Starting phenix.real_space_refine on Thu Mar 5 22:07:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6usf_20863/03_2026/6usf_20863.cif Found real_map, /net/cci-nas-00/data/ceres_data/6usf_20863/03_2026/6usf_20863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6usf_20863/03_2026/6usf_20863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6usf_20863/03_2026/6usf_20863.map" model { file = "/net/cci-nas-00/data/ceres_data/6usf_20863/03_2026/6usf_20863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6usf_20863/03_2026/6usf_20863.cif" } resolution = 3.87 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 Anisotropic ADP refinement not supported. Converting 3066 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 14903 2.51 5 N 3726 2.21 5 O 4276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23022 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3764 Classifications: {'peptide': 464} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 441} Chain breaks: 2 Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2917 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 337} Chain breaks: 1 Chain: "C" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2908 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 336} Chain breaks: 1 Chain: "D" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3764 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 22, 'TRANS': 441} Chain breaks: 2 Chain: "E" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2908 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 336} Chain breaks: 1 Chain: "H" Number of atoms: 1655 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 205} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 205} Chain breaks: 1 bond proxies already assigned to first conformer: 1689 Chain: "L" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1602 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 198} Chain breaks: 1 Chain: "K" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1700 Classifications: {'peptide': 227} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 213} Chain: "M" Number of atoms: 1627 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1658 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'QMR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'QMR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'BMA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.08, per 1000 atoms: 0.26 Number of scatterers: 23022 At special positions: 0 Unit cell: (214.968, 145.517, 177.486, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 4276 8.00 N 3726 7.00 C 14903 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.05 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 200 " distance=2.65 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.05 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.06 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 199 " - pdb=" SG CYS D 200 " distance=2.05 Simple disulfide: pdb=" SG CYS E 130 " - pdb=" SG CYS E 144 " distance=2.05 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.05 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.46 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS K 25 " - pdb=" SG CYS K 99 " distance=2.04 Simple disulfide: pdb=" SG CYS K 154 " - pdb=" SG CYS K 210 " distance=2.03 Simple disulfide: pdb=" SG CYS M 24 " - pdb=" SG CYS M 89 " distance=2.04 Simple disulfide: pdb=" SG CYS M 136 " - pdb=" SG CYS M 196 " distance=2.07 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 Atom "HETATM22965 O5 NAG B 401 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " BMA F 2 " " NAG F 1 " - " NAG B 401 " " NAG G 1 " - " BMA G 2 " " NAG G 1 " - " NAG C 401 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA E 403 " NAG-ASN " NAG A 501 " - " ASN A 148 " " NAG B 401 " - " ASN B 143 " " NAG C 401 " - " ASN C 143 " " NAG D 501 " - " ASN D 148 " " NAG I 1 " - " ASN E 143 " Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 1.1 seconds 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5498 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 40 sheets defined 28.9% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 removed outlier: 3.820A pdb=" N ALA A 10 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.687A pdb=" N CYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 241 removed outlier: 4.233A pdb=" N VAL A 236 " --> pdb=" O CYS A 233 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU A 237 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL A 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 239 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 267 Processing helix chain 'A' and resid 278 through 306 removed outlier: 3.641A pdb=" N TYR A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 removed outlier: 3.793A pdb=" N VAL A 321 " --> pdb=" O TRP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 355 removed outlier: 4.096A pdb=" N THR A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN A 353 " --> pdb=" O TRP A 349 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 361 removed outlier: 3.724A pdb=" N ILE A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.634A pdb=" N VAL A 368 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 382 removed outlier: 3.589A pdb=" N LEU A 380 " --> pdb=" O ARG A 376 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 407 removed outlier: 3.656A pdb=" N PHE A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 407 " --> pdb=" O PHE A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 413 through 422 removed outlier: 3.720A pdb=" N LYS A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.947A pdb=" N ILE A 444 " --> pdb=" O ASN A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 478 removed outlier: 3.712A pdb=" N VAL A 456 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE A 461 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TRP A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE A 467 " --> pdb=" O TRP A 463 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 468 " --> pdb=" O MET A 464 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 477 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 12 removed outlier: 3.510A pdb=" N LEU B 12 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 removed outlier: 3.518A pdb=" N THR B 213 " --> pdb=" O PRO B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.788A pdb=" N CYS B 237 " --> pdb=" O PRO B 234 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY B 238 " --> pdb=" O SER B 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 234 through 238' Processing helix chain 'B' and resid 240 through 262 Processing helix chain 'B' and resid 270 through 298 removed outlier: 3.557A pdb=" N LYS B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 315 removed outlier: 4.316A pdb=" N LYS B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'B' and resid 337 through 352 removed outlier: 3.679A pdb=" N VAL B 344 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG B 347 " --> pdb=" O MET B 343 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP B 351 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 360 Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 209 through 217 removed outlier: 3.637A pdb=" N THR C 213 " --> pdb=" O PRO C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 239 through 262 removed outlier: 3.840A pdb=" N LEU C 243 " --> pdb=" O GLU C 239 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 298 removed outlier: 4.017A pdb=" N HIS C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.670A pdb=" N ALA C 342 " --> pdb=" O TRP C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 352 removed outlier: 3.798A pdb=" N TRP C 351 " --> pdb=" O ARG C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 removed outlier: 3.602A pdb=" N VAL C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE C 359 " --> pdb=" O PHE C 355 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR C 361 " --> pdb=" O CYS C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 365 Processing helix chain 'D' and resid 6 through 19 removed outlier: 3.924A pdb=" N ALA D 10 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 224 Processing helix chain 'D' and resid 224 through 232 removed outlier: 3.528A pdb=" N CYS D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 247 through 270 removed outlier: 4.198A pdb=" N LEU D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE D 270 " --> pdb=" O ILE D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 306 removed outlier: 3.567A pdb=" N GLU D 282 " --> pdb=" O PRO D 278 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N HIS D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 326 removed outlier: 3.509A pdb=" N VAL D 321 " --> pdb=" O TRP D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 353 removed outlier: 3.595A pdb=" N ASN D 348 " --> pdb=" O ASP D 344 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 351 " --> pdb=" O ASP D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 384 removed outlier: 3.901A pdb=" N ALA D 371 " --> pdb=" O GLN D 367 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA D 379 " --> pdb=" O MET D 375 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP D 381 " --> pdb=" O ALA D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.641A pdb=" N GLU D 391 " --> pdb=" O PRO D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 405 Processing helix chain 'D' and resid 407 through 413 Processing helix chain 'D' and resid 415 through 420 removed outlier: 4.582A pdb=" N LYS D 419 " --> pdb=" O ASP D 415 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 415 through 420' Processing helix chain 'D' and resid 425 through 433 removed outlier: 3.802A pdb=" N ALA D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 442 removed outlier: 3.567A pdb=" N ASN D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 478 removed outlier: 3.685A pdb=" N VAL D 456 " --> pdb=" O TYR D 452 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP D 458 " --> pdb=" O ALA D 454 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE D 460 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE D 461 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 462 " --> pdb=" O ASP D 458 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE D 466 " --> pdb=" O LEU D 462 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE D 467 " --> pdb=" O TRP D 463 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR D 473 " --> pdb=" O CYS D 469 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 478 " --> pdb=" O VAL D 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 209 through 225 removed outlier: 3.714A pdb=" N THR E 213 " --> pdb=" O PRO E 209 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ILE E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Proline residue: E 219 - end of helix Processing helix chain 'E' and resid 234 through 238 removed outlier: 3.654A pdb=" N CYS E 237 " --> pdb=" O PRO E 234 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY E 238 " --> pdb=" O SER E 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 234 through 238' Processing helix chain 'E' and resid 239 through 262 removed outlier: 4.134A pdb=" N LEU E 243 " --> pdb=" O GLU E 239 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL E 262 " --> pdb=" O ILE E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 298 removed outlier: 3.601A pdb=" N LYS E 274 " --> pdb=" O PRO E 270 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 315 Processing helix chain 'E' and resid 317 through 321 Processing helix chain 'E' and resid 340 through 358 removed outlier: 3.649A pdb=" N VAL E 344 " --> pdb=" O TYR E 340 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP E 346 " --> pdb=" O ALA E 342 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG E 347 " --> pdb=" O MET E 343 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TRP E 351 " --> pdb=" O ARG E 347 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE E 352 " --> pdb=" O LEU E 348 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL E 356 " --> pdb=" O ILE E 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.716A pdb=" N TRP H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 172 No H-bonds generated for 'chain 'H' and resid 170 through 172' Processing helix chain 'H' and resid 201 through 203 No H-bonds generated for 'chain 'H' and resid 201 through 203' Processing helix chain 'L' and resid 94 through 98 removed outlier: 4.206A pdb=" N VAL L 98 " --> pdb=" O TYR L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 130 removed outlier: 3.697A pdb=" N SER L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY L 130 " --> pdb=" O GLN L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 190 Processing helix chain 'K' and resid 90 through 94 removed outlier: 3.854A pdb=" N ASP K 93 " --> pdb=" O ARG K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 112 Processing helix chain 'K' and resid 170 through 172 No H-bonds generated for 'chain 'K' and resid 170 through 172' Processing helix chain 'K' and resid 201 through 203 No H-bonds generated for 'chain 'K' and resid 201 through 203' Processing helix chain 'M' and resid 123 through 128 Processing helix chain 'M' and resid 185 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.579A pdb=" N VAL A 166 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 51 removed outlier: 7.330A pdb=" N ALA A 45 " --> pdb=" O TRP A 62 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N TRP A 62 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU A 47 " --> pdb=" O ASN A 60 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ASN A 60 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 49 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 68 removed outlier: 4.529A pdb=" N ARG A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 99 removed outlier: 4.169A pdb=" N SER A 155 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG A 214 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE A 185 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 79 through 83 removed outlier: 3.735A pdb=" N SER B 113 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 79 through 83 removed outlier: 3.735A pdb=" N SER B 113 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN B 55 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU B 42 " --> pdb=" O ASN B 55 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N TRP B 57 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA B 40 " --> pdb=" O TRP B 57 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR B 59 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N SER B 38 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N GLU B 61 " --> pdb=" O MET B 36 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N MET B 36 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N GLU B 63 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N GLN B 34 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL B 31 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL B 161 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 33 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 3.645A pdb=" N ARG B 149 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER B 150 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL B 197 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 182 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG B 206 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE B 180 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 92 through 94 removed outlier: 3.645A pdb=" N ARG B 149 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER B 150 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL B 197 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 79 through 82 removed outlier: 3.583A pdb=" N SER C 113 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 79 through 82 removed outlier: 3.583A pdb=" N SER C 113 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE C 51 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N SER C 44 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASN C 55 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU C 63 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR C 32 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL C 31 " --> pdb=" O ASP C 159 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL C 161 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL C 33 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 4.918A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE C 204 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 92 through 94 removed outlier: 4.918A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.551A pdb=" N ASP D 164 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 44 through 51 removed outlier: 7.330A pdb=" N ALA D 45 " --> pdb=" O TRP D 62 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N TRP D 62 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU D 47 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN D 60 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 65 through 68 Processing sheet with id=AB7, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.379A pdb=" N SER D 155 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TYR D 204 " --> pdb=" O THR D 194 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR D 194 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASP D 206 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR D 192 " --> pdb=" O ASP D 206 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR D 208 " --> pdb=" O GLY D 190 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY D 190 " --> pdb=" O THR D 208 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA D 210 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA D 188 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL D 212 " --> pdb=" O VAL D 186 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 80 through 82 Processing sheet with id=AB9, first strand: chain 'E' and resid 80 through 82 removed outlier: 6.733A pdb=" N ASN E 55 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU E 42 " --> pdb=" O ASN E 55 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N TRP E 57 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ALA E 40 " --> pdb=" O TRP E 57 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR E 59 " --> pdb=" O SER E 38 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER E 38 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N GLU E 61 " --> pdb=" O MET E 36 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N MET E 36 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N GLU E 63 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 9.359A pdb=" N GLN E 34 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL E 31 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL E 161 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL E 33 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 92 through 93 removed outlier: 3.637A pdb=" N ARG E 149 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA E 182 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ARG E 206 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE E 180 " --> pdb=" O ARG E 206 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 92 through 93 removed outlier: 3.637A pdb=" N ARG E 149 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AC4, first strand: chain 'H' and resid 61 through 63 removed outlier: 4.937A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.399A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.399A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER H 191 " --> pdb=" O VAL H 183 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 165 through 168 removed outlier: 4.393A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AC9, first strand: chain 'L' and resid 36 through 38 removed outlier: 6.351A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 85 through 87 Processing sheet with id=AD2, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.233A pdb=" N SER L 133 " --> pdb=" O LEU L 183 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU L 183 " --> pdb=" O SER L 133 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL L 135 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU L 181 " --> pdb=" O VAL L 135 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU L 137 " --> pdb=" O SER L 179 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N SER L 179 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASN L 139 " --> pdb=" O LEU L 177 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU L 177 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 147 through 152 Processing sheet with id=AD4, first strand: chain 'K' and resid 6 through 10 Processing sheet with id=AD5, first strand: chain 'K' and resid 14 through 15 removed outlier: 3.978A pdb=" N VAL K 15 " --> pdb=" O THR K 124 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE K 37 " --> pdb=" O TYR K 53 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR K 53 " --> pdb=" O ILE K 37 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP K 39 " --> pdb=" O VAL K 51 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 134 through 138 removed outlier: 6.206A pdb=" N TYR K 190 " --> pdb=" O ASP K 158 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 134 through 138 removed outlier: 6.206A pdb=" N TYR K 190 " --> pdb=" O ASP K 158 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER K 191 " --> pdb=" O VAL K 183 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL K 183 " --> pdb=" O SER K 191 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 164 through 168 removed outlier: 4.413A pdb=" N TYR K 208 " --> pdb=" O VAL K 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 5 through 8 Processing sheet with id=AE1, first strand: chain 'M' and resid 34 through 39 Processing sheet with id=AE2, first strand: chain 'M' and resid 34 through 39 Processing sheet with id=AE3, first strand: chain 'M' and resid 116 through 120 removed outlier: 6.057A pdb=" N TYR M 175 " --> pdb=" O ASN M 140 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 146 through 152 941 hydrogen bonds defined for protein. 2627 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: 4.78 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6599 1.34 - 1.47: 6548 1.47 - 1.59: 10287 1.59 - 1.72: 8 1.72 - 1.85: 178 Bond restraints: 23620 Sorted by residual: bond pdb=" N PRO A 480 " pdb=" CA PRO A 480 " ideal model delta sigma weight residual 1.473 1.707 -0.233 1.32e-02 5.74e+03 3.12e+02 bond pdb=" C04 QMR D 502 " pdb=" C05 QMR D 502 " ideal model delta sigma weight residual 1.536 1.240 0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C05 QMR D 502 " pdb=" C06 QMR D 502 " ideal model delta sigma weight residual 1.536 1.241 0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C04 QMR A 502 " pdb=" C05 QMR A 502 " ideal model delta sigma weight residual 1.536 1.243 0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C05 QMR A 502 " pdb=" C06 QMR A 502 " ideal model delta sigma weight residual 1.536 1.245 0.291 2.00e-02 2.50e+03 2.11e+02 ... (remaining 23615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.65: 32043 6.65 - 13.30: 146 13.30 - 19.95: 14 19.95 - 26.60: 1 26.60 - 33.25: 1 Bond angle restraints: 32205 Sorted by residual: angle pdb=" N CYS A 200 " pdb=" CA CYS A 200 " pdb=" C CYS A 200 " ideal model delta sigma weight residual 109.96 143.21 -33.25 1.49e+00 4.50e-01 4.98e+02 angle pdb=" C PRO A 479 " pdb=" N PRO A 480 " pdb=" CA PRO A 480 " ideal model delta sigma weight residual 118.97 139.03 -20.06 1.04e+00 9.25e-01 3.72e+02 angle pdb=" C ALA B 307 " pdb=" N PRO B 308 " pdb=" CA PRO B 308 " ideal model delta sigma weight residual 118.97 137.39 -18.42 1.04e+00 9.25e-01 3.14e+02 angle pdb=" C LEU H 138 " pdb=" N ALA H 139 " pdb=" CA ALA H 139 " ideal model delta sigma weight residual 120.49 138.84 -18.35 1.42e+00 4.96e-01 1.67e+02 angle pdb=" N CYS A 200 " pdb=" CA CYS A 200 " pdb=" CB CYS A 200 " ideal model delta sigma weight residual 109.51 93.33 16.18 1.58e+00 4.01e-01 1.05e+02 ... (remaining 32200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.35: 12693 20.35 - 40.70: 1290 40.70 - 61.05: 170 61.05 - 81.40: 45 81.40 - 101.75: 15 Dihedral angle restraints: 14213 sinusoidal: 5745 harmonic: 8468 Sorted by residual: dihedral pdb=" CB CYS M 136 " pdb=" SG CYS M 136 " pdb=" SG CYS M 196 " pdb=" CB CYS M 196 " ideal model delta sinusoidal sigma weight residual -86.00 -5.32 -80.68 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CB CYS E 130 " pdb=" SG CYS E 130 " pdb=" SG CYS E 144 " pdb=" CB CYS E 144 " ideal model delta sinusoidal sigma weight residual 93.00 18.56 74.44 1 1.00e+01 1.00e-02 7.03e+01 dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 149 " pdb=" CB CYS A 149 " ideal model delta sinusoidal sigma weight residual 93.00 32.04 60.96 1 1.00e+01 1.00e-02 4.94e+01 ... (remaining 14210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.659: 3737 0.659 - 1.317: 2 1.317 - 1.976: 1 1.976 - 2.634: 1 2.634 - 3.293: 1 Chirality restraints: 3742 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " pdb=" O4 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 0.89 -3.29 2.00e-02 2.50e+03 2.71e+04 chirality pdb=" C1 BMA G 2 " pdb=" O4 NAG G 1 " pdb=" C2 BMA G 2 " pdb=" O5 BMA G 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-02 2.50e+03 1.17e+03 chirality pdb=" C1 BMA F 2 " pdb=" O4 NAG F 1 " pdb=" C2 BMA F 2 " pdb=" O5 BMA F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.43e+02 ... (remaining 3739 not shown) Planarity restraints: 3983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 143 " -0.166 2.00e-02 2.50e+03 1.96e-01 4.82e+02 pdb=" CG ASN B 143 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN B 143 " 0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN B 143 " 0.332 2.00e-02 2.50e+03 pdb=" C1 NAG B 401 " -0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 143 " 0.141 2.00e-02 2.50e+03 1.48e-01 2.75e+02 pdb=" CG ASN C 143 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN C 143 " -0.061 2.00e-02 2.50e+03 pdb=" ND2 ASN C 143 " -0.233 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " 0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 304 " -0.032 2.00e-02 2.50e+03 6.69e-02 4.48e+01 pdb=" C HIS B 304 " 0.116 2.00e-02 2.50e+03 pdb=" O HIS B 304 " -0.044 2.00e-02 2.50e+03 pdb=" N THR B 305 " -0.039 2.00e-02 2.50e+03 ... (remaining 3980 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 255 2.58 - 3.16: 16203 3.16 - 3.74: 34098 3.74 - 4.32: 44974 4.32 - 4.90: 74873 Nonbonded interactions: 170403 Sorted by model distance: nonbonded pdb=" O PRO M 81 " pdb=" CD1 ILE M 108 " model vdw 2.004 3.460 nonbonded pdb=" O VAL B 197 " pdb=" OD1 ASP B 198 " model vdw 2.021 3.040 nonbonded pdb=" O GLN M 39 " pdb=" CB ALA M 85 " model vdw 2.048 3.460 nonbonded pdb=" CB SER E 84 " pdb=" O SER E 108 " model vdw 2.085 3.440 nonbonded pdb=" CB ASN D 102 " pdb=" CE1 PHE D 107 " model vdw 2.156 3.740 ... (remaining 170398 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' selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 2 through 325 or resid 333 through 365)) selection = (chain 'C' and resid 2 through 365) selection = (chain 'E' and resid 2 through 365) } ncs_group { reference = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) } ncs_group { reference = (chain 'H' and (resid 3 through 184 or resid 186 through 229)) selection = (chain 'K' and (resid 3 through 122 or resid 131 through 184 or resid 186 throug \ h 229)) } ncs_group { reference = (chain 'L' and (resid 2 through 23 or resid 25 through 214)) selection = (chain 'M' and (resid 2 through 23 or resid 25 through 108 or resid 113 through \ 214)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 23.020 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 0.016 0.618 23646 Z= 0.743 Angle : 1.685 46.423 32268 Z= 0.908 Chirality : 0.109 3.293 3742 Planarity : 0.011 0.109 3978 Dihedral : 16.343 101.747 8669 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.08 % Allowed : 13.81 % Favored : 86.11 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.48 (0.13), residues: 2834 helix: -4.66 (0.08), residues: 710 sheet: -1.38 (0.18), residues: 819 loop : -2.98 (0.14), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 207 TYR 0.042 0.004 TYR B 340 PHE 0.045 0.004 PHE A 322 TRP 0.043 0.004 TRP H 110 HIS 0.010 0.002 HIS K 38 Details of bonding type rmsd covalent geometry : bond 0.01443 (23620) covalent geometry : angle 1.54639 (32205) SS BOND : bond 0.19477 ( 15) SS BOND : angle 7.15898 ( 30) hydrogen bonds : bond 0.19494 ( 847) hydrogen bonds : angle 8.21066 ( 2627) link_BETA1-4 : bond 0.16543 ( 6) link_BETA1-4 : angle 15.72975 ( 18) link_NAG-ASN : bond 0.19842 ( 5) link_NAG-ASN : angle 23.96688 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8849 (mp0) REVERT: B 77 MET cc_start: 0.8751 (mtp) cc_final: 0.8301 (ttm) REVERT: B 324 MET cc_start: 0.6545 (ptp) cc_final: 0.6112 (ptt) REVERT: B 325 GLN cc_start: 0.6353 (mm110) cc_final: 0.6147 (tp40) REVERT: D 240 TYR cc_start: 0.8500 (t80) cc_final: 0.7893 (t80) REVERT: D 310 ARG cc_start: 0.6596 (tpt170) cc_final: 0.6266 (tpt90) REVERT: D 413 GLN cc_start: 0.8050 (mt0) cc_final: 0.7435 (mp10) REVERT: D 470 LEU cc_start: 0.8649 (tp) cc_final: 0.8375 (tp) REVERT: E 36 MET cc_start: 0.8320 (ppp) cc_final: 0.8028 (ppp) REVERT: H 23 LEU cc_start: 0.6835 (mt) cc_final: 0.6266 (mt) REVERT: H 73 ILE cc_start: 0.8409 (mt) cc_final: 0.8151 (mt) REVERT: H 108 GLU cc_start: 0.8462 (tt0) cc_final: 0.8209 (tm-30) REVERT: H 119 GLN cc_start: 0.8017 (pm20) cc_final: 0.6644 (mm110) REVERT: L 47 LEU cc_start: 0.7425 (tp) cc_final: 0.5417 (tt) REVERT: K 35 PHE cc_start: 0.7692 (m-80) cc_final: 0.7384 (m-80) REVERT: K 81 THR cc_start: 0.6921 (m) cc_final: 0.6631 (p) REVERT: K 83 TYR cc_start: 0.6443 (m-80) cc_final: 0.5999 (m-80) REVERT: M 87 TYR cc_start: 0.5856 (m-80) cc_final: 0.5388 (m-80) REVERT: M 92 TYR cc_start: 0.7866 (p90) cc_final: 0.7446 (p90) outliers start: 2 outliers final: 2 residues processed: 286 average time/residue: 0.1592 time to fit residues: 72.8478 Evaluate side-chains 206 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 204 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain E residue 86 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.0270 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 HIS A 435 GLN B 97 ASN C 26 ASN C 109 ASN C 304 HIS D 119 HIS D 430 GLN D 445 GLN L 91 GLN M 90 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.150181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.114763 restraints weight = 60286.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.112865 restraints weight = 35951.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.111883 restraints weight = 33745.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.111838 restraints weight = 29422.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.112666 restraints weight = 20052.676| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 23646 Z= 0.164 Angle : 0.740 11.180 32268 Z= 0.384 Chirality : 0.046 0.246 3742 Planarity : 0.006 0.083 3978 Dihedral : 8.215 59.632 3343 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.32 % Allowed : 16.71 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.00 (0.14), residues: 2834 helix: -2.46 (0.15), residues: 752 sheet: -0.98 (0.18), residues: 809 loop : -2.28 (0.16), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 22 TYR 0.026 0.002 TYR K 53 PHE 0.023 0.002 PHE B 359 TRP 0.028 0.001 TRP H 110 HIS 0.008 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00360 (23620) covalent geometry : angle 0.73376 (32205) SS BOND : bond 0.00576 ( 15) SS BOND : angle 2.41128 ( 30) hydrogen bonds : bond 0.05845 ( 847) hydrogen bonds : angle 5.89188 ( 2627) link_BETA1-4 : bond 0.00688 ( 6) link_BETA1-4 : angle 2.13812 ( 18) link_NAG-ASN : bond 0.00688 ( 5) link_NAG-ASN : angle 2.48789 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 245 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 TRP cc_start: 0.7747 (t-100) cc_final: 0.6576 (t-100) REVERT: A 350 GLU cc_start: 0.9317 (mt-10) cc_final: 0.8810 (mp0) REVERT: A 392 ASP cc_start: 0.8287 (p0) cc_final: 0.7775 (t70) REVERT: B 77 MET cc_start: 0.8494 (mtp) cc_final: 0.8102 (ttm) REVERT: B 324 MET cc_start: 0.6137 (ptp) cc_final: 0.5866 (ptt) REVERT: B 343 MET cc_start: 0.7961 (tpp) cc_final: 0.7549 (tpp) REVERT: C 21 ILE cc_start: 0.8747 (pt) cc_final: 0.8445 (mt) REVERT: D 240 TYR cc_start: 0.8376 (t80) cc_final: 0.7704 (t80) REVERT: D 310 ARG cc_start: 0.6545 (tpt170) cc_final: 0.6334 (tpt90) REVERT: E 36 MET cc_start: 0.8228 (ppp) cc_final: 0.7912 (ppp) REVERT: E 95 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: H 108 GLU cc_start: 0.8530 (tt0) cc_final: 0.8066 (tm-30) REVERT: H 119 GLN cc_start: 0.7944 (pm20) cc_final: 0.6275 (mm110) REVERT: L 86 THR cc_start: 0.6556 (m) cc_final: 0.6061 (t) REVERT: L 88 TYR cc_start: 0.6758 (m-10) cc_final: 0.5988 (m-10) REVERT: K 63 TYR cc_start: 0.6838 (m-80) cc_final: 0.6340 (m-80) REVERT: K 81 THR cc_start: 0.6766 (m) cc_final: 0.6216 (p) REVERT: K 83 TYR cc_start: 0.6423 (m-80) cc_final: 0.5890 (m-80) outliers start: 60 outliers final: 31 residues processed: 290 average time/residue: 0.1428 time to fit residues: 67.7376 Evaluate side-chains 237 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain M residue 34 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 163 optimal weight: 0.5980 chunk 240 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 306 HIS D 422 ASN E 190 ASN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN H 185 GLN B Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.148074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.116079 restraints weight = 79170.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113020 restraints weight = 67063.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.112742 restraints weight = 38489.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.112233 restraints weight = 31535.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.112646 restraints weight = 26907.286| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 23646 Z= 0.224 Angle : 0.725 9.754 32268 Z= 0.371 Chirality : 0.046 0.233 3742 Planarity : 0.005 0.075 3978 Dihedral : 6.563 59.456 3339 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.26 % Favored : 94.70 % Rotamer: Outliers : 3.17 % Allowed : 18.61 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.20 (0.15), residues: 2834 helix: -1.31 (0.17), residues: 785 sheet: -0.75 (0.18), residues: 790 loop : -1.94 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 299 TYR 0.018 0.002 TYR K 53 PHE 0.031 0.002 PHE A 286 TRP 0.021 0.001 TRP H 110 HIS 0.008 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00522 (23620) covalent geometry : angle 0.71858 (32205) SS BOND : bond 0.00524 ( 15) SS BOND : angle 2.42917 ( 30) hydrogen bonds : bond 0.05402 ( 847) hydrogen bonds : angle 5.47397 ( 2627) link_BETA1-4 : bond 0.00567 ( 6) link_BETA1-4 : angle 2.14960 ( 18) link_NAG-ASN : bond 0.00440 ( 5) link_NAG-ASN : angle 1.85789 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 216 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 TRP cc_start: 0.7745 (t-100) cc_final: 0.6723 (t-100) REVERT: A 392 ASP cc_start: 0.8300 (p0) cc_final: 0.7942 (t70) REVERT: A 405 HIS cc_start: 0.8857 (m-70) cc_final: 0.8532 (m90) REVERT: B 324 MET cc_start: 0.6066 (ptp) cc_final: 0.5707 (ptt) REVERT: B 343 MET cc_start: 0.8011 (tpp) cc_final: 0.7638 (tpp) REVERT: C 21 ILE cc_start: 0.8774 (pt) cc_final: 0.8497 (mt) REVERT: C 352 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.8807 (mt) REVERT: D 240 TYR cc_start: 0.8396 (t80) cc_final: 0.7913 (t80) REVERT: D 310 ARG cc_start: 0.6613 (tpt170) cc_final: 0.6391 (tpt90) REVERT: D 414 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8639 (mt) REVERT: E 95 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8102 (m-80) REVERT: H 108 GLU cc_start: 0.8464 (tt0) cc_final: 0.7978 (tm-30) REVERT: H 112 LYS cc_start: 0.8338 (mttt) cc_final: 0.7458 (mttt) REVERT: L 86 THR cc_start: 0.6825 (m) cc_final: 0.6125 (t) REVERT: L 88 TYR cc_start: 0.6311 (m-10) cc_final: 0.5826 (m-10) REVERT: K 63 TYR cc_start: 0.6766 (m-80) cc_final: 0.6348 (m-80) REVERT: K 81 THR cc_start: 0.6946 (m) cc_final: 0.6416 (p) REVERT: K 83 TYR cc_start: 0.6297 (m-80) cc_final: 0.6076 (m-80) outliers start: 82 outliers final: 51 residues processed: 274 average time/residue: 0.1375 time to fit residues: 62.6204 Evaluate side-chains 250 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 196 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 220 CYS Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 481 TRP Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 357 CYS Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain M residue 34 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 242 optimal weight: 0.3980 chunk 147 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 267 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 173 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 HIS ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.149452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.117439 restraints weight = 64219.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.111974 restraints weight = 50037.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.112075 restraints weight = 48557.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.112641 restraints weight = 29508.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.112852 restraints weight = 21439.513| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 23646 Z= 0.140 Angle : 0.629 12.033 32268 Z= 0.324 Chirality : 0.044 0.243 3742 Planarity : 0.005 0.067 3978 Dihedral : 5.837 57.664 3339 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.03 % Favored : 95.94 % Rotamer: Outliers : 3.52 % Allowed : 19.15 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.67 (0.16), residues: 2834 helix: -0.63 (0.18), residues: 783 sheet: -0.51 (0.18), residues: 793 loop : -1.76 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 299 TYR 0.019 0.001 TYR K 53 PHE 0.027 0.001 PHE A 286 TRP 0.018 0.001 TRP H 110 HIS 0.007 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00320 (23620) covalent geometry : angle 0.62245 (32205) SS BOND : bond 0.00810 ( 15) SS BOND : angle 2.65250 ( 30) hydrogen bonds : bond 0.04469 ( 847) hydrogen bonds : angle 5.07122 ( 2627) link_BETA1-4 : bond 0.00618 ( 6) link_BETA1-4 : angle 1.72560 ( 18) link_NAG-ASN : bond 0.00190 ( 5) link_NAG-ASN : angle 1.58590 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 221 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 TRP cc_start: 0.7792 (t-100) cc_final: 0.7211 (t-100) REVERT: B 77 MET cc_start: 0.8526 (mtp) cc_final: 0.8205 (ttm) REVERT: B 324 MET cc_start: 0.5932 (ptp) cc_final: 0.5578 (ptt) REVERT: B 325 GLN cc_start: 0.6512 (mm-40) cc_final: 0.5652 (tp40) REVERT: B 343 MET cc_start: 0.7992 (tpp) cc_final: 0.7644 (tpp) REVERT: C 21 ILE cc_start: 0.8667 (pt) cc_final: 0.8397 (mt) REVERT: C 95 TYR cc_start: 0.9054 (OUTLIER) cc_final: 0.8837 (m-10) REVERT: C 352 ILE cc_start: 0.9464 (OUTLIER) cc_final: 0.8804 (mt) REVERT: D 163 ILE cc_start: 0.9551 (OUTLIER) cc_final: 0.9270 (mt) REVERT: E 95 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: E 280 MET cc_start: 0.8439 (ttm) cc_final: 0.8087 (mtt) REVERT: H 49 GLU cc_start: 0.6662 (tt0) cc_final: 0.6237 (mm-30) REVERT: H 108 GLU cc_start: 0.8497 (tt0) cc_final: 0.8060 (tm-30) REVERT: L 88 TYR cc_start: 0.6536 (m-80) cc_final: 0.6212 (m-10) REVERT: K 83 TYR cc_start: 0.6309 (m-80) cc_final: 0.6060 (m-80) outliers start: 91 outliers final: 51 residues processed: 289 average time/residue: 0.1455 time to fit residues: 68.9813 Evaluate side-chains 259 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 204 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 481 TRP Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 59 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 140 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 184 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 242 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 19 optimal weight: 0.0670 chunk 165 optimal weight: 2.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN D 405 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.145874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.111088 restraints weight = 81916.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.105649 restraints weight = 57213.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.107380 restraints weight = 37241.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106745 restraints weight = 24646.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.108790 restraints weight = 20788.303| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23646 Z= 0.116 Angle : 0.602 11.732 32268 Z= 0.307 Chirality : 0.043 0.259 3742 Planarity : 0.005 0.060 3978 Dihedral : 5.420 57.393 3339 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.22 % Rotamer: Outliers : 2.86 % Allowed : 20.66 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.32 (0.16), residues: 2834 helix: -0.16 (0.19), residues: 771 sheet: -0.35 (0.18), residues: 796 loop : -1.64 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 62 TYR 0.019 0.001 TYR K 53 PHE 0.028 0.001 PHE A 286 TRP 0.016 0.001 TRP H 110 HIS 0.006 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00261 (23620) covalent geometry : angle 0.59834 (32205) SS BOND : bond 0.00476 ( 15) SS BOND : angle 1.67717 ( 30) hydrogen bonds : bond 0.04036 ( 847) hydrogen bonds : angle 4.80770 ( 2627) link_BETA1-4 : bond 0.00422 ( 6) link_BETA1-4 : angle 1.50592 ( 18) link_NAG-ASN : bond 0.00142 ( 5) link_NAG-ASN : angle 1.54238 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 219 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ASP cc_start: 0.7789 (p0) cc_final: 0.7484 (m-30) REVERT: B 77 MET cc_start: 0.8605 (mtp) cc_final: 0.8291 (ttm) REVERT: B 324 MET cc_start: 0.5606 (ptp) cc_final: 0.5283 (ptt) REVERT: B 343 MET cc_start: 0.8076 (tpp) cc_final: 0.7638 (tpp) REVERT: C 95 TYR cc_start: 0.9069 (OUTLIER) cc_final: 0.8747 (m-10) REVERT: C 352 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.8809 (mt) REVERT: D 400 MET cc_start: 0.8388 (mmm) cc_final: 0.8168 (mpp) REVERT: E 95 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.7933 (m-80) REVERT: E 280 MET cc_start: 0.8507 (ttm) cc_final: 0.8298 (mtt) REVERT: H 108 GLU cc_start: 0.8481 (tt0) cc_final: 0.8065 (tm-30) REVERT: L 86 THR cc_start: 0.6481 (m) cc_final: 0.5659 (t) REVERT: L 88 TYR cc_start: 0.6505 (m-80) cc_final: 0.5901 (m-10) REVERT: L 169 ASP cc_start: 0.6567 (m-30) cc_final: 0.6297 (m-30) REVERT: K 83 TYR cc_start: 0.6613 (m-80) cc_final: 0.6411 (m-80) outliers start: 74 outliers final: 52 residues processed: 275 average time/residue: 0.1355 time to fit residues: 62.6818 Evaluate side-chains 261 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 237 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 357 CYS Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 481 TRP Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 59 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 134 optimal weight: 0.0870 chunk 248 optimal weight: 7.9990 chunk 188 optimal weight: 0.0270 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 0.0030 chunk 247 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 overall best weight: 0.3626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.146158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109350 restraints weight = 73033.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.105642 restraints weight = 44765.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.106646 restraints weight = 37946.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.106713 restraints weight = 25063.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.107437 restraints weight = 20839.533| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 23646 Z= 0.107 Angle : 0.584 9.547 32268 Z= 0.299 Chirality : 0.043 0.248 3742 Planarity : 0.004 0.058 3978 Dihedral : 5.268 63.892 3339 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 2.98 % Allowed : 21.12 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.16), residues: 2834 helix: 0.11 (0.19), residues: 789 sheet: -0.22 (0.18), residues: 794 loop : -1.59 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 299 TYR 0.021 0.001 TYR L 88 PHE 0.025 0.001 PHE A 286 TRP 0.015 0.001 TRP H 110 HIS 0.005 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00237 (23620) covalent geometry : angle 0.58076 (32205) SS BOND : bond 0.00955 ( 15) SS BOND : angle 1.73783 ( 30) hydrogen bonds : bond 0.03784 ( 847) hydrogen bonds : angle 4.64769 ( 2627) link_BETA1-4 : bond 0.00454 ( 6) link_BETA1-4 : angle 1.42590 ( 18) link_NAG-ASN : bond 0.00124 ( 5) link_NAG-ASN : angle 1.47141 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 224 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.8710 (mtp) cc_final: 0.8420 (ttm) REVERT: B 324 MET cc_start: 0.5552 (ptp) cc_final: 0.5112 (ptt) REVERT: B 343 MET cc_start: 0.8188 (tpp) cc_final: 0.7703 (tpp) REVERT: C 95 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.8714 (m-10) REVERT: C 352 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.8784 (mt) REVERT: D 240 TYR cc_start: 0.8295 (t80) cc_final: 0.7575 (t80) REVERT: E 95 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: H 108 GLU cc_start: 0.8602 (tt0) cc_final: 0.8005 (tm-30) REVERT: H 112 LYS cc_start: 0.8036 (mttt) cc_final: 0.7146 (mttt) REVERT: L 86 THR cc_start: 0.6404 (m) cc_final: 0.5959 (m) REVERT: L 88 TYR cc_start: 0.6810 (m-80) cc_final: 0.6185 (m-10) REVERT: L 105 LYS cc_start: 0.6641 (tppt) cc_final: 0.6235 (mtmt) REVERT: L 169 ASP cc_start: 0.6666 (m-30) cc_final: 0.6368 (m-30) REVERT: K 54 ILE cc_start: 0.8864 (tp) cc_final: 0.8362 (mp) outliers start: 77 outliers final: 57 residues processed: 286 average time/residue: 0.1376 time to fit residues: 66.0326 Evaluate side-chains 265 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 205 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 351 TRP Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 481 TRP Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 59 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 275 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 190 optimal weight: 0.9990 chunk 256 optimal weight: 0.0870 chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 268 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 ASN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.148363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.111964 restraints weight = 63083.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.107836 restraints weight = 38210.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.108801 restraints weight = 35243.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.108746 restraints weight = 25176.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.109488 restraints weight = 19722.239| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 23646 Z= 0.128 Angle : 0.594 11.088 32268 Z= 0.302 Chirality : 0.043 0.241 3742 Planarity : 0.004 0.057 3978 Dihedral : 5.172 65.312 3339 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.01 % Rotamer: Outliers : 3.40 % Allowed : 21.28 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.93 (0.16), residues: 2834 helix: 0.38 (0.19), residues: 785 sheet: -0.16 (0.18), residues: 797 loop : -1.55 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 22 TYR 0.032 0.001 TYR M 94 PHE 0.024 0.001 PHE A 286 TRP 0.015 0.001 TRP H 110 HIS 0.005 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00297 (23620) covalent geometry : angle 0.58864 (32205) SS BOND : bond 0.00884 ( 15) SS BOND : angle 2.23696 ( 30) hydrogen bonds : bond 0.03890 ( 847) hydrogen bonds : angle 4.59781 ( 2627) link_BETA1-4 : bond 0.00509 ( 6) link_BETA1-4 : angle 1.41078 ( 18) link_NAG-ASN : bond 0.00160 ( 5) link_NAG-ASN : angle 1.53682 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 220 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: B 77 MET cc_start: 0.8732 (mtp) cc_final: 0.8422 (ttm) REVERT: B 324 MET cc_start: 0.5798 (ptp) cc_final: 0.5435 (ptt) REVERT: B 343 MET cc_start: 0.8084 (tpp) cc_final: 0.7691 (tpp) REVERT: C 95 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.8767 (m-10) REVERT: C 352 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.8743 (mt) REVERT: D 163 ILE cc_start: 0.9564 (OUTLIER) cc_final: 0.9316 (mt) REVERT: D 240 TYR cc_start: 0.8273 (t80) cc_final: 0.7636 (t80) REVERT: D 329 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8701 (mt) REVERT: E 95 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.7888 (m-80) REVERT: H 108 GLU cc_start: 0.8602 (tt0) cc_final: 0.8115 (tm-30) REVERT: L 86 THR cc_start: 0.6434 (m) cc_final: 0.5586 (t) REVERT: L 88 TYR cc_start: 0.6822 (m-80) cc_final: 0.5880 (m-10) REVERT: L 169 ASP cc_start: 0.6726 (m-30) cc_final: 0.6406 (m-30) REVERT: K 53 TYR cc_start: 0.7409 (p90) cc_final: 0.6560 (p90) REVERT: K 54 ILE cc_start: 0.8866 (tp) cc_final: 0.8392 (mp) outliers start: 88 outliers final: 65 residues processed: 293 average time/residue: 0.1389 time to fit residues: 68.1702 Evaluate side-chains 277 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 207 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 351 TRP Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 220 CYS Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 357 CYS Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 481 TRP Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 59 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 166 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 140 optimal weight: 0.3980 chunk 187 optimal weight: 1.9990 chunk 255 optimal weight: 3.9990 chunk 83 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 216 optimal weight: 10.0000 chunk 43 optimal weight: 0.0970 chunk 132 optimal weight: 0.2980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.147889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.110524 restraints weight = 63124.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.107827 restraints weight = 35547.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.107840 restraints weight = 37747.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.108170 restraints weight = 26178.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.108471 restraints weight = 19749.325| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 23646 Z= 0.108 Angle : 0.585 12.689 32268 Z= 0.296 Chirality : 0.042 0.248 3742 Planarity : 0.004 0.054 3978 Dihedral : 5.043 71.778 3339 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.61 % Rotamer: Outliers : 2.82 % Allowed : 21.86 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.72 (0.16), residues: 2834 helix: 0.62 (0.19), residues: 781 sheet: -0.01 (0.18), residues: 791 loop : -1.48 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 101 TYR 0.031 0.001 TYR M 94 PHE 0.023 0.001 PHE A 286 TRP 0.015 0.001 TRP H 110 HIS 0.005 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00250 (23620) covalent geometry : angle 0.57744 (32205) SS BOND : bond 0.00869 ( 15) SS BOND : angle 2.78726 ( 30) hydrogen bonds : bond 0.03546 ( 847) hydrogen bonds : angle 4.46390 ( 2627) link_BETA1-4 : bond 0.00467 ( 6) link_BETA1-4 : angle 1.33442 ( 18) link_NAG-ASN : bond 0.00108 ( 5) link_NAG-ASN : angle 1.48325 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 233 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 ASN cc_start: 0.8353 (t0) cc_final: 0.7971 (t0) REVERT: B 77 MET cc_start: 0.8833 (mtp) cc_final: 0.8503 (ttm) REVERT: B 324 MET cc_start: 0.5671 (ptp) cc_final: 0.5394 (ptt) REVERT: B 343 MET cc_start: 0.8186 (tpp) cc_final: 0.7966 (tpt) REVERT: C 95 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.8680 (m-10) REVERT: C 352 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.8699 (mt) REVERT: D 240 TYR cc_start: 0.8256 (t80) cc_final: 0.7535 (t80) REVERT: D 329 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8793 (mt) REVERT: E 95 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.7940 (m-80) REVERT: E 268 ASP cc_start: 0.8030 (t0) cc_final: 0.7245 (m-30) REVERT: H 9 GLU cc_start: 0.4860 (mp0) cc_final: 0.3843 (pm20) REVERT: H 108 GLU cc_start: 0.8599 (tt0) cc_final: 0.8110 (tm-30) REVERT: H 114 PHE cc_start: 0.6954 (m-10) cc_final: 0.6545 (m-10) REVERT: L 86 THR cc_start: 0.5832 (m) cc_final: 0.5461 (m) REVERT: L 88 TYR cc_start: 0.6866 (m-80) cc_final: 0.6080 (m-10) REVERT: L 105 LYS cc_start: 0.6661 (tppt) cc_final: 0.6057 (mtmt) REVERT: L 169 ASP cc_start: 0.6621 (m-30) cc_final: 0.6299 (m-30) REVERT: K 53 TYR cc_start: 0.7460 (p90) cc_final: 0.6647 (p90) REVERT: K 54 ILE cc_start: 0.8913 (tp) cc_final: 0.8470 (mp) REVERT: K 63 TYR cc_start: 0.6657 (m-80) cc_final: 0.6441 (m-80) outliers start: 73 outliers final: 57 residues processed: 295 average time/residue: 0.1443 time to fit residues: 70.5460 Evaluate side-chains 270 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 209 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 351 TRP Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 481 TRP Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 49 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 150 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 233 optimal weight: 30.0000 chunk 272 optimal weight: 50.0000 chunk 55 optimal weight: 0.0050 chunk 49 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 234 optimal weight: 0.5980 chunk 273 optimal weight: 5.9990 chunk 279 optimal weight: 7.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.148210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115673 restraints weight = 74384.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.110322 restraints weight = 57552.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.111690 restraints weight = 37546.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.111318 restraints weight = 24235.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.112198 restraints weight = 21550.621| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 23646 Z= 0.147 Angle : 0.630 13.679 32268 Z= 0.316 Chirality : 0.044 0.247 3742 Planarity : 0.004 0.057 3978 Dihedral : 5.088 72.267 3339 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.13 % Favored : 95.83 % Rotamer: Outliers : 3.13 % Allowed : 22.05 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.68 (0.16), residues: 2834 helix: 0.68 (0.20), residues: 787 sheet: 0.01 (0.18), residues: 792 loop : -1.49 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 101 TYR 0.026 0.001 TYR M 94 PHE 0.024 0.001 PHE A 286 TRP 0.019 0.001 TRP A 349 HIS 0.005 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00352 (23620) covalent geometry : angle 0.62261 (32205) SS BOND : bond 0.00928 ( 15) SS BOND : angle 2.97537 ( 30) hydrogen bonds : bond 0.03874 ( 847) hydrogen bonds : angle 4.56075 ( 2627) link_BETA1-4 : bond 0.00431 ( 6) link_BETA1-4 : angle 1.35583 ( 18) link_NAG-ASN : bond 0.00188 ( 5) link_NAG-ASN : angle 1.53371 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 210 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8078 (ttm) cc_final: 0.7858 (ttp) REVERT: A 405 HIS cc_start: 0.9017 (OUTLIER) cc_final: 0.8526 (t70) REVERT: B 324 MET cc_start: 0.5847 (ptp) cc_final: 0.5489 (ptt) REVERT: C 95 TYR cc_start: 0.9093 (OUTLIER) cc_final: 0.8871 (m-10) REVERT: C 352 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.8628 (mt) REVERT: D 163 ILE cc_start: 0.9566 (OUTLIER) cc_final: 0.9302 (mt) REVERT: D 218 LEU cc_start: 0.8676 (tt) cc_final: 0.8444 (tp) REVERT: D 240 TYR cc_start: 0.8228 (t80) cc_final: 0.7612 (t80) REVERT: D 329 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8744 (mt) REVERT: D 375 MET cc_start: 0.8418 (mpp) cc_final: 0.8119 (mtp) REVERT: E 95 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.8225 (m-80) REVERT: E 268 ASP cc_start: 0.8012 (t0) cc_final: 0.7171 (m-30) REVERT: H 112 LYS cc_start: 0.8429 (mttt) cc_final: 0.7592 (mmtm) REVERT: L 86 THR cc_start: 0.5667 (m) cc_final: 0.5336 (m) REVERT: L 88 TYR cc_start: 0.6337 (m-80) cc_final: 0.5851 (m-10) REVERT: L 105 LYS cc_start: 0.6760 (tppt) cc_final: 0.6065 (mtmt) REVERT: L 169 ASP cc_start: 0.6580 (m-30) cc_final: 0.6272 (m-30) REVERT: K 53 TYR cc_start: 0.7337 (p90) cc_final: 0.6709 (p90) REVERT: K 54 ILE cc_start: 0.8784 (tp) cc_final: 0.8443 (mp) outliers start: 81 outliers final: 63 residues processed: 276 average time/residue: 0.1403 time to fit residues: 65.2847 Evaluate side-chains 273 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 204 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 351 TRP Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 220 CYS Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 357 CYS Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 481 TRP Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 59 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 76 optimal weight: 0.0470 chunk 140 optimal weight: 0.0980 chunk 3 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 chunk 44 optimal weight: 0.0770 chunk 129 optimal weight: 0.0970 chunk 82 optimal weight: 0.7980 chunk 231 optimal weight: 7.9990 chunk 246 optimal weight: 0.8980 overall best weight: 0.1834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.150594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.116270 restraints weight = 68137.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113332 restraints weight = 41468.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.112433 restraints weight = 39269.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.112869 restraints weight = 26281.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.114056 restraints weight = 18863.056| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.133 23646 Z= 0.107 Angle : 0.608 13.417 32268 Z= 0.302 Chirality : 0.043 0.247 3742 Planarity : 0.004 0.053 3978 Dihedral : 4.926 72.957 3339 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 2.17 % Allowed : 23.06 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.16), residues: 2834 helix: 0.78 (0.19), residues: 791 sheet: 0.09 (0.18), residues: 798 loop : -1.44 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 347 TYR 0.029 0.001 TYR M 94 PHE 0.023 0.001 PHE A 286 TRP 0.023 0.001 TRP A 349 HIS 0.005 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00249 (23620) covalent geometry : angle 0.60078 (32205) SS BOND : bond 0.00910 ( 15) SS BOND : angle 2.92627 ( 30) hydrogen bonds : bond 0.03380 ( 847) hydrogen bonds : angle 4.38746 ( 2627) link_BETA1-4 : bond 0.00489 ( 6) link_BETA1-4 : angle 1.27765 ( 18) link_NAG-ASN : bond 0.00110 ( 5) link_NAG-ASN : angle 1.38627 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 223 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 101 ASN cc_start: 0.8271 (t0) cc_final: 0.7900 (t0) REVERT: A 314 MET cc_start: 0.8413 (tpt) cc_final: 0.8129 (tpt) REVERT: A 405 HIS cc_start: 0.9002 (m170) cc_final: 0.8646 (t70) REVERT: D 240 TYR cc_start: 0.8133 (t80) cc_final: 0.7521 (t80) REVERT: D 329 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8706 (mt) REVERT: D 400 MET cc_start: 0.8071 (tpp) cc_final: 0.7503 (tpp) REVERT: E 95 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8012 (m-80) REVERT: E 268 ASP cc_start: 0.8066 (t0) cc_final: 0.7206 (m-30) REVERT: H 9 GLU cc_start: 0.4723 (mp0) cc_final: 0.3670 (pm20) REVERT: H 110 TRP cc_start: 0.7470 (t60) cc_final: 0.7246 (t-100) REVERT: H 112 LYS cc_start: 0.8234 (mttt) cc_final: 0.7452 (mmtm) REVERT: L 86 THR cc_start: 0.5693 (m) cc_final: 0.5306 (m) REVERT: L 88 TYR cc_start: 0.6616 (m-80) cc_final: 0.6066 (m-10) REVERT: L 105 LYS cc_start: 0.6680 (tppt) cc_final: 0.6033 (mtmt) REVERT: L 169 ASP cc_start: 0.6604 (m-30) cc_final: 0.6316 (m-30) REVERT: K 53 TYR cc_start: 0.7437 (p90) cc_final: 0.6811 (p90) REVERT: K 54 ILE cc_start: 0.8872 (tp) cc_final: 0.8429 (mp) REVERT: K 63 TYR cc_start: 0.6529 (m-80) cc_final: 0.6307 (m-80) outliers start: 56 outliers final: 46 residues processed: 269 average time/residue: 0.1422 time to fit residues: 64.0755 Evaluate side-chains 257 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 209 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 351 TRP Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 220 CYS Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 481 TRP Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 59 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 252 optimal weight: 20.0000 chunk 14 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 88 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 chunk 102 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 353 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.149229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.113487 restraints weight = 63128.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.110831 restraints weight = 39307.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.110442 restraints weight = 32635.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.110243 restraints weight = 31154.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.111260 restraints weight = 20877.249| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 23646 Z= 0.127 Angle : 0.626 13.667 32268 Z= 0.310 Chirality : 0.043 0.246 3742 Planarity : 0.004 0.053 3978 Dihedral : 4.921 73.051 3339 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.22 % Rotamer: Outliers : 2.09 % Allowed : 23.40 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.51 (0.16), residues: 2834 helix: 0.83 (0.19), residues: 791 sheet: 0.11 (0.18), residues: 797 loop : -1.40 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 299 TYR 0.027 0.001 TYR M 94 PHE 0.023 0.001 PHE A 286 TRP 0.019 0.001 TRP A 349 HIS 0.005 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00305 (23620) covalent geometry : angle 0.61665 (32205) SS BOND : bond 0.00972 ( 15) SS BOND : angle 3.39108 ( 30) hydrogen bonds : bond 0.03569 ( 847) hydrogen bonds : angle 4.39641 ( 2627) link_BETA1-4 : bond 0.00438 ( 6) link_BETA1-4 : angle 1.31580 ( 18) link_NAG-ASN : bond 0.00124 ( 5) link_NAG-ASN : angle 1.45059 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4616.40 seconds wall clock time: 80 minutes 23.81 seconds (4823.81 seconds total)