Starting phenix.real_space_refine on Tue Aug 26 23:35:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yd1_39162/08_2025/8yd1_39162_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yd1_39162/08_2025/8yd1_39162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yd1_39162/08_2025/8yd1_39162_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yd1_39162/08_2025/8yd1_39162_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yd1_39162/08_2025/8yd1_39162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yd1_39162/08_2025/8yd1_39162.map" } resolution = 2.81 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= 0.003 sd= 0.016 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: 7 Type Number sf(0) Gaussians P 27 5.49 5 Mg 7 5.21 5 S 177 5.16 5 B 14 2.79 5 C 27296 2.51 5 N 7597 2.21 5 O 8322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 146 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: 43440 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 4496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4496 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 20, 'TRANS': 552} Chain breaks: 2 Chain: "B" Number of atoms: 4414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4414 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 20, 'TRANS': 543} Chain breaks: 3 Chain: "C" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4478 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 20, 'TRANS': 549} Chain breaks: 3 Chain: "D" Number of atoms: 4267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4267 Classifications: {'peptide': 544} Link IDs: {'PTRANS': 18, 'TRANS': 525} Chain breaks: 3 Chain: "E" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2083 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 9, 'TRANS': 258} Chain breaks: 1 Chain: "F" Number of atoms: 3602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3602 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 14, 'TRANS': 441} Chain breaks: 10 Chain: "G" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1389 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "H" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1389 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "I" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1389 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "J" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1389 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "K" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1389 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "L" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1389 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "M" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1389 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "N" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "O" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "P" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "Q" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "R" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "S" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "T" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "a" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 181 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.90, per 1000 atoms: 0.25 Number of scatterers: 43440 At special positions: 0 Unit cell: (125.67, 138.45, 199.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 177 16.00 P 27 15.00 Mg 7 11.99 O 8322 8.00 N 7597 7.00 C 27296 6.00 B 14 5.00 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 Atom "HETATM42769 O3B ATP A 902 .*. O " rejected from bonding due to valence issues. Atom "HETATM42769 O3B ATP A 902 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.88 Conformation dependent library (CDL) restraints added in 2.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10196 Finding SS restraints... Secondary structure from input PDB file: 251 helices and 58 sheets defined 53.3% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 178 through 184 Processing helix chain 'A' and resid 193 through 204 Processing helix chain 'A' and resid 222 through 236 removed outlier: 4.140A pdb=" N VAL A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 257 removed outlier: 3.534A pdb=" N VAL A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 280 removed outlier: 3.505A pdb=" N GLU A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 removed outlier: 3.815A pdb=" N VAL A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 362 through 370 removed outlier: 3.625A pdb=" N ALA A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 390 removed outlier: 3.587A pdb=" N MET A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 399 through 411 removed outlier: 3.626A pdb=" N ILE A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 492 removed outlier: 3.635A pdb=" N VAL A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 509 Processing helix chain 'A' and resid 509 through 515 Processing helix chain 'A' and resid 521 through 537 removed outlier: 3.801A pdb=" N ALA A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 572 removed outlier: 3.566A pdb=" N SER A 563 " --> pdb=" O LYS A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 590 removed outlier: 3.563A pdb=" N THR A 590 " --> pdb=" O ASP A 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 587 through 590' Processing helix chain 'A' and resid 591 through 596 Processing helix chain 'A' and resid 610 through 615 Processing helix chain 'A' and resid 627 through 630 Processing helix chain 'A' and resid 631 through 645 removed outlier: 4.090A pdb=" N TYR A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 636 " --> pdb=" O GLN A 632 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN A 640 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL A 641 " --> pdb=" O SER A 637 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 642 " --> pdb=" O LEU A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 705 removed outlier: 3.525A pdb=" N VAL A 697 " --> pdb=" O MET A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.594A pdb=" N LEU A 710 " --> pdb=" O ARG A 706 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 712 " --> pdb=" O GLU A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 739 removed outlier: 3.843A pdb=" N ARG A 729 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N MET A 730 " --> pdb=" O GLU A 726 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP A 732 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 733 " --> pdb=" O ARG A 729 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG A 737 " --> pdb=" O LEU A 733 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 738 " --> pdb=" O MET A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 763 Processing helix chain 'A' and resid 770 through 781 Processing helix chain 'A' and resid 781 through 791 Processing helix chain 'B' and resid 169 through 175 removed outlier: 3.585A pdb=" N PHE B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 221 through 235 removed outlier: 4.320A pdb=" N VAL B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 263 through 280 removed outlier: 3.710A pdb=" N VAL B 272 " --> pdb=" O ARG B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 292 Processing helix chain 'B' and resid 303 through 314 Proline residue: B 310 - end of helix removed outlier: 3.698A pdb=" N ALA B 313 " --> pdb=" O LYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 332 Processing helix chain 'B' and resid 335 through 341 removed outlier: 3.605A pdb=" N ARG B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 removed outlier: 3.915A pdb=" N GLU B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 371 Processing helix chain 'B' and resid 375 through 390 removed outlier: 3.530A pdb=" N MET B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 388 " --> pdb=" O THR B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 411 removed outlier: 3.570A pdb=" N LEU B 402 " --> pdb=" O LYS B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 490 removed outlier: 3.634A pdb=" N ILE B 484 " --> pdb=" O ASP B 480 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 485 " --> pdb=" O ASP B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 509 Processing helix chain 'B' and resid 509 through 515 Processing helix chain 'B' and resid 521 through 537 removed outlier: 4.322A pdb=" N LYS B 530 " --> pdb=" O LYS B 526 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 531 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 532 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 572 Processing helix chain 'B' and resid 587 through 594 removed outlier: 3.615A pdb=" N THR B 590 " --> pdb=" O ASP B 587 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA B 591 " --> pdb=" O ARG B 588 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 592 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 617 removed outlier: 3.875A pdb=" N ARG B 616 " --> pdb=" O GLU B 612 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS B 617 " --> pdb=" O LYS B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 630 Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.850A pdb=" N LEU B 639 " --> pdb=" O ASN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 705 Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.546A pdb=" N LEU B 710 " --> pdb=" O ARG B 706 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG B 712 " --> pdb=" O GLU B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 742 removed outlier: 3.928A pdb=" N ARG B 729 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 733 " --> pdb=" O ARG B 729 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 738 " --> pdb=" O MET B 734 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLY B 740 " --> pdb=" O SER B 736 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN B 741 " --> pdb=" O ARG B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 763 Processing helix chain 'B' and resid 770 through 781 Processing helix chain 'B' and resid 783 through 791 Processing helix chain 'C' and resid 178 through 184 Processing helix chain 'C' and resid 196 through 205 Processing helix chain 'C' and resid 221 through 236 removed outlier: 3.917A pdb=" N VAL C 226 " --> pdb=" O LYS C 222 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL C 234 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 265 through 280 Processing helix chain 'C' and resid 289 through 292 Processing helix chain 'C' and resid 303 through 315 removed outlier: 3.616A pdb=" N LEU C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) Proline residue: C 310 - end of helix removed outlier: 3.509A pdb=" N ALA C 313 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 329 removed outlier: 3.594A pdb=" N ARG C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 325 through 329' Processing helix chain 'C' and resid 335 through 342 removed outlier: 3.913A pdb=" N GLU C 339 " --> pdb=" O ASP C 335 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG C 341 " --> pdb=" O ALA C 337 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 removed outlier: 4.170A pdb=" N GLU C 357 " --> pdb=" O GLU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 371 Processing helix chain 'C' and resid 375 through 390 removed outlier: 3.507A pdb=" N MET C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 386 " --> pdb=" O ALA C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 414 removed outlier: 5.746A pdb=" N ILE C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 402 " --> pdb=" O LYS C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 492 removed outlier: 3.651A pdb=" N VAL C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 509 removed outlier: 4.027A pdb=" N ARG C 506 " --> pdb=" O ALA C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 515 Processing helix chain 'C' and resid 521 through 537 removed outlier: 3.581A pdb=" N ILE C 532 " --> pdb=" O VAL C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 571 removed outlier: 3.629A pdb=" N SER C 563 " --> pdb=" O LYS C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 596 removed outlier: 3.627A pdb=" N PHE C 595 " --> pdb=" O ALA C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 615 Processing helix chain 'C' and resid 626 through 630 removed outlier: 3.745A pdb=" N LYS C 629 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 636 removed outlier: 3.978A pdb=" N TYR C 635 " --> pdb=" O HIS C 631 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN C 636 " --> pdb=" O GLN C 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 631 through 636' Processing helix chain 'C' and resid 638 through 643 removed outlier: 3.677A pdb=" N LEU C 642 " --> pdb=" O LEU C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 705 removed outlier: 3.534A pdb=" N ASP C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 removed outlier: 3.592A pdb=" N ARG C 712 " --> pdb=" O GLU C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 744 removed outlier: 3.886A pdb=" N ARG C 729 " --> pdb=" O GLU C 725 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP C 732 " --> pdb=" O ILE C 728 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 737 " --> pdb=" O LEU C 733 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER C 744 " --> pdb=" O GLY C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 762 Processing helix chain 'C' and resid 770 through 781 Processing helix chain 'C' and resid 781 through 791 removed outlier: 3.702A pdb=" N LEU C 790 " --> pdb=" O SER C 786 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 174 Processing helix chain 'D' and resid 178 through 184 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 221 through 235 removed outlier: 3.809A pdb=" N VAL D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 243 Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 263 through 280 Processing helix chain 'D' and resid 289 through 293 removed outlier: 3.641A pdb=" N VAL D 293 " --> pdb=" O HIS D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 315 Proline residue: D 310 - end of helix removed outlier: 3.617A pdb=" N ARG D 314 " --> pdb=" O PRO D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 330 removed outlier: 3.631A pdb=" N LYS D 330 " --> pdb=" O ASP D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 341 removed outlier: 3.659A pdb=" N ARG D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG D 341 " --> pdb=" O ALA D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 362 through 371 Processing helix chain 'D' and resid 375 through 390 removed outlier: 3.618A pdb=" N ALA D 386 " --> pdb=" O ALA D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 414 removed outlier: 5.896A pdb=" N ILE D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D 402 " --> pdb=" O LYS D 398 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 490 removed outlier: 3.911A pdb=" N VAL D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 509 Processing helix chain 'D' and resid 509 through 514 Processing helix chain 'D' and resid 523 through 537 removed outlier: 3.654A pdb=" N ALA D 531 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 532 " --> pdb=" O VAL D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 572 Processing helix chain 'D' and resid 610 through 615 Processing helix chain 'D' and resid 626 through 630 Processing helix chain 'D' and resid 638 through 644 removed outlier: 3.948A pdb=" N GLU D 643 " --> pdb=" O LEU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 694 through 705 removed outlier: 3.662A pdb=" N ASN D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 removed outlier: 3.593A pdb=" N ARG D 712 " --> pdb=" O GLU D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 738 removed outlier: 4.032A pdb=" N ILE D 728 " --> pdb=" O ARG D 724 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG D 729 " --> pdb=" O GLU D 725 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP D 732 " --> pdb=" O ILE D 728 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 733 " --> pdb=" O ARG D 729 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET D 734 " --> pdb=" O MET D 730 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER D 736 " --> pdb=" O ASP D 732 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG D 737 " --> pdb=" O LEU D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 762 Processing helix chain 'D' and resid 770 through 782 removed outlier: 4.161A pdb=" N THR D 776 " --> pdb=" O PRO D 772 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN D 778 " --> pdb=" O ARG D 774 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 780 " --> pdb=" O THR D 776 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 781 " --> pdb=" O ILE D 777 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 185 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 221 through 236 removed outlier: 3.754A pdb=" N VAL E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 257 removed outlier: 3.711A pdb=" N LEU E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 278 removed outlier: 3.563A pdb=" N GLU E 267 " --> pdb=" O GLY E 263 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG E 268 " --> pdb=" O ASP E 264 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 308 Processing helix chain 'E' and resid 308 through 313 removed outlier: 3.531A pdb=" N ALA E 313 " --> pdb=" O LYS E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 332 Processing helix chain 'E' and resid 351 through 370 removed outlier: 5.021A pdb=" N ASP E 364 " --> pdb=" O LYS E 360 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ARG E 365 " --> pdb=" O GLY E 361 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 390 removed outlier: 3.992A pdb=" N MET E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL E 380 " --> pdb=" O ASP E 376 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR E 384 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA E 386 " --> pdb=" O ALA E 382 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 399 Processing helix chain 'E' and resid 399 through 414 removed outlier: 3.864A pdb=" N ILE E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 492 removed outlier: 4.112A pdb=" N TRP E 491 " --> pdb=" O VAL E 487 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR E 492 " --> pdb=" O LEU E 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 185 removed outlier: 3.580A pdb=" N GLU F 184 " --> pdb=" O ALA F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 205 removed outlier: 3.636A pdb=" N SER F 205 " --> pdb=" O MET F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 236 removed outlier: 3.522A pdb=" N VAL F 226 " --> pdb=" O LYS F 222 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 278 Processing helix chain 'F' and resid 288 through 292 Processing helix chain 'F' and resid 307 through 313 removed outlier: 3.542A pdb=" N LYS F 311 " --> pdb=" O ILE F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 331 removed outlier: 3.509A pdb=" N ARG F 329 " --> pdb=" O LEU F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 340 removed outlier: 3.614A pdb=" N ARG F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 362 removed outlier: 3.601A pdb=" N GLU F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 370 Processing helix chain 'F' and resid 375 through 385 removed outlier: 3.573A pdb=" N MET F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 390 removed outlier: 3.650A pdb=" N ILE F 390 " --> pdb=" O ALA F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 399 Processing helix chain 'F' and resid 399 through 414 Processing helix chain 'F' and resid 482 through 493 removed outlier: 4.180A pdb=" N GLU F 486 " --> pdb=" O GLU F 482 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU F 488 " --> pdb=" O ILE F 484 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP F 491 " --> pdb=" O VAL F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 513 through 517 removed outlier: 3.819A pdb=" N ARG F 517 " --> pdb=" O LEU F 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 537 removed outlier: 3.508A pdb=" N ILE F 532 " --> pdb=" O VAL F 528 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG F 533 " --> pdb=" O SER F 529 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR F 535 " --> pdb=" O ALA F 531 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA F 537 " --> pdb=" O ARG F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 570 removed outlier: 3.578A pdb=" N SER F 563 " --> pdb=" O LYS F 559 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA F 565 " --> pdb=" O GLU F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 575 No H-bonds generated for 'chain 'F' and resid 573 through 575' Processing helix chain 'F' and resid 609 through 617 Processing helix chain 'F' and resid 632 through 640 removed outlier: 3.682A pdb=" N ASN F 636 " --> pdb=" O GLN F 632 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU F 638 " --> pdb=" O ILE F 634 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN F 640 " --> pdb=" O ASN F 636 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 735 removed outlier: 3.762A pdb=" N ILE F 728 " --> pdb=" O ARG F 724 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG F 729 " --> pdb=" O GLU F 725 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N MET F 730 " --> pdb=" O GLU F 726 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU F 733 " --> pdb=" O ARG F 729 " (cutoff:3.500A) Processing helix chain 'F' and resid 735 through 743 removed outlier: 3.708A pdb=" N GLN F 741 " --> pdb=" O ARG F 737 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 763 Processing helix chain 'F' and resid 772 through 780 removed outlier: 3.568A pdb=" N ILE F 777 " --> pdb=" O LEU F 773 " (cutoff:3.500A) Processing helix chain 'F' and resid 782 through 791 removed outlier: 3.787A pdb=" N LYS F 788 " --> pdb=" O GLN F 784 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 39 Processing helix chain 'G' and resid 49 through 67 Processing helix chain 'G' and resid 83 through 96 Processing helix chain 'G' and resid 110 through 118 removed outlier: 3.720A pdb=" N VAL G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 173 removed outlier: 3.993A pdb=" N ILE G 152 " --> pdb=" O SER G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 183 Processing helix chain 'G' and resid 191 through 195 Processing helix chain 'H' and resid 31 through 39 Processing helix chain 'H' and resid 49 through 67 Processing helix chain 'H' and resid 83 through 96 Processing helix chain 'H' and resid 110 through 118 removed outlier: 3.781A pdb=" N VAL H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 173 removed outlier: 3.992A pdb=" N ILE H 152 " --> pdb=" O SER H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 183 Processing helix chain 'H' and resid 191 through 195 Processing helix chain 'I' and resid 31 through 39 Processing helix chain 'I' and resid 49 through 67 Processing helix chain 'I' and resid 83 through 96 Processing helix chain 'I' and resid 110 through 118 removed outlier: 3.787A pdb=" N VAL I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 173 removed outlier: 3.993A pdb=" N ILE I 152 " --> pdb=" O SER I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 183 Processing helix chain 'I' and resid 191 through 195 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 49 through 67 Processing helix chain 'J' and resid 83 through 96 Processing helix chain 'J' and resid 110 through 118 removed outlier: 3.623A pdb=" N VAL J 114 " --> pdb=" O SER J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 173 removed outlier: 3.993A pdb=" N ILE J 152 " --> pdb=" O SER J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 183 Processing helix chain 'J' and resid 191 through 195 Processing helix chain 'K' and resid 31 through 39 Processing helix chain 'K' and resid 49 through 67 Processing helix chain 'K' and resid 83 through 96 Processing helix chain 'K' and resid 110 through 118 removed outlier: 3.853A pdb=" N VAL K 114 " --> pdb=" O SER K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 173 removed outlier: 3.992A pdb=" N ILE K 152 " --> pdb=" O SER K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 183 Processing helix chain 'K' and resid 191 through 195 Processing helix chain 'L' and resid 31 through 39 Processing helix chain 'L' and resid 49 through 67 Processing helix chain 'L' and resid 83 through 96 Processing helix chain 'L' and resid 110 through 118 removed outlier: 3.797A pdb=" N VAL L 114 " --> pdb=" O SER L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 173 removed outlier: 3.993A pdb=" N ILE L 152 " --> pdb=" O SER L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 183 Processing helix chain 'L' and resid 191 through 195 Processing helix chain 'M' and resid 31 through 39 Processing helix chain 'M' and resid 49 through 67 Processing helix chain 'M' and resid 83 through 96 Processing helix chain 'M' and resid 110 through 118 removed outlier: 3.591A pdb=" N VAL M 114 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 173 removed outlier: 3.993A pdb=" N ILE M 152 " --> pdb=" O SER M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 183 Processing helix chain 'M' and resid 191 through 195 Processing helix chain 'N' and resid 16 through 27 Processing helix chain 'N' and resid 37 through 55 Processing helix chain 'N' and resid 70 through 84 Processing helix chain 'N' and resid 98 through 106 Processing helix chain 'N' and resid 133 through 159 Processing helix chain 'N' and resid 161 through 169 Processing helix chain 'N' and resid 176 through 184 Processing helix chain 'O' and resid 16 through 27 Processing helix chain 'O' and resid 37 through 55 Processing helix chain 'O' and resid 70 through 84 Processing helix chain 'O' and resid 98 through 106 Processing helix chain 'O' and resid 133 through 159 Processing helix chain 'O' and resid 161 through 169 Processing helix chain 'O' and resid 176 through 184 Processing helix chain 'P' and resid 16 through 27 Processing helix chain 'P' and resid 37 through 55 Processing helix chain 'P' and resid 70 through 84 Processing helix chain 'P' and resid 98 through 106 Processing helix chain 'P' and resid 133 through 159 Processing helix chain 'P' and resid 161 through 169 Processing helix chain 'P' and resid 176 through 184 Processing helix chain 'Q' and resid 16 through 27 Processing helix chain 'Q' and resid 37 through 55 Processing helix chain 'Q' and resid 70 through 84 Processing helix chain 'Q' and resid 98 through 106 Processing helix chain 'Q' and resid 133 through 159 Processing helix chain 'Q' and resid 161 through 169 Processing helix chain 'Q' and resid 176 through 184 Processing helix chain 'R' and resid 16 through 27 Processing helix chain 'R' and resid 37 through 55 Processing helix chain 'R' and resid 70 through 84 Processing helix chain 'R' and resid 98 through 106 Processing helix chain 'R' and resid 133 through 159 Processing helix chain 'R' and resid 161 through 169 Processing helix chain 'R' and resid 176 through 184 Processing helix chain 'S' and resid 16 through 27 Processing helix chain 'S' and resid 37 through 55 Processing helix chain 'S' and resid 70 through 84 Processing helix chain 'S' and resid 98 through 106 Processing helix chain 'S' and resid 133 through 159 Processing helix chain 'S' and resid 161 through 169 Processing helix chain 'S' and resid 176 through 184 Processing helix chain 'T' and resid 16 through 27 Processing helix chain 'T' and resid 37 through 55 Processing helix chain 'T' and resid 70 through 84 Processing helix chain 'T' and resid 98 through 106 Processing helix chain 'T' and resid 133 through 159 Processing helix chain 'T' and resid 161 through 169 Processing helix chain 'T' and resid 176 through 184 Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.582A pdb=" N ARG A 176 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLN A 246 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE A 285 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR A 248 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASP A 287 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 250 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 322 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASN A 211 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL A 345 " --> pdb=" O ASN A 211 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL A 213 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 373 through 374 removed outlier: 6.606A pdb=" N SER A 373 " --> pdb=" O VAL A 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 578 through 579 removed outlier: 6.488A pdb=" N ILE A 578 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ASP A 625 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLY A 547 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE A 664 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE A 549 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER A 548 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE A 717 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE A 550 " --> pdb=" O ILE A 717 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 747 through 751 Processing sheet with id=AA5, first strand: chain 'B' and resid 212 through 215 removed outlier: 6.410A pdb=" N VAL B 213 " --> pdb=" O VAL B 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 246 through 249 removed outlier: 6.504A pdb=" N GLN B 246 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N PHE B 285 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR B 248 " --> pdb=" O PHE B 285 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP B 287 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE B 320 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B 284 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ALA B 322 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE B 286 " --> pdb=" O ALA B 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 373 through 374 removed outlier: 7.071A pdb=" N SER B 373 " --> pdb=" O VAL B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 578 through 581 removed outlier: 5.922A pdb=" N GLY B 547 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N PHE B 664 " --> pdb=" O GLY B 547 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE B 549 " --> pdb=" O PHE B 664 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER B 548 " --> pdb=" O ASP B 715 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE B 717 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE B 550 " --> pdb=" O ILE B 717 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 648 removed outlier: 3.504A pdb=" N LEU B 647 " --> pdb=" O VAL B 655 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 748 through 751 removed outlier: 5.744A pdb=" N ALA B 748 " --> pdb=" O VAL B 800 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL B 802 " --> pdb=" O ALA B 748 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL B 750 " --> pdb=" O VAL B 802 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 175 through 177 removed outlier: 6.783A pdb=" N GLN C 246 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE C 285 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR C 248 " --> pdb=" O PHE C 285 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASP C 287 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU C 250 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE C 282 " --> pdb=" O GLN C 318 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE C 320 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU C 284 " --> pdb=" O ILE C 320 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ALA C 322 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE C 286 " --> pdb=" O ALA C 322 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N THR C 324 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL C 213 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL C 347 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE C 215 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 373 through 374 removed outlier: 7.203A pdb=" N SER C 373 " --> pdb=" O VAL C 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 578 through 581 removed outlier: 6.450A pdb=" N SER C 548 " --> pdb=" O ASP C 715 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE C 717 " --> pdb=" O SER C 548 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE C 550 " --> pdb=" O ILE C 717 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 749 through 751 removed outlier: 6.784A pdb=" N VAL C 750 " --> pdb=" O THR C 801 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 175 through 177 removed outlier: 4.815A pdb=" N ASP D 287 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ALA D 322 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE D 286 " --> pdb=" O ALA D 322 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N THR D 324 " --> pdb=" O ILE D 286 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VAL D 213 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL D 347 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE D 215 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 578 through 581 removed outlier: 6.157A pdb=" N ILE D 578 " --> pdb=" O LEU D 623 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP D 625 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE D 580 " --> pdb=" O ASP D 625 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N SER D 548 " --> pdb=" O ASP D 715 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE D 717 " --> pdb=" O SER D 548 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE D 550 " --> pdb=" O ILE D 717 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 646 through 648 Processing sheet with id=AB9, first strand: chain 'E' and resid 249 through 250 removed outlier: 6.602A pdb=" N LEU E 284 " --> pdb=" O ILE E 320 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ALA E 322 " --> pdb=" O LEU E 284 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE E 286 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR E 323 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU E 214 " --> pdb=" O THR E 323 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL E 213 " --> pdb=" O VAL E 345 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 176 through 177 removed outlier: 6.183A pdb=" N GLN F 246 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE F 285 " --> pdb=" O GLN F 246 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TYR F 248 " --> pdb=" O PHE F 285 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N ILE F 320 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU F 284 " --> pdb=" O ILE F 320 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 211 through 212 removed outlier: 6.659A pdb=" N ASN F 211 " --> pdb=" O GLN F 343 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 215 through 216 Processing sheet with id=AC4, first strand: chain 'F' and resid 549 through 550 removed outlier: 3.548A pdb=" N PHE F 664 " --> pdb=" O PHE F 549 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 750 through 751 removed outlier: 6.879A pdb=" N VAL F 750 " --> pdb=" O VAL F 802 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'G' and resid 41 through 43 removed outlier: 6.415A pdb=" N ILE G 42 " --> pdb=" O TYR G 75 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ASN G 77 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N SER G 78 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLN G 107 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG G 131 " --> pdb=" O CYS G 104 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLY G 106 " --> pdb=" O ARG G 131 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU G 133 " --> pdb=" O GLY G 106 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA G 108 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 41 through 43 removed outlier: 6.415A pdb=" N ILE G 42 " --> pdb=" O TYR G 75 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ASN G 77 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N SER G 78 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLN G 107 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N MET G 125 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N THR G 102 " --> pdb=" O MET G 125 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 138 through 146 removed outlier: 6.956A pdb=" N GLY G 141 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLY N 131 " --> pdb=" O GLY G 141 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 41 through 43 removed outlier: 6.414A pdb=" N ILE H 42 " --> pdb=" O TYR H 75 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ASN H 77 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N SER H 78 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLN H 107 " --> pdb=" O SER H 78 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG H 131 " --> pdb=" O CYS H 104 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLY H 106 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU H 133 " --> pdb=" O GLY H 106 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA H 108 " --> pdb=" O LEU H 133 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 41 through 43 removed outlier: 6.414A pdb=" N ILE H 42 " --> pdb=" O TYR H 75 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ASN H 77 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N SER H 78 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLN H 107 " --> pdb=" O SER H 78 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N MET H 125 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N THR H 102 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 138 through 146 removed outlier: 4.026A pdb=" N GLY O 131 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY H 141 " --> pdb=" O VAL O 129 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL O 129 " --> pdb=" O GLY H 141 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE H 143 " --> pdb=" O GLY O 127 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLY O 127 " --> pdb=" O ILE H 143 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 41 through 43 removed outlier: 6.415A pdb=" N ILE I 42 " --> pdb=" O TYR I 75 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ASN I 77 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N SER I 78 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN I 107 " --> pdb=" O SER I 78 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG I 131 " --> pdb=" O CYS I 104 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLY I 106 " --> pdb=" O ARG I 131 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU I 133 " --> pdb=" O GLY I 106 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA I 108 " --> pdb=" O LEU I 133 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 41 through 43 removed outlier: 6.415A pdb=" N ILE I 42 " --> pdb=" O TYR I 75 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ASN I 77 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N SER I 78 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN I 107 " --> pdb=" O SER I 78 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N MET I 125 " --> pdb=" O ILE I 100 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N THR I 102 " --> pdb=" O MET I 125 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 138 through 146 removed outlier: 7.127A pdb=" N GLY I 141 " --> pdb=" O GLY P 131 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLY P 131 " --> pdb=" O GLY I 141 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE I 143 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL P 129 " --> pdb=" O ILE I 143 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 41 through 43 removed outlier: 6.416A pdb=" N ILE J 42 " --> pdb=" O TYR J 75 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ASN J 77 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N SER J 78 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN J 107 " --> pdb=" O SER J 78 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG J 131 " --> pdb=" O CYS J 104 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLY J 106 " --> pdb=" O ARG J 131 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU J 133 " --> pdb=" O GLY J 106 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA J 108 " --> pdb=" O LEU J 133 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 41 through 43 removed outlier: 6.416A pdb=" N ILE J 42 " --> pdb=" O TYR J 75 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ASN J 77 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N SER J 78 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN J 107 " --> pdb=" O SER J 78 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N MET J 125 " --> pdb=" O ILE J 100 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N THR J 102 " --> pdb=" O MET J 125 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 138 through 146 removed outlier: 7.036A pdb=" N GLY J 141 " --> pdb=" O GLY Q 131 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLY Q 131 " --> pdb=" O GLY J 141 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 41 through 43 removed outlier: 6.415A pdb=" N ILE K 42 " --> pdb=" O TYR K 75 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ASN K 77 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N SER K 78 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLN K 107 " --> pdb=" O SER K 78 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG K 131 " --> pdb=" O CYS K 104 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLY K 106 " --> pdb=" O ARG K 131 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU K 133 " --> pdb=" O GLY K 106 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA K 108 " --> pdb=" O LEU K 133 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 41 through 43 removed outlier: 6.415A pdb=" N ILE K 42 " --> pdb=" O TYR K 75 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ASN K 77 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N SER K 78 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLN K 107 " --> pdb=" O SER K 78 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N MET K 125 " --> pdb=" O ILE K 100 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N THR K 102 " --> pdb=" O MET K 125 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 138 through 146 removed outlier: 6.922A pdb=" N GLY K 141 " --> pdb=" O GLY R 131 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLY R 131 " --> pdb=" O GLY K 141 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 41 through 43 removed outlier: 6.415A pdb=" N ILE L 42 " --> pdb=" O TYR L 75 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ASN L 77 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N SER L 78 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN L 107 " --> pdb=" O SER L 78 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG L 131 " --> pdb=" O CYS L 104 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLY L 106 " --> pdb=" O ARG L 131 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU L 133 " --> pdb=" O GLY L 106 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA L 108 " --> pdb=" O LEU L 133 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 41 through 43 removed outlier: 6.415A pdb=" N ILE L 42 " --> pdb=" O TYR L 75 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ASN L 77 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N SER L 78 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN L 107 " --> pdb=" O SER L 78 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N MET L 125 " --> pdb=" O ILE L 100 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N THR L 102 " --> pdb=" O MET L 125 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 138 through 146 removed outlier: 6.957A pdb=" N GLY L 141 " --> pdb=" O GLY S 131 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY S 131 " --> pdb=" O GLY L 141 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 41 through 43 removed outlier: 6.415A pdb=" N ILE M 42 " --> pdb=" O TYR M 75 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ASN M 77 " --> pdb=" O ILE M 42 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N SER M 78 " --> pdb=" O LEU M 105 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN M 107 " --> pdb=" O SER M 78 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG M 131 " --> pdb=" O CYS M 104 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLY M 106 " --> pdb=" O ARG M 131 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU M 133 " --> pdb=" O GLY M 106 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA M 108 " --> pdb=" O LEU M 133 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 41 through 43 removed outlier: 6.415A pdb=" N ILE M 42 " --> pdb=" O TYR M 75 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ASN M 77 " --> pdb=" O ILE M 42 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N SER M 78 " --> pdb=" O LEU M 105 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN M 107 " --> pdb=" O SER M 78 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N MET M 125 " --> pdb=" O ILE M 100 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N THR M 102 " --> pdb=" O MET M 125 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 138 through 146 removed outlier: 7.085A pdb=" N GLY M 141 " --> pdb=" O GLY T 131 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLY T 131 " --> pdb=" O GLY M 141 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE M 143 " --> pdb=" O VAL T 129 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL T 129 " --> pdb=" O ILE M 143 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY M 145 " --> pdb=" O GLY T 127 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.928A pdb=" N ILE N 30 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASN N 65 " --> pdb=" O ILE N 30 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU N 32 " --> pdb=" O ASN N 65 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N SER N 66 " --> pdb=" O MET N 93 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N MET N 95 " --> pdb=" O SER N 66 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.928A pdb=" N ILE N 30 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASN N 65 " --> pdb=" O ILE N 30 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU N 32 " --> pdb=" O ASN N 65 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N SER N 66 " --> pdb=" O MET N 93 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N MET N 95 " --> pdb=" O SER N 66 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N TYR N 113 " --> pdb=" O ILE N 88 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N THR N 90 " --> pdb=" O TYR N 113 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 29 through 32 removed outlier: 6.928A pdb=" N ILE O 30 " --> pdb=" O TYR O 63 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASN O 65 " --> pdb=" O ILE O 30 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU O 32 " --> pdb=" O ASN O 65 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER O 66 " --> pdb=" O MET O 93 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N MET O 95 " --> pdb=" O SER O 66 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 29 through 32 removed outlier: 6.928A pdb=" N ILE O 30 " --> pdb=" O TYR O 63 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASN O 65 " --> pdb=" O ILE O 30 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU O 32 " --> pdb=" O ASN O 65 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER O 66 " --> pdb=" O MET O 93 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N MET O 95 " --> pdb=" O SER O 66 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N TYR O 113 " --> pdb=" O ILE O 88 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N THR O 90 " --> pdb=" O TYR O 113 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 29 through 32 removed outlier: 6.927A pdb=" N ILE P 30 " --> pdb=" O TYR P 63 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN P 65 " --> pdb=" O ILE P 30 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU P 32 " --> pdb=" O ASN P 65 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER P 66 " --> pdb=" O MET P 93 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N MET P 95 " --> pdb=" O SER P 66 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 29 through 32 removed outlier: 6.927A pdb=" N ILE P 30 " --> pdb=" O TYR P 63 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN P 65 " --> pdb=" O ILE P 30 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU P 32 " --> pdb=" O ASN P 65 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER P 66 " --> pdb=" O MET P 93 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N MET P 95 " --> pdb=" O SER P 66 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N TYR P 113 " --> pdb=" O ILE P 88 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N THR P 90 " --> pdb=" O TYR P 113 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 29 through 32 removed outlier: 6.927A pdb=" N ILE Q 30 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN Q 65 " --> pdb=" O ILE Q 30 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU Q 32 " --> pdb=" O ASN Q 65 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER Q 66 " --> pdb=" O MET Q 93 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N MET Q 95 " --> pdb=" O SER Q 66 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 29 through 32 removed outlier: 6.927A pdb=" N ILE Q 30 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN Q 65 " --> pdb=" O ILE Q 30 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU Q 32 " --> pdb=" O ASN Q 65 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER Q 66 " --> pdb=" O MET Q 93 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N MET Q 95 " --> pdb=" O SER Q 66 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N TYR Q 113 " --> pdb=" O ILE Q 88 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N THR Q 90 " --> pdb=" O TYR Q 113 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 29 through 32 removed outlier: 6.927A pdb=" N ILE R 30 " --> pdb=" O TYR R 63 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN R 65 " --> pdb=" O ILE R 30 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU R 32 " --> pdb=" O ASN R 65 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER R 66 " --> pdb=" O MET R 93 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N MET R 95 " --> pdb=" O SER R 66 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 29 through 32 removed outlier: 6.927A pdb=" N ILE R 30 " --> pdb=" O TYR R 63 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN R 65 " --> pdb=" O ILE R 30 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU R 32 " --> pdb=" O ASN R 65 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER R 66 " --> pdb=" O MET R 93 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N MET R 95 " --> pdb=" O SER R 66 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N TYR R 113 " --> pdb=" O ILE R 88 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N THR R 90 " --> pdb=" O TYR R 113 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'S' and resid 29 through 32 removed outlier: 6.927A pdb=" N ILE S 30 " --> pdb=" O TYR S 63 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN S 65 " --> pdb=" O ILE S 30 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU S 32 " --> pdb=" O ASN S 65 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER S 66 " --> pdb=" O MET S 93 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N MET S 95 " --> pdb=" O SER S 66 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG S 119 " --> pdb=" O ALA S 92 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY S 94 " --> pdb=" O ARG S 119 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU S 121 " --> pdb=" O GLY S 94 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA S 96 " --> pdb=" O LEU S 121 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 29 through 32 removed outlier: 6.927A pdb=" N ILE S 30 " --> pdb=" O TYR S 63 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN S 65 " --> pdb=" O ILE S 30 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU S 32 " --> pdb=" O ASN S 65 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER S 66 " --> pdb=" O MET S 93 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N MET S 95 " --> pdb=" O SER S 66 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N TYR S 113 " --> pdb=" O ILE S 88 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N THR S 90 " --> pdb=" O TYR S 113 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'T' and resid 29 through 32 removed outlier: 6.927A pdb=" N ILE T 30 " --> pdb=" O TYR T 63 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASN T 65 " --> pdb=" O ILE T 30 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU T 32 " --> pdb=" O ASN T 65 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER T 66 " --> pdb=" O MET T 93 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N MET T 95 " --> pdb=" O SER T 66 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'T' and resid 29 through 32 removed outlier: 6.927A pdb=" N ILE T 30 " --> pdb=" O TYR T 63 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASN T 65 " --> pdb=" O ILE T 30 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU T 32 " --> pdb=" O ASN T 65 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER T 66 " --> pdb=" O MET T 93 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N MET T 95 " --> pdb=" O SER T 66 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N TYR T 113 " --> pdb=" O ILE T 88 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N THR T 90 " --> pdb=" O TYR T 113 " (cutoff:3.500A) 2079 hydrogen bonds defined for protein. 6090 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: 12.47 Time building geometry restraints manager: 5.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.54: 43327 1.54 - 1.87: 721 1.87 - 2.20: 0 2.20 - 2.53: 0 2.53 - 2.86: 1 Bond restraints: 44049 Sorted by residual: bond pdb=" C LYS F 498 " pdb=" N THR F 505 " ideal model delta sigma weight residual 1.332 2.864 -1.531 1.40e-02 5.10e+03 1.20e+04 bond pdb=" C ALA S 96 " pdb=" N ALA S 97 " ideal model delta sigma weight residual 1.330 1.229 0.100 1.32e-02 5.74e+03 5.79e+01 bond pdb=" B26 BO2 T 201 " pdb=" O28 BO2 T 201 " ideal model delta sigma weight residual 1.356 1.491 -0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" B26 BO2 M 301 " pdb=" O28 BO2 M 301 " ideal model delta sigma weight residual 1.356 1.491 -0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" B26 BO2 P 201 " pdb=" O28 BO2 P 201 " ideal model delta sigma weight residual 1.356 1.491 -0.135 2.00e-02 2.50e+03 4.55e+01 ... (remaining 44044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.93: 59391 8.93 - 17.86: 68 17.86 - 26.79: 0 26.79 - 35.72: 1 35.72 - 44.65: 1 Bond angle restraints: 59461 Sorted by residual: angle pdb=" O LYS F 498 " pdb=" C LYS F 498 " pdb=" N THR F 505 " ideal model delta sigma weight residual 122.46 77.81 44.65 1.19e+00 7.06e-01 1.41e+03 angle pdb=" C LYS F 498 " pdb=" N THR F 505 " pdb=" CA THR F 505 " ideal model delta sigma weight residual 121.54 149.14 -27.60 1.91e+00 2.74e-01 2.09e+02 angle pdb=" CA LYS F 498 " pdb=" C LYS F 498 " pdb=" N THR F 505 " ideal model delta sigma weight residual 115.10 128.92 -13.82 1.26e+00 6.30e-01 1.20e+02 angle pdb=" PB ATP D 903 " pdb=" O3B ATP D 903 " pdb=" PG ATP D 903 " ideal model delta sigma weight residual 139.87 130.36 9.51 1.00e+00 1.00e+00 9.04e+01 angle pdb=" PA ATP A 902 " pdb=" O3A ATP A 902 " pdb=" PB ATP A 902 " ideal model delta sigma weight residual 136.83 127.92 8.91 1.00e+00 1.00e+00 7.94e+01 ... (remaining 59456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.07: 26364 27.07 - 54.13: 621 54.13 - 81.20: 122 81.20 - 108.26: 5 108.26 - 135.33: 5 Dihedral angle restraints: 27117 sinusoidal: 11318 harmonic: 15799 Sorted by residual: dihedral pdb=" CA LYS F 498 " pdb=" C LYS F 498 " pdb=" N THR F 505 " pdb=" CA THR F 505 " ideal model delta harmonic sigma weight residual 180.00 59.55 120.45 0 5.00e+00 4.00e-02 5.80e+02 dihedral pdb=" CD ARG B 340 " pdb=" NE ARG B 340 " pdb=" CZ ARG B 340 " pdb=" NH1 ARG B 340 " ideal model delta sinusoidal sigma weight residual 0.00 80.92 -80.92 1 1.00e+01 1.00e-02 8.09e+01 dihedral pdb=" CD ARG A 340 " pdb=" NE ARG A 340 " pdb=" CZ ARG A 340 " pdb=" NH1 ARG A 340 " ideal model delta sinusoidal sigma weight residual 0.00 -77.42 77.42 1 1.00e+01 1.00e-02 7.51e+01 ... (remaining 27114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 6043 0.089 - 0.179: 721 0.179 - 0.268: 41 0.268 - 0.358: 2 0.358 - 0.447: 9 Chirality restraints: 6816 Sorted by residual: chirality pdb=" CG LEU D 679 " pdb=" CB LEU D 679 " pdb=" CD1 LEU D 679 " pdb=" CD2 LEU D 679 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CG LEU C 679 " pdb=" CB LEU C 679 " pdb=" CD1 LEU C 679 " pdb=" CD2 LEU C 679 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CG LEU K 36 " pdb=" CB LEU K 36 " pdb=" CD1 LEU K 36 " pdb=" CD2 LEU K 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 6813 not shown) Planarity restraints: 7675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BO2 R 201 " 0.329 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C2 BO2 R 201 " 0.151 2.00e-02 2.50e+03 pdb=" C7 BO2 R 201 " -0.074 2.00e-02 2.50e+03 pdb=" N9 BO2 R 201 " -0.504 2.00e-02 2.50e+03 pdb=" O8 BO2 R 201 " 0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BO2 I 301 " 0.173 2.00e-02 2.50e+03 2.72e-01 9.26e+02 pdb=" C18 BO2 I 301 " -0.080 2.00e-02 2.50e+03 pdb=" C21 BO2 I 301 " 0.320 2.00e-02 2.50e+03 pdb=" N20 BO2 I 301 " -0.477 2.00e-02 2.50e+03 pdb=" O19 BO2 I 301 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BO2 L 301 " 0.175 2.00e-02 2.50e+03 2.68e-01 8.97e+02 pdb=" C18 BO2 L 301 " -0.080 2.00e-02 2.50e+03 pdb=" C21 BO2 L 301 " 0.316 2.00e-02 2.50e+03 pdb=" N20 BO2 L 301 " -0.468 2.00e-02 2.50e+03 pdb=" O19 BO2 L 301 " 0.057 2.00e-02 2.50e+03 ... (remaining 7672 not shown) Histogram of nonbonded interaction distances: 0.82 - 1.64: 5 1.64 - 2.45: 177 2.45 - 3.27: 47081 3.27 - 4.08: 117952 4.08 - 4.90: 221336 Warning: very small nonbonded interaction distances. Nonbonded interactions: 386551 Sorted by model distance: nonbonded pdb="MG MG D 902 " pdb=" O3G ATP D 903 " model vdw 0.824 2.170 nonbonded pdb=" OG1 THR B 223 " pdb="MG MG B 901 " model vdw 1.413 2.170 nonbonded pdb="MG MG C 903 " pdb=" O3G ATP C 904 " model vdw 1.479 2.170 nonbonded pdb=" N GLY A 556 " pdb=" O3B ATP A 902 " model vdw 1.511 3.120 nonbonded pdb="MG MG A 901 " pdb=" O2B ATP A 904 " model vdw 1.516 2.170 ... (remaining 386546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 170 through 414 or resid 477 through 668 or resid 679 thro \ ugh 684 or resid 693 through 788 or resid 904)) selection = (chain 'B' and (resid 170 through 299 or resid 304 through 668 or resid 679 thro \ ugh 684 or resid 693 through 788 or resid 904)) selection = (chain 'C' and (resid 170 through 299 or resid 304 through 414 or resid 477 thro \ ugh 668 or resid 679 through 684 or resid 693 through 788 or resid 904)) selection = (chain 'D' and (resid 170 through 299 or resid 304 through 414 or resid 477 thro \ ugh 668 or resid 679 through 788 or resid 903)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 12.710 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: 0.050 Extract box with map and model: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.130 Process input model: 45.080 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.160 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:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.014 1.531 44069 Z= 0.906 Angle : 1.122 44.647 59461 Z= 0.630 Chirality : 0.060 0.447 6816 Planarity : 0.019 0.488 7675 Dihedral : 12.121 135.330 16921 Min Nonbonded Distance : 0.824 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.44 % Favored : 94.45 % Rotamer: Outliers : 0.96 % Allowed : 3.15 % Favored : 95.89 % 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: -4.84 (0.09), residues: 5424 helix: -4.05 (0.05), residues: 2828 sheet: -2.10 (0.23), residues: 437 loop : -1.89 (0.12), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 206 TYR 0.059 0.004 TYR R 63 PHE 0.047 0.004 PHE C 719 TRP 0.028 0.003 TRP A 491 HIS 0.016 0.003 HIS C 515 Details of bonding type rmsd covalent geometry : bond 0.01266 (44049) covalent geometry : angle 1.12239 (59461) hydrogen bonds : bond 0.26174 ( 2009) hydrogen bonds : angle 9.91587 ( 6090) Misc. bond : bond 0.26861 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1491 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 1448 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 226 VAL cc_start: 0.8213 (m) cc_final: 0.7881 (t) REVERT: A 248 TYR cc_start: 0.8701 (m-80) cc_final: 0.8494 (m-80) REVERT: A 256 VAL cc_start: 0.7771 (t) cc_final: 0.7327 (t) REVERT: A 632 GLN cc_start: 0.7765 (mp10) cc_final: 0.7461 (mm-40) REVERT: A 718 VAL cc_start: 0.7726 (t) cc_final: 0.7345 (m) REVERT: A 764 PHE cc_start: 0.7852 (t80) cc_final: 0.7547 (t80) REVERT: B 303 ASP cc_start: 0.7982 (p0) cc_final: 0.7676 (p0) REVERT: B 410 MET cc_start: 0.7989 (mmm) cc_final: 0.7724 (mmm) REVERT: B 592 SER cc_start: 0.9095 (m) cc_final: 0.8693 (t) REVERT: C 323 THR cc_start: 0.9085 (m) cc_final: 0.8853 (p) REVERT: C 324 THR cc_start: 0.8761 (m) cc_final: 0.8551 (p) REVERT: C 339 GLU cc_start: 0.7896 (tt0) cc_final: 0.7612 (tm-30) REVERT: C 548 SER cc_start: 0.8585 (m) cc_final: 0.8322 (m) REVERT: C 667 ASN cc_start: 0.7528 (m-40) cc_final: 0.6737 (m110) REVERT: C 710 LEU cc_start: 0.8547 (mt) cc_final: 0.8319 (mm) REVERT: C 714 ASP cc_start: 0.7516 (m-30) cc_final: 0.7278 (m-30) REVERT: D 260 ARG cc_start: 0.7228 (mtp-110) cc_final: 0.6978 (mtp85) REVERT: D 293 VAL cc_start: 0.8278 (t) cc_final: 0.7968 (m) REVERT: D 389 TYR cc_start: 0.8682 (m-80) cc_final: 0.8400 (m-80) REVERT: D 581 ASP cc_start: 0.7937 (m-30) cc_final: 0.7492 (m-30) REVERT: D 593 ARG cc_start: 0.7435 (mtm180) cc_final: 0.6955 (mmt180) REVERT: D 625 ASP cc_start: 0.7536 (t0) cc_final: 0.7309 (t0) REVERT: D 634 ILE cc_start: 0.8365 (tt) cc_final: 0.8020 (mp) REVERT: D 639 LEU cc_start: 0.8441 (tt) cc_final: 0.8185 (tp) REVERT: D 714 ASP cc_start: 0.6478 (m-30) cc_final: 0.5862 (m-30) REVERT: E 183 MET cc_start: 0.7816 (ttm) cc_final: 0.7604 (tpt) REVERT: E 186 LYS cc_start: 0.8560 (mtmt) cc_final: 0.7591 (ttpt) REVERT: E 231 GLN cc_start: 0.8528 (mt0) cc_final: 0.8309 (mt0) REVERT: E 340 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7972 (ptm-80) REVERT: E 354 HIS cc_start: 0.8357 (t-90) cc_final: 0.8090 (t70) REVERT: E 367 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6822 (mt-10) REVERT: E 410 MET cc_start: 0.8110 (tpp) cc_final: 0.7403 (tmm) REVERT: F 210 ASN cc_start: 0.8364 (p0) cc_final: 0.8122 (p0) REVERT: F 270 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8577 (mmtt) REVERT: F 340 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7512 (mtp-110) REVERT: F 379 MET cc_start: 0.8111 (mtm) cc_final: 0.7710 (mtm) REVERT: F 403 ILE cc_start: 0.8308 (pt) cc_final: 0.8056 (pp) REVERT: F 487 VAL cc_start: 0.7909 (t) cc_final: 0.7570 (p) REVERT: F 498 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6432 (ptpt) REVERT: F 505 THR cc_start: 0.6612 (OUTLIER) cc_final: 0.6349 (t) REVERT: F 514 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7410 (tp) REVERT: G 101 GLN cc_start: 0.8291 (tt0) cc_final: 0.7714 (tt0) REVERT: I 46 VAL cc_start: 0.9399 (m) cc_final: 0.9123 (m) REVERT: I 78 SER cc_start: 0.8916 (t) cc_final: 0.8630 (t) REVERT: I 87 MET cc_start: 0.8658 (mmt) cc_final: 0.8243 (mmt) REVERT: I 101 GLN cc_start: 0.8499 (tt0) cc_final: 0.8268 (tt0) REVERT: J 52 SER cc_start: 0.9048 (t) cc_final: 0.8813 (p) REVERT: K 78 SER cc_start: 0.8881 (t) cc_final: 0.8649 (t) REVERT: L 31 ASN cc_start: 0.8124 (m-40) cc_final: 0.7911 (m110) REVERT: L 34 ASN cc_start: 0.8572 (m-40) cc_final: 0.8315 (m110) REVERT: L 39 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7898 (mm-30) REVERT: L 78 SER cc_start: 0.9075 (t) cc_final: 0.8866 (t) REVERT: N 152 ARG cc_start: 0.8872 (ttp80) cc_final: 0.8653 (ttp80) REVERT: O 40 ILE cc_start: 0.8874 (mm) cc_final: 0.8657 (mp) REVERT: O 152 ARG cc_start: 0.8691 (ttp80) cc_final: 0.8452 (ttp80) REVERT: P 40 ILE cc_start: 0.8986 (mm) cc_final: 0.8784 (mt) REVERT: P 43 ARG cc_start: 0.8175 (tmm160) cc_final: 0.7895 (ttp80) REVERT: P 59 ASP cc_start: 0.8016 (m-30) cc_final: 0.7541 (m-30) REVERT: P 111 LYS cc_start: 0.8774 (mttp) cc_final: 0.8436 (mttt) REVERT: P 190 ILE cc_start: 0.8744 (mm) cc_final: 0.8482 (mt) REVERT: Q 37 ASN cc_start: 0.8738 (p0) cc_final: 0.8470 (p0) REVERT: Q 38 ASP cc_start: 0.8164 (m-30) cc_final: 0.7838 (m-30) REVERT: Q 42 ASN cc_start: 0.8667 (m-40) cc_final: 0.8412 (m-40) REVERT: Q 111 LYS cc_start: 0.8712 (mttp) cc_final: 0.8492 (mttt) REVERT: S 111 LYS cc_start: 0.8752 (mttp) cc_final: 0.8524 (mttt) REVERT: T 37 ASN cc_start: 0.9078 (p0) cc_final: 0.8744 (p0) outliers start: 43 outliers final: 12 residues processed: 1475 average time/residue: 1.0097 time to fit residues: 1753.6844 Evaluate side-chains 804 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 787 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 498 LYS Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain P residue 98 SER Chi-restraints excluded: chain Q residue 98 SER Chi-restraints excluded: chain R residue 98 SER Chi-restraints excluded: chain T residue 98 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 394 optimal weight: 0.9980 chunk 430 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 0.8980 chunk 523 optimal weight: 0.6980 chunk 497 optimal weight: 0.7980 chunk 414 optimal weight: 0.8980 chunk 310 optimal weight: 0.6980 chunk 488 optimal weight: 0.9980 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 211 ASN A 343 GLN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 HIS A 521 GLN A 659 ASN A 667 ASN A 720 HIS B 211 ASN B 521 GLN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 HIS C 246 GLN C 277 ASN C 343 GLN C 346 GLN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 778 GLN ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 GLN D 343 GLN D 346 GLN D 490 ASN D 631 HIS D 640 GLN E 177 ASN E 202 GLN E 246 GLN E 277 ASN F 370 HIS F 636 ASN G 34 ASN G 54 ASN H 31 ASN H 54 ASN H 135 HIS I 107 GLN I 129 ASN I 136 GLN J 54 ASN J 135 HIS L 34 ASN L 107 GLN M 129 ASN ** N 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 HIS ** Q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 117 HIS S 142 GLN T 117 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.116149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.090914 restraints weight = 74121.902| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.96 r_work: 0.3233 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 44069 Z= 0.167 Angle : 0.695 9.936 59461 Z= 0.353 Chirality : 0.045 0.352 6816 Planarity : 0.006 0.080 7675 Dihedral : 10.884 157.944 6563 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.22 % Favored : 95.76 % Rotamer: Outliers : 3.75 % Allowed : 14.79 % Favored : 81.45 % 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: -2.66 (0.10), residues: 5426 helix: -1.71 (0.08), residues: 2907 sheet: -2.09 (0.22), residues: 475 loop : -1.46 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 260 TYR 0.017 0.002 TYR D 261 PHE 0.022 0.002 PHE B 394 TRP 0.033 0.001 TRP F 491 HIS 0.008 0.001 HIS C 354 Details of bonding type rmsd covalent geometry : bond 0.00368 (44049) covalent geometry : angle 0.69513 (59461) hydrogen bonds : bond 0.04322 ( 2009) hydrogen bonds : angle 5.36223 ( 6090) Misc. bond : bond 0.00194 ( 20) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 894 time to evaluate : 1.797 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 242 LEU cc_start: 0.8042 (tt) cc_final: 0.7811 (tt) REVERT: A 248 TYR cc_start: 0.8806 (m-80) cc_final: 0.8540 (m-80) REVERT: A 324 THR cc_start: 0.7725 (p) cc_final: 0.7444 (p) REVERT: A 325 LEU cc_start: 0.7743 (tp) cc_final: 0.7432 (tm) REVERT: A 340 ARG cc_start: 0.7708 (mtt180) cc_final: 0.7462 (mtm180) REVERT: A 395 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6863 (tt) REVERT: A 401 ASP cc_start: 0.7754 (m-30) cc_final: 0.7362 (t0) REVERT: A 410 MET cc_start: 0.8523 (tpt) cc_final: 0.8093 (mpp) REVERT: A 509 ARG cc_start: 0.8053 (mtp-110) cc_final: 0.7687 (ttm110) REVERT: A 667 ASN cc_start: 0.7302 (OUTLIER) cc_final: 0.7101 (t0) REVERT: A 708 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6388 (tp30) REVERT: A 764 PHE cc_start: 0.7807 (t80) cc_final: 0.7362 (t80) REVERT: B 328 TYR cc_start: 0.8961 (t80) cc_final: 0.8032 (t80) REVERT: B 330 LYS cc_start: 0.8758 (mtmt) cc_final: 0.8202 (mtpp) REVERT: B 331 TYR cc_start: 0.8778 (m-80) cc_final: 0.8451 (m-80) REVERT: B 357 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8454 (mm-30) REVERT: B 410 MET cc_start: 0.8993 (mmm) cc_final: 0.8601 (mmm) REVERT: B 564 LYS cc_start: 0.8885 (mttt) cc_final: 0.8654 (mttm) REVERT: B 592 SER cc_start: 0.9211 (m) cc_final: 0.8774 (p) REVERT: B 644 ASP cc_start: 0.7880 (m-30) cc_final: 0.7664 (m-30) REVERT: B 646 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7873 (ptt-90) REVERT: B 693 MET cc_start: 0.5114 (mtp) cc_final: 0.4305 (ptt) REVERT: B 711 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.8375 (t0) REVERT: B 715 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7360 (t0) REVERT: C 176 ARG cc_start: 0.8701 (ttm-80) cc_final: 0.8484 (ttm-80) REVERT: C 323 THR cc_start: 0.8953 (m) cc_final: 0.8535 (p) REVERT: C 327 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7140 (mm-30) REVERT: C 330 LYS cc_start: 0.8943 (mtmt) cc_final: 0.8581 (mtpt) REVERT: C 482 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: C 490 ASN cc_start: 0.7903 (m-40) cc_final: 0.7653 (t0) REVERT: C 714 ASP cc_start: 0.8037 (m-30) cc_final: 0.7730 (m-30) REVERT: D 367 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7385 (mt-10) REVERT: D 371 ARG cc_start: 0.7778 (ptt-90) cc_final: 0.7559 (ppt90) REVERT: D 478 GLU cc_start: 0.8074 (pt0) cc_final: 0.7715 (pt0) REVERT: D 523 ASP cc_start: 0.8147 (t0) cc_final: 0.7490 (t0) REVERT: D 578 ILE cc_start: 0.8064 (mt) cc_final: 0.7857 (mp) REVERT: D 593 ARG cc_start: 0.7688 (mtm180) cc_final: 0.7255 (mmp-170) REVERT: D 622 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.8055 (p) REVERT: D 633 GLU cc_start: 0.7369 (tt0) cc_final: 0.6930 (pt0) REVERT: D 634 ILE cc_start: 0.8013 (tt) cc_final: 0.7648 (mp) REVERT: D 771 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7047 (ptp-170) REVERT: E 199 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8051 (tpt-90) REVERT: E 231 GLN cc_start: 0.8535 (mt0) cc_final: 0.8246 (mt0) REVERT: E 343 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7696 (mm-40) REVERT: E 354 HIS cc_start: 0.8504 (t-90) cc_final: 0.8146 (t-90) REVERT: E 367 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7141 (mt-10) REVERT: E 393 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7722 (ptp90) REVERT: E 410 MET cc_start: 0.7868 (tpp) cc_final: 0.7594 (tpt) REVERT: E 414 ARG cc_start: 0.6448 (mtm-85) cc_final: 0.6105 (mtm-85) REVERT: F 210 ASN cc_start: 0.8421 (p0) cc_final: 0.8129 (p0) REVERT: F 227 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: F 270 LYS cc_start: 0.8910 (mmmt) cc_final: 0.8632 (mmtt) REVERT: F 281 ASP cc_start: 0.6788 (p0) cc_final: 0.6515 (p0) REVERT: F 330 LYS cc_start: 0.8585 (mttt) cc_final: 0.8345 (tppp) REVERT: F 352 VAL cc_start: 0.7828 (m) cc_final: 0.7595 (t) REVERT: F 508 LEU cc_start: 0.7254 (mm) cc_final: 0.7018 (pt) REVERT: F 514 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7227 (tp) REVERT: F 515 HIS cc_start: 0.7872 (OUTLIER) cc_final: 0.7258 (t70) REVERT: F 562 LEU cc_start: 0.7488 (mm) cc_final: 0.7079 (tp) REVERT: F 761 LYS cc_start: 0.6599 (OUTLIER) cc_final: 0.6289 (ptpt) REVERT: G 101 GLN cc_start: 0.8878 (tt0) cc_final: 0.8662 (tt0) REVERT: G 136 GLN cc_start: 0.8883 (pt0) cc_final: 0.8581 (pt0) REVERT: G 190 THR cc_start: 0.8720 (m) cc_final: 0.8500 (p) REVERT: H 46 VAL cc_start: 0.9367 (m) cc_final: 0.9125 (m) REVERT: H 101 GLN cc_start: 0.8713 (tt0) cc_final: 0.8433 (tt0) REVERT: I 89 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8334 (mt) REVERT: J 39 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8384 (mp0) REVERT: J 44 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8227 (tt) REVERT: J 52 SER cc_start: 0.9131 (t) cc_final: 0.8868 (p) REVERT: J 95 TYR cc_start: 0.9088 (t80) cc_final: 0.8832 (t80) REVERT: J 158 GLU cc_start: 0.8693 (tp30) cc_final: 0.8382 (tp30) REVERT: L 47 GLN cc_start: 0.8751 (pt0) cc_final: 0.8392 (pm20) REVERT: M 101 GLN cc_start: 0.8769 (tt0) cc_final: 0.8559 (tt0) REVERT: M 156 GLU cc_start: 0.8801 (tp30) cc_final: 0.8462 (tp30) REVERT: M 192 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8492 (mm-30) REVERT: N 22 GLU cc_start: 0.8102 (tp30) cc_final: 0.7809 (tp30) REVERT: P 34 SER cc_start: 0.9038 (OUTLIER) cc_final: 0.8819 (p) REVERT: P 35 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7766 (tp30) REVERT: P 38 ASP cc_start: 0.8211 (m-30) cc_final: 0.7848 (m-30) REVERT: P 40 ILE cc_start: 0.9035 (mm) cc_final: 0.8762 (mt) REVERT: P 59 ASP cc_start: 0.8734 (m-30) cc_final: 0.8338 (m-30) REVERT: P 111 LYS cc_start: 0.9017 (mttp) cc_final: 0.8655 (mttt) REVERT: P 139 GLN cc_start: 0.8789 (mt0) cc_final: 0.8581 (mt0) REVERT: Q 38 ASP cc_start: 0.8776 (m-30) cc_final: 0.8380 (m-30) REVERT: Q 42 ASN cc_start: 0.8884 (m-40) cc_final: 0.8624 (m-40) REVERT: Q 55 ASP cc_start: 0.8359 (t0) cc_final: 0.7851 (t0) REVERT: Q 164 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8131 (ttt180) REVERT: T 35 GLU cc_start: 0.7965 (pp20) cc_final: 0.7687 (pm20) REVERT: T 37 ASN cc_start: 0.9172 (p0) cc_final: 0.8954 (p0) REVERT: T 38 ASP cc_start: 0.8341 (m-30) cc_final: 0.8117 (m-30) REVERT: T 39 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8181 (tp30) REVERT: T 58 LYS cc_start: 0.8781 (mtmt) cc_final: 0.8531 (mtmt) outliers start: 169 outliers final: 39 residues processed: 1001 average time/residue: 0.8435 time to fit residues: 1013.2187 Evaluate side-chains 785 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 724 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 715 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 579 GLN Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 771 ARG Chi-restraints excluded: chain E residue 199 ARG Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 393 ARG Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 397 ASP Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 761 LYS Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 143 ILE Chi-restraints excluded: chain M residue 192 GLU Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain P residue 34 SER Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain Q residue 164 ARG Chi-restraints excluded: chain R residue 98 SER Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain T residue 39 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 119 optimal weight: 0.9980 chunk 407 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 240 optimal weight: 0.2980 chunk 443 optimal weight: 5.9990 chunk 531 optimal weight: 2.9990 chunk 392 optimal weight: 0.9990 chunk 344 optimal weight: 0.9990 chunk 347 optimal weight: 0.7980 chunk 534 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 GLN A 651 GLN A 667 ASN B 290 HIS B 609 GLN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 ASN B 720 HIS C 636 ASN D 640 GLN ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN F 721 GLN H 31 ASN I 107 GLN J 101 GLN L 34 ASN L 144 GLN ** N 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 160 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.115347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090125 restraints weight = 73992.420| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.95 r_work: 0.3218 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 44069 Z= 0.154 Angle : 0.635 11.296 59461 Z= 0.319 Chirality : 0.044 0.279 6816 Planarity : 0.005 0.071 7675 Dihedral : 10.109 142.913 6536 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.02 % Favored : 95.96 % Rotamer: Outliers : 3.75 % Allowed : 17.33 % Favored : 78.92 % 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: -1.57 (0.11), residues: 5426 helix: -0.61 (0.09), residues: 2933 sheet: -1.96 (0.22), residues: 496 loop : -1.21 (0.14), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 774 TYR 0.023 0.001 TYR F 366 PHE 0.021 0.002 PHE B 394 TRP 0.027 0.001 TRP F 491 HIS 0.011 0.001 HIS J 135 Details of bonding type rmsd covalent geometry : bond 0.00344 (44049) covalent geometry : angle 0.63520 (59461) hydrogen bonds : bond 0.03794 ( 2009) hydrogen bonds : angle 4.82698 ( 6090) Misc. bond : bond 0.00199 ( 20) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 792 time to evaluate : 1.510 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 248 TYR cc_start: 0.8818 (m-80) cc_final: 0.8537 (m-80) REVERT: A 317 LEU cc_start: 0.8166 (tp) cc_final: 0.7858 (tp) REVERT: A 324 THR cc_start: 0.7783 (p) cc_final: 0.7453 (p) REVERT: A 325 LEU cc_start: 0.7807 (tp) cc_final: 0.7539 (tm) REVERT: A 379 MET cc_start: 0.8033 (mtm) cc_final: 0.7700 (mtp) REVERT: A 395 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6846 (mt) REVERT: A 410 MET cc_start: 0.8568 (tpt) cc_final: 0.8237 (mpp) REVERT: A 509 ARG cc_start: 0.8082 (mtp-110) cc_final: 0.7720 (ttm110) REVERT: A 523 ASP cc_start: 0.8163 (p0) cc_final: 0.7804 (m-30) REVERT: A 582 MET cc_start: 0.7466 (mmm) cc_final: 0.7112 (mmm) REVERT: A 667 ASN cc_start: 0.7308 (OUTLIER) cc_final: 0.7019 (t0) REVERT: A 710 LEU cc_start: 0.7812 (mp) cc_final: 0.7320 (mm) REVERT: A 764 PHE cc_start: 0.7795 (t80) cc_final: 0.7479 (t80) REVERT: B 208 THR cc_start: 0.8075 (p) cc_final: 0.7846 (t) REVERT: B 330 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8128 (mtpp) REVERT: B 331 TYR cc_start: 0.8799 (m-80) cc_final: 0.8454 (m-80) REVERT: B 357 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8492 (mm-30) REVERT: B 564 LYS cc_start: 0.8922 (mttt) cc_final: 0.8713 (mttm) REVERT: B 587 ASP cc_start: 0.6891 (m-30) cc_final: 0.6639 (m-30) REVERT: B 629 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7734 (mtpp) REVERT: B 644 ASP cc_start: 0.7839 (m-30) cc_final: 0.7609 (m-30) REVERT: B 711 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8382 (t0) REVERT: B 715 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7469 (t0) REVERT: C 223 THR cc_start: 0.8843 (t) cc_final: 0.8631 (m) REVERT: C 323 THR cc_start: 0.8948 (m) cc_final: 0.8508 (p) REVERT: C 327 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7166 (mm-30) REVERT: C 330 LYS cc_start: 0.8935 (mtmt) cc_final: 0.8546 (mtpt) REVERT: C 415 MET cc_start: 0.6066 (mmm) cc_final: 0.5816 (mmm) REVERT: C 490 ASN cc_start: 0.7974 (m-40) cc_final: 0.7703 (t0) REVERT: C 780 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7186 (tt0) REVERT: D 227 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8188 (mm-30) REVERT: D 260 ARG cc_start: 0.7860 (ttm110) cc_final: 0.7652 (ttp-110) REVERT: D 293 VAL cc_start: 0.8407 (OUTLIER) cc_final: 0.7973 (m) REVERT: D 326 ASP cc_start: 0.8192 (m-30) cc_final: 0.7497 (t0) REVERT: D 367 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: D 478 GLU cc_start: 0.7956 (pt0) cc_final: 0.7555 (pt0) REVERT: D 523 ASP cc_start: 0.8156 (t0) cc_final: 0.7475 (t0) REVERT: D 593 ARG cc_start: 0.7764 (mtm180) cc_final: 0.7338 (mmp-170) REVERT: D 601 TYR cc_start: 0.8351 (m-80) cc_final: 0.7921 (m-80) REVERT: D 634 ILE cc_start: 0.7923 (tt) cc_final: 0.7639 (mp) REVERT: E 187 LEU cc_start: 0.8718 (mt) cc_final: 0.8307 (mt) REVERT: E 227 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8032 (mt-10) REVERT: E 231 GLN cc_start: 0.8578 (mt0) cc_final: 0.8257 (mt0) REVERT: E 267 GLU cc_start: 0.8216 (tp30) cc_final: 0.7939 (tp30) REVERT: E 333 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7119 (mt-10) REVERT: E 339 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5762 (tm-30) REVERT: E 367 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7245 (mt-10) REVERT: E 410 MET cc_start: 0.8013 (tpp) cc_final: 0.7765 (tpt) REVERT: F 210 ASN cc_start: 0.8475 (p0) cc_final: 0.8200 (p0) REVERT: F 227 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7665 (tm-30) REVERT: F 270 LYS cc_start: 0.8924 (mmmt) cc_final: 0.8205 (mmpt) REVERT: F 330 LYS cc_start: 0.8564 (mttt) cc_final: 0.8343 (tppp) REVERT: F 352 VAL cc_start: 0.7785 (m) cc_final: 0.7545 (t) REVERT: F 508 LEU cc_start: 0.7252 (mm) cc_final: 0.7042 (pt) REVERT: F 562 LEU cc_start: 0.7708 (mm) cc_final: 0.7435 (tp) REVERT: F 579 GLN cc_start: 0.7574 (mt0) cc_final: 0.7328 (mt0) REVERT: F 623 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8634 (tm) REVERT: F 773 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7994 (tm) REVERT: G 39 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8355 (mm-30) REVERT: H 57 MET cc_start: 0.8677 (mtp) cc_final: 0.8457 (mtt) REVERT: I 87 MET cc_start: 0.9130 (mmt) cc_final: 0.8829 (mmt) REVERT: J 39 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8314 (mp0) REVERT: J 52 SER cc_start: 0.9143 (t) cc_final: 0.8897 (p) REVERT: J 97 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7493 (mtp180) REVERT: J 158 GLU cc_start: 0.8667 (tp30) cc_final: 0.8428 (tp30) REVERT: L 46 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.8958 (p) REVERT: L 47 GLN cc_start: 0.8752 (pt0) cc_final: 0.8523 (pt0) REVERT: L 89 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8386 (tp) REVERT: M 39 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8572 (mm-30) REVERT: M 44 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7970 (tt) REVERT: M 156 GLU cc_start: 0.8789 (tp30) cc_final: 0.8469 (tp30) REVERT: M 181 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8657 (mtpt) REVERT: N 22 GLU cc_start: 0.8095 (tp30) cc_final: 0.7773 (tp30) REVERT: N 40 ILE cc_start: 0.9218 (mp) cc_final: 0.9008 (mp) REVERT: O 23 ARG cc_start: 0.8588 (mtp85) cc_final: 0.8179 (mtp180) REVERT: O 40 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8834 (mp) REVERT: O 42 ASN cc_start: 0.9080 (m-40) cc_final: 0.8863 (m110) REVERT: O 99 MET cc_start: 0.8946 (tpt) cc_final: 0.8677 (tpt) REVERT: P 35 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7843 (tp30) REVERT: P 38 ASP cc_start: 0.8163 (m-30) cc_final: 0.7805 (m-30) REVERT: P 40 ILE cc_start: 0.8973 (mm) cc_final: 0.8689 (mt) REVERT: P 59 ASP cc_start: 0.8727 (m-30) cc_final: 0.8252 (m-30) REVERT: P 111 LYS cc_start: 0.8925 (mttp) cc_final: 0.8538 (mttt) REVERT: P 139 GLN cc_start: 0.8797 (mt0) cc_final: 0.8595 (mt0) REVERT: P 164 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8470 (ttt180) REVERT: Q 38 ASP cc_start: 0.8704 (m-30) cc_final: 0.8318 (m-30) REVERT: Q 39 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7892 (tp30) REVERT: Q 42 ASN cc_start: 0.8866 (m-40) cc_final: 0.8613 (m-40) REVERT: Q 55 ASP cc_start: 0.8526 (t0) cc_final: 0.8102 (t0) REVERT: Q 164 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8146 (ttt180) REVERT: R 43 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8281 (ttp80) REVERT: S 40 ILE cc_start: 0.9015 (mp) cc_final: 0.8647 (mp) REVERT: T 35 GLU cc_start: 0.8000 (pp20) cc_final: 0.7742 (pm20) REVERT: T 37 ASN cc_start: 0.9190 (p0) cc_final: 0.8960 (p0) REVERT: T 38 ASP cc_start: 0.8298 (m-30) cc_final: 0.8049 (m-30) REVERT: T 39 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8215 (tp30) REVERT: T 58 LYS cc_start: 0.8845 (mtmt) cc_final: 0.8592 (mtmt) REVERT: T 164 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7867 (ttm170) outliers start: 169 outliers final: 51 residues processed: 890 average time/residue: 0.7217 time to fit residues: 778.8413 Evaluate side-chains 760 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 688 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 715 ASP Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 579 GLN Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 339 GLU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 397 ASP Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 773 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain J residue 42 ILE Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 97 ARG Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain L residue 143 ILE Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 98 SER Chi-restraints excluded: chain P residue 164 ARG Chi-restraints excluded: chain Q residue 164 ARG Chi-restraints excluded: chain R residue 98 SER Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 163 GLU Chi-restraints excluded: chain T residue 39 GLU Chi-restraints excluded: chain T residue 164 ARG Chi-restraints excluded: chain a residue 10 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 276 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 348 optimal weight: 0.7980 chunk 359 optimal weight: 5.9990 chunk 373 optimal weight: 2.9990 chunk 275 optimal weight: 9.9990 chunk 541 optimal weight: 8.9990 chunk 265 optimal weight: 9.9990 chunk 403 optimal weight: 0.8980 chunk 201 optimal weight: 0.8980 chunk 444 optimal weight: 0.5980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 GLN A 667 ASN A 704 HIS B 667 ASN B 720 HIS C 636 ASN ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN D 370 HIS D 636 ASN ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 GLN F 721 GLN G 101 GLN H 101 GLN J 101 GLN K 59 GLN K 144 GLN ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.113160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.088538 restraints weight = 73957.478| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.89 r_work: 0.3185 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 44069 Z= 0.183 Angle : 0.634 15.997 59461 Z= 0.316 Chirality : 0.044 0.276 6816 Planarity : 0.004 0.047 7675 Dihedral : 9.714 130.540 6532 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.96 % Favored : 96.02 % Rotamer: Outliers : 3.93 % Allowed : 18.33 % Favored : 77.74 % 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: -1.05 (0.11), residues: 5426 helix: -0.12 (0.10), residues: 2952 sheet: -1.89 (0.22), residues: 502 loop : -1.06 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 774 TYR 0.023 0.001 TYR F 366 PHE 0.019 0.002 PHE C 394 TRP 0.020 0.001 TRP F 491 HIS 0.011 0.001 HIS L 135 Details of bonding type rmsd covalent geometry : bond 0.00418 (44049) covalent geometry : angle 0.63364 (59461) hydrogen bonds : bond 0.03669 ( 2009) hydrogen bonds : angle 4.63885 ( 6090) Misc. bond : bond 0.00165 ( 20) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 729 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7790 (tt) REVERT: A 248 TYR cc_start: 0.8831 (m-80) cc_final: 0.8614 (m-80) REVERT: A 324 THR cc_start: 0.7856 (p) cc_final: 0.7572 (p) REVERT: A 325 LEU cc_start: 0.7873 (tp) cc_final: 0.7590 (tm) REVERT: A 379 MET cc_start: 0.8113 (mtm) cc_final: 0.7763 (mtp) REVERT: A 483 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8023 (mp-120) REVERT: A 509 ARG cc_start: 0.8167 (mtp-110) cc_final: 0.7787 (ttm110) REVERT: A 523 ASP cc_start: 0.8193 (p0) cc_final: 0.7978 (m-30) REVERT: A 582 MET cc_start: 0.7642 (mmm) cc_final: 0.7221 (mmm) REVERT: A 667 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.7170 (t0) REVERT: A 710 LEU cc_start: 0.7862 (mp) cc_final: 0.7409 (mm) REVERT: A 784 GLN cc_start: 0.8791 (mm-40) cc_final: 0.7840 (pt0) REVERT: B 330 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8192 (mtpp) REVERT: B 331 TYR cc_start: 0.8851 (m-80) cc_final: 0.8449 (m-80) REVERT: B 357 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8537 (mm-30) REVERT: B 410 MET cc_start: 0.8875 (mmm) cc_final: 0.8430 (mmm) REVERT: B 564 LYS cc_start: 0.9002 (mttt) cc_final: 0.8792 (mttm) REVERT: B 629 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7869 (mtpp) REVERT: B 715 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7551 (t0) REVERT: C 194 GLU cc_start: 0.8216 (pm20) cc_final: 0.7988 (pm20) REVERT: C 278 THR cc_start: 0.8592 (m) cc_final: 0.8353 (p) REVERT: C 323 THR cc_start: 0.8967 (m) cc_final: 0.8540 (p) REVERT: C 327 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7321 (mm-30) REVERT: C 330 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8572 (mtpt) REVERT: C 410 MET cc_start: 0.8781 (mmp) cc_final: 0.8521 (mmp) REVERT: C 695 GLN cc_start: 0.7261 (mm110) cc_final: 0.6805 (pm20) REVERT: C 780 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7444 (tm-30) REVERT: D 293 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8194 (m) REVERT: D 326 ASP cc_start: 0.8239 (m-30) cc_final: 0.7620 (t0) REVERT: D 367 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: D 478 GLU cc_start: 0.8034 (pt0) cc_final: 0.7826 (pt0) REVERT: D 523 ASP cc_start: 0.8173 (t0) cc_final: 0.7517 (t0) REVERT: D 593 ARG cc_start: 0.7840 (mtm180) cc_final: 0.7494 (mmp-170) REVERT: D 633 GLU cc_start: 0.7446 (tt0) cc_final: 0.6743 (pt0) REVERT: D 634 ILE cc_start: 0.7946 (tt) cc_final: 0.7625 (mp) REVERT: D 693 MET cc_start: 0.4758 (tpp) cc_final: 0.3471 (mpm) REVERT: E 187 LEU cc_start: 0.8818 (mt) cc_final: 0.8245 (mt) REVERT: E 227 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8031 (mt-10) REVERT: E 231 GLN cc_start: 0.8604 (mt0) cc_final: 0.8280 (mt0) REVERT: E 256 VAL cc_start: 0.7245 (OUTLIER) cc_final: 0.6951 (p) REVERT: E 267 GLU cc_start: 0.8238 (tp30) cc_final: 0.8016 (tp30) REVERT: E 339 GLU cc_start: 0.6335 (OUTLIER) cc_final: 0.5876 (tm-30) REVERT: E 367 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7156 (mt-10) REVERT: F 227 GLU cc_start: 0.7848 (tt0) cc_final: 0.7556 (tm-30) REVERT: F 240 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7089 (tp30) REVERT: F 270 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8277 (mmpt) REVERT: F 411 ARG cc_start: 0.7675 (tpt-90) cc_final: 0.7372 (tpt90) REVERT: F 508 LEU cc_start: 0.7334 (mm) cc_final: 0.7104 (pt) REVERT: F 532 ILE cc_start: 0.8572 (tt) cc_final: 0.8305 (mp) REVERT: F 562 LEU cc_start: 0.7773 (mm) cc_final: 0.7558 (tp) REVERT: F 579 GLN cc_start: 0.7577 (mt0) cc_final: 0.7338 (mt0) REVERT: F 582 MET cc_start: 0.5488 (ppp) cc_final: 0.4983 (pmm) REVERT: F 610 LEU cc_start: 0.7124 (pt) cc_final: 0.6837 (tm) REVERT: F 623 LEU cc_start: 0.8907 (tp) cc_final: 0.8551 (tm) REVERT: F 665 THR cc_start: 0.4944 (m) cc_final: 0.4587 (p) REVERT: F 773 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7942 (tm) REVERT: G 39 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8388 (mm-30) REVERT: H 89 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8366 (mt) REVERT: H 202 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8953 (p) REVERT: J 39 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8393 (mp0) REVERT: J 52 SER cc_start: 0.9170 (t) cc_final: 0.8924 (p) REVERT: J 55 ASP cc_start: 0.8555 (m-30) cc_final: 0.8309 (m-30) REVERT: J 97 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7457 (mtp180) REVERT: J 101 GLN cc_start: 0.8733 (tt0) cc_final: 0.8485 (tt0) REVERT: J 158 GLU cc_start: 0.8653 (tp30) cc_final: 0.8405 (tp30) REVERT: K 153 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8544 (mp10) REVERT: L 46 VAL cc_start: 0.9272 (m) cc_final: 0.9007 (p) REVERT: L 47 GLN cc_start: 0.8724 (pt0) cc_final: 0.8513 (pt0) REVERT: M 44 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8013 (tt) REVERT: M 156 GLU cc_start: 0.8727 (tp30) cc_final: 0.8402 (tp30) REVERT: M 181 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8628 (mtpt) REVERT: N 22 GLU cc_start: 0.8145 (tp30) cc_final: 0.7758 (tp30) REVERT: O 23 ARG cc_start: 0.8660 (mtp85) cc_final: 0.8266 (mtp180) REVERT: O 40 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8916 (mp) REVERT: O 164 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8546 (ttt-90) REVERT: P 35 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: P 38 ASP cc_start: 0.8195 (m-30) cc_final: 0.7893 (m-30) REVERT: P 40 ILE cc_start: 0.9064 (mm) cc_final: 0.8817 (mt) REVERT: P 58 LYS cc_start: 0.8950 (ttmt) cc_final: 0.8705 (mtmt) REVERT: P 59 ASP cc_start: 0.8664 (m-30) cc_final: 0.8217 (m-30) REVERT: P 111 LYS cc_start: 0.9015 (mttp) cc_final: 0.8638 (mttt) REVERT: P 164 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8436 (ttt180) REVERT: Q 26 SER cc_start: 0.9356 (OUTLIER) cc_final: 0.9096 (p) REVERT: Q 38 ASP cc_start: 0.8693 (m-30) cc_final: 0.8335 (m-30) REVERT: Q 39 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7894 (tp30) REVERT: Q 42 ASN cc_start: 0.8856 (m-40) cc_final: 0.8643 (m-40) REVERT: Q 55 ASP cc_start: 0.8570 (t0) cc_final: 0.8147 (t0) REVERT: Q 164 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8145 (ttt180) REVERT: R 55 ASP cc_start: 0.8247 (t0) cc_final: 0.7957 (t0) REVERT: S 39 GLU cc_start: 0.8331 (tp30) cc_final: 0.8080 (tp30) REVERT: T 35 GLU cc_start: 0.8055 (pp20) cc_final: 0.7831 (pm20) REVERT: T 37 ASN cc_start: 0.9227 (p0) cc_final: 0.8987 (p0) REVERT: T 38 ASP cc_start: 0.8305 (m-30) cc_final: 0.8093 (m-30) REVERT: T 39 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8147 (tp30) REVERT: T 164 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7641 (ttm170) outliers start: 177 outliers final: 60 residues processed: 835 average time/residue: 0.7491 time to fit residues: 767.2144 Evaluate side-chains 756 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 672 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 715 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 579 GLN Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 667 ASN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 339 GLU Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 758 LEU Chi-restraints excluded: chain F residue 773 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain J residue 42 ILE Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 97 ARG Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 39 GLU Chi-restraints excluded: chain O residue 35 GLU Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 164 ARG Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 98 SER Chi-restraints excluded: chain P residue 164 ARG Chi-restraints excluded: chain Q residue 26 SER Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain Q residue 164 ARG Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain S residue 163 GLU Chi-restraints excluded: chain T residue 22 GLU Chi-restraints excluded: chain T residue 39 GLU Chi-restraints excluded: chain T residue 55 ASP Chi-restraints excluded: chain T residue 86 CYS Chi-restraints excluded: chain T residue 164 ARG Chi-restraints excluded: chain a residue 10 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 413 optimal weight: 0.7980 chunk 265 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 459 optimal weight: 0.9980 chunk 428 optimal weight: 0.5980 chunk 455 optimal weight: 2.9990 chunk 316 optimal weight: 0.9980 chunk 491 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 527 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 ASN A 667 ASN B 632 GLN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 HIS C 277 ASN C 636 ASN ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 GLN H 101 GLN H 135 HIS H 144 GLN K 144 GLN ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 124 GLN S 139 GLN a 22 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.113578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.088973 restraints weight = 73930.119| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.94 r_work: 0.3197 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 44069 Z= 0.153 Angle : 0.611 15.329 59461 Z= 0.304 Chirality : 0.043 0.255 6816 Planarity : 0.004 0.085 7675 Dihedral : 9.438 124.722 6529 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.85 % Favored : 96.13 % Rotamer: Outliers : 3.47 % Allowed : 19.10 % Favored : 77.43 % 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: -0.68 (0.12), residues: 5426 helix: 0.21 (0.10), residues: 2951 sheet: -1.78 (0.23), residues: 488 loop : -0.93 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 260 TYR 0.019 0.001 TYR F 366 PHE 0.025 0.001 PHE F 569 TRP 0.019 0.001 TRP F 491 HIS 0.011 0.001 HIS I 135 Details of bonding type rmsd covalent geometry : bond 0.00346 (44049) covalent geometry : angle 0.61132 (59461) hydrogen bonds : bond 0.03483 ( 2009) hydrogen bonds : angle 4.51347 ( 6090) Misc. bond : bond 0.00119 ( 20) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 745 time to evaluate : 1.569 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 204 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7935 (mt) REVERT: A 242 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7849 (tt) REVERT: A 248 TYR cc_start: 0.8817 (m-80) cc_final: 0.8582 (m-80) REVERT: A 324 THR cc_start: 0.7860 (p) cc_final: 0.7573 (p) REVERT: A 325 LEU cc_start: 0.7818 (tp) cc_final: 0.7566 (tm) REVERT: A 379 MET cc_start: 0.8062 (mtm) cc_final: 0.7720 (mtp) REVERT: A 509 ARG cc_start: 0.8133 (mtp-110) cc_final: 0.7799 (ttm110) REVERT: A 582 MET cc_start: 0.7721 (mmm) cc_final: 0.7276 (mmm) REVERT: A 640 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: A 710 LEU cc_start: 0.7827 (mp) cc_final: 0.7395 (mm) REVERT: A 712 ARG cc_start: 0.7878 (mmm160) cc_final: 0.7623 (mmm160) REVERT: A 784 GLN cc_start: 0.8811 (mm-40) cc_final: 0.7874 (pt0) REVERT: B 330 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8240 (mtpp) REVERT: B 331 TYR cc_start: 0.8861 (m-80) cc_final: 0.8470 (m-80) REVERT: B 357 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8545 (mm-30) REVERT: B 629 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7787 (mtpp) REVERT: B 644 ASP cc_start: 0.7816 (t0) cc_final: 0.7549 (t0) REVERT: B 702 LYS cc_start: 0.7991 (mptt) cc_final: 0.7771 (mttm) REVERT: B 715 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7637 (t0) REVERT: C 176 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8395 (ttt-90) REVERT: C 194 GLU cc_start: 0.8222 (pm20) cc_final: 0.7965 (pm20) REVERT: C 278 THR cc_start: 0.8602 (m) cc_final: 0.8377 (p) REVERT: C 326 ASP cc_start: 0.8169 (m-30) cc_final: 0.7633 (p0) REVERT: C 327 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7384 (mm-30) REVERT: C 780 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7226 (tt0) REVERT: D 293 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8199 (m) REVERT: D 326 ASP cc_start: 0.8245 (m-30) cc_final: 0.7457 (t0) REVERT: D 329 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7903 (mtm110) REVERT: D 506 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8275 (ttt90) REVERT: D 523 ASP cc_start: 0.8210 (t0) cc_final: 0.7559 (t0) REVERT: D 593 ARG cc_start: 0.7836 (mtm180) cc_final: 0.7521 (mmp-170) REVERT: D 633 GLU cc_start: 0.7300 (tt0) cc_final: 0.6702 (pt0) REVERT: D 634 ILE cc_start: 0.7949 (tt) cc_final: 0.7679 (mp) REVERT: D 639 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7708 (mp) REVERT: D 640 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7202 (pm20) REVERT: D 693 MET cc_start: 0.4722 (tpp) cc_final: 0.3353 (mpm) REVERT: E 187 LEU cc_start: 0.8804 (mt) cc_final: 0.8336 (mt) REVERT: E 227 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8073 (mt-10) REVERT: E 231 GLN cc_start: 0.8605 (mt0) cc_final: 0.8271 (mt0) REVERT: E 267 GLU cc_start: 0.8243 (tp30) cc_final: 0.8024 (tp30) REVERT: E 330 LYS cc_start: 0.8817 (ttmt) cc_final: 0.8574 (ttpp) REVERT: E 333 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7393 (mm-30) REVERT: E 339 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.5905 (tm-30) REVERT: E 367 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7072 (mt-10) REVERT: F 227 GLU cc_start: 0.7723 (tt0) cc_final: 0.7469 (tm-30) REVERT: F 240 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7025 (tp30) REVERT: F 270 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8273 (mmpt) REVERT: F 371 ARG cc_start: 0.8196 (ppt170) cc_final: 0.7883 (ppt170) REVERT: F 411 ARG cc_start: 0.7703 (tpt-90) cc_final: 0.7423 (tpt90) REVERT: F 508 LEU cc_start: 0.7349 (mm) cc_final: 0.7137 (pt) REVERT: F 532 ILE cc_start: 0.8585 (tt) cc_final: 0.8382 (mp) REVERT: F 562 LEU cc_start: 0.7842 (mm) cc_final: 0.7638 (tp) REVERT: F 579 GLN cc_start: 0.7660 (mt0) cc_final: 0.7416 (mt0) REVERT: F 610 LEU cc_start: 0.7109 (pt) cc_final: 0.6783 (tm) REVERT: F 623 LEU cc_start: 0.8937 (tp) cc_final: 0.8632 (tm) REVERT: F 665 THR cc_start: 0.4898 (m) cc_final: 0.4514 (p) REVERT: F 773 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7902 (tm) REVERT: G 39 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8415 (mm-30) REVERT: H 89 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8389 (mt) REVERT: J 39 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8440 (mp0) REVERT: J 50 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8235 (t0) REVERT: J 52 SER cc_start: 0.9160 (t) cc_final: 0.8930 (p) REVERT: J 55 ASP cc_start: 0.8564 (m-30) cc_final: 0.8318 (m-30) REVERT: J 158 GLU cc_start: 0.8632 (tp30) cc_final: 0.8399 (tp30) REVERT: K 89 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8331 (mt) REVERT: L 46 VAL cc_start: 0.9271 (m) cc_final: 0.9033 (p) REVERT: M 156 GLU cc_start: 0.8682 (tp30) cc_final: 0.8387 (tp30) REVERT: N 22 GLU cc_start: 0.8184 (tp30) cc_final: 0.7882 (tp30) REVERT: O 23 ARG cc_start: 0.8645 (mtp85) cc_final: 0.8329 (mmm-85) REVERT: O 40 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8897 (mp) REVERT: O 58 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8420 (mtmm) REVERT: O 164 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8572 (ttt-90) REVERT: P 35 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: P 40 ILE cc_start: 0.9061 (mm) cc_final: 0.8814 (mt) REVERT: P 58 LYS cc_start: 0.8963 (ttmt) cc_final: 0.8736 (mtmt) REVERT: P 59 ASP cc_start: 0.8674 (m-30) cc_final: 0.8187 (m-30) REVERT: P 111 LYS cc_start: 0.8997 (mttp) cc_final: 0.8601 (mttt) REVERT: P 164 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8458 (ttt180) REVERT: Q 26 SER cc_start: 0.9351 (OUTLIER) cc_final: 0.9119 (p) REVERT: Q 38 ASP cc_start: 0.8698 (m-30) cc_final: 0.8336 (m-30) REVERT: Q 42 ASN cc_start: 0.8853 (m-40) cc_final: 0.8649 (m-40) REVERT: Q 55 ASP cc_start: 0.8556 (t0) cc_final: 0.8204 (t0) REVERT: Q 58 LYS cc_start: 0.8528 (ttmt) cc_final: 0.8275 (ttmt) REVERT: Q 119 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8704 (mtt90) REVERT: Q 148 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8783 (ttpp) REVERT: Q 164 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8146 (ttt180) REVERT: S 39 GLU cc_start: 0.8330 (tp30) cc_final: 0.8077 (tp30) REVERT: S 40 ILE cc_start: 0.9074 (mp) cc_final: 0.8655 (mp) REVERT: T 35 GLU cc_start: 0.8094 (pp20) cc_final: 0.7882 (pm20) REVERT: T 37 ASN cc_start: 0.9226 (p0) cc_final: 0.8990 (p0) REVERT: T 38 ASP cc_start: 0.8299 (m-30) cc_final: 0.8090 (m-30) REVERT: T 43 ARG cc_start: 0.8599 (tmm-80) cc_final: 0.8345 (tmm-80) REVERT: T 164 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7715 (ttm170) outliers start: 156 outliers final: 69 residues processed: 836 average time/residue: 0.7284 time to fit residues: 740.9167 Evaluate side-chains 779 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 685 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 715 ASP Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 579 GLN Chi-restraints excluded: chain C residue 791 PHE Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 640 GLN Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 339 GLU Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 411 ARG Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 773 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain J residue 42 ILE Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 135 HIS Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain M residue 43 PHE Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain O residue 35 GLU Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 164 ARG Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 98 SER Chi-restraints excluded: chain P residue 164 ARG Chi-restraints excluded: chain Q residue 26 SER Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain Q residue 148 LYS Chi-restraints excluded: chain Q residue 164 ARG Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 163 GLU Chi-restraints excluded: chain T residue 22 GLU Chi-restraints excluded: chain T residue 164 ARG Chi-restraints excluded: chain a residue 4 LEU Chi-restraints excluded: chain a residue 10 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 110 optimal weight: 0.9980 chunk 459 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 438 optimal weight: 0.5980 chunk 428 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 422 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 ASN C 741 GLN ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 GLN H 101 GLN H 135 HIS J 101 GLN K 107 GLN K 144 GLN ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 22 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.112910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.088165 restraints weight = 74120.404| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.96 r_work: 0.3184 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 44069 Z= 0.167 Angle : 0.615 15.189 59461 Z= 0.307 Chirality : 0.044 0.245 6816 Planarity : 0.004 0.077 7675 Dihedral : 9.321 124.170 6529 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.94 % Favored : 96.04 % Rotamer: Outliers : 3.55 % Allowed : 19.90 % Favored : 76.54 % 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: -0.46 (0.12), residues: 5426 helix: 0.39 (0.10), residues: 2950 sheet: -1.70 (0.23), residues: 489 loop : -0.83 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 340 TYR 0.017 0.001 TYR E 261 PHE 0.018 0.001 PHE C 394 TRP 0.017 0.001 TRP F 491 HIS 0.010 0.001 HIS L 135 Details of bonding type rmsd covalent geometry : bond 0.00382 (44049) covalent geometry : angle 0.61528 (59461) hydrogen bonds : bond 0.03471 ( 2009) hydrogen bonds : angle 4.45088 ( 6090) Misc. bond : bond 0.00123 ( 20) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 717 time to evaluate : 1.577 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 242 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7676 (tt) REVERT: A 248 TYR cc_start: 0.8869 (m-80) cc_final: 0.8641 (m-80) REVERT: A 324 THR cc_start: 0.7871 (p) cc_final: 0.7561 (p) REVERT: A 325 LEU cc_start: 0.7900 (tp) cc_final: 0.7624 (tm) REVERT: A 379 MET cc_start: 0.8040 (mtm) cc_final: 0.7694 (mtp) REVERT: A 483 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7966 (mp-120) REVERT: A 509 ARG cc_start: 0.8177 (mtp-110) cc_final: 0.7825 (ttm110) REVERT: A 582 MET cc_start: 0.7779 (mmm) cc_final: 0.7365 (mmm) REVERT: A 710 LEU cc_start: 0.7765 (mp) cc_final: 0.7331 (mm) REVERT: A 716 ILE cc_start: 0.8549 (mt) cc_final: 0.8310 (mp) REVERT: A 784 GLN cc_start: 0.8789 (mm-40) cc_final: 0.7880 (pt0) REVERT: B 330 LYS cc_start: 0.8762 (mtmt) cc_final: 0.8221 (mtpp) REVERT: B 331 TYR cc_start: 0.8874 (m-80) cc_final: 0.8493 (m-80) REVERT: B 357 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8554 (mm-30) REVERT: B 371 ARG cc_start: 0.8850 (mtm180) cc_final: 0.8615 (mtm110) REVERT: B 410 MET cc_start: 0.8852 (mmm) cc_final: 0.8462 (mmm) REVERT: B 644 ASP cc_start: 0.7899 (t0) cc_final: 0.7602 (t0) REVERT: B 666 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.8275 (p) REVERT: B 702 LYS cc_start: 0.7997 (mptt) cc_final: 0.7783 (mttm) REVERT: B 711 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.8290 (t0) REVERT: C 176 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8381 (ttt-90) REVERT: C 194 GLU cc_start: 0.8256 (pm20) cc_final: 0.7985 (pm20) REVERT: C 278 THR cc_start: 0.8633 (m) cc_final: 0.8407 (p) REVERT: C 323 THR cc_start: 0.8981 (m) cc_final: 0.8551 (p) REVERT: C 326 ASP cc_start: 0.8145 (m-30) cc_final: 0.7664 (p0) REVERT: C 327 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7409 (mm-30) REVERT: C 695 GLN cc_start: 0.7049 (mm110) cc_final: 0.6671 (pm20) REVERT: C 698 ASN cc_start: 0.7393 (m-40) cc_final: 0.7159 (m-40) REVERT: C 780 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7268 (tt0) REVERT: D 293 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8241 (m) REVERT: D 506 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8260 (ttt90) REVERT: D 523 ASP cc_start: 0.8281 (t0) cc_final: 0.7654 (t0) REVERT: D 593 ARG cc_start: 0.7925 (mtm180) cc_final: 0.7549 (mmt180) REVERT: D 633 GLU cc_start: 0.7316 (tt0) cc_final: 0.6774 (pt0) REVERT: D 634 ILE cc_start: 0.7874 (tt) cc_final: 0.7585 (mp) REVERT: D 639 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7781 (mp) REVERT: D 693 MET cc_start: 0.4603 (tpp) cc_final: 0.3859 (tpp) REVERT: E 187 LEU cc_start: 0.8886 (mt) cc_final: 0.8302 (mt) REVERT: E 227 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8083 (mt-10) REVERT: E 231 GLN cc_start: 0.8610 (mt0) cc_final: 0.8282 (mt0) REVERT: E 267 GLU cc_start: 0.8194 (tp30) cc_final: 0.7916 (tp30) REVERT: E 330 LYS cc_start: 0.8864 (ttmt) cc_final: 0.8571 (ttpp) REVERT: E 333 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7531 (mm-30) REVERT: E 335 ASP cc_start: 0.7314 (t0) cc_final: 0.6833 (OUTLIER) REVERT: E 339 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.5829 (pm20) REVERT: E 367 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7077 (mt-10) REVERT: F 176 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.7039 (ppt-90) REVERT: F 183 MET cc_start: 0.8582 (mtm) cc_final: 0.8272 (mmm) REVERT: F 240 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7066 (tp30) REVERT: F 270 LYS cc_start: 0.8997 (mmmt) cc_final: 0.8275 (mmpt) REVERT: F 411 ARG cc_start: 0.7717 (tpt-90) cc_final: 0.6985 (tmt170) REVERT: F 508 LEU cc_start: 0.7526 (mm) cc_final: 0.7290 (pt) REVERT: F 532 ILE cc_start: 0.8705 (tt) cc_final: 0.8494 (mp) REVERT: F 562 LEU cc_start: 0.7915 (mm) cc_final: 0.7654 (tp) REVERT: F 580 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8046 (mp) REVERT: F 582 MET cc_start: 0.5445 (pmm) cc_final: 0.4932 (pmm) REVERT: F 610 LEU cc_start: 0.7094 (pt) cc_final: 0.6787 (tm) REVERT: F 623 LEU cc_start: 0.8971 (tp) cc_final: 0.8626 (tm) REVERT: F 665 THR cc_start: 0.4988 (m) cc_final: 0.4729 (p) REVERT: G 39 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8394 (mm-30) REVERT: G 43 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8588 (t80) REVERT: H 89 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8417 (mt) REVERT: H 202 THR cc_start: 0.9398 (p) cc_final: 0.9166 (p) REVERT: I 39 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8467 (tp30) REVERT: J 39 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8535 (mp0) REVERT: J 50 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8256 (t0) REVERT: J 52 SER cc_start: 0.9137 (t) cc_final: 0.8875 (p) REVERT: J 55 ASP cc_start: 0.8572 (m-30) cc_final: 0.8327 (m-30) REVERT: J 97 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7412 (mtp180) REVERT: K 89 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8396 (mt) REVERT: K 153 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8499 (mp10) REVERT: L 46 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.9026 (p) REVERT: N 22 GLU cc_start: 0.8208 (tp30) cc_final: 0.7892 (tp30) REVERT: O 23 ARG cc_start: 0.8661 (mtp85) cc_final: 0.8349 (mmm-85) REVERT: O 40 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8885 (mp) REVERT: O 42 ASN cc_start: 0.9084 (m-40) cc_final: 0.8818 (m110) REVERT: O 58 LYS cc_start: 0.8701 (ttmt) cc_final: 0.8440 (mtmm) REVERT: O 164 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8554 (ttt-90) REVERT: P 35 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: P 40 ILE cc_start: 0.9043 (mm) cc_final: 0.8801 (mt) REVERT: P 58 LYS cc_start: 0.8950 (ttmt) cc_final: 0.8728 (mtmt) REVERT: P 59 ASP cc_start: 0.8669 (m-30) cc_final: 0.8163 (m-30) REVERT: P 111 LYS cc_start: 0.9024 (mttp) cc_final: 0.8593 (mttt) REVERT: P 164 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8211 (ttt-90) REVERT: Q 26 SER cc_start: 0.9370 (OUTLIER) cc_final: 0.9129 (p) REVERT: Q 38 ASP cc_start: 0.8699 (m-30) cc_final: 0.8319 (m-30) REVERT: Q 42 ASN cc_start: 0.8862 (m-40) cc_final: 0.8649 (m-40) REVERT: Q 55 ASP cc_start: 0.8532 (t0) cc_final: 0.8146 (t0) REVERT: Q 119 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8726 (mtt90) REVERT: Q 164 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8120 (ttt180) REVERT: S 39 GLU cc_start: 0.8323 (tp30) cc_final: 0.8059 (tp30) REVERT: S 93 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8902 (ptt) REVERT: T 35 GLU cc_start: 0.8186 (pp20) cc_final: 0.7986 (pm20) REVERT: T 37 ASN cc_start: 0.9237 (p0) cc_final: 0.9011 (p0) REVERT: T 38 ASP cc_start: 0.8296 (m-30) cc_final: 0.8079 (m-30) REVERT: T 43 ARG cc_start: 0.8596 (tmm-80) cc_final: 0.8394 (tmm-80) REVERT: T 164 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7694 (ttm170) outliers start: 160 outliers final: 75 residues processed: 814 average time/residue: 0.8300 time to fit residues: 822.7018 Evaluate side-chains 777 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 675 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 579 GLN Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 339 GLU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 411 ARG Chi-restraints excluded: chain F residue 176 ARG Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 580 ILE Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 758 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain I residue 39 GLU Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain J residue 42 ILE Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 97 ARG Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 135 HIS Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain L residue 143 ILE Chi-restraints excluded: chain M residue 43 PHE Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain O residue 35 GLU Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 164 ARG Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 98 SER Chi-restraints excluded: chain P residue 164 ARG Chi-restraints excluded: chain Q residue 26 SER Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain Q residue 164 ARG Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 163 GLU Chi-restraints excluded: chain T residue 22 GLU Chi-restraints excluded: chain T residue 86 CYS Chi-restraints excluded: chain T residue 164 ARG Chi-restraints excluded: chain a residue 4 LEU Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 22 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 521 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 510 optimal weight: 5.9990 chunk 271 optimal weight: 8.9990 chunk 490 optimal weight: 0.6980 chunk 301 optimal weight: 0.9980 chunk 411 optimal weight: 0.9990 chunk 423 optimal weight: 0.3980 chunk 372 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 ASN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN C 636 ASN C 659 ASN ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 GLN H 101 GLN H 135 HIS K 144 GLN O 117 HIS ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 ASN a 22 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.111668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.086716 restraints weight = 73682.136| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.92 r_work: 0.3153 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 44069 Z= 0.198 Angle : 0.638 14.122 59461 Z= 0.318 Chirality : 0.045 0.258 6816 Planarity : 0.004 0.063 7675 Dihedral : 9.314 122.838 6529 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.81 % Favored : 96.17 % Rotamer: Outliers : 3.93 % Allowed : 19.77 % Favored : 76.30 % 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: -0.37 (0.12), residues: 5426 helix: 0.46 (0.10), residues: 2950 sheet: -1.72 (0.23), residues: 488 loop : -0.77 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 411 TYR 0.019 0.001 TYR D 366 PHE 0.020 0.002 PHE A 394 TRP 0.015 0.001 TRP F 491 HIS 0.011 0.001 HIS L 135 Details of bonding type rmsd covalent geometry : bond 0.00453 (44049) covalent geometry : angle 0.63781 (59461) hydrogen bonds : bond 0.03600 ( 2009) hydrogen bonds : angle 4.47590 ( 6090) Misc. bond : bond 0.00129 ( 20) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 694 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.8777 (mtm) cc_final: 0.8358 (mtm) REVERT: A 204 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7981 (mp) REVERT: A 242 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7738 (tt) REVERT: A 248 TYR cc_start: 0.8873 (m-80) cc_final: 0.8630 (m-80) REVERT: A 325 LEU cc_start: 0.7945 (tp) cc_final: 0.7697 (tm) REVERT: A 379 MET cc_start: 0.8066 (mtm) cc_final: 0.7722 (mtp) REVERT: A 483 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7928 (mp-120) REVERT: A 509 ARG cc_start: 0.8179 (mtp-110) cc_final: 0.7872 (ttm110) REVERT: A 582 MET cc_start: 0.7825 (mmm) cc_final: 0.7502 (mmm) REVERT: A 631 HIS cc_start: 0.8545 (t-90) cc_final: 0.8343 (t-90) REVERT: A 710 LEU cc_start: 0.7763 (mp) cc_final: 0.7366 (mm) REVERT: A 712 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.6758 (mmm160) REVERT: A 716 ILE cc_start: 0.8588 (mt) cc_final: 0.8310 (mp) REVERT: A 784 GLN cc_start: 0.8803 (mm-40) cc_final: 0.7894 (pt0) REVERT: B 330 LYS cc_start: 0.8724 (mtmt) cc_final: 0.8174 (mtpp) REVERT: B 331 TYR cc_start: 0.8889 (m-80) cc_final: 0.8394 (m-80) REVERT: B 357 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8555 (mm-30) REVERT: B 371 ARG cc_start: 0.8861 (mtm180) cc_final: 0.8631 (mtm110) REVERT: B 410 MET cc_start: 0.8900 (mmm) cc_final: 0.8509 (mmm) REVERT: B 528 VAL cc_start: 0.9269 (OUTLIER) cc_final: 0.9058 (p) REVERT: B 644 ASP cc_start: 0.8001 (t0) cc_final: 0.7667 (t0) REVERT: B 803 ASP cc_start: 0.7838 (t0) cc_final: 0.7421 (p0) REVERT: C 176 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8371 (ttt-90) REVERT: C 194 GLU cc_start: 0.8255 (pm20) cc_final: 0.7979 (pm20) REVERT: C 217 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7932 (mt-10) REVERT: C 278 THR cc_start: 0.8681 (m) cc_final: 0.8437 (p) REVERT: C 323 THR cc_start: 0.8986 (m) cc_final: 0.8570 (p) REVERT: C 327 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7637 (mm-30) REVERT: C 555 SER cc_start: 0.8926 (t) cc_final: 0.8629 (p) REVERT: C 695 GLN cc_start: 0.6925 (mm110) cc_final: 0.6569 (pm20) REVERT: C 700 GLU cc_start: 0.6083 (OUTLIER) cc_final: 0.5872 (pm20) REVERT: C 765 ASP cc_start: 0.8507 (t70) cc_final: 0.7967 (p0) REVERT: C 780 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7487 (tm-30) REVERT: D 293 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8236 (m) REVERT: D 506 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8251 (ttt90) REVERT: D 523 ASP cc_start: 0.8316 (t0) cc_final: 0.7682 (t0) REVERT: D 593 ARG cc_start: 0.7970 (mtm180) cc_final: 0.7581 (mmp-170) REVERT: D 633 GLU cc_start: 0.7353 (tt0) cc_final: 0.6753 (pt0) REVERT: D 634 ILE cc_start: 0.7906 (tt) cc_final: 0.7604 (mp) REVERT: D 693 MET cc_start: 0.4525 (tpp) cc_final: 0.4272 (tpp) REVERT: D 714 ASP cc_start: 0.7487 (m-30) cc_final: 0.7067 (m-30) REVERT: E 187 LEU cc_start: 0.8908 (mt) cc_final: 0.8396 (mt) REVERT: E 227 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8120 (mt-10) REVERT: E 231 GLN cc_start: 0.8629 (mt0) cc_final: 0.8388 (mt0) REVERT: E 267 GLU cc_start: 0.8176 (tp30) cc_final: 0.7921 (tp30) REVERT: E 335 ASP cc_start: 0.7390 (t0) cc_final: 0.6926 (OUTLIER) REVERT: E 339 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.5867 (pm20) REVERT: E 367 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7094 (mt-10) REVERT: E 376 ASP cc_start: 0.8147 (m-30) cc_final: 0.7391 (t0) REVERT: F 176 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6917 (ppp80) REVERT: F 183 MET cc_start: 0.8634 (mtm) cc_final: 0.8343 (mmm) REVERT: F 227 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: F 240 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7103 (tp30) REVERT: F 270 LYS cc_start: 0.9005 (mmmt) cc_final: 0.8286 (mmpt) REVERT: F 508 LEU cc_start: 0.7672 (mm) cc_final: 0.7454 (pt) REVERT: F 562 LEU cc_start: 0.7896 (mm) cc_final: 0.7638 (tp) REVERT: F 623 LEU cc_start: 0.8985 (tp) cc_final: 0.8621 (tm) REVERT: F 665 THR cc_start: 0.5136 (m) cc_final: 0.4882 (p) REVERT: G 39 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8459 (mm-30) REVERT: H 202 THR cc_start: 0.9390 (OUTLIER) cc_final: 0.9184 (p) REVERT: I 43 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8574 (m-80) REVERT: I 144 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8145 (mp10) REVERT: J 39 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8530 (mp0) REVERT: J 50 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8250 (t0) REVERT: J 52 SER cc_start: 0.9134 (t) cc_final: 0.8870 (p) REVERT: J 55 ASP cc_start: 0.8534 (m-30) cc_final: 0.8293 (m-30) REVERT: J 97 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7465 (mtp180) REVERT: J 158 GLU cc_start: 0.8618 (tp30) cc_final: 0.8408 (tp30) REVERT: K 89 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8368 (mt) REVERT: K 153 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8508 (mp10) REVERT: L 46 VAL cc_start: 0.9276 (OUTLIER) cc_final: 0.9062 (p) REVERT: L 144 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8220 (mp10) REVERT: M 44 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7998 (tt) REVERT: N 22 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7867 (tp30) REVERT: O 40 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8908 (mp) REVERT: O 42 ASN cc_start: 0.9108 (m-40) cc_final: 0.8835 (m110) REVERT: O 150 MET cc_start: 0.9040 (mmm) cc_final: 0.8669 (mmp) REVERT: O 164 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8565 (ttt-90) REVERT: P 35 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: P 40 ILE cc_start: 0.9035 (mm) cc_final: 0.8805 (mt) REVERT: P 59 ASP cc_start: 0.8652 (m-30) cc_final: 0.8115 (m-30) REVERT: P 111 LYS cc_start: 0.9075 (mttp) cc_final: 0.8641 (mttt) REVERT: P 164 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8199 (ttt-90) REVERT: Q 26 SER cc_start: 0.9391 (OUTLIER) cc_final: 0.9152 (p) REVERT: Q 38 ASP cc_start: 0.8750 (m-30) cc_final: 0.8389 (m-30) REVERT: Q 42 ASN cc_start: 0.8856 (m-40) cc_final: 0.8646 (m-40) REVERT: Q 55 ASP cc_start: 0.8517 (t0) cc_final: 0.8161 (t0) REVERT: Q 58 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8302 (ttmt) REVERT: Q 119 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8732 (mtt90) REVERT: Q 148 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8744 (ttpp) REVERT: Q 164 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8145 (ttt180) REVERT: S 39 GLU cc_start: 0.8285 (tp30) cc_final: 0.8030 (tp30) REVERT: S 40 ILE cc_start: 0.9057 (mp) cc_final: 0.8693 (mp) REVERT: S 93 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8917 (ptt) REVERT: S 120 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8945 (mt) REVERT: T 37 ASN cc_start: 0.9227 (p0) cc_final: 0.9001 (p0) REVERT: T 43 ARG cc_start: 0.8628 (tmm-80) cc_final: 0.8422 (tmm-80) REVERT: T 156 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8567 (tt0) REVERT: T 164 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7666 (ttm170) REVERT: a 21 LEU cc_start: 0.8177 (mm) cc_final: 0.7847 (mt) outliers start: 177 outliers final: 81 residues processed: 805 average time/residue: 0.8269 time to fit residues: 807.8159 Evaluate side-chains 769 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 654 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 579 GLN Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 791 PHE Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 339 GLU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain F residue 176 ARG Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 758 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain I residue 43 PHE Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain J residue 42 ILE Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 97 ARG Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 135 HIS Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain L residue 151 GLU Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 43 PHE Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 22 GLU Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain O residue 35 GLU Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 164 ARG Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 98 SER Chi-restraints excluded: chain P residue 164 ARG Chi-restraints excluded: chain Q residue 26 SER Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain Q residue 148 LYS Chi-restraints excluded: chain Q residue 164 ARG Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 163 GLU Chi-restraints excluded: chain T residue 22 GLU Chi-restraints excluded: chain T residue 34 SER Chi-restraints excluded: chain T residue 86 CYS Chi-restraints excluded: chain T residue 156 GLU Chi-restraints excluded: chain T residue 164 ARG Chi-restraints excluded: chain a residue 4 LEU Chi-restraints excluded: chain a residue 10 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 15 optimal weight: 0.4980 chunk 317 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 360 optimal weight: 0.5980 chunk 487 optimal weight: 5.9990 chunk 196 optimal weight: 0.7980 chunk 457 optimal weight: 0.9990 chunk 207 optimal weight: 0.3980 chunk 178 optimal weight: 5.9990 chunk 445 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 ASN B 369 HIS ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 HIS C 277 ASN C 667 ASN C 798 GLN D 636 ASN E 369 HIS G 144 GLN H 101 GLN H 135 HIS I 101 GLN K 107 GLN K 144 GLN M 31 ASN ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 22 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.113067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.088238 restraints weight = 74113.025| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.95 r_work: 0.3187 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 44069 Z= 0.135 Angle : 0.614 13.221 59461 Z= 0.304 Chirality : 0.043 0.225 6816 Planarity : 0.004 0.073 7675 Dihedral : 9.145 122.415 6529 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.85 % Favored : 96.13 % Rotamer: Outliers : 3.11 % Allowed : 21.08 % Favored : 75.81 % 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: -0.20 (0.12), residues: 5426 helix: 0.66 (0.10), residues: 2934 sheet: -1.73 (0.23), residues: 489 loop : -0.76 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 329 TYR 0.018 0.001 TYR B 328 PHE 0.019 0.001 PHE A 394 TRP 0.015 0.001 TRP F 491 HIS 0.012 0.001 HIS L 135 Details of bonding type rmsd covalent geometry : bond 0.00306 (44049) covalent geometry : angle 0.61416 (59461) hydrogen bonds : bond 0.03310 ( 2009) hydrogen bonds : angle 4.40018 ( 6090) Misc. bond : bond 0.00133 ( 20) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 713 time to evaluate : 1.568 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: A 201 MET cc_start: 0.8765 (mtm) cc_final: 0.8357 (mtm) REVERT: A 204 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7923 (mt) REVERT: A 242 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7637 (tt) REVERT: A 248 TYR cc_start: 0.8841 (m-80) cc_final: 0.8611 (m-80) REVERT: A 325 LEU cc_start: 0.7812 (tp) cc_final: 0.7556 (tm) REVERT: A 371 ARG cc_start: 0.8799 (mpp80) cc_final: 0.8551 (mpp80) REVERT: A 379 MET cc_start: 0.8045 (mtm) cc_final: 0.7700 (mtp) REVERT: A 483 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7906 (mp-120) REVERT: A 509 ARG cc_start: 0.8177 (mtp-110) cc_final: 0.7853 (ttm110) REVERT: A 582 MET cc_start: 0.7826 (mmm) cc_final: 0.7514 (mmm) REVERT: A 710 LEU cc_start: 0.7698 (mp) cc_final: 0.7263 (mm) REVERT: A 712 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6830 (mmm160) REVERT: A 716 ILE cc_start: 0.8566 (mt) cc_final: 0.8290 (mp) REVERT: A 784 GLN cc_start: 0.8777 (mm-40) cc_final: 0.7826 (pt0) REVERT: B 237 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7741 (tt0) REVERT: B 330 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8192 (mtpp) REVERT: B 331 TYR cc_start: 0.8895 (m-80) cc_final: 0.8412 (m-80) REVERT: B 339 GLU cc_start: 0.7801 (tp30) cc_final: 0.7307 (tm-30) REVERT: B 357 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8557 (mm-30) REVERT: B 371 ARG cc_start: 0.8853 (mtm180) cc_final: 0.8599 (mtm110) REVERT: B 387 ASP cc_start: 0.7856 (t0) cc_final: 0.7620 (t0) REVERT: B 410 MET cc_start: 0.8854 (mmm) cc_final: 0.8450 (mmm) REVERT: B 644 ASP cc_start: 0.7996 (t0) cc_final: 0.7350 (t0) REVERT: B 646 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7706 (ptt-90) REVERT: B 702 LYS cc_start: 0.7913 (mttm) cc_final: 0.7549 (mtpp) REVERT: B 711 ASN cc_start: 0.8553 (m-40) cc_final: 0.8185 (t0) REVERT: C 176 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8394 (ttt-90) REVERT: C 194 GLU cc_start: 0.8268 (pm20) cc_final: 0.7982 (pm20) REVERT: C 217 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7912 (mt-10) REVERT: C 278 THR cc_start: 0.8650 (m) cc_final: 0.8436 (p) REVERT: C 323 THR cc_start: 0.8983 (m) cc_final: 0.8565 (p) REVERT: C 326 ASP cc_start: 0.8141 (m-30) cc_final: 0.7686 (p0) REVERT: C 327 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7409 (mm-30) REVERT: C 695 GLN cc_start: 0.6917 (mm110) cc_final: 0.6601 (pm20) REVERT: C 700 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5766 (pm20) REVERT: C 734 MET cc_start: 0.8925 (mtt) cc_final: 0.8699 (mtt) REVERT: C 765 ASP cc_start: 0.8487 (t70) cc_final: 0.7984 (p0) REVERT: D 260 ARG cc_start: 0.7996 (ttp-110) cc_final: 0.7683 (ptm160) REVERT: D 293 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8183 (m) REVERT: D 326 ASP cc_start: 0.8191 (m-30) cc_final: 0.7716 (t0) REVERT: D 501 GLU cc_start: 0.8409 (tp30) cc_final: 0.8163 (tp30) REVERT: D 506 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8250 (ttt90) REVERT: D 523 ASP cc_start: 0.8303 (t0) cc_final: 0.7674 (t0) REVERT: D 593 ARG cc_start: 0.7955 (mtm180) cc_final: 0.7597 (mmp-170) REVERT: D 633 GLU cc_start: 0.7259 (tt0) cc_final: 0.6792 (pt0) REVERT: E 187 LEU cc_start: 0.8921 (mt) cc_final: 0.8355 (mt) REVERT: E 227 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8107 (mt-10) REVERT: E 231 GLN cc_start: 0.8619 (mt0) cc_final: 0.8367 (mt0) REVERT: E 267 GLU cc_start: 0.8169 (tp30) cc_final: 0.7888 (tp30) REVERT: E 306 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8428 (p) REVERT: E 330 LYS cc_start: 0.8836 (ttmt) cc_final: 0.8632 (ttpt) REVERT: E 335 ASP cc_start: 0.7289 (t0) cc_final: 0.6809 (OUTLIER) REVERT: E 339 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.5862 (pm20) REVERT: E 367 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7081 (mt-10) REVERT: E 371 ARG cc_start: 0.6896 (ptm-80) cc_final: 0.6629 (ptm-80) REVERT: E 376 ASP cc_start: 0.8102 (m-30) cc_final: 0.7356 (t0) REVERT: F 183 MET cc_start: 0.8653 (mtm) cc_final: 0.8365 (mmm) REVERT: F 227 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7391 (tm-30) REVERT: F 240 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7102 (tp30) REVERT: F 270 LYS cc_start: 0.9013 (mmmt) cc_final: 0.8298 (mmpt) REVERT: F 562 LEU cc_start: 0.7864 (mm) cc_final: 0.7603 (tp) REVERT: F 665 THR cc_start: 0.5180 (m) cc_final: 0.4909 (p) REVERT: F 725 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7558 (mm-30) REVERT: G 39 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8437 (mm-30) REVERT: G 89 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8344 (mt) REVERT: H 202 THR cc_start: 0.9369 (OUTLIER) cc_final: 0.9149 (p) REVERT: J 50 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8219 (t0) REVERT: J 52 SER cc_start: 0.9117 (t) cc_final: 0.8823 (p) REVERT: J 55 ASP cc_start: 0.8493 (m-30) cc_final: 0.8269 (m-30) REVERT: J 158 GLU cc_start: 0.8592 (tp30) cc_final: 0.8366 (tp30) REVERT: K 153 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8422 (mp10) REVERT: L 46 VAL cc_start: 0.9251 (m) cc_final: 0.9031 (p) REVERT: L 144 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8190 (mp10) REVERT: N 22 GLU cc_start: 0.8164 (tp30) cc_final: 0.7772 (tp30) REVERT: O 40 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8870 (mp) REVERT: P 35 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: P 40 ILE cc_start: 0.9003 (mm) cc_final: 0.8774 (mt) REVERT: P 58 LYS cc_start: 0.8958 (mtmt) cc_final: 0.8674 (mtmm) REVERT: P 59 ASP cc_start: 0.8667 (m-30) cc_final: 0.8127 (m-30) REVERT: P 111 LYS cc_start: 0.8991 (mttp) cc_final: 0.8579 (mttt) REVERT: P 164 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8402 (ttt180) REVERT: Q 26 SER cc_start: 0.9365 (OUTLIER) cc_final: 0.9130 (p) REVERT: Q 38 ASP cc_start: 0.8657 (m-30) cc_final: 0.8274 (m-30) REVERT: Q 42 ASN cc_start: 0.8850 (m-40) cc_final: 0.8624 (m-40) REVERT: Q 55 ASP cc_start: 0.8484 (t0) cc_final: 0.8118 (t0) REVERT: Q 58 LYS cc_start: 0.8544 (ttmt) cc_final: 0.8289 (ttmt) REVERT: Q 119 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8682 (mtt90) REVERT: Q 164 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8140 (ttt180) REVERT: R 111 LYS cc_start: 0.8839 (mttt) cc_final: 0.8638 (mttt) REVERT: S 22 GLU cc_start: 0.8609 (tt0) cc_final: 0.8370 (tm-30) REVERT: S 39 GLU cc_start: 0.8290 (tp30) cc_final: 0.8027 (tp30) REVERT: S 40 ILE cc_start: 0.9043 (mp) cc_final: 0.8623 (mp) REVERT: S 93 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8905 (ptt) REVERT: S 120 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8926 (mt) REVERT: T 43 ARG cc_start: 0.8615 (tmm-80) cc_final: 0.8344 (tmm-80) REVERT: T 59 ASP cc_start: 0.8148 (m-30) cc_final: 0.7661 (m-30) REVERT: T 111 LYS cc_start: 0.9094 (mttm) cc_final: 0.8849 (mttm) REVERT: T 164 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7680 (ttm170) outliers start: 140 outliers final: 74 residues processed: 798 average time/residue: 0.7601 time to fit residues: 737.4204 Evaluate side-chains 768 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 669 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 579 GLN Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 791 PHE Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 339 GLU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 758 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 135 HIS Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain M residue 43 PHE Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain O residue 35 GLU Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 164 ARG Chi-restraints excluded: chain Q residue 26 SER Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain Q residue 164 ARG Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 163 GLU Chi-restraints excluded: chain T residue 22 GLU Chi-restraints excluded: chain T residue 86 CYS Chi-restraints excluded: chain T residue 98 SER Chi-restraints excluded: chain T residue 164 ARG Chi-restraints excluded: chain a residue 4 LEU Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 22 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 454 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 452 optimal weight: 0.9980 chunk 222 optimal weight: 0.2980 chunk 333 optimal weight: 0.7980 chunk 459 optimal weight: 4.9990 chunk 313 optimal weight: 0.8980 chunk 318 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 470 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 ASN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 HIS C 277 ASN C 632 GLN G 101 GLN G 144 GLN H 135 HIS I 101 GLN J 135 HIS K 54 ASN K 107 GLN K 144 GLN M 31 ASN M 107 GLN ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 22 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.113423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.088787 restraints weight = 73562.252| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.94 r_work: 0.3188 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 44069 Z= 0.146 Angle : 0.627 16.291 59461 Z= 0.309 Chirality : 0.044 0.235 6816 Planarity : 0.004 0.071 7675 Dihedral : 9.059 122.256 6529 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.65 % Favored : 96.33 % Rotamer: Outliers : 2.93 % Allowed : 21.46 % Favored : 75.61 % 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: -0.09 (0.12), residues: 5426 helix: 0.76 (0.10), residues: 2946 sheet: -1.68 (0.22), residues: 489 loop : -0.73 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 509 TYR 0.021 0.001 TYR E 328 PHE 0.020 0.001 PHE A 394 TRP 0.013 0.001 TRP F 491 HIS 0.013 0.001 HIS L 135 Details of bonding type rmsd covalent geometry : bond 0.00332 (44049) covalent geometry : angle 0.62650 (59461) hydrogen bonds : bond 0.03291 ( 2009) hydrogen bonds : angle 4.35304 ( 6090) Misc. bond : bond 0.00152 ( 20) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 693 time to evaluate : 1.742 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: A 201 MET cc_start: 0.8793 (mtm) cc_final: 0.8421 (mtm) REVERT: A 204 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7965 (mt) REVERT: A 218 PRO cc_start: 0.8569 (Cg_exo) cc_final: 0.8363 (Cg_endo) REVERT: A 242 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7701 (tt) REVERT: A 248 TYR cc_start: 0.8840 (m-80) cc_final: 0.8579 (m-80) REVERT: A 325 LEU cc_start: 0.7789 (tp) cc_final: 0.7529 (tm) REVERT: A 371 ARG cc_start: 0.8802 (mpp80) cc_final: 0.8569 (mpp80) REVERT: A 379 MET cc_start: 0.8052 (mtm) cc_final: 0.7711 (mtp) REVERT: A 483 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7841 (mp-120) REVERT: A 509 ARG cc_start: 0.8161 (mtp-110) cc_final: 0.7858 (ttm110) REVERT: A 582 MET cc_start: 0.7835 (mmm) cc_final: 0.7568 (mmm) REVERT: A 716 ILE cc_start: 0.8574 (mt) cc_final: 0.8302 (mp) REVERT: A 784 GLN cc_start: 0.8761 (mm-40) cc_final: 0.7814 (pt0) REVERT: B 237 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7775 (tt0) REVERT: B 330 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8211 (mtpp) REVERT: B 331 TYR cc_start: 0.8885 (m-80) cc_final: 0.8472 (m-80) REVERT: B 339 GLU cc_start: 0.7770 (tp30) cc_final: 0.7278 (tm-30) REVERT: B 371 ARG cc_start: 0.8835 (mtm180) cc_final: 0.8590 (mtm110) REVERT: B 387 ASP cc_start: 0.7829 (t0) cc_final: 0.7594 (t0) REVERT: B 392 ASP cc_start: 0.7811 (p0) cc_final: 0.7224 (t70) REVERT: B 528 VAL cc_start: 0.9267 (OUTLIER) cc_final: 0.9065 (p) REVERT: B 609 GLN cc_start: 0.7903 (mt0) cc_final: 0.7656 (mp10) REVERT: B 639 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8375 (tp) REVERT: B 644 ASP cc_start: 0.8030 (t0) cc_final: 0.7376 (t0) REVERT: B 646 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7778 (ptt-90) REVERT: B 702 LYS cc_start: 0.7879 (mttm) cc_final: 0.7508 (mtpp) REVERT: B 711 ASN cc_start: 0.8533 (m-40) cc_final: 0.8153 (t0) REVERT: B 775 ARG cc_start: 0.8530 (mtm-85) cc_final: 0.8244 (mtm-85) REVERT: C 176 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8418 (ttt-90) REVERT: C 194 GLU cc_start: 0.8317 (pm20) cc_final: 0.8026 (pm20) REVERT: C 217 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7910 (mt-10) REVERT: C 278 THR cc_start: 0.8643 (m) cc_final: 0.8435 (p) REVERT: C 323 THR cc_start: 0.8982 (m) cc_final: 0.8561 (p) REVERT: C 326 ASP cc_start: 0.8130 (m-30) cc_final: 0.7695 (p0) REVERT: C 327 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7349 (mm-30) REVERT: C 700 GLU cc_start: 0.6069 (OUTLIER) cc_final: 0.5667 (pm20) REVERT: C 765 ASP cc_start: 0.8459 (t70) cc_final: 0.7987 (p0) REVERT: D 237 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8064 (mp0) REVERT: D 293 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8201 (m) REVERT: D 326 ASP cc_start: 0.8195 (m-30) cc_final: 0.7719 (t0) REVERT: D 501 GLU cc_start: 0.8381 (tp30) cc_final: 0.8148 (tp30) REVERT: D 506 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8254 (ttt90) REVERT: D 523 ASP cc_start: 0.8289 (t0) cc_final: 0.7646 (t0) REVERT: D 582 MET cc_start: 0.7310 (mtp) cc_final: 0.6852 (mmm) REVERT: D 593 ARG cc_start: 0.7930 (mtm180) cc_final: 0.7521 (mmt180) REVERT: D 633 GLU cc_start: 0.7559 (tt0) cc_final: 0.6918 (tp30) REVERT: E 187 LEU cc_start: 0.8935 (mt) cc_final: 0.8409 (mt) REVERT: E 227 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8141 (mt-10) REVERT: E 231 GLN cc_start: 0.8628 (mt0) cc_final: 0.8388 (mt0) REVERT: E 267 GLU cc_start: 0.8170 (tp30) cc_final: 0.7897 (tp30) REVERT: E 306 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8427 (p) REVERT: E 335 ASP cc_start: 0.7170 (t0) cc_final: 0.6746 (t0) REVERT: E 339 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5876 (pm20) REVERT: E 367 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7175 (mt-10) REVERT: E 376 ASP cc_start: 0.8060 (m-30) cc_final: 0.7284 (t0) REVERT: F 176 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6934 (ppp80) REVERT: F 183 MET cc_start: 0.8623 (mtm) cc_final: 0.8341 (mmm) REVERT: F 240 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7108 (tp30) REVERT: F 270 LYS cc_start: 0.9020 (mmmt) cc_final: 0.8305 (mmpt) REVERT: F 562 LEU cc_start: 0.7906 (mm) cc_final: 0.7622 (tp) REVERT: F 665 THR cc_start: 0.5372 (m) cc_final: 0.5036 (p) REVERT: G 39 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8455 (mm-30) REVERT: G 205 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: H 202 THR cc_start: 0.9367 (OUTLIER) cc_final: 0.9121 (p) REVERT: J 50 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8194 (t0) REVERT: J 52 SER cc_start: 0.9108 (t) cc_final: 0.8822 (p) REVERT: J 55 ASP cc_start: 0.8496 (m-30) cc_final: 0.8279 (m-30) REVERT: J 158 GLU cc_start: 0.8579 (tp30) cc_final: 0.8337 (tp30) REVERT: J 195 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8610 (tttp) REVERT: K 153 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8433 (mp10) REVERT: L 46 VAL cc_start: 0.9240 (m) cc_final: 0.9017 (p) REVERT: L 144 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8171 (mp10) REVERT: M 89 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8026 (mt) REVERT: N 22 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7758 (tp30) REVERT: O 23 ARG cc_start: 0.8639 (mtp85) cc_final: 0.8298 (mtm-85) REVERT: O 40 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8862 (mp) REVERT: O 42 ASN cc_start: 0.9085 (m-40) cc_final: 0.8850 (m-40) REVERT: P 35 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: P 40 ILE cc_start: 0.8972 (mm) cc_final: 0.8750 (mt) REVERT: P 59 ASP cc_start: 0.8673 (m-30) cc_final: 0.8139 (m-30) REVERT: P 111 LYS cc_start: 0.8975 (mttp) cc_final: 0.8599 (mttt) REVERT: P 164 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8398 (ttt180) REVERT: Q 26 SER cc_start: 0.9357 (OUTLIER) cc_final: 0.9123 (p) REVERT: Q 38 ASP cc_start: 0.8678 (m-30) cc_final: 0.8291 (m-30) REVERT: Q 42 ASN cc_start: 0.8847 (m-40) cc_final: 0.8635 (m-40) REVERT: Q 55 ASP cc_start: 0.8483 (t0) cc_final: 0.8108 (t0) REVERT: Q 119 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8672 (mtt90) REVERT: Q 164 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8143 (ttt180) REVERT: R 59 ASP cc_start: 0.8408 (m-30) cc_final: 0.8017 (m-30) REVERT: S 22 GLU cc_start: 0.8609 (tt0) cc_final: 0.8394 (tm-30) REVERT: S 39 GLU cc_start: 0.8273 (tp30) cc_final: 0.8001 (tp30) REVERT: S 93 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8886 (ptt) REVERT: S 120 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8922 (mt) REVERT: S 150 MET cc_start: 0.9188 (mmp) cc_final: 0.8924 (mmp) outliers start: 132 outliers final: 69 residues processed: 776 average time/residue: 0.7246 time to fit residues: 683.9508 Evaluate side-chains 757 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 659 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 579 GLN Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 791 PHE Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 339 GLU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 176 ARG Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 758 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 135 HIS Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 195 LYS Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 135 HIS Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain M residue 43 PHE Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 22 GLU Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain O residue 35 GLU Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 164 ARG Chi-restraints excluded: chain Q residue 26 SER Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain Q residue 164 ARG Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 163 GLU Chi-restraints excluded: chain T residue 86 CYS Chi-restraints excluded: chain a residue 4 LEU Chi-restraints excluded: chain a residue 10 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 77 optimal weight: 0.9980 chunk 414 optimal weight: 0.6980 chunk 351 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 408 optimal weight: 0.8980 chunk 517 optimal weight: 0.0870 chunk 474 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 229 optimal weight: 0.7980 chunk 310 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 ASN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 HIS C 277 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 579 GLN G 101 GLN H 135 HIS H 144 GLN I 101 GLN J 101 GLN J 135 HIS K 144 GLN M 31 ASN ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 22 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.114231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.089856 restraints weight = 73691.922| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.93 r_work: 0.3207 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 44069 Z= 0.133 Angle : 0.624 14.175 59461 Z= 0.308 Chirality : 0.043 0.227 6816 Planarity : 0.004 0.119 7675 Dihedral : 8.910 102.022 6529 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.72 % Favored : 96.26 % Rotamer: Outliers : 2.38 % Allowed : 22.46 % Favored : 75.17 % 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: -0.02 (0.12), residues: 5426 helix: 0.82 (0.10), residues: 2947 sheet: -1.67 (0.22), residues: 498 loop : -0.69 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 363 TYR 0.022 0.001 TYR E 328 PHE 0.020 0.001 PHE F 585 TRP 0.013 0.001 TRP F 491 HIS 0.014 0.001 HIS L 135 Details of bonding type rmsd covalent geometry : bond 0.00302 (44049) covalent geometry : angle 0.62430 (59461) hydrogen bonds : bond 0.03195 ( 2009) hydrogen bonds : angle 4.32861 ( 6090) Misc. bond : bond 0.00140 ( 20) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10852 Ramachandran restraints generated. 5426 Oldfield, 0 Emsley, 5426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 694 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.8750 (mtm) cc_final: 0.8332 (mtm) REVERT: A 204 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7930 (mt) REVERT: A 218 PRO cc_start: 0.8554 (Cg_exo) cc_final: 0.8353 (Cg_endo) REVERT: A 242 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7645 (tt) REVERT: A 248 TYR cc_start: 0.8809 (m-80) cc_final: 0.8535 (m-80) REVERT: A 325 LEU cc_start: 0.7714 (tp) cc_final: 0.7429 (tm) REVERT: A 379 MET cc_start: 0.8052 (mtm) cc_final: 0.7703 (mtp) REVERT: A 483 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7592 (mp-120) REVERT: A 509 ARG cc_start: 0.8163 (mtp-110) cc_final: 0.7884 (ttp80) REVERT: A 582 MET cc_start: 0.7836 (mmm) cc_final: 0.7565 (mmm) REVERT: A 716 ILE cc_start: 0.8580 (mt) cc_final: 0.8298 (mp) REVERT: A 784 GLN cc_start: 0.8746 (mm-40) cc_final: 0.7804 (pt0) REVERT: B 237 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7772 (tt0) REVERT: B 330 LYS cc_start: 0.8742 (mtmt) cc_final: 0.8153 (mtpp) REVERT: B 331 TYR cc_start: 0.8874 (m-80) cc_final: 0.8411 (m-80) REVERT: B 339 GLU cc_start: 0.7711 (tp30) cc_final: 0.7201 (tm-30) REVERT: B 371 ARG cc_start: 0.8829 (mtm180) cc_final: 0.8579 (mtm110) REVERT: B 387 ASP cc_start: 0.7757 (t0) cc_final: 0.7511 (t0) REVERT: B 392 ASP cc_start: 0.7771 (p0) cc_final: 0.7202 (t70) REVERT: B 528 VAL cc_start: 0.9269 (OUTLIER) cc_final: 0.9063 (p) REVERT: B 587 ASP cc_start: 0.7483 (m-30) cc_final: 0.7174 (m-30) REVERT: B 644 ASP cc_start: 0.8099 (t0) cc_final: 0.7460 (t0) REVERT: B 646 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7818 (ptt-90) REVERT: B 702 LYS cc_start: 0.7870 (mttm) cc_final: 0.7510 (mtpp) REVERT: B 711 ASN cc_start: 0.8513 (m-40) cc_final: 0.8111 (t0) REVERT: B 775 ARG cc_start: 0.8561 (mtm-85) cc_final: 0.8261 (mtm-85) REVERT: C 176 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8392 (ttt-90) REVERT: C 194 GLU cc_start: 0.8285 (pm20) cc_final: 0.7959 (pm20) REVERT: C 217 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7888 (mt-10) REVERT: C 326 ASP cc_start: 0.8102 (m-30) cc_final: 0.7710 (p0) REVERT: C 327 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7302 (mm-30) REVERT: C 700 GLU cc_start: 0.6096 (OUTLIER) cc_final: 0.5698 (pm20) REVERT: C 765 ASP cc_start: 0.8456 (t70) cc_final: 0.7946 (p0) REVERT: D 237 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8082 (mp0) REVERT: D 260 ARG cc_start: 0.7969 (ttp-110) cc_final: 0.7591 (ptm160) REVERT: D 293 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8197 (m) REVERT: D 326 ASP cc_start: 0.8164 (m-30) cc_final: 0.7651 (t0) REVERT: D 501 GLU cc_start: 0.8333 (tp30) cc_final: 0.7906 (mp0) REVERT: D 523 ASP cc_start: 0.8270 (t0) cc_final: 0.7640 (t0) REVERT: D 582 MET cc_start: 0.7463 (mtp) cc_final: 0.7122 (mmm) REVERT: D 593 ARG cc_start: 0.7883 (mtm180) cc_final: 0.7478 (mmp-170) REVERT: D 622 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8250 (p) REVERT: D 633 GLU cc_start: 0.7566 (tt0) cc_final: 0.6731 (tm-30) REVERT: E 187 LEU cc_start: 0.8922 (mt) cc_final: 0.8392 (mt) REVERT: E 227 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8161 (mt-10) REVERT: E 231 GLN cc_start: 0.8626 (mt0) cc_final: 0.8291 (mt0) REVERT: E 267 GLU cc_start: 0.8150 (tp30) cc_final: 0.7875 (tp30) REVERT: E 306 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8426 (p) REVERT: E 335 ASP cc_start: 0.7083 (t0) cc_final: 0.6697 (t0) REVERT: E 339 GLU cc_start: 0.6250 (pm20) cc_final: 0.5871 (pm20) REVERT: E 376 ASP cc_start: 0.8026 (m-30) cc_final: 0.7229 (t0) REVERT: F 176 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6955 (ppp80) REVERT: F 183 MET cc_start: 0.8695 (mtm) cc_final: 0.8397 (mmm) REVERT: F 240 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7116 (tp30) REVERT: F 270 LYS cc_start: 0.9021 (mmmt) cc_final: 0.8310 (mmpt) REVERT: F 325 LEU cc_start: 0.8146 (mm) cc_final: 0.7921 (mt) REVERT: F 562 LEU cc_start: 0.7851 (mm) cc_final: 0.7584 (tp) REVERT: F 610 LEU cc_start: 0.7428 (pt) cc_final: 0.7013 (tm) REVERT: F 665 THR cc_start: 0.5186 (m) cc_final: 0.4820 (p) REVERT: G 39 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8429 (mm-30) REVERT: G 205 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: H 202 THR cc_start: 0.9390 (OUTLIER) cc_final: 0.9147 (p) REVERT: I 39 GLU cc_start: 0.8636 (mp0) cc_final: 0.8222 (tm-30) REVERT: J 52 SER cc_start: 0.9115 (t) cc_final: 0.8843 (p) REVERT: J 55 ASP cc_start: 0.8493 (m-30) cc_final: 0.8271 (m-30) REVERT: J 158 GLU cc_start: 0.8610 (tp30) cc_final: 0.8365 (tp30) REVERT: J 195 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8593 (tttp) REVERT: K 97 ARG cc_start: 0.7946 (mmm160) cc_final: 0.7595 (mmm160) REVERT: K 153 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8386 (mp10) REVERT: L 46 VAL cc_start: 0.9224 (m) cc_final: 0.8998 (p) REVERT: L 144 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8155 (mp10) REVERT: M 89 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8035 (mt) REVERT: N 22 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7728 (tp30) REVERT: N 83 LEU cc_start: 0.8862 (mt) cc_final: 0.8628 (mm) REVERT: O 23 ARG cc_start: 0.8635 (mtp85) cc_final: 0.8286 (mtm-85) REVERT: O 40 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8833 (mp) REVERT: P 35 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: P 40 ILE cc_start: 0.8952 (mm) cc_final: 0.8737 (mt) REVERT: P 43 ARG cc_start: 0.8465 (tmm-80) cc_final: 0.8189 (ttp80) REVERT: P 59 ASP cc_start: 0.8665 (m-30) cc_final: 0.8143 (m-30) REVERT: P 111 LYS cc_start: 0.8940 (mttp) cc_final: 0.8581 (mttt) REVERT: Q 26 SER cc_start: 0.9351 (OUTLIER) cc_final: 0.9137 (p) REVERT: Q 38 ASP cc_start: 0.8573 (m-30) cc_final: 0.8166 (m-30) REVERT: Q 40 ILE cc_start: 0.8874 (pp) cc_final: 0.8629 (pt) REVERT: Q 42 ASN cc_start: 0.8836 (m-40) cc_final: 0.8626 (m-40) REVERT: Q 55 ASP cc_start: 0.8488 (t0) cc_final: 0.8026 (t0) REVERT: Q 58 LYS cc_start: 0.8506 (ttmt) cc_final: 0.7930 (mtmt) REVERT: Q 119 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8669 (mtt90) REVERT: Q 164 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8136 (ttt180) REVERT: R 170 ASP cc_start: 0.7982 (t0) cc_final: 0.7697 (t0) REVERT: S 22 GLU cc_start: 0.8595 (tt0) cc_final: 0.8386 (tm-30) REVERT: S 39 GLU cc_start: 0.8257 (tp30) cc_final: 0.7984 (tp30) REVERT: S 93 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8866 (ptt) REVERT: S 120 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8921 (mt) REVERT: T 59 ASP cc_start: 0.8049 (m-30) cc_final: 0.7448 (m-30) REVERT: T 111 LYS cc_start: 0.9022 (mttm) cc_final: 0.8748 (mttm) outliers start: 107 outliers final: 66 residues processed: 763 average time/residue: 0.5312 time to fit residues: 500.2291 Evaluate side-chains 753 residues out of total 4502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 662 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 579 GLN Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 791 PHE Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain F residue 176 ARG Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 758 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 135 HIS Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 195 LYS Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 135 HIS Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain L residue 144 GLN Chi-restraints excluded: chain M residue 43 PHE Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 22 GLU Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain O residue 35 GLU Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain Q residue 26 SER Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain Q residue 164 ARG Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 163 GLU Chi-restraints excluded: chain T residue 86 CYS Chi-restraints excluded: chain T residue 98 SER Chi-restraints excluded: chain a residue 4 LEU Chi-restraints excluded: chain a residue 10 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 129 optimal weight: 1.9990 chunk 287 optimal weight: 0.0870 chunk 230 optimal weight: 0.6980 chunk 529 optimal weight: 0.9980 chunk 195 optimal weight: 0.7980 chunk 170 optimal weight: 0.9980 chunk 172 optimal weight: 0.0980 chunk 35 optimal weight: 0.6980 chunk 502 optimal weight: 2.9990 chunk 423 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 ASN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN C 343 GLN D 343 GLN F 579 GLN G 101 GLN I 101 GLN J 101 GLN J 135 HIS ** K 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 GLN M 31 ASN ** O 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 124 GLN R 139 GLN a 22 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.115090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.090905 restraints weight = 73902.074| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.94 r_work: 0.3229 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 44069 Z= 0.123 Angle : 0.614 12.277 59461 Z= 0.305 Chirality : 0.043 0.220 6816 Planarity : 0.004 0.069 7675 Dihedral : 8.755 101.120 6529 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.56 % Favored : 96.42 % Rotamer: Outliers : 2.38 % Allowed : 22.70 % Favored : 74.92 % 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: 0.11 (0.12), residues: 5426 helix: 0.92 (0.10), residues: 2928 sheet: -1.72 (0.22), residues: 479 loop : -0.59 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 329 TYR 0.022 0.001 TYR E 328 PHE 0.018 0.001 PHE A 394 TRP 0.012 0.001 TRP F 491 HIS 0.014 0.001 HIS L 135 Details of bonding type rmsd covalent geometry : bond 0.00277 (44049) covalent geometry : angle 0.61428 (59461) hydrogen bonds : bond 0.03105 ( 2009) hydrogen bonds : angle 4.27589 ( 6090) Misc. bond : bond 0.00132 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18489.46 seconds wall clock time: 315 minutes 11.81 seconds (18911.81 seconds total)