Starting phenix.real_space_refine on Tue Aug 26 12:29:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itu_60879/08_2025/9itu_60879.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itu_60879/08_2025/9itu_60879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9itu_60879/08_2025/9itu_60879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itu_60879/08_2025/9itu_60879.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9itu_60879/08_2025/9itu_60879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itu_60879/08_2025/9itu_60879.map" } resolution = 3.18 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= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 5 5.21 5 S 87 5.16 5 C 23269 2.51 5 N 6574 2.21 5 O 7090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37039 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3749 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 25, 'TRANS': 467} Chain: "B" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3793 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 26, 'TRANS': 471} Chain: "C" Number of atoms: 3948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3948 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 26, 'TRANS': 491} Chain: "D" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3593 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 438} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3593 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 438} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3608 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 440} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 980 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 123} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "S" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 538 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "W" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 549 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "G" Number of atoms: 2215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2215 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain: "Y" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 763 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 1, 'TRANS': 151} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 468 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 12, 'ASN:plan1': 4, 'ARG:plan': 20, 'TYR:plan': 2, 'GLU:plan': 20, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 289 Chain: "V" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 758 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 2, 'TRANS': 149} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 468 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'ASN:plan1': 5, 'PHE:plan': 3, 'GLN:plan1': 12, 'ARG:plan': 20, 'TYR:plan': 2, 'GLU:plan': 20, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 292 Chain: "U" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 713 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 1, 'TRANS': 141} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 437 Unresolved non-hydrogen angles: 545 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'ASN:plan1': 4, 'PHE:plan': 2, 'ARG:plan': 20, 'TYR:plan': 2, 'GLU:plan': 20, 'ASP:plan': 4, 'GLN:plan1': 11, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 279 Chain: "X" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 758 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'PTRANS': 1, 'TRANS': 150} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 465 Unresolved non-hydrogen angles: 582 Unresolved non-hydrogen dihedrals: 363 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 12, 'ASN:plan1': 4, 'ARG:plan': 20, 'TYR:plan': 2, 'GLU:plan': 20, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 289 Chain: "T" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1093 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 700 Unresolved non-hydrogen angles: 918 Unresolved non-hydrogen dihedrals: 588 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 9, 'PHE:plan': 31, 'ASP:plan': 3, 'ASN:plan1': 12, 'ARG:plan': 5, 'GLN:plan1': 3, 'TYR:plan': 6, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 369 Chain: "H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 480 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "J" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "K" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "M" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "N" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "O" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "P" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "Q" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "Z" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1206 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 199} Link IDs: {'PTRANS': 14, 'TRANS': 230} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 773 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 654 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'PHE:plan': 34, 'TYR:plan': 7, 'HIS:plan': 1, 'GLU:plan': 9, 'ASP:plan': 3, 'ASN:plan1': 12, 'ARG:plan': 6, 'GLN:plan1': 4, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 403 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.32, per 1000 atoms: 0.20 Number of scatterers: 37039 At special positions: 0 Unit cell: (126.48, 137.64, 229.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 87 16.00 P 14 15.00 Mg 5 11.99 O 7090 8.00 N 6574 7.00 C 23269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 238.4 nanoseconds 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9566 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 32 sheets defined 59.3% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.891A pdb=" N THR A 88 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.661A pdb=" N LEU A 110 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 208 through 222 Processing helix chain 'A' and resid 223 through 226 Processing helix chain 'A' and resid 244 through 259 Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.513A pdb=" N HIS A 281 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 304 through 315 removed outlier: 4.115A pdb=" N ARG A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 324 removed outlier: 3.725A pdb=" N GLY A 324 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 360 through 366 Processing helix chain 'A' and resid 387 through 408 removed outlier: 4.599A pdb=" N LYS A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 removed outlier: 3.915A pdb=" N GLN A 412 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 436 Processing helix chain 'A' and resid 444 through 457 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 467 through 482 Processing helix chain 'A' and resid 483 through 493 removed outlier: 3.595A pdb=" N ARG A 487 " --> pdb=" O HIS A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 519 Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.576A pdb=" N GLN B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 222 Processing helix chain 'B' and resid 223 through 226 removed outlier: 3.940A pdb=" N GLU B 226 " --> pdb=" O GLY B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'B' and resid 246 through 259 removed outlier: 5.923A pdb=" N MET B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 302 through 303 No H-bonds generated for 'chain 'B' and resid 302 through 303' Processing helix chain 'B' and resid 304 through 315 removed outlier: 3.921A pdb=" N ARG B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 360 through 366 Processing helix chain 'B' and resid 381 through 386 Processing helix chain 'B' and resid 387 through 407 removed outlier: 3.564A pdb=" N GLY B 395 " --> pdb=" O ARG B 391 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS B 396 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN B 403 " --> pdb=" O GLY B 399 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 414 removed outlier: 4.210A pdb=" N PHE B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 435 Processing helix chain 'B' and resid 444 through 457 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 467 through 482 Processing helix chain 'B' and resid 483 through 493 removed outlier: 4.264A pdb=" N ARG B 487 " --> pdb=" O HIS B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 506 Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'C' and resid 5 through 12 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 157 through 164 Processing helix chain 'C' and resid 181 through 192 Processing helix chain 'C' and resid 208 through 222 Processing helix chain 'C' and resid 238 through 259 Proline residue: C 246 - end of helix Processing helix chain 'C' and resid 277 through 292 Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 304 through 314 Processing helix chain 'C' and resid 343 through 353 Processing helix chain 'C' and resid 360 through 366 Processing helix chain 'C' and resid 381 through 386 removed outlier: 3.994A pdb=" N ALA C 384 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 407 removed outlier: 3.787A pdb=" N GLY C 395 " --> pdb=" O ARG C 391 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LYS C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 414 removed outlier: 3.515A pdb=" N ALA C 411 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLN C 412 " --> pdb=" O ALA C 409 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 414 " --> pdb=" O ALA C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 436 Processing helix chain 'C' and resid 444 through 457 Processing helix chain 'C' and resid 464 through 466 No H-bonds generated for 'chain 'C' and resid 464 through 466' Processing helix chain 'C' and resid 467 through 482 Processing helix chain 'C' and resid 483 through 493 removed outlier: 3.671A pdb=" N ARG C 487 " --> pdb=" O HIS C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 519 Processing helix chain 'D' and resid 20 through 24 removed outlier: 4.024A pdb=" N VAL D 24 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 158 through 173 Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 209 through 212 Processing helix chain 'D' and resid 222 through 244 removed outlier: 4.725A pdb=" N GLY D 230 " --> pdb=" O ARG D 226 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE D 240 " --> pdb=" O MET D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 268 Processing helix chain 'D' and resid 280 through 291 removed outlier: 4.169A pdb=" N ARG D 291 " --> pdb=" O GLU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 323 removed outlier: 4.468A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 380 removed outlier: 3.648A pdb=" N ARG D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 388 Processing helix chain 'D' and resid 394 through 410 Processing helix chain 'D' and resid 433 through 443 Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 458 through 468 removed outlier: 3.612A pdb=" N ALA D 468 " --> pdb=" O ALA D 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'E' and resid 134 through 141 Processing helix chain 'E' and resid 158 through 173 Processing helix chain 'E' and resid 194 through 201 Processing helix chain 'E' and resid 207 through 210 Processing helix chain 'E' and resid 222 through 243 removed outlier: 4.846A pdb=" N GLY E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE E 240 " --> pdb=" O MET E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.800A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 288 Processing helix chain 'E' and resid 315 through 323 Processing helix chain 'E' and resid 333 through 338 removed outlier: 4.028A pdb=" N ARG E 338 " --> pdb=" O SER E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 380 removed outlier: 6.519A pdb=" N GLU E 361 " --> pdb=" O ASN E 357 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N GLU E 362 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N HIS E 363 " --> pdb=" O VAL E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 387 Processing helix chain 'E' and resid 388 through 392 Processing helix chain 'E' and resid 396 through 410 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 458 through 467 Processing helix chain 'F' and resid 20 through 24 removed outlier: 4.160A pdb=" N VAL F 24 " --> pdb=" O GLU F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 193 through 201 Processing helix chain 'F' and resid 208 through 210 No H-bonds generated for 'chain 'F' and resid 208 through 210' Processing helix chain 'F' and resid 222 through 243 removed outlier: 4.558A pdb=" N GLY F 230 " --> pdb=" O ARG F 226 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU F 231 " --> pdb=" O LEU F 227 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR F 239 " --> pdb=" O THR F 235 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE F 240 " --> pdb=" O MET F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 269 removed outlier: 3.767A pdb=" N PHE F 257 " --> pdb=" O ASN F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 291 removed outlier: 3.957A pdb=" N ARG F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 323 removed outlier: 4.259A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 380 Processing helix chain 'F' and resid 380 through 387 Processing helix chain 'F' and resid 393 through 410 Processing helix chain 'F' and resid 414 through 418 removed outlier: 3.804A pdb=" N GLN F 418 " --> pdb=" O THR F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 443 Processing helix chain 'F' and resid 449 through 454 Processing helix chain 'F' and resid 458 through 470 removed outlier: 3.642A pdb=" N VAL F 462 " --> pdb=" O ASP F 458 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 92 removed outlier: 4.049A pdb=" N ARG R 91 " --> pdb=" O ILE R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 100 Processing helix chain 'R' and resid 107 through 128 removed outlier: 3.748A pdb=" N LEU R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 109 Processing helix chain 'S' and resid 110 through 112 No H-bonds generated for 'chain 'S' and resid 110 through 112' Processing helix chain 'S' and resid 143 through 154 Processing helix chain 'W' and resid 98 through 109 Processing helix chain 'W' and resid 142 through 152 removed outlier: 3.688A pdb=" N ARG W 146 " --> pdb=" O SER W 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 60 Proline residue: G 44 - end of helix removed outlier: 4.323A pdb=" N GLU G 51 " --> pdb=" O ASP G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 71 removed outlier: 3.586A pdb=" N GLU G 71 " --> pdb=" O THR G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 112 Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 148 through 165 removed outlier: 3.865A pdb=" N ILE G 152 " --> pdb=" O LYS G 148 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL G 155 " --> pdb=" O ALA G 151 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER G 158 " --> pdb=" O GLY G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 286 Proline residue: G 222 - end of helix Processing helix chain 'Y' and resid 9 through 29 removed outlier: 3.690A pdb=" N ALA Y 27 " --> pdb=" O PHE Y 23 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU Y 29 " --> pdb=" O LEU Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 139 Processing helix chain 'Y' and resid 140 through 146 Processing helix chain 'Y' and resid 148 through 160 Processing helix chain 'V' and resid 8 through 29 Processing helix chain 'V' and resid 29 through 113 removed outlier: 3.572A pdb=" N ARG V 62 " --> pdb=" O LEU V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 113 through 121 removed outlier: 4.045A pdb=" N ARG V 117 " --> pdb=" O ALA V 113 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 138 Processing helix chain 'V' and resid 148 through 158 Processing helix chain 'U' and resid 19 through 123 removed outlier: 4.101A pdb=" N PHE U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE U 24 " --> pdb=" O LEU U 20 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) Proline residue: U 32 - end of helix removed outlier: 3.914A pdb=" N ASN U 35 " --> pdb=" O ARG U 31 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG U 43 " --> pdb=" O GLU U 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 123 through 137 Processing helix chain 'U' and resid 148 through 156 Processing helix chain 'X' and resid 10 through 148 Proline residue: X 32 - end of helix Processing helix chain 'X' and resid 149 through 158 removed outlier: 3.791A pdb=" N LEU X 152 " --> pdb=" O HIS X 149 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE X 153 " --> pdb=" O ASP X 150 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU X 157 " --> pdb=" O ALA X 154 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA X 158 " --> pdb=" O GLU X 155 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 71 Processing helix chain 'T' and resid 79 through 99 removed outlier: 4.184A pdb=" N MET T 84 " --> pdb=" O LEU T 80 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU T 89 " --> pdb=" O GLU T 85 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER T 90 " --> pdb=" O PHE T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 114 Processing helix chain 'T' and resid 117 through 125 Processing helix chain 'T' and resid 190 through 209 Processing helix chain 'T' and resid 214 through 219 removed outlier: 4.433A pdb=" N TYR T 217 " --> pdb=" O GLY T 214 " (cutoff:3.500A) Processing helix chain 'T' and resid 231 through 252 Proline residue: T 243 - end of helix Processing helix chain 'T' and resid 253 through 267 Processing helix chain 'T' and resid 275 through 304 Processing helix chain 'H' and resid 3 through 38 removed outlier: 3.707A pdb=" N VAL H 7 " --> pdb=" O GLY H 3 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLY H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Proline residue: H 20 - end of helix removed outlier: 3.741A pdb=" N ILE H 26 " --> pdb=" O VAL H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 72 removed outlier: 3.636A pdb=" N ILE H 51 " --> pdb=" O THR H 47 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY H 52 " --> pdb=" O TYR H 48 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR H 56 " --> pdb=" O GLY H 52 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU H 59 " --> pdb=" O PHE H 55 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 37 removed outlier: 4.630A pdb=" N GLY I 19 " --> pdb=" O LEU I 15 " (cutoff:3.500A) Proline residue: I 20 - end of helix removed outlier: 3.891A pdb=" N GLY I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE I 26 " --> pdb=" O VAL I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 40 No H-bonds generated for 'chain 'I' and resid 38 through 40' Processing helix chain 'I' and resid 41 through 72 Processing helix chain 'J' and resid 3 through 38 Proline residue: J 20 - end of helix removed outlier: 4.260A pdb=" N GLY J 23 " --> pdb=" O GLY J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 72 removed outlier: 3.745A pdb=" N PHE J 50 " --> pdb=" O VAL J 46 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE J 51 " --> pdb=" O THR J 47 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY J 52 " --> pdb=" O TYR J 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 38 removed outlier: 4.434A pdb=" N GLY K 19 " --> pdb=" O LEU K 15 " (cutoff:3.500A) Proline residue: K 20 - end of helix Processing helix chain 'K' and resid 41 through 72 removed outlier: 3.643A pdb=" N LEU K 59 " --> pdb=" O PHE K 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 38 removed outlier: 4.177A pdb=" N VAL L 7 " --> pdb=" O GLY L 3 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLY L 19 " --> pdb=" O LEU L 15 " (cutoff:3.500A) Proline residue: L 20 - end of helix Processing helix chain 'L' and resid 41 through 72 removed outlier: 4.232A pdb=" N THR L 47 " --> pdb=" O ASN L 43 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY L 71 " --> pdb=" O ALA L 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 38 removed outlier: 3.953A pdb=" N GLY M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Proline residue: M 20 - end of helix removed outlier: 3.653A pdb=" N GLY M 25 " --> pdb=" O GLY M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 72 removed outlier: 4.277A pdb=" N ILE M 66 " --> pdb=" O PHE M 62 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA M 67 " --> pdb=" O GLY M 63 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE M 68 " --> pdb=" O LEU M 64 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY M 71 " --> pdb=" O ALA M 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 17 through 38 removed outlier: 3.737A pdb=" N VAL N 28 " --> pdb=" O ILE N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 72 removed outlier: 3.761A pdb=" N GLY N 52 " --> pdb=" O TYR N 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 17 Processing helix chain 'O' and resid 18 through 38 removed outlier: 3.562A pdb=" N SER O 29 " --> pdb=" O GLY O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 72 removed outlier: 4.177A pdb=" N LEU O 59 " --> pdb=" O PHE O 55 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA O 60 " --> pdb=" O THR O 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 15 Processing helix chain 'P' and resid 17 through 38 removed outlier: 3.807A pdb=" N GLY P 25 " --> pdb=" O GLY P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 72 removed outlier: 3.580A pdb=" N PHE P 50 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE P 51 " --> pdb=" O THR P 47 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA P 67 " --> pdb=" O GLY P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 38 removed outlier: 4.596A pdb=" N GLY Q 19 " --> pdb=" O LEU Q 15 " (cutoff:3.500A) Proline residue: Q 20 - end of helix Processing helix chain 'Q' and resid 41 through 72 removed outlier: 3.678A pdb=" N LEU Q 59 " --> pdb=" O PHE Q 55 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE Q 72 " --> pdb=" O PHE Q 68 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 71 Processing helix chain 'Z' and resid 80 through 99 removed outlier: 4.308A pdb=" N MET Z 84 " --> pdb=" O LEU Z 80 " (cutoff:3.500A) Processing helix chain 'Z' and resid 106 through 114 removed outlier: 3.606A pdb=" N ILE Z 113 " --> pdb=" O LEU Z 109 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 122 Processing helix chain 'Z' and resid 190 through 213 Processing helix chain 'Z' and resid 213 through 220 Processing helix chain 'Z' and resid 233 through 267 Proline residue: Z 243 - end of helix removed outlier: 4.705A pdb=" N ILE Z 254 " --> pdb=" O LEU Z 250 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE Z 255 " --> pdb=" O PHE Z 251 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLY Z 257 " --> pdb=" O ASN Z 253 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA Z 265 " --> pdb=" O LEU Z 261 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU Z 267 " --> pdb=" O VAL Z 263 " (cutoff:3.500A) Processing helix chain 'Z' and resid 272 through 304 removed outlier: 3.542A pdb=" N PHE Z 276 " --> pdb=" O LEU Z 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR Z 296 " --> pdb=" O ALA Z 292 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 5.601A pdb=" N ARG A 100 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 52 " --> pdb=" O ALA A 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 5 through 11 current: chain 'A' and resid 39 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 31 removed outlier: 5.601A pdb=" N ARG A 100 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 52 " --> pdb=" O ALA A 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 73 current: chain 'F' and resid 29 through 33 removed outlier: 4.940A pdb=" N ASN F 29 " --> pdb=" O VAL F 45 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS F 55 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLN F 48 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL F 53 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL F 14 " --> pdb=" O ILE F 10 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE F 10 " --> pdb=" O VAL F 14 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG F 16 " --> pdb=" O GLN F 8 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 5 through 11 current: chain 'A' and resid 39 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 106 removed outlier: 4.513A pdb=" N LYS A 132 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.525A pdb=" N TYR A 275 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU A 173 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 261 through 263 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.580A pdb=" N VAL B 95 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR B 98 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE B 53 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU B 52 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG D 16 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE D 10 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL D 14 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL D 57 " --> pdb=" O VAL D 45 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL D 45 " --> pdb=" O VAL D 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 35 removed outlier: 3.556A pdb=" N ALA B 34 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 77 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE B 81 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ALA B 70 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.668A pdb=" N ARG B 134 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS B 132 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AB1, first strand: chain 'B' and resid 261 through 263 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.674A pdb=" N SER C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU C 73 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA C 79 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG E 16 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE E 10 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL E 14 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL E 57 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL E 45 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 31 through 32 removed outlier: 4.221A pdb=" N GLU C 52 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE C 53 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR C 98 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER C 97 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASN C 28 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA W 89 " --> pdb=" O THR W 119 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N HIS W 121 " --> pdb=" O ALA W 89 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL W 91 " --> pdb=" O HIS W 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 103 through 106 removed outlier: 4.912A pdb=" N LYS C 132 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 114 through 115 removed outlier: 6.288A pdb=" N CYS C 200 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL C 231 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TYR C 202 " --> pdb=" O VAL C 231 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 333 through 336 removed outlier: 8.494A pdb=" N ILE C 334 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE C 174 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR C 336 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY C 176 " --> pdb=" O THR C 336 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 261 through 263 Processing sheet with id=AB8, first strand: chain 'D' and resid 33 through 34 Processing sheet with id=AB9, first strand: chain 'D' and resid 79 through 81 Processing sheet with id=AC1, first strand: chain 'D' and resid 90 through 91 removed outlier: 6.250A pdb=" N LYS D 148 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE D 329 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA D 150 " --> pdb=" O ILE D 329 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 202 through 203 Processing sheet with id=AC3, first strand: chain 'E' and resid 79 through 81 Processing sheet with id=AC4, first strand: chain 'E' and resid 90 through 91 removed outlier: 6.240A pdb=" N PHE E 91 " --> pdb=" O PHE E 216 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLN E 218 " --> pdb=" O PHE E 91 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE E 177 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU E 248 " --> pdb=" O PHE E 177 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N MET E 303 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU E 249 " --> pdb=" O MET E 303 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 129 through 130 removed outlier: 4.272A pdb=" N PHE E 143 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 150 through 151 removed outlier: 5.886A pdb=" N ALA E 150 " --> pdb=" O ILE E 329 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 79 through 82 removed outlier: 3.855A pdb=" N GLU F 109 " --> pdb=" O VAL F 82 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 90 through 91 removed outlier: 6.707A pdb=" N SER F 178 " --> pdb=" O VAL F 213 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N VAL F 215 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE F 180 " --> pdb=" O VAL F 215 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 304 through 305 removed outlier: 6.483A pdb=" N THR F 149 " --> pdb=" O GLN F 304 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'R' and resid 13 through 15 removed outlier: 6.717A pdb=" N ILE R 7 " --> pdb=" O ILE R 14 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE R 3 " --> pdb=" O VAL R 19 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL R 19 " --> pdb=" O ILE R 3 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 13 through 15 removed outlier: 6.717A pdb=" N ILE R 7 " --> pdb=" O ILE R 14 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY R 65 " --> pdb=" O LEU R 44 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 31 through 33 removed outlier: 4.089A pdb=" N MET R 21 " --> pdb=" O ILE R 52 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE R 51 " --> pdb=" O THR R 58 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR R 58 " --> pdb=" O ILE R 51 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 117 through 121 removed outlier: 3.549A pdb=" N THR S 92 " --> pdb=" O ILE S 131 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL S 134 " --> pdb=" O GLN S 137 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 139 through 140 removed outlier: 8.709A pdb=" N ALA G 140 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR G 120 " --> pdb=" O ALA G 140 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL G 79 " --> pdb=" O ASP G 117 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N TYR G 119 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU G 81 " --> pdb=" O TYR G 119 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N PHE G 121 " --> pdb=" O LEU G 81 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL G 83 " --> pdb=" O PHE G 121 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N SER G 78 " --> pdb=" O GLU G 170 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N TYR G 172 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA G 80 " --> pdb=" O TYR G 172 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE G 174 " --> pdb=" O ALA G 80 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU G 82 " --> pdb=" O ILE G 174 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N SER G 176 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N VAL G 84 " --> pdb=" O SER G 176 " (cutoff:3.500A) 2488 hydrogen bonds defined for protein. 7242 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: 7.51 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6967 1.32 - 1.45: 8403 1.45 - 1.57: 21970 1.57 - 1.69: 16 1.69 - 1.81: 164 Bond restraints: 37520 Sorted by residual: bond pdb=" O4 PO4 D 503 " pdb=" P PO4 D 503 " ideal model delta sigma weight residual 1.568 1.504 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" N GLY E 153 " pdb=" CA GLY E 153 " ideal model delta sigma weight residual 1.444 1.476 -0.032 1.02e-02 9.61e+03 9.97e+00 bond pdb=" N VAL F 215 " pdb=" CA VAL F 215 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.14e-02 7.69e+03 9.92e+00 bond pdb=" O1 PO4 D 503 " pdb=" P PO4 D 503 " ideal model delta sigma weight residual 1.565 1.502 0.063 2.00e-02 2.50e+03 9.79e+00 bond pdb=" O3 PO4 D 503 " pdb=" P PO4 D 503 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.79e+00 ... (remaining 37515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 48882 1.65 - 3.30: 1836 3.30 - 4.94: 326 4.94 - 6.59: 55 6.59 - 8.24: 13 Bond angle restraints: 51112 Sorted by residual: angle pdb=" C MET Z 228 " pdb=" CA MET Z 228 " pdb=" CB MET Z 228 " ideal model delta sigma weight residual 116.54 109.41 7.13 1.15e+00 7.56e-01 3.85e+01 angle pdb=" N MET D 219 " pdb=" CA MET D 219 " pdb=" C MET D 219 " ideal model delta sigma weight residual 111.33 104.69 6.64 1.21e+00 6.83e-01 3.01e+01 angle pdb=" N GLY D 217 " pdb=" CA GLY D 217 " pdb=" C GLY D 217 " ideal model delta sigma weight residual 112.31 104.07 8.24 1.59e+00 3.96e-01 2.68e+01 angle pdb=" CA GLY D 217 " pdb=" C GLY D 217 " pdb=" O GLY D 217 " ideal model delta sigma weight residual 122.47 117.39 5.08 1.08e+00 8.57e-01 2.21e+01 angle pdb=" C SER C 43 " pdb=" CA SER C 43 " pdb=" CB SER C 43 " ideal model delta sigma weight residual 116.54 111.30 5.24 1.15e+00 7.56e-01 2.08e+01 ... (remaining 51107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 20914 18.00 - 36.00: 1374 36.00 - 54.00: 244 54.00 - 72.00: 52 72.00 - 90.00: 39 Dihedral angle restraints: 22623 sinusoidal: 7740 harmonic: 14883 Sorted by residual: dihedral pdb=" CA LEU D 139 " pdb=" C LEU D 139 " pdb=" N ILE D 140 " pdb=" CA ILE D 140 " ideal model delta harmonic sigma weight residual 180.00 153.82 26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ASP F 192 " pdb=" C ASP F 192 " pdb=" N LEU F 193 " pdb=" CA LEU F 193 " ideal model delta harmonic sigma weight residual 180.00 155.85 24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA TYR B 247 " pdb=" C TYR B 247 " pdb=" N ALA B 248 " pdb=" CA ALA B 248 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 22620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 5142 0.067 - 0.134: 896 0.134 - 0.200: 97 0.200 - 0.267: 10 0.267 - 0.334: 7 Chirality restraints: 6152 Sorted by residual: chirality pdb=" C2' ATP B 602 " pdb=" C1' ATP B 602 " pdb=" C3' ATP B 602 " pdb=" O2' ATP B 602 " both_signs ideal model delta sigma weight residual False -2.68 -3.01 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB ILE Q 41 " pdb=" CA ILE Q 41 " pdb=" CG1 ILE Q 41 " pdb=" CG2 ILE Q 41 " both_signs ideal model delta sigma weight residual False 2.64 2.96 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C2' ATP C 602 " pdb=" C1' ATP C 602 " pdb=" C3' ATP C 602 " pdb=" O2' ATP C 602 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 6149 not shown) Planarity restraints: 6786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN O 43 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C ASN O 43 " -0.058 2.00e-02 2.50e+03 pdb=" O ASN O 43 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG O 44 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 34 " 0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO R 35 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO R 35 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO R 35 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE I 53 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C ILE I 53 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE I 53 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA I 54 " 0.015 2.00e-02 2.50e+03 ... (remaining 6783 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 164 2.49 - 3.09: 29466 3.09 - 3.69: 58847 3.69 - 4.30: 82980 4.30 - 4.90: 137771 Nonbonded interactions: 309228 Sorted by model distance: nonbonded pdb="MG MG B 601 " pdb=" O2B ATP B 602 " model vdw 1.885 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1G ATP C 602 " model vdw 1.886 2.170 nonbonded pdb=" O1B ADP D 501 " pdb="MG MG D 502 " model vdw 1.910 2.170 nonbonded pdb=" O1B ADP F 501 " pdb="MG MG F 502 " model vdw 1.923 2.170 nonbonded pdb="MG MG D 502 " pdb=" O3 PO4 D 503 " model vdw 1.923 2.170 ... (remaining 309223 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 'B' and (resid 27 through 519 or resid 601 through 602)) selection = (chain 'C' and (resid 27 through 519 or resid 601 through 602)) } ncs_group { reference = (chain 'D' and resid 3 through 468) selection = chain 'E' selection = (chain 'F' and resid 3 through 468) } ncs_group { reference = chain 'H' selection = (chain 'I' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'J' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'K' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'L' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'M' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'N' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'O' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'P' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'Q' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) } ncs_group { reference = chain 'S' selection = (chain 'W' and resid 86 through 154) } ncs_group { reference = chain 'T' selection = (chain 'Z' and (resid 31 through 135 or resid 188 through 304)) } ncs_group { reference = (chain 'U' and resid 17 through 158) selection = (chain 'V' and resid 17 through 158) selection = (chain 'X' and resid 17 through 158) selection = (chain 'Y' and resid 17 through 158) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 29.900 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 : 0.006 0.064 37520 Z= 0.298 Angle : 0.757 8.239 51112 Z= 0.460 Chirality : 0.050 0.334 6152 Planarity : 0.005 0.071 6786 Dihedral : 13.391 89.997 13057 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.54 % Favored : 94.43 % Rotamer: Outliers : 0.12 % Allowed : 0.88 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.12), residues: 5184 helix: 1.60 (0.10), residues: 2827 sheet: -1.10 (0.24), residues: 484 loop : -1.22 (0.15), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 188 TYR 0.028 0.002 TYR E 377 PHE 0.022 0.002 PHE D 322 TRP 0.003 0.001 TRP C 471 HIS 0.008 0.002 HIS D 195 Details of bonding type rmsd covalent geometry : bond 0.00557 (37520) covalent geometry : angle 0.75697 (51112) hydrogen bonds : bond 0.14847 ( 2477) hydrogen bonds : angle 5.93929 ( 7242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 628 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8400 (p0) cc_final: 0.8175 (p0) REVERT: A 340 ASP cc_start: 0.8701 (t0) cc_final: 0.7933 (p0) REVERT: B 74 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8736 (mt-10) REVERT: B 376 ILE cc_start: 0.9085 (tp) cc_final: 0.8866 (pt) REVERT: B 464 PRO cc_start: 0.5590 (Cg_endo) cc_final: 0.5326 (Cg_exo) REVERT: D 51 ASN cc_start: 0.8745 (m110) cc_final: 0.8426 (p0) REVERT: D 311 ASP cc_start: 0.8324 (t0) cc_final: 0.7922 (t0) REVERT: E 189 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8458 (mt-10) REVERT: E 364 TYR cc_start: 0.8674 (t80) cc_final: 0.8373 (t80) REVERT: E 392 LEU cc_start: 0.9063 (mm) cc_final: 0.8824 (tp) REVERT: F 398 LEU cc_start: 0.9009 (tp) cc_final: 0.8784 (tp) REVERT: W 107 ARG cc_start: 0.7915 (ppt170) cc_final: 0.7671 (ptm-80) REVERT: W 110 GLN cc_start: 0.8895 (pt0) cc_final: 0.8335 (pp30) REVERT: W 151 GLN cc_start: 0.8597 (tt0) cc_final: 0.8283 (tp-100) REVERT: G 24 MET cc_start: 0.8393 (mmt) cc_final: 0.7912 (mtt) REVERT: G 50 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7913 (mtm-85) REVERT: G 157 ILE cc_start: 0.8475 (pt) cc_final: 0.8267 (pt) REVERT: G 261 ASP cc_start: 0.8748 (m-30) cc_final: 0.8523 (m-30) REVERT: H 35 ILE cc_start: 0.7439 (tp) cc_final: 0.6999 (tt) REVERT: I 64 LEU cc_start: 0.7450 (mm) cc_final: 0.7136 (mt) REVERT: J 48 TYR cc_start: 0.6710 (m-80) cc_final: 0.5709 (m-80) REVERT: L 44 ARG cc_start: 0.3541 (mmm160) cc_final: 0.3010 (mmp-170) REVERT: L 68 PHE cc_start: 0.7134 (m-80) cc_final: 0.6529 (t80) REVERT: N 32 VAL cc_start: 0.7512 (m) cc_final: 0.7190 (m) REVERT: N 48 TYR cc_start: 0.6192 (m-10) cc_final: 0.5850 (m-80) REVERT: O 41 ILE cc_start: 0.6404 (tp) cc_final: 0.5934 (mt) REVERT: O 53 ILE cc_start: 0.6982 (mt) cc_final: 0.6743 (mt) REVERT: Q 44 ARG cc_start: 0.7677 (tpt170) cc_final: 0.7439 (ttt180) REVERT: Q 56 THR cc_start: 0.7783 (p) cc_final: 0.7558 (p) outliers start: 4 outliers final: 1 residues processed: 632 average time/residue: 0.2099 time to fit residues: 214.8591 Evaluate side-chains 408 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 406 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 ARG Chi-restraints excluded: chain O residue 24 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 394 optimal weight: 50.0000 chunk 430 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 chunk 497 optimal weight: 50.0000 chunk 414 optimal weight: 50.0000 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 8.9990 chunk 223 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN B 309 HIS B 437 GLN D 29 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN D 412 GLN E 205 ASN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 GLN ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 ASN G 204 ASN H 5 ASN H 33 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.126022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.080162 restraints weight = 78320.812| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.93 r_work: 0.3051 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 37520 Z= 0.351 Angle : 0.736 8.254 51112 Z= 0.387 Chirality : 0.050 0.265 6152 Planarity : 0.005 0.063 6786 Dihedral : 6.711 89.355 5714 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.36 % Allowed : 9.68 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.12), residues: 5184 helix: 1.35 (0.10), residues: 2846 sheet: -1.29 (0.23), residues: 514 loop : -1.18 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 37 TYR 0.023 0.002 TYR A 358 PHE 0.026 0.002 PHE N 62 TRP 0.004 0.001 TRP A 471 HIS 0.009 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00826 (37520) covalent geometry : angle 0.73643 (51112) hydrogen bonds : bond 0.04885 ( 2477) hydrogen bonds : angle 4.80892 ( 7242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 401 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8602 (p0) cc_final: 0.8277 (p0) REVERT: A 358 TYR cc_start: 0.7486 (m-80) cc_final: 0.7275 (m-10) REVERT: A 380 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8341 (mtt180) REVERT: B 340 ASP cc_start: 0.9014 (t0) cc_final: 0.8572 (t0) REVERT: B 498 LYS cc_start: 0.7936 (ptmm) cc_final: 0.7435 (ptmm) REVERT: C 262 MET cc_start: 0.9128 (mmm) cc_final: 0.8921 (mmm) REVERT: D 59 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8572 (mmp) REVERT: D 311 ASP cc_start: 0.8592 (t0) cc_final: 0.8178 (t0) REVERT: D 432 LYS cc_start: 0.8846 (tppt) cc_final: 0.8514 (tppt) REVERT: E 312 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8743 (m-30) REVERT: E 358 ILE cc_start: 0.8980 (mp) cc_final: 0.8715 (mp) REVERT: F 191 ASN cc_start: 0.6643 (m110) cc_final: 0.6440 (m-40) REVERT: F 398 LEU cc_start: 0.8914 (tp) cc_final: 0.8714 (tp) REVERT: R 21 MET cc_start: 0.3478 (tpp) cc_final: 0.2910 (tpp) REVERT: R 67 MET cc_start: 0.8241 (ptt) cc_final: 0.7766 (tmm) REVERT: R 102 ARG cc_start: 0.8913 (ttt180) cc_final: 0.8557 (tmt170) REVERT: S 136 ASP cc_start: 0.7552 (t70) cc_final: 0.6987 (t0) REVERT: W 107 ARG cc_start: 0.8071 (ppt170) cc_final: 0.7818 (ptm-80) REVERT: W 110 GLN cc_start: 0.9150 (pt0) cc_final: 0.8646 (pp30) REVERT: W 139 LEU cc_start: 0.5850 (OUTLIER) cc_final: 0.5610 (tp) REVERT: W 151 GLN cc_start: 0.8674 (tt0) cc_final: 0.8428 (tp40) REVERT: G 50 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7939 (ttp-110) REVERT: G 261 ASP cc_start: 0.8760 (m-30) cc_final: 0.8538 (m-30) REVERT: I 48 TYR cc_start: 0.7593 (m-80) cc_final: 0.6771 (m-80) REVERT: I 64 LEU cc_start: 0.7247 (mm) cc_final: 0.6873 (mt) REVERT: I 70 ILE cc_start: 0.5224 (mm) cc_final: 0.5017 (mt) REVERT: J 48 TYR cc_start: 0.6948 (m-80) cc_final: 0.6207 (m-80) REVERT: L 44 ARG cc_start: 0.3385 (mmm160) cc_final: 0.3024 (mmm160) REVERT: L 68 PHE cc_start: 0.7067 (m-80) cc_final: 0.6382 (t80) REVERT: M 43 ASN cc_start: 0.7192 (m-40) cc_final: 0.6781 (p0) REVERT: N 55 PHE cc_start: 0.7993 (m-80) cc_final: 0.7535 (m-10) REVERT: O 15 LEU cc_start: 0.6073 (mt) cc_final: 0.5826 (mt) REVERT: P 15 LEU cc_start: 0.8026 (mt) cc_final: 0.7660 (tp) REVERT: Q 29 SER cc_start: 0.8001 (p) cc_final: 0.7406 (m) outliers start: 78 outliers final: 39 residues processed: 449 average time/residue: 0.1906 time to fit residues: 143.5750 Evaluate side-chains 399 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 355 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 143 PHE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain S residue 108 GLU Chi-restraints excluded: chain W residue 139 LEU Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 50 ARG Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 72 PHE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 33 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 425 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 229 optimal weight: 0.7980 chunk 336 optimal weight: 0.8980 chunk 328 optimal weight: 0.8980 chunk 420 optimal weight: 40.0000 chunk 103 optimal weight: 0.1980 chunk 174 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 504 optimal weight: 50.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS B 309 HIS D 164 GLN ** F 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 101 GLN K 33 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.130293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.084792 restraints weight = 77443.498| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.96 r_work: 0.3143 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37520 Z= 0.131 Angle : 0.564 8.352 51112 Z= 0.296 Chirality : 0.044 0.225 6152 Planarity : 0.004 0.063 6786 Dihedral : 6.307 89.116 5712 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.15 % Allowed : 12.89 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.12), residues: 5184 helix: 1.58 (0.10), residues: 2786 sheet: -1.22 (0.23), residues: 491 loop : -1.08 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 297 TYR 0.037 0.001 TYR H 48 PHE 0.033 0.001 PHE I 62 TRP 0.002 0.001 TRP B 471 HIS 0.006 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00288 (37520) covalent geometry : angle 0.56428 (51112) hydrogen bonds : bond 0.04114 ( 2477) hydrogen bonds : angle 4.43599 ( 7242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 426 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8620 (p0) cc_final: 0.8247 (p0) REVERT: A 340 ASP cc_start: 0.8712 (t0) cc_final: 0.7884 (p0) REVERT: B 340 ASP cc_start: 0.8952 (t0) cc_final: 0.8554 (t0) REVERT: B 498 LYS cc_start: 0.7849 (ptmm) cc_final: 0.7613 (ptmm) REVERT: C 335 GLU cc_start: 0.8433 (tt0) cc_final: 0.8209 (tt0) REVERT: D 311 ASP cc_start: 0.8592 (t0) cc_final: 0.8184 (t0) REVERT: D 432 LYS cc_start: 0.8732 (tppt) cc_final: 0.8422 (tppt) REVERT: E 23 GLU cc_start: 0.8128 (mp0) cc_final: 0.7573 (mp0) REVERT: E 202 ILE cc_start: 0.7234 (OUTLIER) cc_final: 0.6906 (pt) REVERT: E 358 ILE cc_start: 0.8919 (mp) cc_final: 0.8627 (mp) REVERT: F 191 ASN cc_start: 0.6472 (m110) cc_final: 0.5939 (m-40) REVERT: F 398 LEU cc_start: 0.8944 (tp) cc_final: 0.8728 (tp) REVERT: R 21 MET cc_start: 0.3919 (tpp) cc_final: 0.3486 (tpp) REVERT: R 56 GLU cc_start: 0.7580 (tm-30) cc_final: 0.6485 (pt0) REVERT: R 102 ARG cc_start: 0.8856 (ttt180) cc_final: 0.8569 (tmt170) REVERT: S 133 ARG cc_start: 0.7894 (ttt-90) cc_final: 0.7634 (ttt-90) REVERT: S 136 ASP cc_start: 0.7319 (t70) cc_final: 0.6719 (t0) REVERT: W 101 GLN cc_start: 0.6112 (OUTLIER) cc_final: 0.5865 (tp40) REVERT: W 107 ARG cc_start: 0.7994 (ppt170) cc_final: 0.7712 (ptm-80) REVERT: W 110 GLN cc_start: 0.9148 (pt0) cc_final: 0.8642 (pp30) REVERT: W 120 TYR cc_start: 0.8597 (m-80) cc_final: 0.7721 (m-80) REVERT: W 139 LEU cc_start: 0.5775 (OUTLIER) cc_final: 0.5533 (tp) REVERT: W 151 GLN cc_start: 0.8619 (tt0) cc_final: 0.8299 (tp-100) REVERT: G 24 MET cc_start: 0.8598 (mmt) cc_final: 0.8229 (mtt) REVERT: G 71 GLU cc_start: 0.6349 (mm-30) cc_final: 0.6016 (mm-30) REVERT: G 112 MET cc_start: 0.7130 (mpp) cc_final: 0.6412 (mpp) REVERT: G 261 ASP cc_start: 0.8767 (m-30) cc_final: 0.8549 (m-30) REVERT: I 48 TYR cc_start: 0.7486 (m-80) cc_final: 0.6741 (m-80) REVERT: I 64 LEU cc_start: 0.7031 (mm) cc_final: 0.6597 (mt) REVERT: K 4 LEU cc_start: 0.4834 (pp) cc_final: 0.4470 (tt) REVERT: K 49 MET cc_start: 0.7275 (ttp) cc_final: 0.7072 (ptt) REVERT: L 44 ARG cc_start: 0.3391 (mmm160) cc_final: 0.2978 (mmm160) REVERT: L 68 PHE cc_start: 0.7061 (m-80) cc_final: 0.6409 (t80) REVERT: L 72 PHE cc_start: 0.2186 (t80) cc_final: 0.1937 (t80) REVERT: M 43 ASN cc_start: 0.7054 (m-40) cc_final: 0.6706 (p0) REVERT: M 70 ILE cc_start: 0.5968 (mm) cc_final: 0.5167 (mm) REVERT: P 15 LEU cc_start: 0.8052 (mt) cc_final: 0.7512 (tp) REVERT: P 66 ILE cc_start: 0.7180 (mm) cc_final: 0.6766 (tt) REVERT: Q 29 SER cc_start: 0.7890 (p) cc_final: 0.7446 (m) REVERT: Q 48 TYR cc_start: 0.5725 (m-80) cc_final: 0.5430 (m-10) outliers start: 71 outliers final: 38 residues processed: 469 average time/residue: 0.1921 time to fit residues: 151.0470 Evaluate side-chains 411 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 370 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 143 PHE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain W residue 101 GLN Chi-restraints excluded: chain W residue 139 LEU Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain H residue 72 PHE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain P residue 33 GLN Chi-restraints excluded: chain Q residue 24 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 383 optimal weight: 40.0000 chunk 369 optimal weight: 40.0000 chunk 53 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 470 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 295 optimal weight: 10.0000 chunk 258 optimal weight: 4.9990 chunk 409 optimal weight: 50.0000 chunk 435 optimal weight: 20.0000 chunk 381 optimal weight: 10.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN B 309 HIS C 116 ASN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 GLN ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 GLN ** N 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.123288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.077650 restraints weight = 78503.375| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.89 r_work: 0.2988 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.098 37520 Z= 0.424 Angle : 0.778 12.844 51112 Z= 0.407 Chirality : 0.052 0.356 6152 Planarity : 0.006 0.059 6786 Dihedral : 6.616 89.324 5708 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.93 % Allowed : 14.77 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.12), residues: 5184 helix: 1.19 (0.10), residues: 2840 sheet: -1.54 (0.22), residues: 540 loop : -1.37 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 44 TYR 0.019 0.002 TYR B 247 PHE 0.042 0.002 PHE I 62 TRP 0.005 0.001 TRP A 471 HIS 0.009 0.002 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.01003 (37520) covalent geometry : angle 0.77826 (51112) hydrogen bonds : bond 0.04870 ( 2477) hydrogen bonds : angle 4.73715 ( 7242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 367 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8555 (p0) cc_final: 0.8120 (p0) REVERT: A 277 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7681 (m-30) REVERT: A 457 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8320 (m-40) REVERT: B 340 ASP cc_start: 0.9024 (t0) cc_final: 0.8544 (t0) REVERT: B 498 LYS cc_start: 0.8075 (ptmm) cc_final: 0.7590 (ptmm) REVERT: B 514 GLU cc_start: 0.7531 (tt0) cc_final: 0.6894 (tm-30) REVERT: C 308 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8999 (tp) REVERT: D 59 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8502 (mmp) REVERT: D 143 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8434 (m-10) REVERT: D 311 ASP cc_start: 0.8581 (t0) cc_final: 0.8108 (t0) REVERT: E 23 GLU cc_start: 0.8305 (mp0) cc_final: 0.7844 (mp0) REVERT: E 202 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7210 (pt) REVERT: E 312 ASP cc_start: 0.9117 (OUTLIER) cc_final: 0.8887 (m-30) REVERT: E 358 ILE cc_start: 0.8972 (mp) cc_final: 0.8584 (mp) REVERT: E 395 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7910 (tm-30) REVERT: E 466 TYR cc_start: 0.7403 (m-80) cc_final: 0.7158 (m-10) REVERT: R 21 MET cc_start: 0.4576 (tpp) cc_final: 0.3856 (tpp) REVERT: R 127 ARG cc_start: 0.7974 (mtm180) cc_final: 0.7518 (mmm-85) REVERT: S 136 ASP cc_start: 0.7609 (t70) cc_final: 0.6792 (t0) REVERT: W 107 ARG cc_start: 0.8089 (ppt170) cc_final: 0.7868 (ptm-80) REVERT: W 110 GLN cc_start: 0.9154 (pt0) cc_final: 0.8642 (pp30) REVERT: W 151 GLN cc_start: 0.8701 (tt0) cc_final: 0.8472 (tp40) REVERT: G 24 MET cc_start: 0.8615 (mmt) cc_final: 0.8327 (mtt) REVERT: G 51 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8241 (pm20) REVERT: G 195 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7051 (tp30) REVERT: G 261 ASP cc_start: 0.8791 (m-30) cc_final: 0.8562 (m-30) REVERT: H 33 GLN cc_start: 0.8254 (mt0) cc_final: 0.7829 (mm110) REVERT: H 49 MET cc_start: 0.7710 (ptt) cc_final: 0.7489 (ppp) REVERT: I 37 ARG cc_start: 0.6433 (tmm-80) cc_final: 0.6227 (tmm-80) REVERT: I 48 TYR cc_start: 0.7574 (m-80) cc_final: 0.6910 (m-80) REVERT: I 64 LEU cc_start: 0.6951 (mm) cc_final: 0.6485 (mt) REVERT: I 70 ILE cc_start: 0.5499 (mm) cc_final: 0.5289 (mm) REVERT: J 37 ARG cc_start: 0.7612 (mpt-90) cc_final: 0.7129 (tpm170) REVERT: J 48 TYR cc_start: 0.7225 (m-80) cc_final: 0.6428 (m-80) REVERT: K 4 LEU cc_start: 0.4949 (pp) cc_final: 0.4560 (tt) REVERT: K 49 MET cc_start: 0.7694 (ttp) cc_final: 0.7110 (ptt) REVERT: K 50 PHE cc_start: 0.8379 (m-10) cc_final: 0.8017 (t80) REVERT: L 44 ARG cc_start: 0.3451 (mmm160) cc_final: 0.2885 (mmm160) REVERT: L 68 PHE cc_start: 0.7277 (m-80) cc_final: 0.6711 (t80) REVERT: L 72 PHE cc_start: 0.2394 (t80) cc_final: 0.2119 (t80) REVERT: M 43 ASN cc_start: 0.7179 (m-40) cc_final: 0.6756 (p0) REVERT: N 11 LEU cc_start: 0.6943 (tp) cc_final: 0.6628 (tt) REVERT: O 49 MET cc_start: 0.7408 (ttp) cc_final: 0.7205 (ptm) REVERT: P 15 LEU cc_start: 0.8195 (mt) cc_final: 0.7797 (tp) REVERT: Q 29 SER cc_start: 0.8125 (p) cc_final: 0.7622 (m) outliers start: 130 outliers final: 87 residues processed: 462 average time/residue: 0.2055 time to fit residues: 158.5006 Evaluate side-chains 443 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 347 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 143 PHE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain W residue 117 HIS Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 139 LEU Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain K residue 59 LEU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 35 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 3 optimal weight: 0.0470 chunk 36 optimal weight: 2.9990 chunk 421 optimal weight: 30.0000 chunk 396 optimal weight: 50.0000 chunk 330 optimal weight: 0.7980 chunk 196 optimal weight: 0.8980 chunk 485 optimal weight: 5.9990 chunk 335 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 365 optimal weight: 50.0000 chunk 422 optimal weight: 5.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 218 GLN ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.127915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.082613 restraints weight = 77590.780| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.97 r_work: 0.3102 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 37520 Z= 0.139 Angle : 0.569 11.077 51112 Z= 0.298 Chirality : 0.044 0.259 6152 Planarity : 0.004 0.060 6786 Dihedral : 6.189 88.432 5708 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.72 % Allowed : 16.73 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.12), residues: 5184 helix: 1.47 (0.10), residues: 2833 sheet: -1.38 (0.24), residues: 497 loop : -1.19 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 110 TYR 0.021 0.001 TYR K 48 PHE 0.043 0.001 PHE I 62 TRP 0.003 0.001 TRP B 471 HIS 0.005 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00315 (37520) covalent geometry : angle 0.56876 (51112) hydrogen bonds : bond 0.03967 ( 2477) hydrogen bonds : angle 4.36703 ( 7242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 406 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8548 (p0) cc_final: 0.8124 (p0) REVERT: A 340 ASP cc_start: 0.8782 (t0) cc_final: 0.7833 (p0) REVERT: A 457 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8257 (m110) REVERT: B 262 MET cc_start: 0.9089 (tpp) cc_final: 0.8727 (tpt) REVERT: B 340 ASP cc_start: 0.8965 (t0) cc_final: 0.8536 (t0) REVERT: B 498 LYS cc_start: 0.8061 (ptmm) cc_final: 0.7590 (pttp) REVERT: B 514 GLU cc_start: 0.7525 (tt0) cc_final: 0.6931 (tm-30) REVERT: C 262 MET cc_start: 0.9059 (mmm) cc_final: 0.8846 (mmm) REVERT: C 308 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8800 (tp) REVERT: D 51 ASN cc_start: 0.8892 (m110) cc_final: 0.8387 (p0) REVERT: D 143 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8314 (m-10) REVERT: D 311 ASP cc_start: 0.8659 (t0) cc_final: 0.8193 (t0) REVERT: E 23 GLU cc_start: 0.8313 (mp0) cc_final: 0.7809 (mp0) REVERT: E 202 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.7045 (pt) REVERT: E 358 ILE cc_start: 0.8917 (mp) cc_final: 0.8566 (mp) REVERT: E 395 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7869 (tm-30) REVERT: E 466 TYR cc_start: 0.7407 (m-80) cc_final: 0.7172 (m-10) REVERT: F 206 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8618 (p) REVERT: R 21 MET cc_start: 0.5125 (tpp) cc_final: 0.3937 (tpp) REVERT: R 67 MET cc_start: 0.8084 (ttt) cc_final: 0.7331 (tmm) REVERT: R 102 ARG cc_start: 0.8875 (ttt180) cc_final: 0.8591 (tmt170) REVERT: S 136 ASP cc_start: 0.7439 (t70) cc_final: 0.6717 (t0) REVERT: W 107 ARG cc_start: 0.7984 (ppt170) cc_final: 0.7718 (ptm-80) REVERT: W 110 GLN cc_start: 0.9106 (pt0) cc_final: 0.8423 (pp30) REVERT: W 151 GLN cc_start: 0.8644 (tt0) cc_final: 0.8373 (tp40) REVERT: G 24 MET cc_start: 0.8602 (mmt) cc_final: 0.8393 (mtt) REVERT: G 51 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8096 (pm20) REVERT: I 37 ARG cc_start: 0.6549 (tmm-80) cc_final: 0.6177 (tmm-80) REVERT: I 48 TYR cc_start: 0.7642 (m-80) cc_final: 0.6893 (m-80) REVERT: I 64 LEU cc_start: 0.7218 (mm) cc_final: 0.6691 (mt) REVERT: J 37 ARG cc_start: 0.7703 (mpt-90) cc_final: 0.7324 (tpp-160) REVERT: J 48 TYR cc_start: 0.7324 (m-80) cc_final: 0.5966 (m-80) REVERT: K 4 LEU cc_start: 0.5054 (pp) cc_final: 0.4615 (tt) REVERT: K 49 MET cc_start: 0.7618 (ttp) cc_final: 0.7012 (ptt) REVERT: K 50 PHE cc_start: 0.8343 (m-10) cc_final: 0.7974 (t80) REVERT: L 44 ARG cc_start: 0.3315 (mmm160) cc_final: 0.2782 (mmm160) REVERT: L 59 LEU cc_start: 0.6807 (pt) cc_final: 0.6592 (mt) REVERT: L 68 PHE cc_start: 0.7249 (m-80) cc_final: 0.6645 (t80) REVERT: M 43 ASN cc_start: 0.7123 (m-40) cc_final: 0.6700 (p0) REVERT: N 11 LEU cc_start: 0.6997 (tp) cc_final: 0.6754 (tt) REVERT: P 15 LEU cc_start: 0.8008 (mt) cc_final: 0.7597 (tp) REVERT: Q 29 SER cc_start: 0.8114 (p) cc_final: 0.7616 (m) REVERT: Q 48 TYR cc_start: 0.5807 (m-80) cc_final: 0.5548 (m-80) outliers start: 90 outliers final: 56 residues processed: 468 average time/residue: 0.2218 time to fit residues: 173.8845 Evaluate side-chains 435 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 373 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 143 PHE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain W residue 117 HIS Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 139 LEU Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain K residue 59 LEU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 6 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 166 optimal weight: 0.8980 chunk 386 optimal weight: 50.0000 chunk 197 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 302 optimal weight: 9.9990 chunk 391 optimal weight: 7.9990 chunk 339 optimal weight: 3.9990 chunk 305 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 137 GLN W 101 GLN H 33 GLN H 38 ASN O 5 ASN ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.128811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.083783 restraints weight = 77142.670| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.91 r_work: 0.3127 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 37520 Z= 0.131 Angle : 0.569 13.807 51112 Z= 0.294 Chirality : 0.044 0.270 6152 Planarity : 0.004 0.089 6786 Dihedral : 5.923 84.137 5708 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.03 % Allowed : 17.37 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.12), residues: 5184 helix: 1.59 (0.10), residues: 2830 sheet: -1.32 (0.23), residues: 512 loop : -1.06 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 107 TYR 0.025 0.001 TYR E 364 PHE 0.050 0.001 PHE N 62 TRP 0.004 0.001 TRP B 471 HIS 0.005 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00293 (37520) covalent geometry : angle 0.56921 (51112) hydrogen bonds : bond 0.03825 ( 2477) hydrogen bonds : angle 4.21608 ( 7242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 422 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8522 (p0) cc_final: 0.8101 (p0) REVERT: A 340 ASP cc_start: 0.8751 (t0) cc_final: 0.7769 (p0) REVERT: A 457 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8123 (m-40) REVERT: B 262 MET cc_start: 0.9088 (tpp) cc_final: 0.8726 (tpt) REVERT: B 340 ASP cc_start: 0.8930 (t0) cc_final: 0.8572 (t0) REVERT: B 498 LYS cc_start: 0.8020 (ptmm) cc_final: 0.7547 (pttp) REVERT: B 514 GLU cc_start: 0.7655 (tt0) cc_final: 0.7103 (tm-30) REVERT: C 308 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8779 (tp) REVERT: D 51 ASN cc_start: 0.8856 (m110) cc_final: 0.8401 (p0) REVERT: D 59 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8679 (mmp) REVERT: D 143 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8282 (m-80) REVERT: D 177 PHE cc_start: 0.8762 (m-80) cc_final: 0.8502 (m-10) REVERT: D 311 ASP cc_start: 0.8656 (t0) cc_final: 0.8184 (t0) REVERT: E 23 GLU cc_start: 0.8273 (mp0) cc_final: 0.7753 (mp0) REVERT: E 202 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.7013 (pt) REVERT: E 285 MET cc_start: 0.8860 (tpp) cc_final: 0.8477 (mmt) REVERT: E 358 ILE cc_start: 0.8919 (mp) cc_final: 0.8598 (mp) REVERT: E 395 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7894 (tm-30) REVERT: E 466 TYR cc_start: 0.7381 (m-80) cc_final: 0.7157 (m-10) REVERT: F 22 ASP cc_start: 0.8766 (t0) cc_final: 0.8557 (t0) REVERT: R 21 MET cc_start: 0.5187 (tpp) cc_final: 0.4056 (tpp) REVERT: R 67 MET cc_start: 0.8080 (ttt) cc_final: 0.7316 (tmm) REVERT: R 102 ARG cc_start: 0.8893 (ttt180) cc_final: 0.8617 (tmt170) REVERT: S 136 ASP cc_start: 0.7492 (t70) cc_final: 0.6729 (t0) REVERT: W 110 GLN cc_start: 0.9068 (pt0) cc_final: 0.8398 (pp30) REVERT: W 151 GLN cc_start: 0.8620 (tt0) cc_final: 0.8329 (tp40) REVERT: G 51 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8127 (pm20) REVERT: H 49 MET cc_start: 0.7461 (ptt) cc_final: 0.7129 (ppp) REVERT: I 48 TYR cc_start: 0.7536 (m-80) cc_final: 0.6753 (m-80) REVERT: I 64 LEU cc_start: 0.7201 (mm) cc_final: 0.6747 (mt) REVERT: J 37 ARG cc_start: 0.7651 (mpt-90) cc_final: 0.7060 (tpp-160) REVERT: J 44 ARG cc_start: 0.6502 (tpt-90) cc_final: 0.6161 (tpt-90) REVERT: J 48 TYR cc_start: 0.7145 (m-80) cc_final: 0.5902 (m-80) REVERT: K 4 LEU cc_start: 0.4947 (pp) cc_final: 0.4249 (tt) REVERT: K 49 MET cc_start: 0.7605 (ttp) cc_final: 0.6996 (ptt) REVERT: K 50 PHE cc_start: 0.8381 (m-10) cc_final: 0.7973 (t80) REVERT: L 44 ARG cc_start: 0.3103 (mmm160) cc_final: 0.2496 (mmm160) REVERT: L 68 PHE cc_start: 0.7210 (m-80) cc_final: 0.6636 (t80) REVERT: M 43 ASN cc_start: 0.6995 (m-40) cc_final: 0.6556 (p0) REVERT: N 11 LEU cc_start: 0.6850 (tp) cc_final: 0.6599 (tt) REVERT: O 49 MET cc_start: 0.7347 (ttp) cc_final: 0.6960 (ptm) REVERT: O 50 PHE cc_start: 0.7825 (m-10) cc_final: 0.7601 (m-10) REVERT: P 15 LEU cc_start: 0.7960 (mt) cc_final: 0.7566 (tp) REVERT: Q 29 SER cc_start: 0.8111 (p) cc_final: 0.7615 (m) REVERT: Q 42 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6169 (mp0) REVERT: Q 48 TYR cc_start: 0.5721 (m-80) cc_final: 0.5050 (m-80) outliers start: 100 outliers final: 57 residues processed: 493 average time/residue: 0.2090 time to fit residues: 173.3081 Evaluate side-chains 450 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 387 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 143 PHE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 139 LEU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 6 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 289 optimal weight: 0.9980 chunk 358 optimal weight: 50.0000 chunk 507 optimal weight: 50.0000 chunk 436 optimal weight: 3.9990 chunk 444 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 317 optimal weight: 5.9990 chunk 353 optimal weight: 50.0000 chunk 283 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 137 GLN ** N 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 5 ASN ** P 33 GLN ** 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 = 0.3965 r_free = 0.3965 target = 0.125502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.080764 restraints weight = 78405.577| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.17 r_work: 0.3022 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 37520 Z= 0.247 Angle : 0.635 14.291 51112 Z= 0.331 Chirality : 0.046 0.328 6152 Planarity : 0.005 0.071 6786 Dihedral : 6.087 88.560 5708 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.30 % Allowed : 18.28 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.12), residues: 5184 helix: 1.55 (0.10), residues: 2808 sheet: -1.49 (0.22), residues: 538 loop : -1.11 (0.15), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG W 104 TYR 0.026 0.002 TYR E 364 PHE 0.053 0.002 PHE I 62 TRP 0.003 0.001 TRP A 471 HIS 0.006 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00582 (37520) covalent geometry : angle 0.63531 (51112) hydrogen bonds : bond 0.04140 ( 2477) hydrogen bonds : angle 4.34587 ( 7242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 391 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8571 (p0) cc_final: 0.8133 (p0) REVERT: A 340 ASP cc_start: 0.8824 (t0) cc_final: 0.7678 (p0) REVERT: A 457 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.7729 (m110) REVERT: B 340 ASP cc_start: 0.8982 (t0) cc_final: 0.8530 (t0) REVERT: B 498 LYS cc_start: 0.8047 (ptmm) cc_final: 0.7491 (ptmm) REVERT: B 514 GLU cc_start: 0.7956 (tt0) cc_final: 0.7445 (tm-30) REVERT: C 308 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8921 (tp) REVERT: D 51 ASN cc_start: 0.8948 (m110) cc_final: 0.8433 (p0) REVERT: D 59 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8662 (mmp) REVERT: D 143 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8352 (m-80) REVERT: D 177 PHE cc_start: 0.8795 (m-80) cc_final: 0.8567 (m-10) REVERT: D 311 ASP cc_start: 0.8671 (t0) cc_final: 0.8192 (t0) REVERT: E 23 GLU cc_start: 0.8402 (mp0) cc_final: 0.7879 (mp0) REVERT: E 202 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.7131 (pt) REVERT: E 333 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.6813 (ptp90) REVERT: E 358 ILE cc_start: 0.8960 (mp) cc_final: 0.8587 (mp) REVERT: E 395 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7972 (tm-30) REVERT: E 466 TYR cc_start: 0.7572 (m-80) cc_final: 0.7302 (m-10) REVERT: R 4 HIS cc_start: 0.7316 (OUTLIER) cc_final: 0.6729 (t70) REVERT: R 21 MET cc_start: 0.5430 (tpp) cc_final: 0.4500 (tpp) REVERT: R 102 ARG cc_start: 0.8899 (ttt180) cc_final: 0.8602 (tmt170) REVERT: R 127 ARG cc_start: 0.8132 (mtm180) cc_final: 0.7654 (mmm-85) REVERT: S 136 ASP cc_start: 0.7566 (t70) cc_final: 0.6661 (t0) REVERT: W 103 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8612 (mm-30) REVERT: W 110 GLN cc_start: 0.9064 (pt0) cc_final: 0.8382 (pp30) REVERT: W 151 GLN cc_start: 0.8669 (tt0) cc_final: 0.8393 (tp40) REVERT: G 51 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8107 (pm20) REVERT: I 29 SER cc_start: 0.7718 (p) cc_final: 0.7379 (m) REVERT: I 48 TYR cc_start: 0.7505 (m-80) cc_final: 0.6766 (m-80) REVERT: I 64 LEU cc_start: 0.7246 (mm) cc_final: 0.6872 (mt) REVERT: J 37 ARG cc_start: 0.7653 (mpt-90) cc_final: 0.7165 (tpp-160) REVERT: K 4 LEU cc_start: 0.4674 (pp) cc_final: 0.4256 (tt) REVERT: K 50 PHE cc_start: 0.8433 (m-10) cc_final: 0.8021 (t80) REVERT: L 44 ARG cc_start: 0.2940 (mmm160) cc_final: 0.2447 (mmm160) REVERT: L 68 PHE cc_start: 0.7184 (m-80) cc_final: 0.6527 (t80) REVERT: M 43 ASN cc_start: 0.7034 (m-40) cc_final: 0.6644 (p0) REVERT: P 15 LEU cc_start: 0.8098 (mt) cc_final: 0.7684 (tp) REVERT: P 41 ILE cc_start: 0.6106 (OUTLIER) cc_final: 0.5765 (tp) REVERT: Q 42 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6105 (mp0) outliers start: 109 outliers final: 63 residues processed: 475 average time/residue: 0.2056 time to fit residues: 162.4275 Evaluate side-chains 436 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 364 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 143 PHE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain S residue 122 VAL Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 139 LEU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain P residue 41 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 161 optimal weight: 5.9990 chunk 419 optimal weight: 20.0000 chunk 320 optimal weight: 7.9990 chunk 368 optimal weight: 6.9990 chunk 322 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 283 optimal weight: 2.9990 chunk 318 optimal weight: 4.9990 chunk 178 optimal weight: 0.7980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** N 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 5 ASN ** P 33 GLN ** 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 = 0.3973 r_free = 0.3973 target = 0.125921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.082055 restraints weight = 76187.927| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.86 r_work: 0.3072 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 37520 Z= 0.198 Angle : 0.615 11.415 51112 Z= 0.320 Chirality : 0.045 0.240 6152 Planarity : 0.004 0.070 6786 Dihedral : 6.056 87.379 5708 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.81 % Allowed : 19.24 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.12), residues: 5184 helix: 1.58 (0.10), residues: 2817 sheet: -1.43 (0.23), residues: 530 loop : -1.14 (0.15), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG W 107 TYR 0.024 0.001 TYR E 364 PHE 0.059 0.002 PHE I 62 TRP 0.005 0.001 TRP B 471 HIS 0.005 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00468 (37520) covalent geometry : angle 0.61450 (51112) hydrogen bonds : bond 0.03982 ( 2477) hydrogen bonds : angle 4.30098 ( 7242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 389 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8531 (p0) cc_final: 0.8085 (p0) REVERT: A 340 ASP cc_start: 0.8775 (t0) cc_final: 0.7746 (p0) REVERT: A 457 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8010 (m110) REVERT: B 335 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8608 (pt0) REVERT: B 340 ASP cc_start: 0.8945 (t0) cc_final: 0.8509 (t0) REVERT: B 498 LYS cc_start: 0.8045 (ptmm) cc_final: 0.7788 (pttp) REVERT: B 514 GLU cc_start: 0.8020 (tt0) cc_final: 0.7546 (tm-30) REVERT: C 308 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8848 (tp) REVERT: D 51 ASN cc_start: 0.8856 (m110) cc_final: 0.8343 (p0) REVERT: D 59 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8666 (mmp) REVERT: D 143 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8244 (m-80) REVERT: D 177 PHE cc_start: 0.8783 (m-80) cc_final: 0.8547 (m-10) REVERT: D 311 ASP cc_start: 0.8623 (t0) cc_final: 0.8131 (t0) REVERT: D 380 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8526 (pp) REVERT: E 23 GLU cc_start: 0.8331 (mp0) cc_final: 0.7820 (mp0) REVERT: E 202 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.7109 (pt) REVERT: E 214 MET cc_start: 0.8927 (mtp) cc_final: 0.8688 (mtp) REVERT: E 333 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.6774 (ptp90) REVERT: E 358 ILE cc_start: 0.8964 (mp) cc_final: 0.8587 (mp) REVERT: E 395 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7919 (tm-30) REVERT: E 466 TYR cc_start: 0.7440 (m-80) cc_final: 0.7219 (m-10) REVERT: R 21 MET cc_start: 0.5455 (tpp) cc_final: 0.4521 (tpp) REVERT: R 102 ARG cc_start: 0.8868 (ttt180) cc_final: 0.8604 (tmt170) REVERT: R 127 ARG cc_start: 0.7998 (mtm180) cc_final: 0.7629 (mmm-85) REVERT: S 136 ASP cc_start: 0.7488 (t70) cc_final: 0.6591 (t0) REVERT: W 110 GLN cc_start: 0.9016 (pt0) cc_final: 0.8324 (pp30) REVERT: W 151 GLN cc_start: 0.8681 (tt0) cc_final: 0.8416 (tp40) REVERT: G 51 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8090 (pm20) REVERT: G 71 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6440 (mm-30) REVERT: I 29 SER cc_start: 0.7572 (p) cc_final: 0.7247 (m) REVERT: I 48 TYR cc_start: 0.7528 (m-80) cc_final: 0.6779 (m-80) REVERT: I 64 LEU cc_start: 0.7222 (mm) cc_final: 0.6710 (mt) REVERT: J 37 ARG cc_start: 0.7739 (mpt-90) cc_final: 0.7061 (tpp-160) REVERT: J 57 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7952 (mp0) REVERT: K 37 ARG cc_start: 0.7913 (mmt90) cc_final: 0.7478 (mpt-90) REVERT: K 50 PHE cc_start: 0.8406 (m-10) cc_final: 0.7991 (t80) REVERT: K 62 PHE cc_start: 0.6965 (t80) cc_final: 0.6739 (t80) REVERT: L 44 ARG cc_start: 0.3030 (mmm160) cc_final: 0.2475 (mmm160) REVERT: L 68 PHE cc_start: 0.7249 (m-80) cc_final: 0.6553 (t80) REVERT: M 43 ASN cc_start: 0.6954 (m-40) cc_final: 0.6609 (p0) REVERT: P 15 LEU cc_start: 0.8152 (mt) cc_final: 0.7836 (tp) REVERT: Q 48 TYR cc_start: 0.5830 (m-80) cc_final: 0.5467 (m-80) outliers start: 93 outliers final: 71 residues processed: 461 average time/residue: 0.2287 time to fit residues: 174.9817 Evaluate side-chains 455 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 375 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain C residue 519 SER Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 423 ARG Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 143 PHE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain S residue 122 VAL Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 139 LEU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain Q residue 53 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 172 optimal weight: 3.9990 chunk 421 optimal weight: 30.0000 chunk 256 optimal weight: 0.8980 chunk 431 optimal weight: 8.9990 chunk 407 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 474 optimal weight: 4.9990 chunk 410 optimal weight: 50.0000 chunk 458 optimal weight: 9.9990 chunk 303 optimal weight: 10.0000 chunk 191 optimal weight: 0.1980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 368 GLN ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 33 GLN ** 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 = 0.3981 r_free = 0.3981 target = 0.126483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.081333 restraints weight = 78113.893| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.97 r_work: 0.3067 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37520 Z= 0.181 Angle : 0.603 9.778 51112 Z= 0.314 Chirality : 0.045 0.285 6152 Planarity : 0.004 0.064 6786 Dihedral : 5.992 85.091 5708 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.75 % Allowed : 19.36 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.12), residues: 5184 helix: 1.62 (0.10), residues: 2811 sheet: -1.39 (0.23), residues: 505 loop : -1.14 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG W 107 TYR 0.027 0.002 TYR G 168 PHE 0.063 0.001 PHE I 62 TRP 0.004 0.001 TRP B 471 HIS 0.005 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00427 (37520) covalent geometry : angle 0.60310 (51112) hydrogen bonds : bond 0.03913 ( 2477) hydrogen bonds : angle 4.26104 ( 7242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 391 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8534 (p0) cc_final: 0.8085 (p0) REVERT: A 340 ASP cc_start: 0.8778 (t0) cc_final: 0.7748 (p0) REVERT: A 457 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.7996 (m110) REVERT: B 262 MET cc_start: 0.9118 (tpp) cc_final: 0.8756 (tpt) REVERT: B 335 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8608 (pt0) REVERT: B 340 ASP cc_start: 0.8938 (t0) cc_final: 0.8508 (t0) REVERT: B 514 GLU cc_start: 0.8071 (tt0) cc_final: 0.7654 (tm-30) REVERT: C 308 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8840 (tp) REVERT: D 51 ASN cc_start: 0.8876 (m110) cc_final: 0.8385 (p0) REVERT: D 59 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8672 (mmp) REVERT: D 101 MET cc_start: 0.9311 (mpp) cc_final: 0.9079 (mmm) REVERT: D 143 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8215 (m-80) REVERT: D 177 PHE cc_start: 0.8811 (m-80) cc_final: 0.8588 (m-10) REVERT: D 311 ASP cc_start: 0.8638 (t0) cc_final: 0.8148 (t0) REVERT: D 380 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8455 (pp) REVERT: D 423 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8201 (ptp90) REVERT: E 23 GLU cc_start: 0.8341 (mp0) cc_final: 0.7874 (mp0) REVERT: E 202 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7168 (pt) REVERT: E 214 MET cc_start: 0.8923 (mtp) cc_final: 0.8721 (mtp) REVERT: E 333 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.6759 (ptp90) REVERT: E 358 ILE cc_start: 0.8949 (mp) cc_final: 0.8609 (mp) REVERT: E 395 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7953 (tm-30) REVERT: R 21 MET cc_start: 0.5492 (tpp) cc_final: 0.4613 (tpp) REVERT: R 102 ARG cc_start: 0.8855 (ttt180) cc_final: 0.8588 (tmt170) REVERT: S 136 ASP cc_start: 0.7345 (t70) cc_final: 0.6414 (t0) REVERT: W 110 GLN cc_start: 0.8995 (pt0) cc_final: 0.8366 (pp30) REVERT: W 120 TYR cc_start: 0.8519 (m-80) cc_final: 0.8232 (m-80) REVERT: W 151 GLN cc_start: 0.8648 (tt0) cc_final: 0.8391 (tp40) REVERT: G 51 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8029 (pm20) REVERT: H 18 ILE cc_start: 0.6511 (OUTLIER) cc_final: 0.6259 (pt) REVERT: I 29 SER cc_start: 0.7656 (p) cc_final: 0.7288 (m) REVERT: I 48 TYR cc_start: 0.7493 (m-80) cc_final: 0.6753 (m-80) REVERT: I 64 LEU cc_start: 0.7167 (mm) cc_final: 0.6712 (mt) REVERT: J 37 ARG cc_start: 0.7692 (mpt-90) cc_final: 0.7054 (tpp-160) REVERT: K 37 ARG cc_start: 0.7684 (mmt90) cc_final: 0.7114 (mpt-90) REVERT: K 62 PHE cc_start: 0.6944 (t80) cc_final: 0.6720 (t80) REVERT: L 44 ARG cc_start: 0.2936 (mmm160) cc_final: 0.2335 (mmm160) REVERT: L 68 PHE cc_start: 0.7328 (m-80) cc_final: 0.6569 (t80) REVERT: M 43 ASN cc_start: 0.6949 (m-40) cc_final: 0.6619 (p0) REVERT: O 55 PHE cc_start: 0.8396 (t80) cc_final: 0.8172 (t80) REVERT: P 15 LEU cc_start: 0.8124 (mt) cc_final: 0.7700 (tp) REVERT: Q 48 TYR cc_start: 0.5790 (m-80) cc_final: 0.5442 (m-80) outliers start: 91 outliers final: 64 residues processed: 459 average time/residue: 0.2147 time to fit residues: 163.9974 Evaluate side-chains 438 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 363 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain C residue 519 SER Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 423 ARG Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 143 PHE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain S residue 122 VAL Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 139 LEU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 187 optimal weight: 7.9990 chunk 265 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 71 optimal weight: 0.5980 chunk 185 optimal weight: 0.0770 chunk 499 optimal weight: 10.0000 chunk 453 optimal weight: 8.9990 chunk 377 optimal weight: 50.0000 chunk 139 optimal weight: 1.9990 overall best weight: 1.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 GLN ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 33 GLN ** 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 = 0.4001 r_free = 0.4001 target = 0.127485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.083830 restraints weight = 75571.451| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.89 r_work: 0.3109 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 37520 Z= 0.147 Angle : 0.599 11.213 51112 Z= 0.310 Chirality : 0.045 0.270 6152 Planarity : 0.004 0.063 6786 Dihedral : 5.890 82.419 5708 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.48 % Allowed : 19.91 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.12), residues: 5184 helix: 1.67 (0.10), residues: 2814 sheet: -1.35 (0.23), residues: 498 loop : -1.10 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG S 107 TYR 0.026 0.001 TYR G 168 PHE 0.065 0.001 PHE I 62 TRP 0.006 0.001 TRP B 471 HIS 0.005 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00343 (37520) covalent geometry : angle 0.59914 (51112) hydrogen bonds : bond 0.03801 ( 2477) hydrogen bonds : angle 4.20843 ( 7242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 377 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8520 (p0) cc_final: 0.8086 (p0) REVERT: A 340 ASP cc_start: 0.8718 (t0) cc_final: 0.7711 (p0) REVERT: A 457 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.8101 (m-40) REVERT: B 72 ASN cc_start: 0.9004 (m-40) cc_final: 0.8626 (t0) REVERT: B 262 MET cc_start: 0.9122 (tpp) cc_final: 0.8769 (tpt) REVERT: B 335 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8596 (pt0) REVERT: B 340 ASP cc_start: 0.8924 (t0) cc_final: 0.8550 (t0) REVERT: B 498 LYS cc_start: 0.8244 (ptpt) cc_final: 0.7923 (ttpt) REVERT: C 131 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: C 308 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8803 (tp) REVERT: D 51 ASN cc_start: 0.8812 (m110) cc_final: 0.8385 (p0) REVERT: D 59 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8667 (mmp) REVERT: D 101 MET cc_start: 0.9287 (mpp) cc_final: 0.9073 (mmm) REVERT: D 143 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.8142 (m-80) REVERT: D 177 PHE cc_start: 0.8801 (m-80) cc_final: 0.8559 (m-10) REVERT: D 311 ASP cc_start: 0.8616 (t0) cc_final: 0.8128 (t0) REVERT: D 423 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8176 (ptp90) REVERT: E 23 GLU cc_start: 0.8315 (mp0) cc_final: 0.7854 (mp0) REVERT: E 202 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7111 (pt) REVERT: E 333 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.6770 (ptp90) REVERT: E 358 ILE cc_start: 0.8937 (mp) cc_final: 0.8609 (mp) REVERT: E 395 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7941 (tm-30) REVERT: R 21 MET cc_start: 0.5506 (tpp) cc_final: 0.4575 (tpp) REVERT: R 102 ARG cc_start: 0.8835 (ttt180) cc_final: 0.8587 (tmt170) REVERT: S 136 ASP cc_start: 0.7429 (t70) cc_final: 0.6493 (t0) REVERT: W 104 ARG cc_start: 0.8323 (ttp-110) cc_final: 0.7759 (ptt90) REVERT: W 110 GLN cc_start: 0.9001 (pt0) cc_final: 0.8390 (pp30) REVERT: W 151 GLN cc_start: 0.8516 (tt0) cc_final: 0.8309 (tp40) REVERT: G 51 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7989 (pm20) REVERT: H 18 ILE cc_start: 0.6669 (OUTLIER) cc_final: 0.6429 (pt) REVERT: I 11 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7951 (mt) REVERT: I 48 TYR cc_start: 0.7456 (m-80) cc_final: 0.6706 (m-80) REVERT: I 64 LEU cc_start: 0.7204 (mm) cc_final: 0.6739 (mt) REVERT: J 37 ARG cc_start: 0.7727 (mpt-90) cc_final: 0.7072 (tpp-160) REVERT: K 37 ARG cc_start: 0.7736 (mmt90) cc_final: 0.7340 (mpt-90) REVERT: K 62 PHE cc_start: 0.6899 (t80) cc_final: 0.6684 (t80) REVERT: L 44 ARG cc_start: 0.2923 (mmm160) cc_final: 0.2349 (mmm160) REVERT: L 61 ILE cc_start: 0.6851 (mm) cc_final: 0.6447 (tt) REVERT: L 68 PHE cc_start: 0.7274 (m-80) cc_final: 0.6576 (t80) REVERT: M 43 ASN cc_start: 0.6902 (m-40) cc_final: 0.6577 (p0) REVERT: O 55 PHE cc_start: 0.8402 (t80) cc_final: 0.8192 (t80) REVERT: Q 35 ILE cc_start: 0.7863 (tt) cc_final: 0.7624 (pt) REVERT: Q 48 TYR cc_start: 0.5694 (m-80) cc_final: 0.5334 (m-80) outliers start: 82 outliers final: 59 residues processed: 437 average time/residue: 0.2275 time to fit residues: 166.4926 Evaluate side-chains 436 residues out of total 4181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 365 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain C residue 519 SER Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 423 ARG Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 143 PHE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain S residue 122 VAL Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 139 LEU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain Q residue 53 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 147 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 chunk 304 optimal weight: 0.6980 chunk 130 optimal weight: 0.0970 chunk 63 optimal weight: 0.0970 chunk 203 optimal weight: 0.8980 chunk 183 optimal weight: 0.0870 chunk 209 optimal weight: 0.8980 chunk 224 optimal weight: 6.9990 chunk 361 optimal weight: 50.0000 chunk 142 optimal weight: 2.9990 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 33 GLN ** 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 = 0.4034 r_free = 0.4034 target = 0.129794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.086577 restraints weight = 75290.739| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.90 r_work: 0.3159 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 37520 Z= 0.120 Angle : 0.585 10.783 51112 Z= 0.302 Chirality : 0.044 0.296 6152 Planarity : 0.004 0.062 6786 Dihedral : 5.689 78.276 5708 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.88 % Allowed : 20.88 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.12), residues: 5184 helix: 1.77 (0.10), residues: 2827 sheet: -1.24 (0.23), residues: 508 loop : -1.06 (0.15), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG S 107 TYR 0.026 0.001 TYR J 48 PHE 0.067 0.001 PHE I 62 TRP 0.006 0.001 TRP B 471 HIS 0.004 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00268 (37520) covalent geometry : angle 0.58481 (51112) hydrogen bonds : bond 0.03613 ( 2477) hydrogen bonds : angle 4.09496 ( 7242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9949.15 seconds wall clock time: 170 minutes 27.41 seconds (10227.41 seconds total)