Starting phenix.real_space_refine on Sun Jul 5 05:08:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6usf_20863/07_2026/6usf_20863.cif Found real_map, /net/cci-nas-00/data/ceres_data/6usf_20863/07_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_20863/07_2026/6usf_20863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6usf_20863/07_2026/6usf_20863.map" model { file = "/net/cci-nas-00/data/ceres_data/6usf_20863/07_2026/6usf_20863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6usf_20863/07_2026/6usf_20863.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6usf_20863/07_2026/6usf_20863.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6usf_20863/07_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-6108/lib/python3.11/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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 5.71, per 1000 atoms: 0.25 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: 2.07 Conformation dependent library (CDL) restraints added in 1.3 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: 0.74 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: 4.37 Time building geometry restraints manager: 2.62 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 - 17.32: 12037 17.32 - 34.65: 1554 34.65 - 51.97: 296 51.97 - 69.29: 52 69.29 - 86.62: 17 Dihedral angle restraints: 13956 sinusoidal: 5488 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 13953 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: 4.550 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.260 Find NCS groups from input model: 0.530 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 : 15.661 86.617 8412 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/Z covalent geometry : bond 0.01443 / 0.67 (23620) covalent geometry : angle 1.54639 / 0.88 (32205) SS BOND : bond 0.19477 / 11.85 ( 15) SS BOND : angle 7.15898 / 4.78 ( 30) hydrogen bonds : bond 0.19494 / 12.79 ( 847) hydrogen bonds : angle 8.21066 / 5.66 ( 2627) link_BETA1-4 : bond 0.16543 / 8.47 ( 6) link_BETA1-4 : angle 15.72975 / 9.25 ( 18) link_NAG-ASN : bond 0.19842 / 10.66 ( 5) link_NAG-ASN : angle 23.96688 / 11.79 ( 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 : 0.902 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: 0.1583 time to fit residues: 72.5005 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 : 0.868 ------------------------------------------------------------------------------- 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... A 405 HIS A 435 GLN B 60 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.149744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.116015 restraints weight = 60065.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.110375 restraints weight = 42213.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.110959 restraints weight = 36844.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.110974 restraints weight = 26968.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.112334 restraints weight = 21293.011| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 23646 Z= 0.161 Angle : 0.736 11.151 32268 Z= 0.381 Chirality : 0.046 0.307 3742 Planarity : 0.006 0.082 3978 Dihedral : 6.879 55.935 3086 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.44 % Allowed : 16.56 % Favored : 81.01 % 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: -2.97 (0.14), residues: 2834 helix: -2.43 (0.15), residues: 752 sheet: -0.97 (0.18), residues: 809 loop : -2.26 (0.16), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 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/Z covalent geometry : bond 0.00347 / 0.16 (23620) covalent geometry : angle 0.72978 / 0.38 (32205) SS BOND : bond 0.00542 / 0.29 ( 15) SS BOND : angle 2.36774 / 1.68 ( 30) hydrogen bonds : bond 0.05754 / 3.79 ( 847) hydrogen bonds : angle 5.86217 / 4.01 ( 2627) link_BETA1-4 : bond 0.00480 / 0.23 ( 6) link_BETA1-4 : angle 2.02263 / 1.14 ( 18) link_NAG-ASN : bond 0.01122 / 0.55 ( 5) link_NAG-ASN : angle 2.61236 / 1.36 ( 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 309 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 246 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 TRP cc_start: 0.7801 (t-100) cc_final: 0.6630 (t-100) REVERT: A 350 GLU cc_start: 0.9345 (mt-10) cc_final: 0.8836 (mp0) REVERT: A 392 ASP cc_start: 0.8270 (p0) cc_final: 0.7824 (t70) REVERT: B 77 MET cc_start: 0.8464 (mtp) cc_final: 0.8054 (ttm) REVERT: B 324 MET cc_start: 0.6130 (ptp) cc_final: 0.5854 (ptt) REVERT: B 325 GLN cc_start: 0.6149 (mm110) cc_final: 0.5771 (tp40) REVERT: B 343 MET cc_start: 0.7884 (tpp) cc_final: 0.7432 (tpp) REVERT: C 21 ILE cc_start: 0.8702 (pt) cc_final: 0.8407 (mt) REVERT: D 163 ILE cc_start: 0.9350 (mt) cc_final: 0.9130 (mt) REVERT: D 310 ARG cc_start: 0.6537 (tpt170) cc_final: 0.6326 (tpt90) REVERT: E 36 MET cc_start: 0.8226 (ppp) cc_final: 0.7905 (ppp) REVERT: E 95 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.7992 (m-80) REVERT: H 9 GLU cc_start: 0.6169 (mp0) cc_final: 0.5955 (mp0) REVERT: H 61 THR cc_start: 0.8234 (p) cc_final: 0.7705 (p) REVERT: H 108 GLU cc_start: 0.8562 (tt0) cc_final: 0.8076 (tm-30) REVERT: H 119 GLN cc_start: 0.7942 (pm20) cc_final: 0.6324 (mm110) REVERT: L 86 THR cc_start: 0.6559 (m) cc_final: 0.5955 (t) REVERT: L 88 TYR cc_start: 0.6975 (m-10) cc_final: 0.6163 (m-10) REVERT: K 63 TYR cc_start: 0.6882 (m-80) cc_final: 0.6300 (m-80) REVERT: K 81 THR cc_start: 0.6766 (m) cc_final: 0.6166 (p) REVERT: K 83 TYR cc_start: 0.6432 (m-80) cc_final: 0.5863 (m-80) outliers start: 63 outliers final: 31 residues processed: 294 average time/residue: 0.1460 time to fit residues: 70.1792 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 : 0.766 ------------------------------------------------------------------------------- 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 77 THR Chi-restraints excluded: chain L residue 37 TYR 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: 0.9990 chunk 240 optimal weight: 7.9990 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: 9.9990 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: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 HIS D 306 HIS D 422 ASN E 190 ASN H 85 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.146813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.114404 restraints weight = 79205.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.109846 restraints weight = 58922.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.110790 restraints weight = 34198.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.110438 restraints weight = 24143.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111280 restraints weight = 21303.437| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 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 = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 23646 Z= 0.283 Angle : 0.776 10.310 32268 Z= 0.397 Chirality : 0.048 0.226 3742 Planarity : 0.006 0.075 3978 Dihedral : 6.301 47.076 3082 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.86 % Favored : 94.10 % Rotamer: Outliers : 3.83 % Allowed : 18.30 % Favored : 77.87 % 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: -1.25 (0.17), residues: 765 sheet: -0.78 (0.19), residues: 781 loop : -1.96 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 155 TYR 0.019 0.002 TYR L 95 PHE 0.032 0.002 PHE A 286 TRP 0.022 0.002 TRP H 110 HIS 0.008 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.28 (23620) covalent geometry : angle 0.77124 / 0.40 (32205) SS BOND : bond 0.00649 / 0.34 ( 15) SS BOND : angle 2.38168 / 1.52 ( 30) hydrogen bonds : bond 0.05818 / 3.88 ( 847) hydrogen bonds : angle 5.60093 / 3.84 ( 2627) link_BETA1-4 : bond 0.00412 / 0.21 ( 6) link_BETA1-4 : angle 1.66875 / 0.87 ( 18) link_NAG-ASN : bond 0.00607 / 0.31 ( 5) link_NAG-ASN : angle 2.12069 / 1.13 ( 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 313 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 214 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 ASP cc_start: 0.8262 (p0) cc_final: 0.7899 (t70) REVERT: B 324 MET cc_start: 0.6222 (ptp) cc_final: 0.5850 (ptt) REVERT: B 343 MET cc_start: 0.8037 (tpp) cc_final: 0.7615 (tpp) REVERT: C 21 ILE cc_start: 0.8787 (pt) cc_final: 0.8497 (mt) REVERT: C 352 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.8855 (mt) REVERT: D 310 ARG cc_start: 0.6638 (tpt170) cc_final: 0.6420 (tpt90) REVERT: D 414 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8638 (mt) REVERT: E 95 TYR cc_start: 0.9062 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: H 108 GLU cc_start: 0.8479 (tt0) cc_final: 0.7983 (tm-30) REVERT: H 112 LYS cc_start: 0.8326 (mttt) cc_final: 0.7456 (mttt) REVERT: H 119 GLN cc_start: 0.8075 (pm20) cc_final: 0.6410 (mm110) REVERT: L 86 THR cc_start: 0.6889 (m) cc_final: 0.6152 (t) REVERT: L 88 TYR cc_start: 0.6525 (m-10) cc_final: 0.5855 (m-10) REVERT: K 63 TYR cc_start: 0.6860 (m-80) cc_final: 0.6366 (m-80) REVERT: K 81 THR cc_start: 0.6951 (m) cc_final: 0.6340 (p) REVERT: K 83 TYR cc_start: 0.6420 (m-80) cc_final: 0.6108 (m-80) outliers start: 99 outliers final: 65 residues processed: 286 average time/residue: 0.1291 time to fit residues: 61.3589 Evaluate side-chains 265 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 197 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 230 LEU 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 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 455 MET 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 225 SER 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 B residue 350 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 216 LEU 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 345 ILE 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 228 ILE Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 357 CYS 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 L residue 75 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: 0.2980 chunk 147 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 173 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 GLN B Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.149111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.116798 restraints weight = 64124.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.110976 restraints weight = 51300.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.111425 restraints weight = 43363.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.111761 restraints weight = 34736.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.113419 restraints weight = 25073.192| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 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 = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 23646 Z= 0.146 Angle : 0.639 12.133 32268 Z= 0.329 Chirality : 0.045 0.265 3742 Planarity : 0.005 0.067 3978 Dihedral : 5.733 52.394 3082 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.87 % Rotamer: Outliers : 3.56 % Allowed : 19.34 % Favored : 77.10 % Cbeta Deviations : 0.04 % 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: -1.70 (0.16), residues: 2834 helix: -0.67 (0.18), residues: 789 sheet: -0.57 (0.18), residues: 787 loop : -1.73 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 22 TYR 0.020 0.001 TYR K 53 PHE 0.026 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/Z covalent geometry : bond 0.00334 / 0.15 (23620) covalent geometry : angle 0.63307 / 0.33 (32205) SS BOND : bond 0.00760 / 0.38 ( 15) SS BOND : angle 2.49340 / 1.52 ( 30) hydrogen bonds : bond 0.04574 / 3.03 ( 847) hydrogen bonds : angle 5.13256 / 3.51 ( 2627) link_BETA1-4 : bond 0.00439 / 0.22 ( 6) link_BETA1-4 : angle 1.35678 / 0.70 ( 18) link_NAG-ASN : bond 0.00191 / 0.10 ( 5) link_NAG-ASN : angle 1.61507 / 0.88 ( 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 303 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 211 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 TRP cc_start: 0.7740 (t-100) cc_final: 0.6931 (t-100) REVERT: B 77 MET cc_start: 0.8489 (mtp) cc_final: 0.8178 (ttm) REVERT: B 324 MET cc_start: 0.5757 (ptp) cc_final: 0.5432 (ptt) REVERT: B 343 MET cc_start: 0.8034 (tpp) cc_final: 0.7689 (tpp) REVERT: C 21 ILE cc_start: 0.8672 (pt) cc_final: 0.8406 (mt) REVERT: C 352 ILE cc_start: 0.9463 (OUTLIER) cc_final: 0.8820 (mt) REVERT: D 329 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8654 (mt) REVERT: E 95 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: E 280 MET cc_start: 0.8376 (ttm) cc_final: 0.8033 (mtt) REVERT: H 108 GLU cc_start: 0.8468 (tt0) cc_final: 0.8049 (tm-30) REVERT: L 88 TYR cc_start: 0.6489 (m-80) cc_final: 0.6176 (m-10) REVERT: K 83 TYR cc_start: 0.6288 (m-80) cc_final: 0.6003 (m-80) outliers start: 92 outliers final: 61 residues processed: 288 average time/residue: 0.1322 time to fit residues: 63.0305 Evaluate side-chains 263 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 199 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 168 MET Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 237 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 465 PHE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 145 THR 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 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 C residue 357 CYS 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 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 329 LEU 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 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 313 VAL Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain H residue 40 VAL 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 L residue 12 LEU Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain K residue 8 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 140 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 184 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 chunk 242 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 188 optimal weight: 0.0030 chunk 42 optimal weight: 0.0570 chunk 19 optimal weight: 0.9980 chunk 165 optimal weight: 0.8980 overall best weight: 0.3508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN D 405 HIS ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.150501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.118828 restraints weight = 85582.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.115681 restraints weight = 74828.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.117517 restraints weight = 33192.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117349 restraints weight = 20340.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.118249 restraints weight = 18964.378| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23646 Z= 0.107 Angle : 0.596 12.068 32268 Z= 0.302 Chirality : 0.043 0.258 3742 Planarity : 0.005 0.059 3978 Dihedral : 5.196 32.658 3082 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.22 % Rotamer: Outliers : 2.94 % Allowed : 20.50 % Favored : 76.56 % 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: -0.20 (0.19), residues: 793 sheet: -0.36 (0.18), residues: 802 loop : -1.61 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 101 TYR 0.020 0.001 TYR K 53 PHE 0.029 0.001 PHE A 286 TRP 0.017 0.001 TRP H 110 HIS 0.006 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (23620) covalent geometry : angle 0.59211 / 0.30 (32205) SS BOND : bond 0.00955 / 0.46 ( 15) SS BOND : angle 1.71387 / 1.08 ( 30) hydrogen bonds : bond 0.03886 / 2.56 ( 847) hydrogen bonds : angle 4.76109 / 3.25 ( 2627) link_BETA1-4 : bond 0.00408 / 0.20 ( 6) link_BETA1-4 : angle 1.32044 / 0.67 ( 18) link_NAG-ASN : bond 0.00121 / 0.06 ( 5) link_NAG-ASN : angle 1.49025 / 0.79 ( 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 297 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 221 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.8503 (mtp) cc_final: 0.8211 (ttm) REVERT: B 324 MET cc_start: 0.5707 (ptp) cc_final: 0.5475 (ptt) REVERT: B 343 MET cc_start: 0.8024 (tpp) cc_final: 0.7633 (tpp) REVERT: C 352 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.8712 (mt) REVERT: D 240 TYR cc_start: 0.8194 (t80) cc_final: 0.7605 (t80) REVERT: D 400 MET cc_start: 0.8299 (mmm) cc_final: 0.8079 (tpp) REVERT: E 95 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.7886 (m-80) REVERT: H 108 GLU cc_start: 0.8396 (tt0) cc_final: 0.7954 (tm-30) REVERT: H 112 LYS cc_start: 0.8281 (mttt) cc_final: 0.7277 (mttt) REVERT: L 37 TYR cc_start: 0.6283 (m-80) cc_final: 0.5972 (m-10) REVERT: L 86 THR cc_start: 0.6192 (m) cc_final: 0.5421 (t) REVERT: L 88 TYR cc_start: 0.5809 (m-80) cc_final: 0.5326 (m-10) REVERT: L 169 ASP cc_start: 0.6292 (m-30) cc_final: 0.6063 (m-30) outliers start: 76 outliers final: 51 residues processed: 282 average time/residue: 0.1319 time to fit residues: 61.6713 Evaluate side-chains 256 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 241 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 356 LEU Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 145 THR 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 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 304 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 359 ILE 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 175 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 40 LYS 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 Chi-restraints excluded: chain M residue 63 PHE 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: 2.9990 chunk 7 optimal weight: 0.0370 chunk 19 optimal weight: 0.3980 chunk 247 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4026 r_free = 0.4026 target = 0.148070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.115257 restraints weight = 75204.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110275 restraints weight = 55479.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.111593 restraints weight = 38397.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.111321 restraints weight = 24020.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.112146 restraints weight = 21745.344| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- 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: 8 | |-----------------------------------------------------------------------------| |-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: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 23646 Z= 0.131 Angle : 0.599 9.531 32268 Z= 0.306 Chirality : 0.043 0.258 3742 Planarity : 0.004 0.058 3978 Dihedral : 5.154 63.366 3082 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 3.64 % Allowed : 20.81 % Favored : 75.55 % 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: -1.11 (0.16), residues: 2834 helix: 0.14 (0.19), residues: 793 sheet: -0.27 (0.18), residues: 797 loop : -1.59 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 299 TYR 0.019 0.001 TYR M 94 PHE 0.024 0.001 PHE A 286 TRP 0.015 0.001 TRP H 110 HIS 0.006 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (23620) covalent geometry : angle 0.59514 / 0.30 (32205) SS BOND : bond 0.00949 / 0.45 ( 15) SS BOND : angle 1.95477 / 1.13 ( 30) hydrogen bonds : bond 0.04011 / 2.66 ( 847) hydrogen bonds : angle 4.70686 / 3.22 ( 2627) link_BETA1-4 : bond 0.00397 / 0.20 ( 6) link_BETA1-4 : angle 1.32108 / 0.68 ( 18) link_NAG-ASN : bond 0.00198 / 0.10 ( 5) link_NAG-ASN : angle 1.48961 / 0.80 ( 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 304 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 210 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.8610 (mtp) cc_final: 0.8324 (ttm) REVERT: B 324 MET cc_start: 0.5714 (ptp) cc_final: 0.5427 (ptt) REVERT: B 343 MET cc_start: 0.8100 (tpp) cc_final: 0.7679 (tpp) REVERT: C 95 TYR cc_start: 0.9028 (OUTLIER) cc_final: 0.8736 (m-10) REVERT: C 352 ILE cc_start: 0.9477 (OUTLIER) cc_final: 0.8760 (mt) REVERT: D 163 ILE cc_start: 0.9555 (OUTLIER) cc_final: 0.9272 (mt) REVERT: D 240 TYR cc_start: 0.8251 (t80) cc_final: 0.7604 (t80) REVERT: D 329 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8643 (mt) REVERT: E 95 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: H 108 GLU cc_start: 0.8553 (tt0) cc_final: 0.8099 (tm-30) REVERT: L 86 THR cc_start: 0.6138 (m) cc_final: 0.5691 (m) REVERT: L 88 TYR cc_start: 0.6303 (m-80) cc_final: 0.5770 (m-10) REVERT: L 105 LYS cc_start: 0.6645 (tppt) cc_final: 0.6226 (mtmt) REVERT: L 169 ASP cc_start: 0.6608 (m-30) cc_final: 0.6314 (m-30) REVERT: K 54 ILE cc_start: 0.8815 (tp) cc_final: 0.8382 (mp) outliers start: 94 outliers final: 69 residues processed: 290 average time/residue: 0.1382 time to fit residues: 66.9109 Evaluate side-chains 276 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 202 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 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 225 ILE Chi-restraints excluded: chain A residue 230 LEU 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 293 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 460 ILE 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 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 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 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 359 ILE 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 180 ILE 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 40 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 47 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 275 optimal weight: 30.0000 chunk 4 optimal weight: 0.0470 chunk 35 optimal weight: 0.5980 chunk 190 optimal weight: 0.5980 chunk 256 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 174 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3983 r_free = 0.3983 target = 0.145954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.101714 restraints weight = 61571.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.099966 restraints weight = 36512.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.099979 restraints weight = 28158.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.100775 restraints weight = 25446.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.100827 restraints weight = 19197.480| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.119 23646 Z= 0.123 Angle : 0.595 12.338 32268 Z= 0.303 Chirality : 0.043 0.261 3742 Planarity : 0.004 0.056 3978 Dihedral : 5.054 71.674 3082 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.12 % Rotamer: Outliers : 3.71 % Allowed : 20.97 % 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: -0.91 (0.16), residues: 2834 helix: 0.42 (0.19), residues: 785 sheet: -0.16 (0.18), residues: 791 loop : -1.54 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 101 TYR 0.022 0.001 TYR K 53 PHE 0.024 0.001 PHE A 286 TRP 0.016 0.001 TRP H 110 HIS 0.007 0.001 HIS C 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (23620) covalent geometry : angle 0.58730 / 0.30 (32205) SS BOND : bond 0.00960 / 0.46 ( 15) SS BOND : angle 2.85368 / 1.68 ( 30) hydrogen bonds : bond 0.03856 / 2.54 ( 847) hydrogen bonds : angle 4.58414 / 3.14 ( 2627) link_BETA1-4 : bond 0.00486 / 0.23 ( 6) link_BETA1-4 : angle 1.29931 / 0.67 ( 18) link_NAG-ASN : bond 0.00129 / 0.06 ( 5) link_NAG-ASN : angle 1.51742 / 0.81 ( 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 307 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 211 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 TRP cc_start: 0.7761 (t-100) cc_final: 0.7337 (t-100) REVERT: B 77 MET cc_start: 0.8866 (mtp) cc_final: 0.8567 (ttm) REVERT: B 324 MET cc_start: 0.5573 (ptp) cc_final: 0.5300 (ptt) REVERT: B 343 MET cc_start: 0.8139 (tpp) cc_final: 0.7732 (tpp) REVERT: C 95 TYR cc_start: 0.8919 (OUTLIER) cc_final: 0.8675 (m-10) REVERT: C 352 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.8794 (mt) REVERT: D 163 ILE cc_start: 0.9551 (OUTLIER) cc_final: 0.9309 (mt) REVERT: D 240 TYR cc_start: 0.8339 (t80) cc_final: 0.7540 (t80) REVERT: E 95 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.7977 (m-80) REVERT: E 268 ASP cc_start: 0.8123 (t0) cc_final: 0.7255 (m-30) REVERT: H 108 GLU cc_start: 0.8593 (tt0) cc_final: 0.8105 (tm-30) REVERT: L 86 THR cc_start: 0.6285 (m) cc_final: 0.5744 (m) REVERT: L 88 TYR cc_start: 0.6845 (m-80) cc_final: 0.6241 (m-10) REVERT: L 105 LYS cc_start: 0.6632 (tppt) cc_final: 0.6282 (mtmt) REVERT: L 169 ASP cc_start: 0.6731 (m-30) cc_final: 0.6404 (m-30) REVERT: K 53 TYR cc_start: 0.7446 (p90) cc_final: 0.6658 (p90) REVERT: K 54 ILE cc_start: 0.8884 (tp) cc_final: 0.8462 (mp) outliers start: 96 outliers final: 74 residues processed: 289 average time/residue: 0.1336 time to fit residues: 64.2216 Evaluate side-chains 279 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 201 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 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 230 LEU 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 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 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 103 GLU Chi-restraints excluded: chain C residue 145 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 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 405 HIS Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 481 TRP Chi-restraints excluded: chain E residue 61 GLU 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 248 LEU 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 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 47 LEU 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 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 Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 86 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 166 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 255 optimal weight: 0.0000 chunk 83 optimal weight: 0.0000 chunk 66 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 chunk 216 optimal weight: 50.0000 chunk 43 optimal weight: 0.0020 chunk 132 optimal weight: 0.5980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.147060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.109914 restraints weight = 62617.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.107766 restraints weight = 34593.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.107213 restraints weight = 36100.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.107580 restraints weight = 25825.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.108230 restraints weight = 18489.479| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 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 = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.134 23646 Z= 0.106 Angle : 0.584 13.082 32268 Z= 0.295 Chirality : 0.042 0.268 3742 Planarity : 0.004 0.054 3978 Dihedral : 4.872 72.369 3082 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.43 % Favored : 96.54 % Rotamer: Outliers : 2.79 % Allowed : 22.05 % Favored : 75.16 % 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: -0.73 (0.16), residues: 2834 helix: 0.62 (0.19), residues: 787 sheet: -0.02 (0.18), residues: 787 loop : -1.49 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 299 TYR 0.025 0.001 TYR M 94 PHE 0.023 0.001 PHE A 286 TRP 0.014 0.001 TRP H 110 HIS 0.007 0.001 HIS C 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (23620) covalent geometry : angle 0.57639 / 0.29 (32205) SS BOND : bond 0.00921 / 0.44 ( 15) SS BOND : angle 2.91134 / 1.71 ( 30) hydrogen bonds : bond 0.03475 / 2.29 ( 847) hydrogen bonds : angle 4.42320 / 3.03 ( 2627) link_BETA1-4 : bond 0.00469 / 0.23 ( 6) link_BETA1-4 : angle 1.22328 / 0.63 ( 18) link_NAG-ASN : bond 0.00076 / 0.04 ( 5) link_NAG-ASN : angle 1.42944 / 0.76 ( 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 311 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 239 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 ASN cc_start: 0.8329 (t0) cc_final: 0.7948 (t0) REVERT: A 349 TRP cc_start: 0.7734 (t-100) cc_final: 0.7448 (t-100) REVERT: A 405 HIS cc_start: 0.8892 (m90) cc_final: 0.8553 (t70) REVERT: B 77 MET cc_start: 0.8763 (mtp) cc_final: 0.8436 (ttm) REVERT: B 324 MET cc_start: 0.5656 (ptp) cc_final: 0.5372 (ptt) REVERT: B 343 MET cc_start: 0.8192 (tpp) cc_final: 0.7987 (tpt) REVERT: C 95 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.8583 (m-10) REVERT: D 163 ILE cc_start: 0.9557 (OUTLIER) cc_final: 0.9305 (mt) REVERT: D 240 TYR cc_start: 0.8192 (t80) cc_final: 0.7495 (t80) REVERT: E 95 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: E 107 TYR cc_start: 0.8943 (m-80) cc_final: 0.8681 (m-10) REVERT: E 268 ASP cc_start: 0.8051 (t0) cc_final: 0.7211 (m-30) REVERT: H 112 LYS cc_start: 0.8177 (mttt) cc_final: 0.7368 (mmtm) REVERT: L 86 THR cc_start: 0.5928 (m) cc_final: 0.5392 (m) REVERT: L 88 TYR cc_start: 0.6684 (m-80) cc_final: 0.6088 (m-10) REVERT: L 105 LYS cc_start: 0.6725 (tppt) cc_final: 0.6478 (mtmt) REVERT: L 169 ASP cc_start: 0.6653 (m-30) cc_final: 0.6339 (m-30) REVERT: K 53 TYR cc_start: 0.7456 (p90) cc_final: 0.6739 (p90) REVERT: K 54 ILE cc_start: 0.8879 (tp) cc_final: 0.8477 (mp) REVERT: K 83 TYR cc_start: 0.6214 (m-80) cc_final: 0.5865 (t80) outliers start: 72 outliers final: 53 residues processed: 300 average time/residue: 0.1385 time to fit residues: 69.0379 Evaluate side-chains 265 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 209 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 83 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 194 THR 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 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 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 257 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 269 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 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 163 ILE Chi-restraints excluded: chain D residue 326 VAL 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 214 ILE 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 40 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 32 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 Chi-restraints excluded: chain M residue 59 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 150 optimal weight: 0.5980 chunk 151 optimal weight: 0.7980 chunk 233 optimal weight: 10.0000 chunk 272 optimal weight: 30.0000 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 234 optimal weight: 0.7980 chunk 273 optimal weight: 5.9990 chunk 279 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4022 r_free = 0.4022 target = 0.147950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.115486 restraints weight = 74422.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.109967 restraints weight = 58383.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.111305 restraints weight = 39036.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111078 restraints weight = 24306.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.111858 restraints weight = 21577.347| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 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 = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 23646 Z= 0.168 Angle : 0.640 13.194 32268 Z= 0.321 Chirality : 0.044 0.256 3742 Planarity : 0.004 0.057 3978 Dihedral : 4.961 72.347 3082 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 2.90 % Allowed : 22.55 % Favored : 74.55 % 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: -0.72 (0.16), residues: 2834 helix: 0.62 (0.19), residues: 789 sheet: -0.02 (0.18), residues: 791 loop : -1.49 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 101 TYR 0.020 0.001 TYR K 53 PHE 0.023 0.001 PHE A 286 TRP 0.017 0.001 TRP D 349 HIS 0.006 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (23620) covalent geometry : angle 0.63089 / 0.32 (32205) SS BOND : bond 0.00977 / 0.45 ( 15) SS BOND : angle 3.29737 / 1.92 ( 30) hydrogen bonds : bond 0.04029 / 2.67 ( 847) hydrogen bonds : angle 4.53155 / 3.11 ( 2627) link_BETA1-4 : bond 0.00407 / 0.20 ( 6) link_BETA1-4 : angle 1.34440 / 0.69 ( 18) link_NAG-ASN : bond 0.00233 / 0.12 ( 5) link_NAG-ASN : angle 1.54070 / 0.82 ( 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 284 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 209 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 349 TRP cc_start: 0.7663 (t-100) cc_final: 0.7417 (t-100) REVERT: A 405 HIS cc_start: 0.8819 (m90) cc_final: 0.8498 (t70) REVERT: A 408 ASP cc_start: 0.8002 (p0) cc_final: 0.7751 (m-30) REVERT: B 324 MET cc_start: 0.5802 (ptp) cc_final: 0.5514 (ptt) REVERT: B 343 MET cc_start: 0.8039 (tpp) cc_final: 0.7663 (tpp) REVERT: C 352 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.8664 (mt) REVERT: D 163 ILE cc_start: 0.9575 (OUTLIER) cc_final: 0.9315 (mt) REVERT: D 240 TYR cc_start: 0.8197 (t80) cc_final: 0.7601 (t80) REVERT: D 329 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8729 (mt) REVERT: E 95 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.8162 (m-80) REVERT: E 268 ASP cc_start: 0.7988 (t0) cc_final: 0.7136 (m-30) REVERT: H 108 GLU cc_start: 0.8419 (tt0) cc_final: 0.8066 (tm-30) REVERT: L 86 THR cc_start: 0.5923 (m) cc_final: 0.5038 (t) REVERT: L 88 TYR cc_start: 0.6562 (m-80) cc_final: 0.5749 (m-10) REVERT: L 169 ASP cc_start: 0.6550 (m-30) cc_final: 0.6236 (m-30) REVERT: K 53 TYR cc_start: 0.7325 (p90) cc_final: 0.6681 (p90) REVERT: K 54 ILE cc_start: 0.8774 (tp) cc_final: 0.8461 (mp) REVERT: K 86 MET cc_start: 0.5743 (mpp) cc_final: 0.5098 (mpp) outliers start: 75 outliers final: 63 residues processed: 274 average time/residue: 0.1264 time to fit residues: 58.4148 Evaluate side-chains 272 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 205 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 194 THR 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 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 37 VAL Chi-restraints excluded: chain B residue 214 ILE 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 103 GLU 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 265 THR Chi-restraints excluded: chain C residue 269 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 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 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 61 GLU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 248 LEU 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 40 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 12 LEU 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 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: 0.8980 chunk 140 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 109 optimal weight: 0.4980 chunk 89 optimal weight: 0.0270 chunk 148 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 129 optimal weight: 0.0970 chunk 82 optimal weight: 0.7980 chunk 231 optimal weight: 5.9990 chunk 246 optimal weight: 10.0000 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 353 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.146505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.110329 restraints weight = 67471.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106238 restraints weight = 41637.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.106892 restraints weight = 39759.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.107043 restraints weight = 27338.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.107955 restraints weight = 20787.021| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 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 = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.130 23646 Z= 0.113 Angle : 0.610 13.011 32268 Z= 0.304 Chirality : 0.043 0.259 3742 Planarity : 0.004 0.054 3978 Dihedral : 4.854 72.582 3082 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.71 % Favored : 96.26 % Rotamer: Outliers : 2.51 % Allowed : 23.02 % Favored : 74.47 % 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: -0.57 (0.16), residues: 2834 helix: 0.76 (0.20), residues: 791 sheet: 0.08 (0.18), residues: 792 loop : -1.43 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 101 TYR 0.024 0.001 TYR M 94 PHE 0.023 0.001 PHE C 359 TRP 0.016 0.001 TRP D 349 HIS 0.005 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (23620) covalent geometry : angle 0.60012 / 0.30 (32205) SS BOND : bond 0.01000 / 0.45 ( 15) SS BOND : angle 3.35473 / 1.95 ( 30) hydrogen bonds : bond 0.03602 / 2.37 ( 847) hydrogen bonds : angle 4.38870 / 3.01 ( 2627) link_BETA1-4 : bond 0.00444 / 0.22 ( 6) link_BETA1-4 : angle 1.24590 / 0.64 ( 18) link_NAG-ASN : bond 0.00076 / 0.04 ( 5) link_NAG-ASN : angle 1.44052 / 0.76 ( 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: 65 poor density : 214 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 101 ASN cc_start: 0.8312 (t0) cc_final: 0.7933 (t0) REVERT: A 349 TRP cc_start: 0.7800 (t-100) cc_final: 0.7501 (t-100) REVERT: A 408 ASP cc_start: 0.8141 (p0) cc_final: 0.7813 (m-30) REVERT: B 324 MET cc_start: 0.5818 (ptp) cc_final: 0.5451 (ptt) REVERT: C 352 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.8640 (mt) REVERT: D 163 ILE cc_start: 0.9564 (OUTLIER) cc_final: 0.9326 (mt) REVERT: D 240 TYR cc_start: 0.8145 (t80) cc_final: 0.7508 (t80) REVERT: D 329 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8701 (mt) REVERT: E 95 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.7975 (m-80) REVERT: E 268 ASP cc_start: 0.8021 (t0) cc_final: 0.7199 (m-30) REVERT: H 108 GLU cc_start: 0.8475 (tt0) cc_final: 0.8060 (tm-30) REVERT: L 88 TYR cc_start: 0.6588 (m-80) cc_final: 0.5909 (m-10) REVERT: L 105 LYS cc_start: 0.6939 (mmmt) cc_final: 0.5795 (mtmt) REVERT: L 169 ASP cc_start: 0.6608 (m-30) cc_final: 0.6309 (m-30) REVERT: K 53 TYR cc_start: 0.7435 (p90) cc_final: 0.6855 (p90) REVERT: K 54 ILE cc_start: 0.8830 (tp) cc_final: 0.8440 (mp) REVERT: K 86 MET cc_start: 0.5503 (mpp) cc_final: 0.4880 (mpp) outliers start: 65 outliers final: 59 residues processed: 268 average time/residue: 0.1215 time to fit residues: 55.1614 Evaluate side-chains 272 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 209 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 83 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 194 THR 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 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 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 103 GLU 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 257 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 321 LEU 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 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 481 TRP Chi-restraints excluded: chain E residue 61 GLU 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 313 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 84 PHE 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: 10.0000 chunk 14 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4031 r_free = 0.4031 target = 0.148392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113016 restraints weight = 63296.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111104 restraints weight = 38496.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109534 restraints weight = 35764.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.109461 restraints weight = 35853.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.109831 restraints weight = 25235.985| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 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 = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 23646 Z= 0.139 Angle : 0.636 15.375 32268 Z= 0.316 Chirality : 0.043 0.259 3742 Planarity : 0.004 0.055 3978 Dihedral : 4.872 72.560 3082 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.87 % Rotamer: Outliers : 2.75 % Allowed : 23.06 % Favored : 74.20 % 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: -0.56 (0.16), residues: 2834 helix: 0.80 (0.20), residues: 791 sheet: 0.05 (0.18), residues: 799 loop : -1.41 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 376 TYR 0.027 0.001 TYR M 94 PHE 0.023 0.001 PHE A 286 TRP 0.020 0.001 TRP D 349 HIS 0.005 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (23620) covalent geometry : angle 0.62659 / 0.31 (32205) SS BOND : bond 0.00964 / 0.44 ( 15) SS BOND : angle 3.31946 / 1.93 ( 30) hydrogen bonds : bond 0.03869 / 2.56 ( 847) hydrogen bonds : angle 4.45640 / 3.04 ( 2627) link_BETA1-4 : bond 0.00395 / 0.18 ( 6) link_BETA1-4 : angle 1.31869 / 0.68 ( 18) link_NAG-ASN : bond 0.00197 / 0.10 ( 5) link_NAG-ASN : angle 1.50646 / 0.80 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4283.28 seconds wall clock time: 74 minutes 47.83 seconds (4487.83 seconds total)