" O2 TTX C 602 " 0.017 2.00e-02 2.50e+03 ... (remaining 4907 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2968 2.74 - 3.28: 28276 3.28 - 3.82: 46792 3.82 - 4.36: 56362 4.36 - 4.90: 95491 Nonbonded interactions: 229889 Sorted by model distance: nonbonded pdb=" O GLN B 187 " pdb=" OH TYR B 221 " model vdw 2.198 3.040 nonbonded pdb=" O GLU A 474 " pdb=" OG SER A 478 " model vdw 2.211 3.040 nonbonded pdb=" O GLN B 84 " pdb=" OG SER B 87 " model vdw 2.221 3.040 nonbonded pdb=" O PRO F 337 " pdb=" OG1 THR F 341 " model vdw 2.223 3.040 nonbonded pdb=" O PHE d 169 " pdb=" OG1 THR d 173 " model vdw 2.224 3.040 ... (remaining 229884 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 7 through 503) selection = (chain 'B' and resid 7 through 503) selection = (chain 'C' and resid 7 through 503) } ncs_group { reference = (chain 'D' and resid 18 through 494) selection = (chain 'E' and resid 18 through 494) selection = (chain 'F' and resid 18 through 494) } 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 group one per residue 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: 6.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 25.790 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.100 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 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 : 0.007 0.077 27897 Z= 0.362 Angle : 1.017 23.891 37815 Z= 0.620 Chirality : 0.055 0.339 4448 Planarity : 0.009 0.360 4910 Dihedral : 16.025 158.970 10478 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.58 % Favored : 92.31 % Rotamer: Outliers : 0.51 % Allowed : 12.18 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.78 (0.11), residues: 3551 helix: -2.02 (0.11), residues: 1446 sheet: -2.83 (0.20), residues: 511 loop : -2.79 (0.13), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 140 TYR 0.029 0.003 TYR g 214 PHE 0.029 0.003 PHE F 441 TRP 0.004 0.001 TRP e 15 HIS 0.007 0.002 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00735 / 0.36 (27897) covalent geometry : angle 1.01658 / 0.62 (37815) hydrogen bonds : bond 0.16875 / 10.90 ( 1236) hydrogen bonds : angle 7.67413 / 5.27 ( 3657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 748 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7459 (tp30) cc_final: 0.6868 (tp30) REVERT: A 385 LEU cc_start: 0.7696 (tt) cc_final: 0.7113 (tt) REVERT: A 389 GLN cc_start: 0.6813 (mt0) cc_final: 0.6264 (tm-30) REVERT: B 173 GLN cc_start: 0.7432 (tp-100) cc_final: 0.7218 (tp40) REVERT: B 227 GLU cc_start: 0.6760 (pm20) cc_final: 0.6491 (pm20) REVERT: B 297 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7401 (ttp80) REVERT: B 314 MET cc_start: 0.7431 (ttt) cc_final: 0.6934 (tmm) REVERT: B 376 MET cc_start: 0.6702 (tpp) cc_final: 0.6376 (mmt) REVERT: B 382 LYS cc_start: 0.7119 (tmtt) cc_final: 0.6793 (tttp) REVERT: B 410 GLN cc_start: 0.7181 (tp40) cc_final: 0.6670 (tp40) REVERT: C 49 MET cc_start: 0.6471 (tpt) cc_final: 0.5927 (tpt) REVERT: C 241 TYR cc_start: 0.8030 (m-80) cc_final: 0.7457 (m-80) REVERT: C 433 GLU cc_start: 0.7156 (mp0) cc_final: 0.6826 (mp0) REVERT: C 455 ARG cc_start: 0.6306 (mtp180) cc_final: 0.6065 (mmm-85) REVERT: D 27 ILE cc_start: 0.8533 (mm) cc_final: 0.8320 (mp) REVERT: D 40 MET cc_start: 0.7452 (tpp) cc_final: 0.7044 (tpt) REVERT: D 66 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7404 (mm-40) REVERT: D 208 GLU cc_start: 0.6652 (tt0) cc_final: 0.6336 (tt0) REVERT: D 247 MET cc_start: 0.6677 (ttp) cc_final: 0.6424 (ttp) REVERT: D 260 PHE cc_start: 0.8492 (m-80) cc_final: 0.8191 (m-80) REVERT: D 277 ARG cc_start: 0.6741 (mmt180) cc_final: 0.6367 (mmt180) REVERT: D 299 GLN cc_start: 0.8407 (pm20) cc_final: 0.8156 (pm20) REVERT: D 306 MET cc_start: 0.6613 (tpp) cc_final: 0.6302 (tpp) REVERT: D 310 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7714 (tp40) REVERT: D 354 ARG cc_start: 0.7242 (tpp80) cc_final: 0.6981 (tpp-160) REVERT: D 359 LYS cc_start: 0.7987 (tptt) cc_final: 0.7636 (tppt) REVERT: D 392 LYS cc_start: 0.8401 (mttm) cc_final: 0.7889 (mtpt) REVERT: E 145 LYS cc_start: 0.6550 (tptp) cc_final: 0.5779 (ttpp) REVERT: E 167 LYS cc_start: 0.8275 (mtmm) cc_final: 0.7691 (mtmm) REVERT: E 272 ILE cc_start: 0.9163 (mp) cc_final: 0.8565 (tp) REVERT: E 292 MET cc_start: 0.5986 (mtp) cc_final: 0.5683 (ttp) REVERT: E 482 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6789 (tp30) REVERT: F 112 ASN cc_start: 0.8135 (p0) cc_final: 0.7680 (p0) REVERT: F 116 GLU cc_start: 0.6577 (tm-30) cc_final: 0.6122 (tm-30) REVERT: F 184 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6816 (tp30) REVERT: F 217 LYS cc_start: 0.8075 (mttt) cc_final: 0.7849 (mtpt) REVERT: F 280 GLN cc_start: 0.6639 (tm-30) cc_final: 0.6410 (tm-30) REVERT: F 298 TYR cc_start: 0.7539 (m-80) cc_final: 0.7206 (m-80) REVERT: F 306 MET cc_start: 0.7909 (tpp) cc_final: 0.7251 (tpt) REVERT: F 311 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7553 (tm-30) REVERT: F 374 MET cc_start: 0.7683 (mmp) cc_final: 0.7350 (mmm) REVERT: F 383 GLU cc_start: 0.7151 (mp0) cc_final: 0.6818 (mp0) REVERT: F 454 THR cc_start: 0.7399 (p) cc_final: 0.7060 (p) REVERT: d 78 TYR cc_start: 0.7054 (m-80) cc_final: 0.6430 (m-80) REVERT: d 113 TYR cc_start: 0.7117 (t80) cc_final: 0.6734 (t80) REVERT: d 156 ASN cc_start: 0.5754 (p0) cc_final: 0.5546 (p0) REVERT: d 160 GLU cc_start: 0.6177 (tt0) cc_final: 0.5858 (tt0) REVERT: d 231 LYS cc_start: 0.6638 (mttt) cc_final: 0.6379 (mtpp) REVERT: e 121 ARG cc_start: 0.5691 (tpp80) cc_final: 0.5422 (tpp80) REVERT: g 163 LYS cc_start: 0.7838 (mmtm) cc_final: 0.7086 (tptp) REVERT: g 224 ASP cc_start: 0.7653 (m-30) cc_final: 0.7447 (m-30) REVERT: g 257 LEU cc_start: 0.7375 (pp) cc_final: 0.7005 (pt) REVERT: g 270 MET cc_start: 0.5783 (ppp) cc_final: 0.5115 (ppp) REVERT: g 300 LEU cc_start: 0.7609 (tt) cc_final: 0.6495 (mt) outliers start: 15 outliers final: 8 residues processed: 759 average time/residue: 0.2264 time to fit residues: 257.5890 Evaluate side-chains 565 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 557 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain g residue 258 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.2980 chunk 298 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN A 214 GLN ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 GLN B 398 GLN C 208 GLN D 210 ASN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 GLN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN ** d 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 199 GLN g 192 GLN g 290 GLN g 361 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.150883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.133527 restraints weight = 45720.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.135688 restraints weight = 27674.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.137103 restraints weight = 18577.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138032 restraints weight = 13953.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138560 restraints weight = 11356.064| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27897 Z= 0.151 Angle : 0.679 21.049 37815 Z= 0.344 Chirality : 0.045 0.294 4448 Planarity : 0.005 0.053 4910 Dihedral : 7.138 148.142 3918 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.52 % Favored : 94.45 % Rotamer: Outliers : 2.96 % Allowed : 16.40 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.13), residues: 3551 helix: -0.60 (0.13), residues: 1464 sheet: -2.50 (0.21), residues: 488 loop : -2.34 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 425 TYR 0.023 0.002 TYR B 144 PHE 0.021 0.002 PHE D 149 TRP 0.002 0.000 TRP e 57 HIS 0.004 0.001 HIS F 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (27897) covalent geometry : angle 0.67890 / 0.34 (37815) hydrogen bonds : bond 0.04433 / 2.94 ( 1236) hydrogen bonds : angle 5.54552 / 3.81 ( 3657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 623 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.6138 (mp0) cc_final: 0.5685 (pm20) REVERT: A 166 GLU cc_start: 0.7651 (tp30) cc_final: 0.6969 (tp30) REVERT: A 385 LEU cc_start: 0.7424 (tt) cc_final: 0.7058 (tt) REVERT: A 389 GLN cc_start: 0.6708 (mt0) cc_final: 0.6116 (tm-30) REVERT: A 420 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7216 (tp) REVERT: B 114 LYS cc_start: 0.7772 (mtpt) cc_final: 0.7364 (mtpp) REVERT: B 314 MET cc_start: 0.7587 (ttt) cc_final: 0.7235 (tmm) REVERT: B 376 MET cc_start: 0.6756 (tpp) cc_final: 0.6520 (mmt) REVERT: B 410 GLN cc_start: 0.6633 (tp40) cc_final: 0.6413 (tp40) REVERT: C 49 MET cc_start: 0.6400 (tpt) cc_final: 0.5990 (tpt) REVERT: C 208 GLN cc_start: 0.5713 (OUTLIER) cc_final: 0.5366 (mm-40) REVERT: C 241 TYR cc_start: 0.7876 (m-80) cc_final: 0.7358 (m-80) REVERT: C 292 PHE cc_start: 0.7698 (t80) cc_final: 0.7440 (t80) REVERT: C 321 GLU cc_start: 0.6839 (tm-30) cc_final: 0.6535 (tm-30) REVERT: C 351 ASN cc_start: 0.7323 (m110) cc_final: 0.7071 (p0) REVERT: C 433 GLU cc_start: 0.7267 (mp0) cc_final: 0.6993 (mp0) REVERT: C 468 ASN cc_start: 0.6878 (t0) cc_final: 0.6489 (t0) REVERT: D 66 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7333 (mm110) REVERT: D 260 PHE cc_start: 0.8436 (m-80) cc_final: 0.8098 (m-80) REVERT: D 277 ARG cc_start: 0.6745 (mmt180) cc_final: 0.6470 (mmt180) REVERT: D 299 GLN cc_start: 0.8336 (pm20) cc_final: 0.7971 (pm20) REVERT: D 310 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7647 (mm-40) REVERT: D 389 GLN cc_start: 0.7343 (pt0) cc_final: 0.7120 (pt0) REVERT: D 392 LYS cc_start: 0.8367 (mttm) cc_final: 0.7897 (mtpt) REVERT: D 488 MET cc_start: 0.7392 (ttp) cc_final: 0.7092 (ttp) REVERT: E 145 LYS cc_start: 0.6315 (tptp) cc_final: 0.5512 (ttpp) REVERT: E 167 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7585 (mtmm) REVERT: E 277 ARG cc_start: 0.6776 (mmt-90) cc_final: 0.6407 (mmt-90) REVERT: E 292 MET cc_start: 0.5827 (mtp) cc_final: 0.5514 (mtp) REVERT: E 306 MET cc_start: 0.7579 (tpp) cc_final: 0.7242 (tpp) REVERT: E 397 ARG cc_start: 0.8095 (tpt170) cc_final: 0.7514 (tpm170) REVERT: E 482 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6903 (tp30) REVERT: F 270 LEU cc_start: 0.8518 (tp) cc_final: 0.8216 (mp) REVERT: F 280 GLN cc_start: 0.6650 (tm-30) cc_final: 0.6336 (tm-30) REVERT: F 298 TYR cc_start: 0.7348 (m-80) cc_final: 0.7086 (m-80) REVERT: F 306 MET cc_start: 0.7817 (tpp) cc_final: 0.7363 (tpt) REVERT: F 311 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7604 (tm-30) REVERT: F 386 GLU cc_start: 0.6073 (mm-30) cc_final: 0.5846 (mm-30) REVERT: F 398 TYR cc_start: 0.8290 (t80) cc_final: 0.8028 (t80) REVERT: F 425 ARG cc_start: 0.7339 (mmm-85) cc_final: 0.6317 (mmm160) REVERT: F 465 GLU cc_start: 0.5817 (OUTLIER) cc_final: 0.5609 (mp0) REVERT: F 488 MET cc_start: 0.6190 (tmm) cc_final: 0.5951 (tmm) REVERT: d 78 TYR cc_start: 0.6956 (m-80) cc_final: 0.6156 (m-80) REVERT: d 210 LYS cc_start: 0.6983 (tmtt) cc_final: 0.6742 (tmtt) REVERT: d 231 LYS cc_start: 0.6158 (mttt) cc_final: 0.5886 (mtpp) REVERT: e 35 PRO cc_start: 0.4487 (Cg_exo) cc_final: 0.4188 (Cg_endo) REVERT: e 63 MET cc_start: 0.5524 (tmm) cc_final: 0.5175 (tmm) REVERT: g 73 ARG cc_start: 0.6642 (tpm170) cc_final: 0.6213 (tpm170) REVERT: g 76 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: g 179 TYR cc_start: 0.5397 (m-80) cc_final: 0.5049 (m-80) REVERT: g 236 LYS cc_start: 0.6134 (mmtm) cc_final: 0.5856 (mmtt) REVERT: g 270 MET cc_start: 0.5570 (ppp) cc_final: 0.5312 (ppp) REVERT: g 290 GLN cc_start: 0.6147 (tp40) cc_final: 0.5839 (tp-100) REVERT: g 303 GLN cc_start: 0.6771 (mt0) cc_final: 0.6548 (mt0) outliers start: 87 outliers final: 58 residues processed: 674 average time/residue: 0.2003 time to fit residues: 208.3635 Evaluate side-chains 611 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 549 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 252 TYR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 208 GLN Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 484 THR Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 109 GLU Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain g residue 76 GLN Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 258 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 41 optimal weight: 0.9980 chunk 326 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 267 optimal weight: 0.7980 chunk 208 optimal weight: 0.0030 chunk 298 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 173 GLN B 398 GLN B 473 GLN D 25 GLN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 GLN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 GLN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 GLN ** d 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.151250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.133694 restraints weight = 45622.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135819 restraints weight = 27597.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137244 restraints weight = 18804.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.138118 restraints weight = 14029.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.138760 restraints weight = 11470.043| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27897 Z= 0.144 Angle : 0.657 19.832 37815 Z= 0.329 Chirality : 0.045 0.258 4448 Planarity : 0.004 0.052 4910 Dihedral : 6.768 140.404 3918 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.86 % Favored : 94.11 % Rotamer: Outliers : 3.98 % Allowed : 18.78 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.13), residues: 3551 helix: -0.11 (0.13), residues: 1474 sheet: -2.45 (0.21), residues: 499 loop : -2.11 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 52 TYR 0.020 0.001 TYR B 144 PHE 0.022 0.001 PHE D 149 TRP 0.002 0.000 TRP e 57 HIS 0.004 0.001 HIS F 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (27897) covalent geometry : angle 0.65737 / 0.33 (37815) hydrogen bonds : bond 0.04074 / 2.72 ( 1236) hydrogen bonds : angle 5.15285 / 3.55 ( 3657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 587 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.6010 (mp0) cc_final: 0.5705 (pm20) REVERT: A 166 GLU cc_start: 0.7687 (tp30) cc_final: 0.6981 (tp30) REVERT: A 171 ASP cc_start: 0.7945 (t0) cc_final: 0.7493 (t0) REVERT: A 199 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7158 (mt) REVERT: A 385 LEU cc_start: 0.7252 (tt) cc_final: 0.6890 (tt) REVERT: A 389 GLN cc_start: 0.7082 (mt0) cc_final: 0.6085 (tm-30) REVERT: A 450 GLU cc_start: 0.5680 (tp30) cc_final: 0.4835 (tm-30) REVERT: B 122 ILE cc_start: 0.8307 (mm) cc_final: 0.8020 (mm) REVERT: B 410 GLN cc_start: 0.6590 (tp40) cc_final: 0.6354 (tp40) REVERT: C 49 MET cc_start: 0.6435 (tpt) cc_final: 0.6032 (tpt) REVERT: C 269 GLN cc_start: 0.7683 (mp-120) cc_final: 0.7478 (mp10) REVERT: C 321 GLU cc_start: 0.6789 (tm-30) cc_final: 0.6552 (tm-30) REVERT: C 433 GLU cc_start: 0.7293 (mp0) cc_final: 0.6699 (mp0) REVERT: C 468 ASN cc_start: 0.6811 (t0) cc_final: 0.6435 (t0) REVERT: D 66 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7352 (mm110) REVERT: D 247 MET cc_start: 0.6354 (ttp) cc_final: 0.6027 (ttm) REVERT: D 260 PHE cc_start: 0.8486 (m-80) cc_final: 0.8146 (m-80) REVERT: D 277 ARG cc_start: 0.6805 (mmt180) cc_final: 0.6513 (mmt180) REVERT: D 299 GLN cc_start: 0.8363 (pm20) cc_final: 0.8088 (pm20) REVERT: D 310 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7584 (mm-40) REVERT: D 374 MET cc_start: 0.7041 (mmt) cc_final: 0.6473 (mmt) REVERT: D 392 LYS cc_start: 0.8405 (mttm) cc_final: 0.7971 (mtpt) REVERT: E 145 LYS cc_start: 0.6256 (tptp) cc_final: 0.5559 (ttpp) REVERT: E 167 LYS cc_start: 0.8129 (mtmm) cc_final: 0.7652 (mtmm) REVERT: E 273 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8032 (t0) REVERT: E 277 ARG cc_start: 0.6782 (mmt-90) cc_final: 0.6354 (mmt-90) REVERT: E 306 MET cc_start: 0.7594 (tpp) cc_final: 0.7181 (tpp) REVERT: E 482 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6832 (tp30) REVERT: F 68 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7653 (tt) REVERT: F 270 LEU cc_start: 0.8557 (tp) cc_final: 0.8223 (mp) REVERT: F 280 GLN cc_start: 0.6643 (tm-30) cc_final: 0.6351 (tm-30) REVERT: F 298 TYR cc_start: 0.7333 (m-80) cc_final: 0.6879 (m-80) REVERT: F 306 MET cc_start: 0.7827 (tpp) cc_final: 0.7278 (tpt) REVERT: F 398 TYR cc_start: 0.8317 (t80) cc_final: 0.8051 (t80) REVERT: F 418 ARG cc_start: 0.5697 (mtt-85) cc_final: 0.5359 (ttp-110) REVERT: F 488 MET cc_start: 0.6170 (tmm) cc_final: 0.5695 (tmm) REVERT: d 78 TYR cc_start: 0.7080 (m-80) cc_final: 0.6191 (m-80) REVERT: d 82 LEU cc_start: 0.6129 (OUTLIER) cc_final: 0.5505 (mt) REVERT: d 231 LYS cc_start: 0.5949 (mttt) cc_final: 0.5714 (mtpp) REVERT: e 20 LYS cc_start: 0.4787 (mmmt) cc_final: 0.4465 (mmmt) REVERT: e 35 PRO cc_start: 0.4379 (Cg_exo) cc_final: 0.4102 (Cg_endo) REVERT: e 63 MET cc_start: 0.5652 (tmm) cc_final: 0.4879 (tmm) REVERT: g 76 GLN cc_start: 0.7788 (pt0) cc_final: 0.7525 (tm-30) REVERT: g 179 TYR cc_start: 0.5538 (m-80) cc_final: 0.5327 (m-10) REVERT: g 270 MET cc_start: 0.5762 (ppp) cc_final: 0.5532 (ppp) REVERT: g 290 GLN cc_start: 0.6179 (tp40) cc_final: 0.5854 (tp-100) REVERT: g 300 LEU cc_start: 0.7462 (tt) cc_final: 0.6240 (mt) REVERT: g 303 GLN cc_start: 0.6656 (mt0) cc_final: 0.6454 (mt0) outliers start: 117 outliers final: 86 residues processed: 657 average time/residue: 0.1964 time to fit residues: 201.9432 Evaluate side-chains 624 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 534 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 252 TYR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 66 GLN Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 420 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 484 THR Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 109 GLU Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 103 LEU Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 165 ASN Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 231 LEU Chi-restraints excluded: chain g residue 258 THR Chi-restraints excluded: chain g residue 355 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 129 optimal weight: 3.9990 chunk 296 optimal weight: 2.9990 chunk 163 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 223 optimal weight: 0.5980 chunk 222 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 185 optimal weight: 0.0040 chunk 187 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN C 148 GLN C 372 GLN D 66 GLN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 GLN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 ASN d 141 HIS ** g 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 286 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.150885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.133610 restraints weight = 45235.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.135666 restraints weight = 27319.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136953 restraints weight = 18578.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137887 restraints weight = 13931.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138414 restraints weight = 11367.202| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27897 Z= 0.141 Angle : 0.645 19.681 37815 Z= 0.322 Chirality : 0.044 0.218 4448 Planarity : 0.004 0.053 4910 Dihedral : 6.539 134.027 3918 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.69 % Favored : 94.28 % Rotamer: Outliers : 4.29 % Allowed : 19.46 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.13), residues: 3551 helix: 0.18 (0.13), residues: 1472 sheet: -2.30 (0.21), residues: 511 loop : -1.95 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG g 45 TYR 0.019 0.001 TYR F 475 PHE 0.022 0.001 PHE D 149 TRP 0.002 0.000 TRP e 57 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (27897) covalent geometry : angle 0.64451 / 0.32 (37815) hydrogen bonds : bond 0.03891 / 2.60 ( 1236) hydrogen bonds : angle 4.96870 / 3.43 ( 3657) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 555 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.5947 (mp0) cc_final: 0.5651 (pm20) REVERT: A 166 GLU cc_start: 0.7654 (tp30) cc_final: 0.6985 (tp30) REVERT: A 171 ASP cc_start: 0.7863 (t0) cc_final: 0.7459 (t0) REVERT: A 199 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7128 (mt) REVERT: A 385 LEU cc_start: 0.7263 (tt) cc_final: 0.6933 (tt) REVERT: A 389 GLN cc_start: 0.7120 (mt0) cc_final: 0.6132 (tm-30) REVERT: A 450 GLU cc_start: 0.5663 (tp30) cc_final: 0.4794 (tm-30) REVERT: B 122 ILE cc_start: 0.8261 (mm) cc_final: 0.7853 (mm) REVERT: B 314 MET cc_start: 0.7465 (ttt) cc_final: 0.7000 (tmm) REVERT: B 410 GLN cc_start: 0.6554 (tp40) cc_final: 0.6316 (tp40) REVERT: C 266 LYS cc_start: 0.7603 (mmmt) cc_final: 0.7031 (tptp) REVERT: C 269 GLN cc_start: 0.7655 (mp-120) cc_final: 0.7338 (mp10) REVERT: C 321 GLU cc_start: 0.6836 (tm-30) cc_final: 0.6575 (tm-30) REVERT: C 433 GLU cc_start: 0.7485 (mp0) cc_final: 0.6822 (mp0) REVERT: D 66 GLN cc_start: 0.7760 (mm110) cc_final: 0.7347 (mm110) REVERT: D 247 MET cc_start: 0.6303 (ttp) cc_final: 0.6026 (ttm) REVERT: D 277 ARG cc_start: 0.6652 (mmt180) cc_final: 0.6408 (mmt180) REVERT: D 299 GLN cc_start: 0.8358 (pm20) cc_final: 0.8055 (pm20) REVERT: D 310 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7597 (mm-40) REVERT: D 392 LYS cc_start: 0.8374 (mttm) cc_final: 0.8101 (mtpt) REVERT: E 145 LYS cc_start: 0.6372 (tptp) cc_final: 0.5694 (ttpp) REVERT: E 167 LYS cc_start: 0.8160 (mtmm) cc_final: 0.7657 (mtmm) REVERT: E 214 MET cc_start: 0.6726 (mmt) cc_final: 0.5866 (mtt) REVERT: E 273 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7930 (t0) REVERT: E 306 MET cc_start: 0.7598 (tpp) cc_final: 0.7172 (tpp) REVERT: E 397 ARG cc_start: 0.8058 (tpt90) cc_final: 0.7839 (tpt170) REVERT: E 448 TYR cc_start: 0.7411 (t80) cc_final: 0.7176 (t80) REVERT: F 298 TYR cc_start: 0.7331 (m-80) cc_final: 0.6888 (m-80) REVERT: F 306 MET cc_start: 0.7795 (tpp) cc_final: 0.7383 (tpt) REVERT: F 398 TYR cc_start: 0.8301 (t80) cc_final: 0.8000 (t80) REVERT: F 425 ARG cc_start: 0.7187 (mmm-85) cc_final: 0.6704 (mmm160) REVERT: F 488 MET cc_start: 0.6106 (tmm) cc_final: 0.5773 (tmm) REVERT: d 78 TYR cc_start: 0.6690 (m-80) cc_final: 0.6092 (m-80) REVERT: d 82 LEU cc_start: 0.6150 (OUTLIER) cc_final: 0.5544 (mt) REVERT: d 176 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6365 (mm-30) REVERT: d 231 LYS cc_start: 0.5841 (mttt) cc_final: 0.5604 (mtpp) REVERT: e 1 MET cc_start: 0.2755 (tmm) cc_final: 0.2510 (tmm) REVERT: e 35 PRO cc_start: 0.4433 (Cg_exo) cc_final: 0.3959 (Cg_endo) REVERT: g 73 ARG cc_start: 0.6832 (tpm170) cc_final: 0.6234 (tpm170) REVERT: g 76 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7242 (tm-30) REVERT: g 123 VAL cc_start: 0.6499 (t) cc_final: 0.6187 (t) REVERT: g 270 MET cc_start: 0.5718 (ppp) cc_final: 0.5476 (ppp) REVERT: g 290 GLN cc_start: 0.6199 (tp40) cc_final: 0.5887 (tp-100) REVERT: g 300 LEU cc_start: 0.7482 (tt) cc_final: 0.6226 (mt) outliers start: 126 outliers final: 85 residues processed: 633 average time/residue: 0.1954 time to fit residues: 193.8621 Evaluate side-chains 608 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 519 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 252 TYR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 354 ARG Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 484 THR Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 109 GLU Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 13 SER Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 103 LEU Chi-restraints excluded: chain g residue 76 GLN Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 165 ASN Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 231 LEU Chi-restraints excluded: chain g residue 258 THR Chi-restraints excluded: chain g residue 355 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 235 optimal weight: 0.6980 chunk 147 optimal weight: 0.6980 chunk 76 optimal weight: 0.1980 chunk 182 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 288 optimal weight: 0.0970 chunk 132 optimal weight: 0.6980 chunk 333 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 173 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 GLN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.151038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.133789 restraints weight = 45449.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135943 restraints weight = 27219.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.136808 restraints weight = 18764.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137712 restraints weight = 14023.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138121 restraints weight = 11469.072| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27897 Z= 0.119 Angle : 0.626 19.554 37815 Z= 0.310 Chirality : 0.043 0.212 4448 Planarity : 0.004 0.050 4910 Dihedral : 6.291 127.573 3918 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.18 % Favored : 94.79 % Rotamer: Outliers : 4.08 % Allowed : 20.82 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.42 (0.14), residues: 3551 helix: 0.42 (0.13), residues: 1474 sheet: -2.11 (0.21), residues: 515 loop : -1.83 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 291 TYR 0.020 0.001 TYR F 475 PHE 0.021 0.001 PHE D 149 TRP 0.002 0.000 TRP e 57 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (27897) covalent geometry : angle 0.62613 / 0.31 (37815) hydrogen bonds : bond 0.03626 / 2.44 ( 1236) hydrogen bonds : angle 4.79583 / 3.32 ( 3657) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 571 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7673 (tp30) cc_final: 0.7190 (tp30) REVERT: A 171 ASP cc_start: 0.7817 (t0) cc_final: 0.7440 (t0) REVERT: A 199 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7101 (mt) REVERT: A 385 LEU cc_start: 0.7277 (tt) cc_final: 0.6959 (tt) REVERT: A 389 GLN cc_start: 0.7284 (mt0) cc_final: 0.6044 (tm-30) REVERT: A 450 GLU cc_start: 0.5746 (tp30) cc_final: 0.4871 (tm-30) REVERT: B 122 ILE cc_start: 0.8188 (mm) cc_final: 0.7831 (mm) REVERT: B 188 GLN cc_start: 0.7078 (pt0) cc_final: 0.6776 (mt0) REVERT: B 314 MET cc_start: 0.7506 (ttt) cc_final: 0.7045 (tmm) REVERT: B 498 MET cc_start: 0.7718 (tpp) cc_final: 0.7500 (tpp) REVERT: C 49 MET cc_start: 0.6352 (tpt) cc_final: 0.5951 (tpt) REVERT: C 269 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7093 (mp10) REVERT: C 321 GLU cc_start: 0.6819 (tm-30) cc_final: 0.6533 (tm-30) REVERT: C 336 ILE cc_start: 0.8213 (mt) cc_final: 0.7954 (mt) REVERT: D 66 GLN cc_start: 0.7719 (mm110) cc_final: 0.7327 (mm110) REVERT: D 277 ARG cc_start: 0.6713 (mmt180) cc_final: 0.6467 (mmt180) REVERT: D 310 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7568 (mm-40) REVERT: D 428 GLU cc_start: 0.7650 (tt0) cc_final: 0.7331 (tt0) REVERT: E 40 MET cc_start: 0.6069 (tpp) cc_final: 0.5860 (mmt) REVERT: E 145 LYS cc_start: 0.6391 (tptp) cc_final: 0.5725 (ttpp) REVERT: E 167 LYS cc_start: 0.8128 (mtmm) cc_final: 0.7683 (mtmm) REVERT: E 267 ASP cc_start: 0.6687 (t0) cc_final: 0.6462 (t70) REVERT: E 273 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7892 (t0) REVERT: E 277 ARG cc_start: 0.6867 (mmt-90) cc_final: 0.6346 (mmt-90) REVERT: E 306 MET cc_start: 0.7640 (tpp) cc_final: 0.7179 (tpp) REVERT: E 343 PHE cc_start: 0.7294 (m-80) cc_final: 0.7032 (m-80) REVERT: E 397 ARG cc_start: 0.8046 (tpt90) cc_final: 0.7817 (tpt170) REVERT: E 448 TYR cc_start: 0.7405 (t80) cc_final: 0.7139 (t80) REVERT: F 298 TYR cc_start: 0.7325 (m-80) cc_final: 0.6905 (m-80) REVERT: F 306 MET cc_start: 0.7839 (tpp) cc_final: 0.7413 (tpt) REVERT: F 398 TYR cc_start: 0.8295 (t80) cc_final: 0.7978 (t80) REVERT: F 425 ARG cc_start: 0.7256 (mmm-85) cc_final: 0.6759 (mmm160) REVERT: F 488 MET cc_start: 0.6232 (tmm) cc_final: 0.5858 (tmm) REVERT: d 78 TYR cc_start: 0.6634 (m-80) cc_final: 0.6090 (m-80) REVERT: d 82 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5816 (mt) REVERT: d 176 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6219 (mm-30) REVERT: d 231 LYS cc_start: 0.5699 (mttt) cc_final: 0.5485 (mtpp) REVERT: e 23 ILE cc_start: 0.2219 (mm) cc_final: 0.1862 (mm) REVERT: e 35 PRO cc_start: 0.4350 (Cg_exo) cc_final: 0.3906 (Cg_endo) REVERT: e 63 MET cc_start: 0.5639 (tmm) cc_final: 0.5327 (tmm) REVERT: g 73 ARG cc_start: 0.6591 (tpm170) cc_final: 0.6065 (tpm170) REVERT: g 76 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: g 123 VAL cc_start: 0.6450 (t) cc_final: 0.6099 (t) REVERT: g 270 MET cc_start: 0.5719 (ppp) cc_final: 0.5435 (ppp) REVERT: g 290 GLN cc_start: 0.6270 (tp40) cc_final: 0.5911 (tp-100) REVERT: g 300 LEU cc_start: 0.7384 (tt) cc_final: 0.6071 (mt) REVERT: g 303 GLN cc_start: 0.6520 (mt0) cc_final: 0.6135 (mt0) outliers start: 120 outliers final: 85 residues processed: 644 average time/residue: 0.1971 time to fit residues: 199.0251 Evaluate side-chains 620 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 530 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 252 TYR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 247 MET Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 354 ARG Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 138 LEU Chi-restraints excluded: chain d residue 161 ILE Chi-restraints excluded: chain d residue 180 VAL Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 13 SER Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 103 LEU Chi-restraints excluded: chain g residue 64 MET Chi-restraints excluded: chain g residue 76 GLN Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 165 ASN Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 231 LEU Chi-restraints excluded: chain g residue 258 THR Chi-restraints excluded: chain g residue 355 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 258 optimal weight: 0.7980 chunk 143 optimal weight: 0.2980 chunk 287 optimal weight: 0.5980 chunk 148 optimal weight: 0.8980 chunk 309 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 195 optimal weight: 0.0770 chunk 209 optimal weight: 5.9990 chunk 261 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 173 GLN B 66 ASN B 497 GLN D 67 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.152809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136106 restraints weight = 45352.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137224 restraints weight = 31630.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138695 restraints weight = 23207.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.139187 restraints weight = 17360.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.139399 restraints weight = 14148.118| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27897 Z= 0.124 Angle : 0.628 19.495 37815 Z= 0.312 Chirality : 0.044 0.335 4448 Planarity : 0.004 0.050 4910 Dihedral : 6.184 122.752 3918 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.46 % Favored : 94.51 % Rotamer: Outliers : 3.98 % Allowed : 22.01 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.24 (0.14), residues: 3551 helix: 0.57 (0.14), residues: 1473 sheet: -2.10 (0.21), residues: 512 loop : -1.70 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 456 TYR 0.022 0.001 TYR F 475 PHE 0.026 0.001 PHE B 390 TRP 0.003 0.000 TRP e 57 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (27897) covalent geometry : angle 0.62758 / 0.31 (37815) hydrogen bonds : bond 0.03591 / 2.41 ( 1236) hydrogen bonds : angle 4.71005 / 3.27 ( 3657) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 558 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.5804 (tmm160) cc_final: 0.5546 (tmm160) REVERT: A 171 ASP cc_start: 0.7859 (t0) cc_final: 0.7473 (t0) REVERT: A 199 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7075 (mt) REVERT: A 385 LEU cc_start: 0.7192 (tt) cc_final: 0.6854 (tt) REVERT: A 389 GLN cc_start: 0.7273 (mt0) cc_final: 0.6092 (tm-30) REVERT: A 450 GLU cc_start: 0.5809 (tp30) cc_final: 0.4942 (tm-30) REVERT: B 17 ILE cc_start: 0.6583 (OUTLIER) cc_final: 0.6382 (tt) REVERT: B 122 ILE cc_start: 0.8218 (mm) cc_final: 0.7880 (mm) REVERT: B 188 GLN cc_start: 0.7161 (pt0) cc_final: 0.6870 (mt0) REVERT: C 49 MET cc_start: 0.6491 (tpt) cc_final: 0.6163 (tpt) REVERT: C 75 VAL cc_start: 0.7822 (t) cc_final: 0.7525 (p) REVERT: C 266 LYS cc_start: 0.7558 (mmmt) cc_final: 0.6860 (tptp) REVERT: C 269 GLN cc_start: 0.7628 (mp-120) cc_final: 0.7015 (mp10) REVERT: C 321 GLU cc_start: 0.6752 (tm-30) cc_final: 0.6478 (tm-30) REVERT: C 336 ILE cc_start: 0.8208 (mt) cc_final: 0.7907 (mt) REVERT: D 66 GLN cc_start: 0.7601 (mm110) cc_final: 0.7220 (mm110) REVERT: D 208 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5990 (tp30) REVERT: D 277 ARG cc_start: 0.6733 (mmt180) cc_final: 0.6492 (mmt180) REVERT: D 284 GLU cc_start: 0.7207 (tt0) cc_final: 0.6829 (mt-10) REVERT: D 310 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7520 (mm-40) REVERT: D 374 MET cc_start: 0.6594 (mmt) cc_final: 0.6002 (mmt) REVERT: E 145 LYS cc_start: 0.6301 (tptp) cc_final: 0.5671 (ttpp) REVERT: E 167 LYS cc_start: 0.8166 (mtmm) cc_final: 0.7726 (mtmm) REVERT: E 168 ILE cc_start: 0.8931 (mm) cc_final: 0.8625 (mt) REVERT: E 231 LYS cc_start: 0.7278 (ptmt) cc_final: 0.7009 (pttt) REVERT: E 267 ASP cc_start: 0.7006 (t0) cc_final: 0.6590 (t70) REVERT: E 273 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7930 (t0) REVERT: E 277 ARG cc_start: 0.6905 (mmt-90) cc_final: 0.6413 (mmt-90) REVERT: E 306 MET cc_start: 0.7630 (tpp) cc_final: 0.7189 (tpp) REVERT: E 343 PHE cc_start: 0.7255 (m-80) cc_final: 0.6982 (m-80) REVERT: E 397 ARG cc_start: 0.8042 (tpt90) cc_final: 0.7774 (tpt170) REVERT: F 298 TYR cc_start: 0.7295 (m-80) cc_final: 0.6891 (m-80) REVERT: F 306 MET cc_start: 0.7909 (tpp) cc_final: 0.7437 (tpt) REVERT: F 398 TYR cc_start: 0.8298 (t80) cc_final: 0.7983 (t80) REVERT: F 425 ARG cc_start: 0.7181 (mmm-85) cc_final: 0.6676 (mmm160) REVERT: F 475 TYR cc_start: 0.6886 (t80) cc_final: 0.6636 (t80) REVERT: F 488 MET cc_start: 0.6102 (tmm) cc_final: 0.5703 (tmm) REVERT: d 78 TYR cc_start: 0.6526 (m-80) cc_final: 0.6097 (m-80) REVERT: d 82 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5627 (mt) REVERT: d 130 ASP cc_start: 0.6441 (OUTLIER) cc_final: 0.6074 (m-30) REVERT: d 176 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6324 (mm-30) REVERT: e 35 PRO cc_start: 0.4285 (Cg_exo) cc_final: 0.3845 (Cg_endo) REVERT: g 73 ARG cc_start: 0.6768 (tpm170) cc_final: 0.6222 (tpm170) REVERT: g 76 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: g 123 VAL cc_start: 0.6485 (t) cc_final: 0.6138 (t) REVERT: g 270 MET cc_start: 0.5689 (ppp) cc_final: 0.5450 (ppp) REVERT: g 290 GLN cc_start: 0.6248 (tp40) cc_final: 0.5965 (tp-100) REVERT: g 300 LEU cc_start: 0.7505 (tt) cc_final: 0.6311 (mt) outliers start: 117 outliers final: 88 residues processed: 630 average time/residue: 0.1980 time to fit residues: 195.5990 Evaluate side-chains 623 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 528 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 130 ASP Chi-restraints excluded: chain d residue 180 VAL Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 103 LEU Chi-restraints excluded: chain g residue 64 MET Chi-restraints excluded: chain g residue 76 GLN Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 165 ASN Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 231 LEU Chi-restraints excluded: chain g residue 258 THR Chi-restraints excluded: chain g residue 355 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 58 optimal weight: 4.9990 chunk 326 optimal weight: 0.5980 chunk 241 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 335 optimal weight: 0.9990 chunk 279 optimal weight: 1.9990 chunk 232 optimal weight: 0.6980 chunk 341 optimal weight: 0.9980 chunk 35 optimal weight: 0.0770 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN C 256 HIS D 67 GLN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.151801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135124 restraints weight = 45296.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.136372 restraints weight = 31354.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137782 restraints weight = 24274.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138324 restraints weight = 17262.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.138674 restraints weight = 13567.661| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27897 Z= 0.148 Angle : 0.647 19.474 37815 Z= 0.320 Chirality : 0.044 0.223 4448 Planarity : 0.004 0.051 4910 Dihedral : 6.224 121.225 3918 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.91 % Favored : 94.06 % Rotamer: Outliers : 4.15 % Allowed : 22.90 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.23 (0.14), residues: 3551 helix: 0.56 (0.14), residues: 1477 sheet: -2.10 (0.21), residues: 519 loop : -1.67 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 16 TYR 0.023 0.002 TYR C 237 PHE 0.023 0.001 PHE D 149 TRP 0.002 0.001 TRP e 57 HIS 0.003 0.001 HIS F 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (27897) covalent geometry : angle 0.64668 / 0.32 (37815) hydrogen bonds : bond 0.03740 / 2.51 ( 1236) hydrogen bonds : angle 4.73840 / 3.28 ( 3657) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 547 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.5887 (tmm160) cc_final: 0.5656 (tmm160) REVERT: A 166 GLU cc_start: 0.7699 (tp30) cc_final: 0.6995 (tp30) REVERT: A 171 ASP cc_start: 0.7912 (t0) cc_final: 0.7539 (t0) REVERT: A 199 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7129 (mt) REVERT: A 385 LEU cc_start: 0.7257 (tt) cc_final: 0.6966 (tt) REVERT: A 389 GLN cc_start: 0.7222 (mt0) cc_final: 0.6091 (tm-30) REVERT: A 450 GLU cc_start: 0.5799 (tp30) cc_final: 0.4890 (tm-30) REVERT: B 17 ILE cc_start: 0.6639 (OUTLIER) cc_final: 0.6415 (tt) REVERT: B 188 GLN cc_start: 0.7258 (pt0) cc_final: 0.6994 (mt0) REVERT: B 314 MET cc_start: 0.7543 (ttt) cc_final: 0.7138 (tmm) REVERT: C 49 MET cc_start: 0.6420 (tpt) cc_final: 0.6141 (tpt) REVERT: C 266 LYS cc_start: 0.7536 (mmmt) cc_final: 0.6874 (tptp) REVERT: C 269 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7086 (mp10) REVERT: C 321 GLU cc_start: 0.6609 (tm-30) cc_final: 0.6359 (tm-30) REVERT: C 336 ILE cc_start: 0.8225 (mt) cc_final: 0.7958 (mt) REVERT: D 66 GLN cc_start: 0.7577 (mm110) cc_final: 0.7261 (mm110) REVERT: D 208 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.6025 (tp30) REVERT: D 284 GLU cc_start: 0.7233 (tt0) cc_final: 0.6978 (mt-10) REVERT: D 310 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7582 (mm-40) REVERT: D 374 MET cc_start: 0.6493 (mmt) cc_final: 0.5892 (mmt) REVERT: E 145 LYS cc_start: 0.6358 (tptp) cc_final: 0.5688 (ttpp) REVERT: E 167 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7738 (mtmm) REVERT: E 231 LYS cc_start: 0.7270 (ptmt) cc_final: 0.6998 (pttt) REVERT: E 267 ASP cc_start: 0.7074 (t0) cc_final: 0.6795 (t70) REVERT: E 273 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7916 (t0) REVERT: E 277 ARG cc_start: 0.7063 (mmt-90) cc_final: 0.6522 (mmt-90) REVERT: E 306 MET cc_start: 0.7665 (tpp) cc_final: 0.7221 (tpp) REVERT: E 343 PHE cc_start: 0.7142 (m-80) cc_final: 0.6863 (m-80) REVERT: E 397 ARG cc_start: 0.8020 (tpt90) cc_final: 0.7731 (tpt170) REVERT: F 270 LEU cc_start: 0.8630 (tp) cc_final: 0.8175 (mp) REVERT: F 298 TYR cc_start: 0.7291 (m-80) cc_final: 0.6913 (m-80) REVERT: F 306 MET cc_start: 0.7919 (tpp) cc_final: 0.7435 (tpt) REVERT: F 398 TYR cc_start: 0.8292 (t80) cc_final: 0.7849 (t80) REVERT: F 425 ARG cc_start: 0.7201 (mmm-85) cc_final: 0.6784 (mmm160) REVERT: F 462 LEU cc_start: 0.7370 (mt) cc_final: 0.7125 (mt) REVERT: F 488 MET cc_start: 0.6208 (tmm) cc_final: 0.5799 (tmm) REVERT: d 78 TYR cc_start: 0.6596 (m-80) cc_final: 0.6227 (m-80) REVERT: d 82 LEU cc_start: 0.6099 (OUTLIER) cc_final: 0.5712 (mt) REVERT: d 130 ASP cc_start: 0.6431 (OUTLIER) cc_final: 0.5975 (m-30) REVERT: d 176 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6285 (mm-30) REVERT: e 35 PRO cc_start: 0.4306 (Cg_exo) cc_final: 0.3886 (Cg_endo) REVERT: e 63 MET cc_start: 0.5560 (tmm) cc_final: 0.5359 (tmm) REVERT: g 76 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: g 123 VAL cc_start: 0.6436 (t) cc_final: 0.6130 (t) REVERT: g 270 MET cc_start: 0.5698 (ppp) cc_final: 0.5466 (ppp) REVERT: g 290 GLN cc_start: 0.6281 (tp40) cc_final: 0.6005 (tp-100) REVERT: g 300 LEU cc_start: 0.7540 (tt) cc_final: 0.6422 (mt) REVERT: g 312 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7395 (tp) outliers start: 122 outliers final: 93 residues processed: 626 average time/residue: 0.1927 time to fit residues: 189.4392 Evaluate side-chains 625 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 523 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 130 ASP Chi-restraints excluded: chain d residue 180 VAL Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 13 SER Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 103 LEU Chi-restraints excluded: chain g residue 64 MET Chi-restraints excluded: chain g residue 76 GLN Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 165 ASN Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 231 LEU Chi-restraints excluded: chain g residue 258 THR Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 312 LEU Chi-restraints excluded: chain g residue 355 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 216 optimal weight: 0.8980 chunk 346 optimal weight: 3.9990 chunk 335 optimal weight: 0.9990 chunk 299 optimal weight: 0.8980 chunk 302 optimal weight: 0.8980 chunk 244 optimal weight: 0.0870 chunk 65 optimal weight: 0.3980 chunk 281 optimal weight: 0.4980 chunk 49 optimal weight: 5.9990 chunk 71 optimal weight: 0.0770 chunk 33 optimal weight: 0.5980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN D 67 GLN D 310 GLN D 325 GLN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.152944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135856 restraints weight = 45533.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.137694 restraints weight = 32154.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.138563 restraints weight = 22378.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.139232 restraints weight = 17649.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139695 restraints weight = 13945.411| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27897 Z= 0.120 Angle : 0.640 19.393 37815 Z= 0.315 Chirality : 0.043 0.189 4448 Planarity : 0.004 0.055 4910 Dihedral : 6.020 116.485 3918 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.07 % Favored : 94.90 % Rotamer: Outliers : 4.15 % Allowed : 23.21 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.06 (0.14), residues: 3551 helix: 0.69 (0.14), residues: 1482 sheet: -1.97 (0.21), residues: 524 loop : -1.59 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 355 TYR 0.023 0.001 TYR C 237 PHE 0.021 0.001 PHE D 149 TRP 0.002 0.000 TRP e 57 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (27897) covalent geometry : angle 0.63991 / 0.31 (37815) hydrogen bonds : bond 0.03505 / 2.35 ( 1236) hydrogen bonds : angle 4.63428 / 3.21 ( 3657) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 562 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7760 (tp30) cc_final: 0.7094 (tp30) REVERT: A 171 ASP cc_start: 0.7851 (t0) cc_final: 0.7487 (t0) REVERT: A 199 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7072 (mt) REVERT: A 385 LEU cc_start: 0.7209 (tt) cc_final: 0.6914 (tt) REVERT: A 389 GLN cc_start: 0.7200 (mt0) cc_final: 0.6065 (tm-30) REVERT: A 450 GLU cc_start: 0.5864 (tp30) cc_final: 0.5112 (tm-30) REVERT: B 17 ILE cc_start: 0.6594 (OUTLIER) cc_final: 0.6254 (tt) REVERT: B 48 VAL cc_start: 0.7695 (m) cc_final: 0.7464 (p) REVERT: B 122 ILE cc_start: 0.8265 (mm) cc_final: 0.7933 (mm) REVERT: B 188 GLN cc_start: 0.7213 (pt0) cc_final: 0.6983 (mt0) REVERT: B 290 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7276 (p0) REVERT: B 314 MET cc_start: 0.7507 (ttt) cc_final: 0.7198 (tmm) REVERT: C 49 MET cc_start: 0.6423 (tpt) cc_final: 0.6124 (tpt) REVERT: C 75 VAL cc_start: 0.7895 (t) cc_final: 0.7567 (p) REVERT: C 171 ASP cc_start: 0.6894 (m-30) cc_final: 0.6577 (m-30) REVERT: C 266 LYS cc_start: 0.7518 (mmmt) cc_final: 0.6825 (tptp) REVERT: C 269 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7040 (mp10) REVERT: C 321 GLU cc_start: 0.6556 (tm-30) cc_final: 0.6280 (tm-30) REVERT: D 66 GLN cc_start: 0.7440 (mm110) cc_final: 0.7172 (mm110) REVERT: D 284 GLU cc_start: 0.7044 (tt0) cc_final: 0.6767 (mt-10) REVERT: D 374 MET cc_start: 0.6357 (mmt) cc_final: 0.5822 (mmt) REVERT: E 145 LYS cc_start: 0.6360 (tptp) cc_final: 0.5683 (ttpp) REVERT: E 167 LYS cc_start: 0.8161 (mtmm) cc_final: 0.7740 (mtmm) REVERT: E 267 ASP cc_start: 0.7032 (t0) cc_final: 0.6822 (t70) REVERT: E 273 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7851 (t0) REVERT: E 277 ARG cc_start: 0.7060 (mmt-90) cc_final: 0.6531 (mmt-90) REVERT: E 306 MET cc_start: 0.7696 (tpp) cc_final: 0.7278 (tpp) REVERT: E 309 LEU cc_start: 0.7986 (mt) cc_final: 0.7725 (mt) REVERT: E 397 ARG cc_start: 0.8024 (tpt90) cc_final: 0.7716 (tpt170) REVERT: F 270 LEU cc_start: 0.8591 (tp) cc_final: 0.8175 (mp) REVERT: F 298 TYR cc_start: 0.7252 (m-80) cc_final: 0.6915 (m-80) REVERT: F 306 MET cc_start: 0.7876 (tpp) cc_final: 0.7477 (tpt) REVERT: F 398 TYR cc_start: 0.8277 (t80) cc_final: 0.7848 (t80) REVERT: F 425 ARG cc_start: 0.7147 (mmm-85) cc_final: 0.6754 (mmm160) REVERT: F 462 LEU cc_start: 0.7378 (mt) cc_final: 0.7137 (mt) REVERT: F 488 MET cc_start: 0.6229 (tmm) cc_final: 0.5874 (tmm) REVERT: d 78 TYR cc_start: 0.6587 (m-80) cc_final: 0.6179 (m-80) REVERT: d 82 LEU cc_start: 0.6106 (OUTLIER) cc_final: 0.5733 (mt) REVERT: d 130 ASP cc_start: 0.6366 (OUTLIER) cc_final: 0.5963 (m-30) REVERT: e 35 PRO cc_start: 0.4297 (Cg_exo) cc_final: 0.3869 (Cg_endo) REVERT: e 63 MET cc_start: 0.5613 (tmm) cc_final: 0.5282 (tmm) REVERT: g 73 ARG cc_start: 0.6684 (tpm170) cc_final: 0.6146 (tpm170) REVERT: g 76 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: g 123 VAL cc_start: 0.6479 (t) cc_final: 0.6206 (t) REVERT: g 270 MET cc_start: 0.5785 (ppp) cc_final: 0.5556 (ppp) REVERT: g 290 GLN cc_start: 0.6348 (tp40) cc_final: 0.6053 (tp-100) REVERT: g 300 LEU cc_start: 0.7545 (tt) cc_final: 0.6213 (mt) REVERT: g 303 GLN cc_start: 0.6767 (mt0) cc_final: 0.6511 (mt0) outliers start: 122 outliers final: 91 residues processed: 644 average time/residue: 0.1971 time to fit residues: 199.3287 Evaluate side-chains 626 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 527 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 496 GLU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 130 ASP Chi-restraints excluded: chain d residue 180 VAL Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 13 SER Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 103 LEU Chi-restraints excluded: chain g residue 64 MET Chi-restraints excluded: chain g residue 76 GLN Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 165 ASN Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 231 LEU Chi-restraints excluded: chain g residue 258 THR Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 355 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 212 optimal weight: 2.9990 chunk 325 optimal weight: 0.9990 chunk 233 optimal weight: 0.0570 chunk 297 optimal weight: 0.8980 chunk 228 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 350 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 197 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 265 optimal weight: 0.7980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 ASN D 67 GLN D 133 HIS ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 102 ASN ** g 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.153206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136225 restraints weight = 45511.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.138232 restraints weight = 31729.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139315 restraints weight = 20700.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.140685 restraints weight = 15179.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.140717 restraints weight = 12465.884| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27897 Z= 0.130 Angle : 0.658 19.498 37815 Z= 0.326 Chirality : 0.044 0.234 4448 Planarity : 0.004 0.053 4910 Dihedral : 5.990 113.647 3918 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.63 % Favored : 94.34 % Rotamer: Outliers : 3.71 % Allowed : 24.02 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.04 (0.14), residues: 3551 helix: 0.72 (0.14), residues: 1481 sheet: -1.99 (0.21), residues: 537 loop : -1.57 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 279 TYR 0.030 0.001 TYR g 179 PHE 0.033 0.001 PHE B 399 TRP 0.001 0.000 TRP e 57 HIS 0.006 0.001 HIS F 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (27897) covalent geometry : angle 0.65756 / 0.33 (37815) hydrogen bonds : bond 0.03562 / 2.39 ( 1236) hydrogen bonds : angle 4.66685 / 3.22 ( 3657) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 541 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7722 (tp30) cc_final: 0.7075 (tp30) REVERT: A 171 ASP cc_start: 0.7776 (t0) cc_final: 0.7411 (t0) REVERT: A 199 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7206 (mt) REVERT: A 271 TYR cc_start: 0.7371 (t80) cc_final: 0.7127 (t80) REVERT: A 385 LEU cc_start: 0.7244 (tt) cc_final: 0.6975 (tt) REVERT: A 389 GLN cc_start: 0.7251 (mt0) cc_final: 0.6124 (tm-30) REVERT: A 450 GLU cc_start: 0.5883 (tp30) cc_final: 0.5125 (tm-30) REVERT: B 17 ILE cc_start: 0.6562 (OUTLIER) cc_final: 0.6346 (tt) REVERT: B 48 VAL cc_start: 0.7652 (m) cc_final: 0.7442 (p) REVERT: B 122 ILE cc_start: 0.8287 (mm) cc_final: 0.7944 (mm) REVERT: B 314 MET cc_start: 0.7466 (ttt) cc_final: 0.7111 (tmm) REVERT: C 49 MET cc_start: 0.6369 (tpt) cc_final: 0.6088 (tpt) REVERT: C 171 ASP cc_start: 0.6871 (m-30) cc_final: 0.6564 (m-30) REVERT: C 266 LYS cc_start: 0.7535 (mmmt) cc_final: 0.6846 (tptp) REVERT: C 269 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7065 (mp10) REVERT: C 321 GLU cc_start: 0.6541 (tm-30) cc_final: 0.6254 (tm-30) REVERT: D 66 GLN cc_start: 0.7518 (mm110) cc_final: 0.7192 (mm110) REVERT: D 284 GLU cc_start: 0.7093 (tt0) cc_final: 0.6698 (mt-10) REVERT: D 374 MET cc_start: 0.6318 (mmt) cc_final: 0.5800 (mmt) REVERT: D 392 LYS cc_start: 0.8465 (mmtp) cc_final: 0.8195 (mmmm) REVERT: E 145 LYS cc_start: 0.6315 (tptp) cc_final: 0.5640 (ttpp) REVERT: E 167 LYS cc_start: 0.8199 (mtmm) cc_final: 0.7772 (mtmm) REVERT: E 231 LYS cc_start: 0.7244 (ptmt) cc_final: 0.6962 (pttt) REVERT: E 277 ARG cc_start: 0.7044 (mmt-90) cc_final: 0.6500 (mmt-90) REVERT: E 309 LEU cc_start: 0.8018 (mt) cc_final: 0.7724 (mt) REVERT: E 397 ARG cc_start: 0.8005 (tpt90) cc_final: 0.7721 (tpt170) REVERT: F 270 LEU cc_start: 0.8592 (tp) cc_final: 0.8173 (mp) REVERT: F 298 TYR cc_start: 0.7262 (m-80) cc_final: 0.6892 (m-80) REVERT: F 306 MET cc_start: 0.7815 (tpp) cc_final: 0.7247 (tpt) REVERT: F 398 TYR cc_start: 0.8283 (t80) cc_final: 0.7854 (t80) REVERT: F 425 ARG cc_start: 0.7176 (mmm-85) cc_final: 0.6792 (mmm160) REVERT: F 462 LEU cc_start: 0.7375 (mt) cc_final: 0.7105 (mt) REVERT: F 488 MET cc_start: 0.6266 (tmm) cc_final: 0.5881 (tmm) REVERT: d 78 TYR cc_start: 0.6574 (m-80) cc_final: 0.6272 (m-80) REVERT: d 82 LEU cc_start: 0.6081 (OUTLIER) cc_final: 0.5728 (mt) REVERT: d 130 ASP cc_start: 0.6400 (OUTLIER) cc_final: 0.5981 (m-30) REVERT: g 270 MET cc_start: 0.5847 (ppp) cc_final: 0.5615 (ppp) REVERT: g 290 GLN cc_start: 0.6462 (tp40) cc_final: 0.6187 (tp-100) REVERT: g 300 LEU cc_start: 0.7545 (tt) cc_final: 0.6185 (mt) REVERT: g 303 GLN cc_start: 0.6844 (mt0) cc_final: 0.6571 (mt0) outliers start: 109 outliers final: 88 residues processed: 611 average time/residue: 0.1979 time to fit residues: 189.7543 Evaluate side-chains 613 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 520 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 496 GLU Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 130 ASP Chi-restraints excluded: chain d residue 180 VAL Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 165 ASN Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 231 LEU Chi-restraints excluded: chain g residue 258 THR Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 355 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 296 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 263 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 139 optimal weight: 0.1980 chunk 307 optimal weight: 0.9990 chunk 91 optimal weight: 0.0050 chunk 4 optimal weight: 0.9980 chunk 290 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN D 67 GLN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 HIS ** g 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.152671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.135953 restraints weight = 45547.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137194 restraints weight = 30668.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138304 restraints weight = 22318.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139361 restraints weight = 15848.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139365 restraints weight = 12949.661| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 27897 Z= 0.140 Angle : 0.678 19.466 37815 Z= 0.335 Chirality : 0.045 0.245 4448 Planarity : 0.004 0.053 4910 Dihedral : 5.976 111.312 3918 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.52 % Favored : 94.45 % Rotamer: Outliers : 3.44 % Allowed : 24.36 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.02 (0.14), residues: 3551 helix: 0.74 (0.14), residues: 1478 sheet: -2.00 (0.21), residues: 535 loop : -1.54 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG d 77 TYR 0.032 0.002 TYR E 162 PHE 0.031 0.001 PHE B 390 TRP 0.002 0.000 TRP e 15 HIS 0.003 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (27897) covalent geometry : angle 0.67849 / 0.33 (37815) hydrogen bonds : bond 0.03633 / 2.44 ( 1236) hydrogen bonds : angle 4.68040 / 3.23 ( 3657) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 534 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.6597 (mmm) cc_final: 0.5847 (tpp) REVERT: A 166 GLU cc_start: 0.7735 (tp30) cc_final: 0.7080 (tp30) REVERT: A 171 ASP cc_start: 0.7790 (t0) cc_final: 0.7437 (t0) REVERT: A 199 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7192 (mt) REVERT: A 385 LEU cc_start: 0.7213 (tt) cc_final: 0.6930 (tt) REVERT: A 389 GLN cc_start: 0.7271 (mt0) cc_final: 0.6137 (tm-30) REVERT: A 450 GLU cc_start: 0.5857 (tp30) cc_final: 0.5149 (tm-30) REVERT: B 17 ILE cc_start: 0.6493 (OUTLIER) cc_final: 0.6282 (tt) REVERT: B 122 ILE cc_start: 0.8259 (mm) cc_final: 0.7896 (mm) REVERT: B 188 GLN cc_start: 0.6901 (mt0) cc_final: 0.6555 (mt0) REVERT: B 314 MET cc_start: 0.7464 (ttt) cc_final: 0.7131 (tmm) REVERT: C 49 MET cc_start: 0.6334 (tpt) cc_final: 0.6116 (tpt) REVERT: C 171 ASP cc_start: 0.6845 (m-30) cc_final: 0.6544 (m-30) REVERT: C 266 LYS cc_start: 0.7518 (mmmt) cc_final: 0.6843 (tptp) REVERT: C 269 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7091 (mp10) REVERT: C 321 GLU cc_start: 0.6502 (tm-30) cc_final: 0.6259 (tm-30) REVERT: D 66 GLN cc_start: 0.7520 (mm110) cc_final: 0.7219 (mm110) REVERT: D 71 ASN cc_start: 0.6492 (p0) cc_final: 0.6188 (p0) REVERT: D 284 GLU cc_start: 0.7147 (tt0) cc_final: 0.6798 (mt-10) REVERT: D 374 MET cc_start: 0.6328 (mmt) cc_final: 0.5804 (mmt) REVERT: D 392 LYS cc_start: 0.8484 (mmtp) cc_final: 0.8182 (mmmm) REVERT: E 145 LYS cc_start: 0.6302 (tptp) cc_final: 0.5640 (ttpp) REVERT: E 167 LYS cc_start: 0.8215 (mtmm) cc_final: 0.7753 (mtmm) REVERT: E 231 LYS cc_start: 0.7297 (ptmt) cc_final: 0.7026 (pttt) REVERT: E 277 ARG cc_start: 0.7022 (mmt-90) cc_final: 0.6518 (mmt-90) REVERT: E 309 LEU cc_start: 0.8041 (mt) cc_final: 0.7697 (mt) REVERT: E 397 ARG cc_start: 0.8019 (tpt90) cc_final: 0.7713 (tpt170) REVERT: F 270 LEU cc_start: 0.8562 (tp) cc_final: 0.8182 (mp) REVERT: F 298 TYR cc_start: 0.7256 (m-80) cc_final: 0.6894 (m-80) REVERT: F 306 MET cc_start: 0.7773 (tpp) cc_final: 0.7357 (tpt) REVERT: F 398 TYR cc_start: 0.8323 (t80) cc_final: 0.7846 (t80) REVERT: F 425 ARG cc_start: 0.7196 (mmm-85) cc_final: 0.6802 (mmm160) REVERT: F 462 LEU cc_start: 0.7391 (mt) cc_final: 0.7125 (mt) REVERT: F 488 MET cc_start: 0.6293 (tmm) cc_final: 0.5888 (tmm) REVERT: d 78 TYR cc_start: 0.6599 (m-80) cc_final: 0.6207 (m-80) REVERT: d 82 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5739 (mt) REVERT: d 130 ASP cc_start: 0.6414 (OUTLIER) cc_final: 0.5990 (m-30) REVERT: d 210 LYS cc_start: 0.7085 (tmtt) cc_final: 0.6811 (tmtt) REVERT: g 144 ARG cc_start: 0.6385 (mmt-90) cc_final: 0.6028 (mmt-90) REVERT: g 270 MET cc_start: 0.5921 (ppp) cc_final: 0.5647 (ppp) REVERT: g 290 GLN cc_start: 0.6299 (tp40) cc_final: 0.6092 (tp-100) REVERT: g 300 LEU cc_start: 0.7556 (tt) cc_final: 0.6195 (mt) REVERT: g 303 GLN cc_start: 0.6849 (mt0) cc_final: 0.6571 (mt0) outliers start: 101 outliers final: 84 residues processed: 605 average time/residue: 0.1951 time to fit residues: 185.8401 Evaluate side-chains 610 residues out of total 2939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 521 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 496 GLU Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 130 ASP Chi-restraints excluded: chain d residue 180 VAL Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 165 ASN Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 258 THR Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 355 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 107 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 chunk 255 optimal weight: 0.0270 chunk 159 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 242 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 76 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 324 optimal weight: 0.5980 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN D 42 ASN D 67 GLN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 135 ASN ** g 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.153902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136759 restraints weight = 45199.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.138914 restraints weight = 33150.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.140262 restraints weight = 22078.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140578 restraints weight = 14105.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.141124 restraints weight = 13145.419| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 27897 Z= 0.125 Angle : 0.673 19.441 37815 Z= 0.331 Chirality : 0.044 0.181 4448 Planarity : 0.004 0.053 4910 Dihedral : 5.895 106.736 3918 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.46 % Favored : 94.51 % Rotamer: Outliers : 3.23 % Allowed : 24.77 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.94 (0.14), residues: 3551 helix: 0.80 (0.14), residues: 1480 sheet: -1.90 (0.21), residues: 535 loop : -1.52 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 134 TYR 0.043 0.001 TYR E 162 PHE 0.030 0.001 PHE B 390 TRP 0.003 0.000 TRP e 15 HIS 0.003 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (27897) covalent geometry : angle 0.67330 / 0.33 (37815) hydrogen bonds : bond 0.03501 / 2.34 ( 1236) hydrogen bonds : angle 4.64829 / 3.22 ( 3657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5082.08 seconds wall clock time: 88 minutes 51.13 seconds (5331.13 seconds total)