Starting phenix.real_space_refine on Wed Aug 27 03:09:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ycx_39157/08_2025/8ycx_39157_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ycx_39157/08_2025/8ycx_39157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ycx_39157/08_2025/8ycx_39157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ycx_39157/08_2025/8ycx_39157.map" model { file = "/net/cci-nas-00/data/ceres_data/8ycx_39157/08_2025/8ycx_39157_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ycx_39157/08_2025/8ycx_39157_trim.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 29 5.49 5 Mg 7 5.21 5 S 183 5.16 5 B 14 2.79 5 C 29179 2.51 5 N 8132 2.21 5 O 8913 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 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: 46457 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 4652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4652 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 21, 'TRANS': 573} Chain breaks: 1 Chain: "B" Number of atoms: 4653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4653 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 21, 'TRANS': 573} Chain breaks: 1 Chain: "C" Number of atoms: 4618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4618 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 21, 'TRANS': 568} Chain breaks: 2 Chain: "D" Number of atoms: 4365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4365 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 19, 'TRANS': 537} Chain breaks: 3 Chain: "E" Number of atoms: 3986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3986 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 17, 'TRANS': 489} Chain breaks: 5 Chain: "F" Number of atoms: 4096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4096 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 17, 'TRANS': 499} Chain breaks: 7 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: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1383 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "I" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1375 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain: "J" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1383 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "K" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1383 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} 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: "U" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 173 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 91 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 12.18, per 1000 atoms: 0.26 Number of scatterers: 46457 At special positions: 0 Unit cell: (135.61, 139.87, 203.06, 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 183 16.00 P 29 15.00 Mg 7 11.99 O 8913 8.00 N 8132 7.00 C 29179 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 "HETATM46060 O3A ADP F 901 .*. O " rejected from bonding due to valence issues. Atom "HETATM46063 O5' ADP F 901 .*. O " rejected from bonding due to valence issues. Atom "HETATM46060 O3A ADP F 901 .*. O " rejected from bonding due to valence issues. Atom "HETATM46060 O3A ADP F 901 .*. O " rejected from bonding due to valence issues. Atom "HETATM45884 O5' ATP B 903 .*. O " rejected from bonding due to valence issues. Atom "HETATM45788 O5' ATP A 902 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 2.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10876 Finding SS restraints... Secondary structure from input PDB file: 279 helices and 62 sheets defined 54.3% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 193 through 203 Processing helix chain 'A' and resid 221 through 236 removed outlier: 3.713A pdb=" N VAL A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 263 through 280 removed outlier: 3.504A pdb=" N LEU A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 removed outlier: 3.751A pdb=" N LEU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 288 through 293' Processing helix chain 'A' and resid 304 through 314 Proline residue: A 310 - end of helix Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.812A pdb=" N ARG A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.661A pdb=" N GLU A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 370 removed outlier: 4.926A pdb=" N ASP A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 390 removed outlier: 3.506A pdb=" N ALA A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 412 removed outlier: 5.589A pdb=" N ILE A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 493 Processing helix chain 'A' and resid 500 through 509 removed outlier: 3.520A pdb=" N ARG A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 507 " --> pdb=" O GLU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 515 Processing helix chain 'A' and resid 521 through 537 Processing helix chain 'A' and resid 558 through 572 removed outlier: 3.612A pdb=" N SER A 563 " --> pdb=" O LYS A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 596 Processing helix chain 'A' and resid 610 through 616 Processing helix chain 'A' and resid 627 through 630 Processing helix chain 'A' and resid 631 through 644 removed outlier: 3.934A pdb=" N TYR A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A 636 " --> pdb=" O GLN A 632 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN A 640 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL A 641 " --> pdb=" O SER A 637 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 642 " --> pdb=" O LEU A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 705 Processing helix chain 'A' and resid 706 through 712 removed outlier: 3.895A pdb=" N ARG A 712 " --> pdb=" O GLU A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 743 removed outlier: 3.948A pdb=" N ARG A 729 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP A 732 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 733 " --> pdb=" O ARG A 729 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 737 " --> pdb=" O LEU A 733 " (cutoff:3.500A) removed outlier: 3.664A 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 178 through 185 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 221 through 235 removed outlier: 3.636A pdb=" N VAL B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 289 through 293 Processing helix chain 'B' and resid 303 through 314 removed outlier: 3.633A pdb=" N ILE B 307 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Proline residue: B 310 - end of helix removed outlier: 3.556A pdb=" N ALA B 313 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 332 Processing helix chain 'B' and resid 335 through 341 removed outlier: 3.623A pdb=" N ARG B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 removed outlier: 3.505A 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: 3.557A pdb=" N MET B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 414 removed outlier: 5.626A pdb=" N ILE B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG B 414 " --> pdb=" O MET B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 493 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 Processing helix chain 'B' and resid 558 through 571 removed outlier: 3.528A pdb=" N SER B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 585 No H-bonds generated for 'chain 'B' and resid 583 through 585' Processing helix chain 'B' and resid 587 through 590 Processing helix chain 'B' and resid 591 through 596 Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.604A pdb=" N LYS B 613 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 630 Processing helix chain 'B' and resid 638 through 644 removed outlier: 3.514A pdb=" N LEU B 642 " --> pdb=" O LEU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 705 Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.550A pdb=" N LEU B 710 " --> pdb=" O ARG B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 743 removed outlier: 3.609A pdb=" N ARG B 729 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 736 " --> pdb=" O ASP B 732 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG B 737 " --> pdb=" O LEU B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 746 No H-bonds generated for 'chain 'B' and resid 744 through 746' Processing helix chain 'B' and resid 752 through 763 Processing helix chain 'B' and resid 770 through 781 Processing helix chain 'B' and resid 781 through 791 removed outlier: 3.908A pdb=" N GLU B 787 " --> pdb=" O ASP B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 810 removed outlier: 3.796A pdb=" N ASP B 808 " --> pdb=" O ASP B 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 174 removed outlier: 3.818A pdb=" N PHE C 174 " --> pdb=" O VAL C 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 170 through 174' Processing helix chain 'C' and resid 178 through 184 Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 221 through 236 removed outlier: 3.585A pdb=" N VAL C 226 " --> pdb=" O LYS C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 263 through 280 Processing helix chain 'C' and resid 289 through 293 Processing helix chain 'C' and resid 303 through 314 Proline residue: C 310 - end of helix removed outlier: 3.505A pdb=" N ALA C 313 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 Processing helix chain 'C' and resid 335 through 342 removed outlier: 3.549A pdb=" N ARG C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 341 " --> pdb=" O ALA C 337 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 362 through 370 Processing helix chain 'C' and resid 375 through 390 removed outlier: 3.740A pdb=" N LEU C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 412 removed outlier: 5.894A pdb=" N ILE C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 402 " --> pdb=" O LYS C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 493 Processing helix chain 'C' and resid 500 through 509 Processing helix chain 'C' and resid 509 through 515 Processing helix chain 'C' and resid 521 through 537 removed outlier: 3.534A pdb=" N ALA C 527 " --> pdb=" O ASP C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 572 removed outlier: 3.542A pdb=" N SER C 563 " --> pdb=" O LYS C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 586 removed outlier: 3.958A pdb=" N HIS C 586 " --> pdb=" O GLY C 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 583 through 586' Processing helix chain 'C' and resid 588 through 590 No H-bonds generated for 'chain 'C' and resid 588 through 590' Processing helix chain 'C' and resid 591 through 596 Processing helix chain 'C' and resid 608 through 617 Processing helix chain 'C' and resid 626 through 630 Processing helix chain 'C' and resid 631 through 638 removed outlier: 4.060A pdb=" N TYR C 635 " --> pdb=" O HIS C 631 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN C 636 " --> pdb=" O GLN C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 644 removed outlier: 3.713A pdb=" N LEU C 642 " --> pdb=" O LEU C 638 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU C 643 " --> pdb=" O LEU C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 705 removed outlier: 3.629A pdb=" N GLN C 695 " --> pdb=" O GLU C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.757A pdb=" N ARG C 712 " --> pdb=" O GLU C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 742 removed outlier: 3.885A pdb=" N ASP C 732 " --> pdb=" O ILE C 728 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 733 " --> pdb=" O ARG C 729 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 736 " --> pdb=" O ASP C 732 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG C 737 " --> pdb=" O LEU C 733 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 738 " --> pdb=" O MET C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 763 Processing helix chain 'C' and resid 770 through 781 Processing helix chain 'C' and resid 781 through 789 Processing helix chain 'D' and resid 169 through 173 removed outlier: 3.716A pdb=" N GLN D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 169 through 173' Processing helix chain 'D' and resid 178 through 184 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 222 through 236 removed outlier: 3.517A pdb=" N VAL D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 263 through 280 removed outlier: 3.607A pdb=" N ARG D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 293 Processing helix chain 'D' and resid 303 through 313 Proline residue: D 310 - end of helix Processing helix chain 'D' and resid 325 through 332 removed outlier: 3.521A pdb=" N ARG D 329 " --> pdb=" O LEU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 342 removed outlier: 3.839A pdb=" N ARG D 341 " --> pdb=" O ALA D 337 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 337 through 342' Processing helix chain 'D' and resid 351 through 362 removed outlier: 3.559A pdb=" N GLU D 357 " --> pdb=" O GLU D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 371 Processing helix chain 'D' and resid 375 through 390 removed outlier: 3.998A pdb=" N LEU D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 415 removed outlier: 5.833A pdb=" N ILE D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 492 removed outlier: 3.542A pdb=" N ASN D 490 " --> pdb=" O GLU D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 509 removed outlier: 3.604A pdb=" N THR D 505 " --> pdb=" O GLU D 501 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG D 506 " --> pdb=" O ALA D 502 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 507 " --> pdb=" O GLU D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 514 Processing helix chain 'D' and resid 521 through 537 removed outlier: 3.522A pdb=" N THR D 535 " --> pdb=" O ALA D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 571 Processing helix chain 'D' and resid 590 through 594 removed outlier: 3.900A pdb=" N ARG D 593 " --> pdb=" O THR D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 616 removed outlier: 3.546A pdb=" N VAL D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 630 removed outlier: 3.521A pdb=" N ALA D 630 " --> pdb=" O ILE D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 635 Processing helix chain 'D' and resid 638 through 645 removed outlier: 3.706A pdb=" N LEU D 642 " --> pdb=" O LEU D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 703 Processing helix chain 'D' and resid 706 through 713 removed outlier: 3.731A pdb=" N LEU D 710 " --> pdb=" O ARG D 706 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG D 712 " --> pdb=" O GLU D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 742 removed outlier: 3.766A pdb=" N ILE D 728 " --> pdb=" O ARG D 724 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG D 729 " --> pdb=" O GLU D 725 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 738 " --> pdb=" O MET D 734 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY D 740 " --> pdb=" O SER D 736 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN D 741 " --> pdb=" O ARG D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 763 removed outlier: 3.530A pdb=" N ALA D 757 " --> pdb=" O ASP D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 781 Processing helix chain 'D' and resid 781 through 791 Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.532A pdb=" N GLN E 173 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE E 174 " --> pdb=" O LEU E 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 170 through 174' Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 222 through 235 Processing helix chain 'E' and resid 251 through 257 Processing helix chain 'E' and resid 263 through 280 removed outlier: 3.840A pdb=" N ARG E 268 " --> pdb=" O ASP E 264 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU E 275 " --> pdb=" O LYS E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 293 removed outlier: 3.580A pdb=" N VAL E 293 " --> pdb=" O HIS E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 313 Proline residue: E 310 - end of helix Processing helix chain 'E' and resid 325 through 331 Processing helix chain 'E' and resid 335 through 340 removed outlier: 4.005A pdb=" N ARG E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 362 removed outlier: 3.700A pdb=" N GLU E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY E 361 " --> pdb=" O GLU E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 370 removed outlier: 3.546A pdb=" N ALA E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS E 369 " --> pdb=" O ARG E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 390 removed outlier: 4.159A pdb=" N MET E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL E 380 " --> pdb=" O ASP E 376 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU E 385 " --> pdb=" O ALA E 381 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA E 386 " --> pdb=" O ALA E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 411 removed outlier: 5.574A pdb=" N ILE E 400 " --> pdb=" O PRO E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 481 through 492 Processing helix chain 'E' and resid 504 through 509 removed outlier: 3.560A pdb=" N LEU E 508 " --> pdb=" O THR E 504 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG E 509 " --> pdb=" O THR E 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 504 through 509' Processing helix chain 'E' and resid 509 through 516 removed outlier: 4.000A pdb=" N GLU E 513 " --> pdb=" O ARG E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 531 removed outlier: 3.604A pdb=" N ALA E 531 " --> pdb=" O ALA E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 536 Processing helix chain 'E' and resid 559 through 571 removed outlier: 3.890A pdb=" N PHE E 571 " --> pdb=" O ALA E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 585 removed outlier: 3.529A pdb=" N PHE E 585 " --> pdb=" O MET E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 590 No H-bonds generated for 'chain 'E' and resid 588 through 590' Processing helix chain 'E' and resid 591 through 596 removed outlier: 3.771A pdb=" N PHE E 595 " --> pdb=" O ALA E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 630 Processing helix chain 'E' and resid 638 through 644 removed outlier: 3.503A pdb=" N LEU E 642 " --> pdb=" O LEU E 638 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU E 643 " --> pdb=" O LEU E 639 " (cutoff:3.500A) Processing helix chain 'E' and resid 707 through 711 removed outlier: 3.544A pdb=" N ASN E 711 " --> pdb=" O PRO E 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 707 through 711' Processing helix chain 'E' and resid 725 through 743 removed outlier: 3.600A pdb=" N ARG E 729 " --> pdb=" O GLU E 725 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER E 736 " --> pdb=" O ASP E 732 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG E 737 " --> pdb=" O LEU E 733 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL E 738 " --> pdb=" O MET E 734 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN E 741 " --> pdb=" O ARG E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 744 through 746 No H-bonds generated for 'chain 'E' and resid 744 through 746' Processing helix chain 'E' and resid 752 through 763 removed outlier: 3.831A pdb=" N ALA E 757 " --> pdb=" O ASP E 753 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG E 762 " --> pdb=" O LEU E 758 " (cutoff:3.500A) Processing helix chain 'E' and resid 772 through 781 removed outlier: 3.637A pdb=" N THR E 776 " --> pdb=" O PRO E 772 " (cutoff:3.500A) Processing helix chain 'E' and resid 785 through 789 removed outlier: 3.577A pdb=" N LYS E 788 " --> pdb=" O LEU E 785 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE E 789 " --> pdb=" O SER E 786 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 785 through 789' Processing helix chain 'F' and resid 179 through 185 Processing helix chain 'F' and resid 193 through 204 removed outlier: 3.701A pdb=" N ILE F 197 " --> pdb=" O ARG F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 234 removed outlier: 3.512A pdb=" N VAL F 226 " --> pdb=" O LYS F 222 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 269 Processing helix chain 'F' and resid 274 through 279 Processing helix chain 'F' and resid 288 through 292 Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 351 through 362 removed outlier: 3.563A pdb=" N ILE F 356 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 370 removed outlier: 3.790A pdb=" N TYR F 366 " --> pdb=" O LEU F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 381 Processing helix chain 'F' and resid 381 through 390 removed outlier: 3.510A pdb=" N TYR F 389 " --> pdb=" O LEU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 415 removed outlier: 5.612A pdb=" N ILE F 400 " --> pdb=" O PRO F 396 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET F 415 " --> pdb=" O ARG F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 490 Processing helix chain 'F' and resid 495 through 500 Processing helix chain 'F' and resid 512 through 517 Processing helix chain 'F' and resid 521 through 536 removed outlier: 3.841A pdb=" N LYS F 530 " --> pdb=" O LYS F 526 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA F 531 " --> pdb=" O ALA F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 570 removed outlier: 3.785A pdb=" N SER F 563 " --> pdb=" O LYS F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 587 through 592 Processing helix chain 'F' and resid 610 through 617 removed outlier: 3.715A pdb=" N ARG F 615 " --> pdb=" O THR F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 633 through 643 removed outlier: 3.994A pdb=" N SER F 637 " --> pdb=" O GLU F 633 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU F 639 " --> pdb=" O TYR F 635 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLN F 640 " --> pdb=" O ASN F 636 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL F 641 " --> pdb=" O SER F 637 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU F 642 " --> pdb=" O LEU F 638 " (cutoff:3.500A) Processing helix chain 'F' and resid 693 through 705 removed outlier: 3.857A pdb=" N GLU F 700 " --> pdb=" O LYS F 696 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS F 702 " --> pdb=" O ASN F 698 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS F 703 " --> pdb=" O ASP F 699 " (cutoff:3.500A) Processing helix chain 'F' and resid 709 through 713 removed outlier: 3.647A pdb=" N ARG F 712 " --> pdb=" O PHE F 709 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE F 713 " --> pdb=" O LEU F 710 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 709 through 713' Processing helix chain 'F' and resid 725 through 744 removed outlier: 4.038A pdb=" N ARG F 729 " --> pdb=" O GLU F 725 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET F 730 " --> pdb=" O GLU F 726 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP F 732 " --> pdb=" O ILE F 728 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG F 737 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL F 738 " --> pdb=" O MET F 734 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER F 744 " --> pdb=" O GLY F 740 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 763 removed outlier: 3.606A pdb=" N LEU F 758 " --> pdb=" O ALA F 754 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU F 759 " --> pdb=" O ALA F 755 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS F 761 " --> pdb=" O ALA F 757 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 781 removed outlier: 4.199A pdb=" N ARG F 774 " --> pdb=" O ALA F 770 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG F 775 " --> pdb=" O ARG F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 781 through 791 removed outlier: 3.834A pdb=" N GLU F 787 " --> pdb=" O ASP F 783 " (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 82 through 96 Processing helix chain 'G' and resid 110 through 118 removed outlier: 3.627A pdb=" N VAL G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 171 removed outlier: 3.635A pdb=" N ILE G 152 " --> pdb=" O SER G 148 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS G 171 " --> pdb=" O THR G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 183 Processing helix chain 'G' and resid 191 through 196 removed outlier: 3.805A pdb=" N ASP G 196 " --> pdb=" O GLU G 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 39 Processing helix chain 'H' and resid 49 through 67 Processing helix chain 'H' and resid 82 through 96 Processing helix chain 'H' and resid 110 through 118 Processing helix chain 'H' and resid 147 through 171 removed outlier: 3.635A pdb=" N ILE H 152 " --> pdb=" O SER H 148 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS H 171 " --> pdb=" O THR H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 183 Processing helix chain 'H' and resid 191 through 196 removed outlier: 3.806A pdb=" N ASP H 196 " --> pdb=" O GLU H 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 39 Processing helix chain 'I' and resid 49 through 67 Processing helix chain 'I' and resid 82 through 96 Processing helix chain 'I' and resid 110 through 118 removed outlier: 3.562A pdb=" N VAL I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 171 removed outlier: 3.635A pdb=" N ILE I 152 " --> pdb=" O SER I 148 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS I 171 " --> pdb=" O THR I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 183 Processing helix chain 'I' and resid 191 through 196 removed outlier: 3.806A pdb=" N ASP I 196 " --> pdb=" O GLU I 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 39 Processing helix chain 'J' and resid 49 through 67 Processing helix chain 'J' and resid 82 through 96 Processing helix chain 'J' and resid 111 through 118 Processing helix chain 'J' and resid 147 through 171 removed outlier: 3.636A pdb=" N ILE J 152 " --> pdb=" O SER J 148 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS J 171 " --> pdb=" O THR J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 183 Processing helix chain 'J' and resid 191 through 196 removed outlier: 3.806A pdb=" N ASP J 196 " --> pdb=" O GLU J 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 39 Processing helix chain 'K' and resid 49 through 67 Processing helix chain 'K' and resid 82 through 96 Processing helix chain 'K' and resid 110 through 118 Processing helix chain 'K' and resid 147 through 171 removed outlier: 3.635A pdb=" N ILE K 152 " --> pdb=" O SER K 148 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS K 171 " --> pdb=" O THR K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 183 Processing helix chain 'K' and resid 191 through 196 removed outlier: 3.807A pdb=" N ASP K 196 " --> pdb=" O GLU K 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 39 Processing helix chain 'L' and resid 49 through 67 Processing helix chain 'L' and resid 82 through 96 Processing helix chain 'L' and resid 111 through 118 Processing helix chain 'L' and resid 147 through 171 removed outlier: 3.635A pdb=" N ILE L 152 " --> pdb=" O SER L 148 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS L 171 " --> pdb=" O THR L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 183 Processing helix chain 'L' and resid 191 through 196 removed outlier: 3.807A pdb=" N ASP L 196 " --> pdb=" O GLU L 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 39 Processing helix chain 'M' and resid 49 through 67 Processing helix chain 'M' and resid 82 through 96 Processing helix chain 'M' and resid 110 through 118 Processing helix chain 'M' and resid 147 through 171 removed outlier: 3.635A pdb=" N ILE M 152 " --> pdb=" O SER M 148 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS M 171 " --> pdb=" O THR M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 183 Processing helix chain 'M' and resid 191 through 196 removed outlier: 3.806A pdb=" N ASP M 196 " --> pdb=" O GLU M 192 " (cutoff:3.500A) 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: 5.940A pdb=" N GLN A 246 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE A 285 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR A 248 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ASP A 287 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 250 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 322 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASN A 211 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A 345 " --> pdb=" O ASN A 211 " (cutoff:3.500A) removed outlier: 6.266A 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: 6.830A 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 581 removed outlier: 6.339A pdb=" N ILE A 578 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP A 625 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE A 580 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLY A 547 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N PHE A 664 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE A 549 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER A 548 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE A 717 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 6.023A 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 removed outlier: 6.949A pdb=" N ALA A 748 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR A 801 " --> pdb=" O ALA A 748 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A 750 " --> pdb=" O THR A 801 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N ASP A 803 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 175 through 177 removed outlier: 6.346A pdb=" N GLN B 246 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE B 285 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N TYR B 248 " --> pdb=" O PHE B 285 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP B 287 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU B 250 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE B 320 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU B 284 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ALA B 322 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE B 286 " --> pdb=" O ALA B 322 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N THR B 324 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N THR B 323 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU B 214 " --> pdb=" O THR B 323 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL B 213 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 373 through 374 removed outlier: 6.345A pdb=" N SER B 373 " --> pdb=" O VAL B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 577 through 581 removed outlier: 6.329A pdb=" N ILE B 578 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP B 625 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE B 580 " --> pdb=" O ASP B 625 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 646 through 648 removed outlier: 3.611A pdb=" N LEU B 647 " --> pdb=" O VAL B 655 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 748 through 749 removed outlier: 6.437A pdb=" N ALA B 748 " --> pdb=" O VAL B 799 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 823 " --> pdb=" O GLN B 798 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 802 through 803 Processing sheet with id=AB2, first strand: chain 'C' and resid 175 through 177 removed outlier: 6.525A pdb=" N GLN C 246 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE C 285 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR C 248 " --> pdb=" O PHE C 285 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASP C 287 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU C 250 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE C 320 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU C 284 " --> pdb=" O ILE C 320 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ALA C 322 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE C 286 " --> pdb=" O ALA C 322 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N THR C 324 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL C 213 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 373 through 374 removed outlier: 6.567A 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 Processing sheet with id=AB5, first strand: chain 'C' and resid 748 through 751 Processing sheet with id=AB6, first strand: chain 'D' and resid 175 through 177 removed outlier: 3.520A pdb=" N ARG D 176 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASP D 287 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE D 282 " --> pdb=" O GLN D 318 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE D 320 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU D 284 " --> pdb=" O ILE D 320 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ALA D 322 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE D 286 " --> pdb=" O ALA D 322 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N THR D 324 " --> pdb=" O ILE D 286 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N THR D 323 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU D 214 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL D 213 " --> pdb=" O VAL D 345 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 373 through 374 removed outlier: 6.887A pdb=" N SER D 373 " --> pdb=" O VAL D 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 577 through 581 removed outlier: 6.188A pdb=" N ILE D 578 " --> pdb=" O LEU D 623 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP D 625 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE D 580 " --> pdb=" O ASP D 625 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL D 622 " --> pdb=" O ILE D 663 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR D 665 " --> pdb=" O VAL D 622 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE D 624 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLY D 547 " --> pdb=" O LEU D 662 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N PHE D 664 " --> pdb=" O GLY D 547 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE D 549 " --> pdb=" O PHE D 664 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N SER D 666 " --> pdb=" O PHE D 549 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE D 551 " --> pdb=" O SER D 666 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 646 through 648 Processing sheet with id=AC1, first strand: chain 'D' and resid 747 through 749 removed outlier: 6.791A pdb=" N ALA D 748 " --> pdb=" O VAL D 799 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 246 through 248 removed outlier: 6.260A pdb=" N GLN E 246 " --> pdb=" O ILE E 283 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE E 285 " --> pdb=" O GLN E 246 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR E 248 " --> pdb=" O PHE E 285 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP E 287 " --> pdb=" O TYR E 248 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE E 282 " --> pdb=" O GLN E 318 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE E 320 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU E 284 " --> pdb=" O ILE E 320 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ALA E 322 " --> pdb=" O LEU E 284 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE E 286 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N THR E 324 " --> pdb=" O ILE E 286 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N THR E 323 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU E 214 " --> pdb=" O THR E 323 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL E 213 " --> pdb=" O VAL E 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 373 through 374 removed outlier: 7.501A pdb=" N SER E 373 " --> pdb=" O VAL E 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 548 through 551 removed outlier: 6.979A pdb=" N SER E 620 " --> pdb=" O VAL E 661 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE E 663 " --> pdb=" O SER E 620 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL E 622 " --> pdb=" O ILE E 663 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N THR E 665 " --> pdb=" O VAL E 622 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE E 624 " --> pdb=" O THR E 665 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE E 578 " --> pdb=" O LEU E 623 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP E 625 " --> pdb=" O ILE E 578 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 646 through 648 Processing sheet with id=AC6, first strand: chain 'F' and resid 248 through 249 removed outlier: 6.761A pdb=" N TYR F 248 " --> pdb=" O PHE F 285 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU F 284 " --> pdb=" O ILE F 320 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ALA F 322 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N THR F 323 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU F 214 " --> pdb=" O THR F 323 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 373 through 374 removed outlier: 7.405A pdb=" N SER F 373 " --> pdb=" O VAL F 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 578 through 581 removed outlier: 7.151A pdb=" N ILE F 578 " --> pdb=" O LEU F 623 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ASP F 625 " --> pdb=" O ILE F 578 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE F 580 " --> pdb=" O ASP F 625 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL F 622 " --> pdb=" O VAL F 661 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER F 548 " --> pdb=" O ASP F 715 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE F 717 " --> pdb=" O SER F 548 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE F 550 " --> pdb=" O ILE F 717 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 646 through 648 Processing sheet with id=AD1, first strand: chain 'G' and resid 41 through 43 removed outlier: 8.590A pdb=" N SER G 78 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN G 107 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG G 131 " --> pdb=" O CYS G 104 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY G 106 " --> pdb=" O ARG G 131 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU G 133 " --> pdb=" O GLY G 106 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA G 108 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 41 through 43 removed outlier: 8.590A pdb=" N SER G 78 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN G 107 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET G 125 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N THR G 102 " --> pdb=" O MET G 125 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 138 through 146 removed outlier: 3.839A pdb=" N GLY N 131 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLY G 141 " --> pdb=" O VAL N 129 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL N 129 " --> pdb=" O GLY G 141 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE G 143 " --> pdb=" O GLY N 127 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLY N 127 " --> pdb=" O ILE G 143 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 41 through 43 removed outlier: 8.590A pdb=" N SER H 78 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN H 107 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 41 through 43 removed outlier: 8.590A pdb=" N SER H 78 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN H 107 " --> pdb=" O SER H 78 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET H 125 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N THR H 102 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 138 through 146 removed outlier: 7.132A pdb=" N GLY H 141 " --> pdb=" O GLY O 131 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLY O 131 " --> pdb=" O GLY H 141 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 41 through 43 removed outlier: 8.591A pdb=" N SER I 78 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLN I 107 " --> pdb=" O SER I 78 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG I 131 " --> pdb=" O CYS I 104 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY I 106 " --> pdb=" O ARG I 131 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU I 133 " --> pdb=" O GLY I 106 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA I 108 " --> pdb=" O LEU I 133 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 41 through 43 removed outlier: 8.591A pdb=" N SER I 78 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLN I 107 " --> pdb=" O SER I 78 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET I 125 " --> pdb=" O ILE I 100 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N THR I 102 " --> pdb=" O MET I 125 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 138 through 146 removed outlier: 7.035A pdb=" N GLY I 141 " --> pdb=" O GLY P 131 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLY P 131 " --> pdb=" O GLY I 141 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 41 through 43 removed outlier: 8.591A pdb=" N SER J 78 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN J 107 " --> pdb=" O SER J 78 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG J 131 " --> pdb=" O CYS J 104 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY J 106 " --> pdb=" O ARG J 131 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU J 133 " --> pdb=" O GLY J 106 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA J 108 " --> pdb=" O LEU J 133 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 41 through 43 removed outlier: 8.591A pdb=" N SER J 78 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN J 107 " --> pdb=" O SER J 78 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET J 125 " --> pdb=" O ILE J 100 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N THR J 102 " --> pdb=" O MET J 125 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 138 through 146 removed outlier: 3.783A pdb=" N GLY Q 131 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY J 141 " --> pdb=" O VAL Q 129 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL Q 129 " --> pdb=" O GLY J 141 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE J 143 " --> pdb=" O GLY Q 127 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY Q 127 " --> pdb=" O ILE J 143 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 41 through 43 removed outlier: 8.591A pdb=" N SER K 78 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLN K 107 " --> pdb=" O SER K 78 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG K 131 " --> pdb=" O CYS K 104 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY K 106 " --> pdb=" O ARG K 131 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU K 133 " --> pdb=" O GLY K 106 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA K 108 " --> pdb=" O LEU K 133 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 41 through 43 removed outlier: 8.591A pdb=" N SER K 78 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLN K 107 " --> pdb=" O SER K 78 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET K 125 " --> pdb=" O ILE K 100 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N THR K 102 " --> pdb=" O MET K 125 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 138 through 146 removed outlier: 6.912A pdb=" N GLY K 141 " --> pdb=" O GLY R 131 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY R 131 " --> pdb=" O GLY K 141 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 41 through 43 removed outlier: 8.590A pdb=" N SER L 78 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN L 107 " --> pdb=" O SER L 78 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG L 131 " --> pdb=" O CYS L 104 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY L 106 " --> pdb=" O ARG L 131 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU L 133 " --> pdb=" O GLY L 106 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA L 108 " --> pdb=" O LEU L 133 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 41 through 43 removed outlier: 8.590A pdb=" N SER L 78 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN L 107 " --> pdb=" O SER L 78 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET L 125 " --> pdb=" O ILE L 100 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N THR L 102 " --> pdb=" O MET L 125 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 138 through 146 removed outlier: 7.093A pdb=" N GLY L 141 " --> pdb=" O GLY S 131 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLY S 131 " --> pdb=" O GLY L 141 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 41 through 43 removed outlier: 8.591A pdb=" N SER M 78 " --> pdb=" O LEU M 105 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN M 107 " --> pdb=" O SER M 78 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG M 131 " --> pdb=" O CYS M 104 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY M 106 " --> pdb=" O ARG M 131 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU M 133 " --> pdb=" O GLY M 106 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA M 108 " --> pdb=" O LEU M 133 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 41 through 43 removed outlier: 8.591A pdb=" N SER M 78 " --> pdb=" O LEU M 105 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN M 107 " --> pdb=" O SER M 78 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET M 125 " --> pdb=" O ILE M 100 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N THR M 102 " --> pdb=" O MET M 125 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 138 through 146 removed outlier: 7.087A pdb=" N GLY M 141 " --> pdb=" O GLY T 131 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLY T 131 " --> pdb=" O GLY M 141 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.595A pdb=" N ILE N 30 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASN N 65 " --> pdb=" O ILE N 30 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU N 32 " --> pdb=" O ASN N 65 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER N 66 " --> pdb=" O MET N 93 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N MET N 95 " --> pdb=" O SER N 66 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.595A pdb=" N ILE N 30 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASN N 65 " --> pdb=" O ILE N 30 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU N 32 " --> pdb=" O ASN N 65 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER N 66 " --> pdb=" O MET N 93 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N MET N 95 " --> pdb=" O SER N 66 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N TYR N 113 " --> pdb=" O ILE N 88 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N THR N 90 " --> pdb=" O TYR N 113 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 29 through 32 removed outlier: 6.594A pdb=" N ILE O 30 " --> pdb=" O TYR O 63 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASN O 65 " --> pdb=" O ILE O 30 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU O 32 " --> pdb=" O ASN O 65 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER O 66 " --> pdb=" O MET O 93 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N MET O 95 " --> pdb=" O SER O 66 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 29 through 32 removed outlier: 6.594A pdb=" N ILE O 30 " --> pdb=" O TYR O 63 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASN O 65 " --> pdb=" O ILE O 30 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU O 32 " --> pdb=" O ASN O 65 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER O 66 " --> pdb=" O MET O 93 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N MET O 95 " --> pdb=" O SER O 66 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N TYR O 113 " --> pdb=" O ILE O 88 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N THR O 90 " --> pdb=" O TYR O 113 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 29 through 32 removed outlier: 6.595A pdb=" N ILE P 30 " --> pdb=" O TYR P 63 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASN P 65 " --> pdb=" O ILE P 30 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU P 32 " --> pdb=" O ASN P 65 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER P 66 " --> pdb=" O MET P 93 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N MET P 95 " --> pdb=" O SER P 66 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 29 through 32 removed outlier: 6.595A pdb=" N ILE P 30 " --> pdb=" O TYR P 63 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASN P 65 " --> pdb=" O ILE P 30 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU P 32 " --> pdb=" O ASN P 65 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER P 66 " --> pdb=" O MET P 93 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N MET P 95 " --> pdb=" O SER P 66 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N TYR P 113 " --> pdb=" O ILE P 88 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N THR P 90 " --> pdb=" O TYR P 113 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Q' and resid 29 through 32 removed outlier: 6.595A pdb=" N ILE Q 30 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASN Q 65 " --> pdb=" O ILE Q 30 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU Q 32 " --> pdb=" O ASN Q 65 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER Q 66 " --> pdb=" O MET Q 93 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N MET Q 95 " --> pdb=" O SER Q 66 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 29 through 32 removed outlier: 6.595A pdb=" N ILE Q 30 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASN Q 65 " --> pdb=" O ILE Q 30 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU Q 32 " --> pdb=" O ASN Q 65 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER Q 66 " --> pdb=" O MET Q 93 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N MET Q 95 " --> pdb=" O SER Q 66 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N TYR Q 113 " --> pdb=" O ILE Q 88 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N THR Q 90 " --> pdb=" O TYR Q 113 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'R' and resid 29 through 32 removed outlier: 6.595A pdb=" N ILE R 30 " --> pdb=" O TYR R 63 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASN R 65 " --> pdb=" O ILE R 30 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU R 32 " --> pdb=" O ASN R 65 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER R 66 " --> pdb=" O MET R 93 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N MET R 95 " --> pdb=" O SER R 66 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'R' and resid 29 through 32 removed outlier: 6.595A pdb=" N ILE R 30 " --> pdb=" O TYR R 63 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASN R 65 " --> pdb=" O ILE R 30 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU R 32 " --> pdb=" O ASN R 65 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER R 66 " --> pdb=" O MET R 93 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N MET R 95 " --> pdb=" O SER R 66 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N TYR R 113 " --> pdb=" O ILE R 88 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N THR R 90 " --> pdb=" O TYR R 113 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'S' and resid 29 through 32 removed outlier: 6.595A pdb=" N ILE S 30 " --> pdb=" O TYR S 63 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASN S 65 " --> pdb=" O ILE S 30 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU S 32 " --> pdb=" O ASN S 65 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER S 66 " --> pdb=" O MET S 93 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N MET S 95 " --> pdb=" O SER S 66 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG S 119 " --> pdb=" O ALA S 92 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY S 94 " --> pdb=" O ARG S 119 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU S 121 " --> pdb=" O GLY S 94 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA S 96 " --> pdb=" O LEU S 121 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 29 through 32 removed outlier: 6.595A pdb=" N ILE S 30 " --> pdb=" O TYR S 63 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASN S 65 " --> pdb=" O ILE S 30 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU S 32 " --> pdb=" O ASN S 65 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER S 66 " --> pdb=" O MET S 93 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N MET S 95 " --> pdb=" O SER S 66 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N TYR S 113 " --> pdb=" O ILE S 88 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N THR S 90 " --> pdb=" O TYR S 113 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'T' and resid 29 through 32 removed outlier: 6.595A pdb=" N ILE T 30 " --> pdb=" O TYR T 63 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ASN T 65 " --> pdb=" O ILE T 30 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU T 32 " --> pdb=" O ASN T 65 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER T 66 " --> pdb=" O MET T 93 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N MET T 95 " --> pdb=" O SER T 66 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU T 121 " --> pdb=" O ALA T 96 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'T' and resid 29 through 32 removed outlier: 6.595A pdb=" N ILE T 30 " --> pdb=" O TYR T 63 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ASN T 65 " --> pdb=" O ILE T 30 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU T 32 " --> pdb=" O ASN T 65 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER T 66 " --> pdb=" O MET T 93 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N MET T 95 " --> pdb=" O SER T 66 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N TYR T 113 " --> pdb=" O ILE T 88 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N THR T 90 " --> pdb=" O TYR T 113 " (cutoff:3.500A) 2273 hydrogen bonds defined for protein. 6636 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: 16.90 Time building geometry restraints manager: 5.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11556 1.33 - 1.45: 8513 1.45 - 1.57: 26646 1.57 - 1.69: 62 1.69 - 1.81: 344 Bond restraints: 47121 Sorted by residual: bond pdb=" B26 BO2 T 201 " pdb=" O28 BO2 T 201 " ideal model delta sigma weight residual 1.356 1.495 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" B26 BO2 R 201 " pdb=" O28 BO2 R 201 " ideal model delta sigma weight residual 1.356 1.494 -0.138 2.00e-02 2.50e+03 4.74e+01 bond pdb=" B26 BO2 G 301 " pdb=" O28 BO2 G 301 " ideal model delta sigma weight residual 1.356 1.493 -0.137 2.00e-02 2.50e+03 4.69e+01 bond pdb=" B26 BO2 I 301 " pdb=" O28 BO2 I 301 " ideal model delta sigma weight residual 1.356 1.492 -0.136 2.00e-02 2.50e+03 4.65e+01 bond pdb=" B26 BO2 O 201 " pdb=" O28 BO2 O 201 " ideal model delta sigma weight residual 1.356 1.492 -0.136 2.00e-02 2.50e+03 4.61e+01 ... (remaining 47116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 61255 2.53 - 5.05: 1984 5.05 - 7.58: 247 7.58 - 10.10: 79 10.10 - 12.63: 43 Bond angle restraints: 63608 Sorted by residual: angle pdb=" PB ATP C 902 " pdb=" O3B ATP C 902 " pdb=" PG ATP C 902 " ideal model delta sigma weight residual 139.87 128.61 11.26 1.00e+00 1.00e+00 1.27e+02 angle pdb=" PB ATP A 904 " pdb=" O3B ATP A 904 " pdb=" PG ATP A 904 " ideal model delta sigma weight residual 139.87 129.45 10.42 1.00e+00 1.00e+00 1.09e+02 angle pdb=" PB ATP E 902 " pdb=" O3B ATP E 902 " pdb=" PG ATP E 902 " ideal model delta sigma weight residual 139.87 131.43 8.44 1.00e+00 1.00e+00 7.12e+01 angle pdb=" PB ATP B 902 " pdb=" O3B ATP B 902 " pdb=" PG ATP B 902 " ideal model delta sigma weight residual 139.87 131.56 8.31 1.00e+00 1.00e+00 6.91e+01 angle pdb=" PA ATP B 903 " pdb=" O3A ATP B 903 " pdb=" PB ATP B 903 " ideal model delta sigma weight residual 136.83 128.54 8.29 1.00e+00 1.00e+00 6.87e+01 ... (remaining 63603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.19: 28221 27.19 - 54.39: 606 54.39 - 81.58: 132 81.58 - 108.77: 7 108.77 - 135.96: 6 Dihedral angle restraints: 28972 sinusoidal: 12106 harmonic: 16866 Sorted by residual: dihedral pdb=" CD ARG E 771 " pdb=" NE ARG E 771 " pdb=" CZ ARG E 771 " pdb=" NH1 ARG E 771 " ideal model delta sinusoidal sigma weight residual 0.00 78.60 -78.60 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" O1B ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PB ADP A 901 " pdb=" PA ADP A 901 " ideal model delta sinusoidal sigma weight residual 300.00 164.03 135.96 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" C2' ADP F 901 " pdb=" C1' ADP F 901 " pdb=" N9 ADP F 901 " pdb=" C4 ADP F 901 " ideal model delta sinusoidal sigma weight residual 91.55 -145.52 -122.94 1 2.00e+01 2.50e-03 3.70e+01 ... (remaining 28969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 6606 0.097 - 0.195: 621 0.195 - 0.292: 36 0.292 - 0.389: 4 0.389 - 0.487: 1 Chirality restraints: 7268 Sorted by residual: chirality pdb=" CA ARG E 771 " pdb=" N ARG E 771 " pdb=" C ARG E 771 " pdb=" CB ARG E 771 " both_signs ideal model delta sigma weight residual False 2.51 3.00 -0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CA ALA E 770 " pdb=" N ALA E 770 " pdb=" C ALA E 770 " pdb=" CB ALA E 770 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA ASN F 211 " pdb=" N ASN F 211 " pdb=" C ASN F 211 " pdb=" CB ASN F 211 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 7265 not shown) Planarity restraints: 8230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BO2 P 201 " 0.328 2.00e-02 2.50e+03 2.81e-01 9.89e+02 pdb=" C2 BO2 P 201 " 0.153 2.00e-02 2.50e+03 pdb=" C7 BO2 P 201 " -0.073 2.00e-02 2.50e+03 pdb=" N9 BO2 P 201 " -0.501 2.00e-02 2.50e+03 pdb=" O8 BO2 P 201 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BO2 S 201 " 0.188 2.00e-02 2.50e+03 2.62e-01 8.55e+02 pdb=" C18 BO2 S 201 " -0.086 2.00e-02 2.50e+03 pdb=" C21 BO2 S 201 " 0.311 2.00e-02 2.50e+03 pdb=" N20 BO2 S 201 " -0.449 2.00e-02 2.50e+03 pdb=" O19 BO2 S 201 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BO2 O 201 " 0.188 2.00e-02 2.50e+03 2.55e-01 8.15e+02 pdb=" C18 BO2 O 201 " -0.085 2.00e-02 2.50e+03 pdb=" C21 BO2 O 201 " 0.304 2.00e-02 2.50e+03 pdb=" N20 BO2 O 201 " -0.436 2.00e-02 2.50e+03 pdb=" O19 BO2 O 201 " 0.029 2.00e-02 2.50e+03 ... (remaining 8227 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 15 1.81 - 2.58: 505 2.58 - 3.36: 60815 3.36 - 4.13: 124681 4.13 - 4.90: 230638 Nonbonded interactions: 416654 Sorted by model distance: nonbonded pdb=" CD GLU F 561 " pdb=" C8 ADP F 901 " model vdw 1.040 2.792 nonbonded pdb=" OE2 GLU B 194 " pdb=" OE2 GLU B 198 " model vdw 1.139 3.040 nonbonded pdb=" OE2 GLU F 561 " pdb=" C8 ADP F 901 " model vdw 1.184 3.260 nonbonded pdb=" NH1 ARG F 771 " pdb=" O5' ADP F 901 " model vdw 1.292 3.120 nonbonded pdb=" CZ ARG F 771 " pdb=" O3A ADP F 901 " model vdw 1.359 2.616 ... (remaining 416649 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 254 or resid 264 through 294 or resid 308 thro \ ugh 414 or resid 477 through 500 or resid 509 through 594 or resid 609 through 6 \ 68 or resid 679 through 684 or resid 692 through 800)) selection = (chain 'B' and (resid 170 through 254 or resid 264 through 294 or resid 308 thro \ ugh 414 or resid 477 through 500 or resid 509 through 594 or resid 609 through 6 \ 68 or resid 679 through 684 or resid 692 through 800)) selection = (chain 'C' and (resid 170 through 254 or resid 264 through 294 or resid 308 thro \ ugh 500 or resid 509 through 594 or resid 609 through 668 or resid 679 through 6 \ 84 or resid 692 through 800)) selection = (chain 'D' and (resid 170 through 254 or resid 264 through 294 or resid 308 thro \ ugh 414 or resid 477 through 500 or resid 509 through 594 or resid 609 through 6 \ 68 or resid 679 through 800)) selection = (chain 'F' and (resid 170 through 414 or resid 477 through 684 or resid 692 thro \ ugh 800)) } ncs_group { reference = (chain 'G' and resid 32 through 301) selection = (chain 'H' and resid 32 through 301) selection = chain 'I' selection = (chain 'J' and resid 32 through 301) selection = (chain 'K' and resid 32 through 301) selection = (chain 'L' and resid 32 through 301) selection = (chain 'M' and resid 32 through 301) } 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: 15.160 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 0.900 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 51.260 Find NCS groups from input model: 1.580 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:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 0.015 0.880 47153 Z= 1.110 Angle : 1.112 12.629 63608 Z= 0.617 Chirality : 0.058 0.487 7268 Planarity : 0.014 0.484 8230 Dihedral : 11.982 135.964 18096 Min Nonbonded Distance : 1.040 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.56 % Favored : 94.24 % Rotamer: Outliers : 0.81 % Allowed : 3.36 % Favored : 95.83 % 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: -4.68 (0.08), residues: 5812 helix: -3.76 (0.05), residues: 3052 sheet: -2.52 (0.18), residues: 538 loop : -1.89 (0.12), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 341 TYR 0.058 0.004 TYR R 63 PHE 0.048 0.004 PHE B 719 TRP 0.014 0.002 TRP C 491 HIS 0.015 0.003 HIS E 515 Details of bonding type rmsd covalent geometry : bond 0.01054 (47121) covalent geometry : angle 1.11171 (63608) hydrogen bonds : bond 0.24423 ( 2189) hydrogen bonds : angle 9.44670 ( 6636) Misc. bond : bond 0.38454 ( 32) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1360 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 1321 time to evaluate : 1.432 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 271 LYS cc_start: 0.8368 (mttt) cc_final: 0.8054 (ttmm) REVERT: A 326 ASP cc_start: 0.7837 (m-30) cc_final: 0.7625 (m-30) REVERT: A 644 ASP cc_start: 0.7181 (t0) cc_final: 0.6893 (t0) REVERT: B 267 GLU cc_start: 0.8041 (tt0) cc_final: 0.7837 (tt0) REVERT: B 696 LYS cc_start: 0.8652 (tppt) cc_final: 0.8325 (tptp) REVERT: C 679 LEU cc_start: 0.8740 (tp) cc_final: 0.8510 (tp) REVERT: D 251 ASP cc_start: 0.7664 (t0) cc_final: 0.7436 (t70) REVERT: E 327 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7547 (mt-10) REVERT: E 331 TYR cc_start: 0.8846 (m-80) cc_final: 0.8551 (m-80) REVERT: E 595 PHE cc_start: 0.8276 (m-80) cc_final: 0.7937 (m-10) REVERT: E 634 ILE cc_start: 0.8803 (mt) cc_final: 0.8367 (pp) REVERT: E 773 LEU cc_start: 0.8301 (tp) cc_final: 0.7873 (mt) REVERT: F 309 LYS cc_start: 0.6065 (OUTLIER) cc_final: 0.5536 (tmtm) REVERT: F 338 LEU cc_start: 0.8840 (tp) cc_final: 0.8405 (tp) REVERT: F 371 ARG cc_start: 0.7642 (pmt-80) cc_final: 0.5602 (ppt90) REVERT: F 490 ASN cc_start: 0.8515 (m-40) cc_final: 0.8003 (m-40) REVERT: F 647 LEU cc_start: 0.6239 (mt) cc_final: 0.5851 (mt) REVERT: G 33 TYR cc_start: 0.8183 (m-80) cc_final: 0.7930 (m-80) REVERT: G 35 LYS cc_start: 0.9105 (tptm) cc_final: 0.8216 (mttt) REVERT: G 42 ILE cc_start: 0.9179 (pt) cc_final: 0.8828 (pp) REVERT: G 160 MET cc_start: 0.8000 (mtt) cc_final: 0.7771 (mtm) REVERT: H 35 LYS cc_start: 0.8983 (tptm) cc_final: 0.8430 (mttt) REVERT: H 156 GLU cc_start: 0.7809 (tp30) cc_final: 0.7406 (tp30) REVERT: H 160 MET cc_start: 0.8124 (mtt) cc_final: 0.7890 (mtp) REVERT: I 156 GLU cc_start: 0.7864 (tp30) cc_final: 0.7655 (tp30) REVERT: J 127 LEU cc_start: 0.8609 (mm) cc_final: 0.8339 (mt) REVERT: K 129 ASN cc_start: 0.8353 (m-40) cc_final: 0.8077 (m110) REVERT: L 35 LYS cc_start: 0.8957 (tptm) cc_final: 0.8643 (tptt) REVERT: M 95 TYR cc_start: 0.7747 (t80) cc_final: 0.7545 (t80) REVERT: M 196 ASP cc_start: 0.7672 (m-30) cc_final: 0.7374 (m-30) REVERT: R 58 LYS cc_start: 0.8517 (mttp) cc_final: 0.8275 (mtmm) REVERT: S 59 ASP cc_start: 0.7948 (m-30) cc_final: 0.7717 (m-30) REVERT: U 19 GLU cc_start: 0.8069 (pm20) cc_final: 0.7851 (pm20) outliers start: 39 outliers final: 16 residues processed: 1350 average time/residue: 0.8622 time to fit residues: 1383.5199 Evaluate side-chains 810 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 793 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 692 ARG Chi-restraints excluded: chain B residue 796 PRO Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 772 PRO Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain P 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: 579 random chunks: chunk 394 optimal weight: 0.9990 chunk 430 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 chunk 265 optimal weight: 20.0000 chunk 523 optimal weight: 0.5980 chunk 497 optimal weight: 0.3980 chunk 414 optimal weight: 3.9990 chunk 310 optimal weight: 7.9990 chunk 488 optimal weight: 0.9990 chunk 366 optimal weight: 0.5980 chunk 223 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 277 ASN A 391 ASN A 490 ASN A 515 HIS A 521 GLN A 609 GLN ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN A 667 ASN A 704 HIS ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN B 636 ASN B 659 ASN B 704 HIS B 720 HIS B 778 GLN B 806 ASN C 177 ASN C 277 ASN ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 HIS C 704 HIS ** C 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 806 ASN D 391 ASN D 720 HIS D 778 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN ** E 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN E 515 HIS E 631 HIS E 651 GLN E 778 GLN F 177 ASN F 202 GLN ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 631 HIS F 632 GLN F 741 GLN G 34 ASN ** G 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 GLN H 94 GLN H 101 GLN I 144 GLN J 135 HIS K 31 ASN K 135 HIS L 34 ASN M 34 ASN M 59 GLN M 129 ASN M 135 HIS M 136 GLN ** N 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 ASN O 124 GLN ** P 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 124 GLN ** Q 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 HIS R 42 ASN S 117 HIS S 124 GLN ** T 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.121989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.093282 restraints weight = 74960.620| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.92 r_work: 0.3370 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 47153 Z= 0.151 Angle : 0.680 10.367 63608 Z= 0.346 Chirality : 0.044 0.303 7268 Planarity : 0.006 0.120 8230 Dihedral : 11.060 131.956 6995 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 2.57 % Allowed : 12.24 % Favored : 85.18 % 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: -2.45 (0.10), residues: 5812 helix: -1.40 (0.08), residues: 3161 sheet: -2.38 (0.18), residues: 564 loop : -1.43 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 193 TYR 0.014 0.002 TYR E 635 PHE 0.033 0.002 PHE F 394 TRP 0.011 0.001 TRP B 807 HIS 0.014 0.001 HIS B 586 Details of bonding type rmsd covalent geometry : bond 0.00325 (47121) covalent geometry : angle 0.67958 (63608) hydrogen bonds : bond 0.04251 ( 2189) hydrogen bonds : angle 5.47275 ( 6636) Misc. bond : bond 0.00208 ( 32) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1023 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 899 time to evaluate : 1.410 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: A 261 TYR cc_start: 0.8288 (m-80) cc_final: 0.8005 (m-80) REVERT: A 327 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7633 (mt-10) REVERT: A 340 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.6212 (tpp-160) REVERT: A 509 ARG cc_start: 0.7946 (mtm110) cc_final: 0.7690 (ptp90) REVERT: A 632 GLN cc_start: 0.7204 (tp-100) cc_final: 0.6789 (tp-100) REVERT: A 640 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: A 646 ARG cc_start: 0.8286 (mtp-110) cc_final: 0.7972 (mtm110) REVERT: A 708 GLU cc_start: 0.8314 (tt0) cc_final: 0.7976 (tp30) REVERT: B 696 LYS cc_start: 0.8778 (tppt) cc_final: 0.8357 (tptm) REVERT: B 791 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8396 (t80) REVERT: C 183 MET cc_start: 0.9156 (mtp) cc_final: 0.8948 (mtm) REVERT: C 242 LEU cc_start: 0.8824 (tp) cc_final: 0.8597 (tt) REVERT: C 343 GLN cc_start: 0.8774 (tp40) cc_final: 0.8511 (mm110) REVERT: C 388 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.7294 (ttp-170) REVERT: C 588 ARG cc_start: 0.8633 (ptp-110) cc_final: 0.8120 (ttp80) REVERT: C 724 ARG cc_start: 0.8450 (tpp80) cc_final: 0.8244 (mtt90) REVERT: D 251 ASP cc_start: 0.8058 (t0) cc_final: 0.7729 (t70) REVERT: D 700 GLU cc_start: 0.8379 (tt0) cc_final: 0.8007 (tt0) REVERT: D 737 ARG cc_start: 0.8516 (ttp80) cc_final: 0.8228 (tmt-80) REVERT: D 747 MET cc_start: 0.1645 (mmt) cc_final: 0.1093 (mtp) REVERT: E 260 ARG cc_start: 0.8030 (ptp-110) cc_final: 0.7649 (ptt-90) REVERT: E 327 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7810 (mt-10) REVERT: E 331 TYR cc_start: 0.9169 (m-80) cc_final: 0.8910 (m-80) REVERT: E 357 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8311 (mp0) REVERT: E 568 ASN cc_start: 0.6584 (m-40) cc_final: 0.6014 (m-40) REVERT: E 582 MET cc_start: 0.8058 (tpp) cc_final: 0.7572 (tpp) REVERT: E 595 PHE cc_start: 0.8112 (m-80) cc_final: 0.7687 (m-10) REVERT: E 627 ILE cc_start: 0.7733 (pt) cc_final: 0.7342 (pp) REVERT: E 634 ILE cc_start: 0.8704 (mt) cc_final: 0.8338 (pp) REVERT: E 764 PHE cc_start: 0.7725 (t80) cc_final: 0.7497 (t80) REVERT: F 308 LEU cc_start: 0.5238 (OUTLIER) cc_final: 0.5016 (mm) REVERT: F 309 LYS cc_start: 0.6570 (OUTLIER) cc_final: 0.5925 (tmtt) REVERT: F 371 ARG cc_start: 0.8033 (pmt-80) cc_final: 0.7457 (ppt90) REVERT: F 411 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7820 (mmt90) REVERT: F 483 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7325 (mt0) REVERT: G 31 ASN cc_start: 0.8300 (t0) cc_final: 0.8092 (t0) REVERT: G 33 TYR cc_start: 0.8059 (m-80) cc_final: 0.7802 (m-80) REVERT: G 42 ILE cc_start: 0.9064 (pt) cc_final: 0.8802 (pp) REVERT: G 74 MET cc_start: 0.7587 (ttt) cc_final: 0.7125 (mtp) REVERT: G 190 THR cc_start: 0.6685 (m) cc_final: 0.6417 (p) REVERT: G 196 ASP cc_start: 0.7702 (m-30) cc_final: 0.7289 (m-30) REVERT: H 35 LYS cc_start: 0.9020 (tptm) cc_final: 0.8489 (mttt) REVERT: H 42 ILE cc_start: 0.7650 (mt) cc_final: 0.7396 (mt) REVERT: H 190 THR cc_start: 0.7856 (m) cc_final: 0.7518 (p) REVERT: I 144 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8122 (mp-120) REVERT: J 127 LEU cc_start: 0.8417 (mm) cc_final: 0.8197 (mt) REVERT: K 97 ARG cc_start: 0.6598 (ttt180) cc_final: 0.6299 (mmp-170) REVERT: K 129 ASN cc_start: 0.8330 (m-40) cc_final: 0.8078 (m-40) REVERT: L 35 LYS cc_start: 0.8710 (tptm) cc_final: 0.8501 (tptt) REVERT: L 39 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6904 (mt-10) REVERT: L 49 ASP cc_start: 0.6074 (p0) cc_final: 0.5837 (p0) REVERT: L 52 SER cc_start: 0.7255 (t) cc_final: 0.7052 (p) REVERT: L 74 MET cc_start: 0.8324 (ttt) cc_final: 0.7886 (ttt) REVERT: L 124 ARG cc_start: 0.7355 (mtm180) cc_final: 0.6975 (mtm180) REVERT: L 125 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6635 (mpt) REVERT: L 129 ASN cc_start: 0.7595 (m-40) cc_final: 0.7373 (m-40) REVERT: L 165 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: L 201 ASP cc_start: 0.7627 (m-30) cc_final: 0.7237 (m-30) REVERT: M 95 TYR cc_start: 0.7533 (t80) cc_final: 0.7328 (t80) REVERT: M 105 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7172 (mm) REVERT: M 196 ASP cc_start: 0.7494 (m-30) cc_final: 0.7165 (m-30) REVERT: M 201 ASP cc_start: 0.6662 (m-30) cc_final: 0.6365 (m-30) REVERT: N 59 ASP cc_start: 0.8854 (m-30) cc_final: 0.8571 (m-30) REVERT: P 35 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8409 (tt0) REVERT: P 192 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.5676 (mpp80) REVERT: Q 55 ASP cc_start: 0.8550 (t0) cc_final: 0.8143 (t0) REVERT: R 35 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8150 (tp30) REVERT: S 59 ASP cc_start: 0.8599 (m-30) cc_final: 0.8250 (m-30) REVERT: S 111 LYS cc_start: 0.9035 (mttt) cc_final: 0.8776 (mttt) outliers start: 124 outliers final: 20 residues processed: 970 average time/residue: 0.7815 time to fit residues: 921.1644 Evaluate side-chains 780 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 744 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 637 SER Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain F residue 483 GLN Chi-restraints excluded: chain F residue 802 VAL Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain L residue 125 MET Chi-restraints excluded: chain L residue 165 GLU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 190 ILE Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 98 SER Chi-restraints excluded: chain P residue 192 ARG Chi-restraints excluded: chain R residue 35 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 318 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 360 optimal weight: 3.9990 chunk 320 optimal weight: 5.9990 chunk 578 optimal weight: 7.9990 chunk 275 optimal weight: 0.0050 chunk 138 optimal weight: 0.4980 chunk 342 optimal weight: 0.7980 chunk 287 optimal weight: 0.9990 chunk 519 optimal weight: 0.5980 chunk 227 optimal weight: 6.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS A 346 GLN A 688 ASN ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 688 ASN ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN D 698 ASN D 720 HIS ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 235 HIS ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 HIS F 741 GLN G 129 ASN G 144 GLN H 101 GLN I 107 GLN K 136 GLN M 59 GLN M 129 ASN N 42 ASN O 139 GLN P 42 ASN ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 ASN T 42 ASN T 124 GLN T 139 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.120987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.092575 restraints weight = 74639.862| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.86 r_work: 0.3360 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 47153 Z= 0.139 Angle : 0.630 9.506 63608 Z= 0.316 Chirality : 0.043 0.292 7268 Planarity : 0.005 0.116 8230 Dihedral : 10.352 118.623 6973 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.16 % Favored : 95.78 % Rotamer: Outliers : 2.86 % Allowed : 14.38 % Favored : 82.76 % 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: -1.28 (0.11), residues: 5812 helix: -0.22 (0.09), residues: 3160 sheet: -2.36 (0.18), residues: 570 loop : -1.17 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 509 TYR 0.013 0.001 TYR D 601 PHE 0.026 0.001 PHE F 394 TRP 0.012 0.001 TRP B 807 HIS 0.011 0.001 HIS B 586 Details of bonding type rmsd covalent geometry : bond 0.00305 (47121) covalent geometry : angle 0.63004 (63608) hydrogen bonds : bond 0.03633 ( 2189) hydrogen bonds : angle 4.96416 ( 6636) Misc. bond : bond 0.00272 ( 32) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 816 time to evaluate : 1.115 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: A 267 GLU cc_start: 0.8305 (tp30) cc_final: 0.7827 (tm-30) REVERT: A 327 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7485 (mt-10) REVERT: A 329 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7720 (mpt180) REVERT: A 340 ARG cc_start: 0.6566 (OUTLIER) cc_final: 0.5872 (tpp-160) REVERT: A 509 ARG cc_start: 0.7910 (mtm110) cc_final: 0.7665 (ptp90) REVERT: A 632 GLN cc_start: 0.7149 (tp-100) cc_final: 0.6693 (tp-100) REVERT: A 640 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8057 (tp40) REVERT: A 646 ARG cc_start: 0.8263 (mtp-110) cc_final: 0.7854 (mtm110) REVERT: A 653 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7767 (ttm170) REVERT: A 708 GLU cc_start: 0.8294 (tt0) cc_final: 0.7935 (tp30) REVERT: A 734 MET cc_start: 0.9240 (mtt) cc_final: 0.8958 (mtt) REVERT: B 243 LYS cc_start: 0.8727 (tppt) cc_final: 0.8341 (tptm) REVERT: B 371 ARG cc_start: 0.8792 (mpp80) cc_final: 0.8561 (mtm110) REVERT: B 513 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8335 (mm-30) REVERT: B 672 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7602 (p0) REVERT: B 696 LYS cc_start: 0.8798 (tppt) cc_final: 0.8455 (tptm) REVERT: C 195 LYS cc_start: 0.8942 (mtmm) cc_final: 0.8703 (mtpp) REVERT: C 588 ARG cc_start: 0.8633 (ptp-110) cc_final: 0.8218 (ttp80) REVERT: C 606 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7628 (mp0) REVERT: D 412 ILE cc_start: 0.8721 (mp) cc_final: 0.8434 (mm) REVERT: D 616 ARG cc_start: 0.8206 (mmt90) cc_final: 0.7889 (mmt90) REVERT: D 651 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.7936 (mm-40) REVERT: D 700 GLU cc_start: 0.8392 (tt0) cc_final: 0.8065 (tt0) REVERT: E 198 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8225 (tp30) REVERT: E 260 ARG cc_start: 0.8023 (ptp-110) cc_final: 0.7645 (ptt-90) REVERT: E 327 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7557 (mt-10) REVERT: E 330 LYS cc_start: 0.9410 (ttpp) cc_final: 0.9000 (ttpt) REVERT: E 331 TYR cc_start: 0.9080 (m-80) cc_final: 0.8648 (m-80) REVERT: E 510 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7306 (tmm) REVERT: E 534 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7345 (mtt90) REVERT: E 582 MET cc_start: 0.8050 (tpp) cc_final: 0.7607 (tpp) REVERT: E 593 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8241 (mmt180) REVERT: E 627 ILE cc_start: 0.7811 (pt) cc_final: 0.7377 (pp) REVERT: E 640 GLN cc_start: 0.8100 (mt0) cc_final: 0.7749 (mt0) REVERT: E 646 ARG cc_start: 0.7555 (mtt90) cc_final: 0.6656 (mmp80) REVERT: E 730 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7780 (ptp) REVERT: F 308 LEU cc_start: 0.4784 (tp) cc_final: 0.4467 (mm) REVERT: F 309 LYS cc_start: 0.6717 (OUTLIER) cc_final: 0.6164 (tmtt) REVERT: F 371 ARG cc_start: 0.7999 (pmt-80) cc_final: 0.7515 (ppt90) REVERT: F 373 SER cc_start: 0.8649 (t) cc_final: 0.8444 (p) REVERT: F 379 MET cc_start: 0.7556 (mmm) cc_final: 0.7014 (mtt) REVERT: G 33 TYR cc_start: 0.8196 (m-80) cc_final: 0.7970 (m-80) REVERT: G 74 MET cc_start: 0.7782 (ttt) cc_final: 0.7190 (ttm) REVERT: G 87 MET cc_start: 0.6225 (mmt) cc_final: 0.5892 (mmm) REVERT: G 196 ASP cc_start: 0.7738 (m-30) cc_final: 0.7334 (m-30) REVERT: G 201 ASP cc_start: 0.6601 (m-30) cc_final: 0.6222 (m-30) REVERT: H 35 LYS cc_start: 0.8949 (tptm) cc_final: 0.8350 (mttt) REVERT: H 39 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8292 (mm-30) REVERT: H 190 THR cc_start: 0.8015 (m) cc_final: 0.7741 (p) REVERT: I 87 MET cc_start: 0.7741 (mmt) cc_final: 0.6978 (mmt) REVERT: J 127 LEU cc_start: 0.8540 (mm) cc_final: 0.8291 (mt) REVERT: J 138 SER cc_start: 0.8747 (m) cc_final: 0.8527 (p) REVERT: K 125 MET cc_start: 0.6985 (mpp) cc_final: 0.6650 (mpp) REVERT: K 129 ASN cc_start: 0.8371 (m-40) cc_final: 0.8109 (m-40) REVERT: L 35 LYS cc_start: 0.8738 (tptm) cc_final: 0.8516 (tptt) REVERT: L 39 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6903 (mt-10) REVERT: L 129 ASN cc_start: 0.7574 (m-40) cc_final: 0.7236 (m110) REVERT: L 165 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7628 (mt-10) REVERT: L 201 ASP cc_start: 0.7650 (m-30) cc_final: 0.7328 (m-30) REVERT: M 95 TYR cc_start: 0.7436 (t80) cc_final: 0.7158 (t80) REVERT: M 105 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7196 (mm) REVERT: M 125 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6442 (ptp) REVERT: M 144 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8243 (mp10) REVERT: M 201 ASP cc_start: 0.6715 (m-30) cc_final: 0.6337 (m-30) REVERT: N 168 ASP cc_start: 0.8763 (m-30) cc_final: 0.8501 (m-30) REVERT: P 35 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8172 (tp30) REVERT: P 55 ASP cc_start: 0.8598 (t0) cc_final: 0.8395 (t0) REVERT: P 58 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8656 (mttp) REVERT: P 192 ARG cc_start: 0.6591 (OUTLIER) cc_final: 0.5721 (mpp80) REVERT: Q 55 ASP cc_start: 0.8461 (t0) cc_final: 0.8049 (t0) REVERT: Q 58 LYS cc_start: 0.9109 (mttm) cc_final: 0.8811 (mtpp) REVERT: R 58 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8780 (mtmm) REVERT: S 59 ASP cc_start: 0.8574 (m-30) cc_final: 0.8155 (m-30) REVERT: S 111 LYS cc_start: 0.8990 (mttt) cc_final: 0.8729 (mttt) REVERT: T 22 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8125 (tm-30) outliers start: 138 outliers final: 38 residues processed: 902 average time/residue: 0.5309 time to fit residues: 588.4960 Evaluate side-chains 780 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 722 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain A residue 653 ARG Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 675 LYS Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 637 SER Chi-restraints excluded: chain D residue 651 GLN Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 510 MET Chi-restraints excluded: chain E residue 534 ARG Chi-restraints excluded: chain E residue 593 ARG Chi-restraints excluded: chain E residue 730 MET Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 143 ILE Chi-restraints excluded: chain M residue 144 GLN Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 58 LYS Chi-restraints excluded: chain P residue 98 SER Chi-restraints excluded: chain P residue 192 ARG Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain T residue 163 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 362 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 518 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 264 optimal weight: 0.8980 chunk 292 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 360 optimal weight: 7.9990 chunk 449 optimal weight: 0.9990 chunk 506 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN C 586 HIS ** C 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 ASN D 720 HIS ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 741 GLN G 34 ASN G 129 ASN H 107 GLN I 107 GLN ** M 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 59 GLN M 94 GLN M 129 ASN N 139 GLN O 42 ASN ** O 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 117 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.117304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.088881 restraints weight = 75082.943| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.78 r_work: 0.3298 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 47153 Z= 0.212 Angle : 0.656 9.970 63608 Z= 0.328 Chirality : 0.045 0.289 7268 Planarity : 0.005 0.139 8230 Dihedral : 10.231 123.081 6966 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 3.71 % Allowed : 14.98 % Favored : 81.30 % 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: -0.75 (0.11), residues: 5812 helix: 0.26 (0.09), residues: 3156 sheet: -2.20 (0.19), residues: 568 loop : -0.99 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 509 TYR 0.028 0.002 TYR C 366 PHE 0.025 0.002 PHE F 394 TRP 0.015 0.001 TRP B 807 HIS 0.008 0.001 HIS B 586 Details of bonding type rmsd covalent geometry : bond 0.00483 (47121) covalent geometry : angle 0.65593 (63608) hydrogen bonds : bond 0.03741 ( 2189) hydrogen bonds : angle 4.85131 ( 6636) Misc. bond : bond 0.00248 ( 32) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 757 time to evaluate : 1.125 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 261 TYR cc_start: 0.8416 (m-80) cc_final: 0.8147 (m-80) REVERT: A 267 GLU cc_start: 0.8318 (tp30) cc_final: 0.7714 (tm-30) REVERT: A 327 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7581 (mt-10) REVERT: A 339 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8260 (pt0) REVERT: A 340 ARG cc_start: 0.6395 (OUTLIER) cc_final: 0.6190 (tpp-160) REVERT: A 509 ARG cc_start: 0.7954 (mtm110) cc_final: 0.7631 (ptp90) REVERT: A 604 TYR cc_start: 0.8017 (p90) cc_final: 0.7292 (p90) REVERT: A 644 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7109 (p0) REVERT: A 646 ARG cc_start: 0.8371 (mtp-110) cc_final: 0.7827 (mtm110) REVERT: A 653 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7715 (ttm170) REVERT: A 708 GLU cc_start: 0.8309 (tt0) cc_final: 0.8000 (tp30) REVERT: A 734 MET cc_start: 0.9247 (mtt) cc_final: 0.8828 (mtt) REVERT: A 780 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: B 371 ARG cc_start: 0.8827 (mpp80) cc_final: 0.8604 (mtm110) REVERT: B 672 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7699 (p0) REVERT: B 695 GLN cc_start: 0.8365 (mm110) cc_final: 0.7940 (mp10) REVERT: B 696 LYS cc_start: 0.8839 (tppt) cc_final: 0.8563 (tptm) REVERT: B 767 VAL cc_start: 0.8955 (m) cc_final: 0.8631 (t) REVERT: C 195 LYS cc_start: 0.8938 (mtmm) cc_final: 0.8688 (mtpp) REVERT: C 523 ASP cc_start: 0.8647 (m-30) cc_final: 0.8390 (p0) REVERT: C 573 ASP cc_start: 0.8278 (t0) cc_final: 0.8044 (t0) REVERT: C 588 ARG cc_start: 0.8645 (ptp-110) cc_final: 0.8252 (ttp80) REVERT: C 606 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7609 (mp0) REVERT: C 747 MET cc_start: 0.8732 (mtt) cc_final: 0.8487 (mtt) REVERT: C 803 ASP cc_start: 0.7672 (t0) cc_final: 0.7469 (t0) REVERT: D 700 GLU cc_start: 0.8431 (tt0) cc_final: 0.8071 (tt0) REVERT: E 198 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8221 (tp30) REVERT: E 260 ARG cc_start: 0.8095 (ptp-110) cc_final: 0.7854 (ptt-90) REVERT: E 324 THR cc_start: 0.9014 (m) cc_final: 0.8750 (p) REVERT: E 326 ASP cc_start: 0.8441 (p0) cc_final: 0.8216 (p0) REVERT: E 327 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7682 (mt-10) REVERT: E 330 LYS cc_start: 0.9412 (ttpp) cc_final: 0.9064 (ttpp) REVERT: E 331 TYR cc_start: 0.9207 (m-80) cc_final: 0.8807 (m-80) REVERT: E 509 ARG cc_start: 0.7832 (pmt-80) cc_final: 0.7359 (ppt90) REVERT: E 510 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7757 (tmm) REVERT: E 533 ARG cc_start: 0.7755 (mtm180) cc_final: 0.7407 (mtt-85) REVERT: E 582 MET cc_start: 0.8059 (tpp) cc_final: 0.7619 (tpp) REVERT: E 593 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7938 (mmt180) REVERT: E 623 LEU cc_start: 0.7863 (tp) cc_final: 0.7634 (tm) REVERT: E 627 ILE cc_start: 0.7852 (pt) cc_final: 0.7381 (pp) REVERT: E 646 ARG cc_start: 0.7528 (mtt90) cc_final: 0.6865 (mmp80) REVERT: E 659 ASN cc_start: 0.7669 (m-40) cc_final: 0.7418 (t0) REVERT: F 184 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8414 (pp20) REVERT: F 194 GLU cc_start: 0.7939 (tp30) cc_final: 0.7680 (tp30) REVERT: F 309 LYS cc_start: 0.6841 (OUTLIER) cc_final: 0.6462 (tmtt) REVERT: F 371 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.6477 (ppt170) REVERT: F 373 SER cc_start: 0.8804 (t) cc_final: 0.8532 (p) REVERT: F 411 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7475 (ttm170) REVERT: F 415 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7110 (ptp) REVERT: F 483 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7646 (mp10) REVERT: F 496 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8371 (t) REVERT: F 640 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7774 (tm-30) REVERT: F 659 ASN cc_start: 0.8696 (t0) cc_final: 0.8470 (t0) REVERT: F 711 ASN cc_start: 0.8120 (p0) cc_final: 0.7222 (p0) REVERT: G 33 TYR cc_start: 0.8376 (m-80) cc_final: 0.8132 (m-80) REVERT: G 74 MET cc_start: 0.7730 (ttt) cc_final: 0.7316 (mtp) REVERT: G 207 ARG cc_start: 0.7159 (tpp80) cc_final: 0.6491 (mtm-85) REVERT: H 35 LYS cc_start: 0.9078 (tptm) cc_final: 0.8525 (mttt) REVERT: H 64 GLU cc_start: 0.8019 (tt0) cc_final: 0.7661 (tt0) REVERT: H 70 ARG cc_start: 0.6496 (OUTLIER) cc_final: 0.6188 (ttp-170) REVERT: H 181 LYS cc_start: 0.9018 (mtpp) cc_final: 0.8722 (mtmp) REVERT: H 190 THR cc_start: 0.8028 (m) cc_final: 0.7762 (p) REVERT: I 35 LYS cc_start: 0.8618 (tptm) cc_final: 0.8174 (mptt) REVERT: I 87 MET cc_start: 0.7711 (mmt) cc_final: 0.7049 (mmt) REVERT: K 42 ILE cc_start: 0.7860 (mt) cc_final: 0.7414 (mm) REVERT: K 97 ARG cc_start: 0.6638 (mtm180) cc_final: 0.5432 (tpt170) REVERT: K 125 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7004 (mpp) REVERT: K 129 ASN cc_start: 0.8384 (m-40) cc_final: 0.8131 (m-40) REVERT: L 35 LYS cc_start: 0.8724 (tptm) cc_final: 0.8506 (tptt) REVERT: L 39 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6851 (mt-10) REVERT: L 57 MET cc_start: 0.7331 (mtt) cc_final: 0.7091 (mtp) REVERT: L 165 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: L 201 ASP cc_start: 0.7722 (m-30) cc_final: 0.7319 (m-30) REVERT: M 95 TYR cc_start: 0.7455 (t80) cc_final: 0.7173 (t80) REVERT: M 105 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7269 (mm) REVERT: M 125 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.6425 (ptp) REVERT: M 144 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8286 (mp10) REVERT: M 196 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7148 (m-30) REVERT: N 59 ASP cc_start: 0.8812 (m-30) cc_final: 0.8529 (m-30) REVERT: O 55 ASP cc_start: 0.8531 (t0) cc_final: 0.8184 (t0) REVERT: P 35 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: P 58 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8697 (mttp) REVERT: R 55 ASP cc_start: 0.8389 (t0) cc_final: 0.8088 (t0) REVERT: R 58 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8676 (mtmm) REVERT: S 59 ASP cc_start: 0.8636 (m-30) cc_final: 0.8286 (m-30) REVERT: S 109 LYS cc_start: 0.9099 (mmmm) cc_final: 0.8880 (tppt) REVERT: S 182 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: U 16 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7923 (ptp90) outliers start: 179 outliers final: 55 residues processed: 858 average time/residue: 0.5201 time to fit residues: 548.5822 Evaluate side-chains 781 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 698 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 653 ARG Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 589 PHE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 675 LYS Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain C residue 675 LYS Chi-restraints excluded: chain C residue 706 ARG Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 799 VAL Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 637 SER Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 510 MET Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 593 ARG Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain F residue 483 GLN Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 640 GLN Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain J residue 85 SER 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 142 VAL Chi-restraints excluded: chain L residue 165 GLU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 143 ILE Chi-restraints excluded: chain M residue 144 GLN Chi-restraints excluded: chain M residue 196 ASP Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain O residue 86 CYS Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 58 LYS Chi-restraints excluded: chain P residue 98 SER Chi-restraints excluded: chain P residue 192 ARG Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain S residue 182 GLU Chi-restraints excluded: chain S residue 190 ILE Chi-restraints excluded: chain T residue 163 GLU Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 16 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 443 optimal weight: 0.9990 chunk 266 optimal weight: 20.0000 chunk 538 optimal weight: 0.5980 chunk 212 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 567 optimal weight: 0.6980 chunk 216 optimal weight: 0.1980 chunk 171 optimal weight: 0.8980 chunk 440 optimal weight: 0.9990 chunk 353 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 720 HIS ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 579 GLN F 741 GLN F 806 ASN G 31 ASN G 34 ASN G 129 ASN H 107 GLN I 144 GLN L 107 GLN L 129 ASN M 59 GLN O 42 ASN ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.119365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.090695 restraints weight = 74284.213| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.91 r_work: 0.3329 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 47153 Z= 0.140 Angle : 0.600 9.751 63608 Z= 0.300 Chirality : 0.043 0.235 7268 Planarity : 0.004 0.066 8230 Dihedral : 9.855 122.964 6966 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.22 % Favored : 95.75 % Rotamer: Outliers : 3.34 % Allowed : 16.06 % Favored : 80.60 % 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: -0.36 (0.11), residues: 5812 helix: 0.61 (0.09), residues: 3160 sheet: -2.14 (0.19), residues: 545 loop : -0.86 (0.14), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 260 TYR 0.015 0.001 TYR C 366 PHE 0.024 0.001 PHE F 394 TRP 0.012 0.001 TRP B 807 HIS 0.008 0.001 HIS B 586 Details of bonding type rmsd covalent geometry : bond 0.00313 (47121) covalent geometry : angle 0.60048 (63608) hydrogen bonds : bond 0.03328 ( 2189) hydrogen bonds : angle 4.66565 ( 6636) Misc. bond : bond 0.00189 ( 32) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 759 time to evaluate : 1.111 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: A 261 TYR cc_start: 0.8435 (m-80) cc_final: 0.8206 (m-80) REVERT: A 262 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6316 (mtm110) REVERT: A 267 GLU cc_start: 0.8339 (tp30) cc_final: 0.7706 (tm-30) REVERT: A 283 ILE cc_start: 0.9094 (mt) cc_final: 0.8880 (mt) REVERT: A 327 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7558 (mt-10) REVERT: A 329 ARG cc_start: 0.7998 (mtm180) cc_final: 0.7723 (mpt180) REVERT: A 330 LYS cc_start: 0.8492 (mtpm) cc_final: 0.8270 (mptt) REVERT: A 339 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8291 (pt0) REVERT: A 509 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7656 (ptp90) REVERT: A 543 LYS cc_start: 0.8390 (mtmt) cc_final: 0.8176 (mtmm) REVERT: A 653 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7814 (ttm170) REVERT: A 692 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8250 (ttp-110) REVERT: A 708 GLU cc_start: 0.8349 (tt0) cc_final: 0.7974 (tp30) REVERT: A 734 MET cc_start: 0.9228 (mtt) cc_final: 0.8964 (mtt) REVERT: A 780 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8178 (mt-10) REVERT: B 201 MET cc_start: 0.8806 (mtt) cc_final: 0.8539 (mtt) REVERT: B 371 ARG cc_start: 0.8805 (mpp80) cc_final: 0.8568 (mtm110) REVERT: B 672 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7713 (p0) REVERT: B 695 GLN cc_start: 0.8322 (mm110) cc_final: 0.7886 (mp10) REVERT: B 696 LYS cc_start: 0.8777 (tppt) cc_final: 0.8510 (tptm) REVERT: B 767 VAL cc_start: 0.8962 (m) cc_final: 0.8573 (t) REVERT: C 195 LYS cc_start: 0.8940 (mtmm) cc_final: 0.8699 (mtpp) REVERT: C 217 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8348 (mm-30) REVERT: C 523 ASP cc_start: 0.8634 (m-30) cc_final: 0.8366 (p0) REVERT: C 573 ASP cc_start: 0.8290 (t0) cc_final: 0.8048 (t0) REVERT: C 588 ARG cc_start: 0.8552 (ptp-110) cc_final: 0.8201 (ttp80) REVERT: C 606 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7534 (mp0) REVERT: C 747 MET cc_start: 0.8698 (mtt) cc_final: 0.8498 (mtt) REVERT: D 658 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8590 (mttp) REVERT: D 700 GLU cc_start: 0.8394 (tt0) cc_final: 0.8029 (tt0) REVERT: E 260 ARG cc_start: 0.8048 (ptp-110) cc_final: 0.7716 (ptt-90) REVERT: E 324 THR cc_start: 0.8960 (m) cc_final: 0.8155 (p) REVERT: E 326 ASP cc_start: 0.8436 (p0) cc_final: 0.8188 (p0) REVERT: E 327 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7268 (mt-10) REVERT: E 330 LYS cc_start: 0.9442 (ttpp) cc_final: 0.9155 (ttpt) REVERT: E 331 TYR cc_start: 0.9214 (m-80) cc_final: 0.8935 (m-80) REVERT: E 509 ARG cc_start: 0.7803 (pmt-80) cc_final: 0.7572 (ppt90) REVERT: E 510 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7643 (tmm) REVERT: E 533 ARG cc_start: 0.7783 (mtm180) cc_final: 0.7430 (mtt-85) REVERT: E 582 MET cc_start: 0.8015 (tpp) cc_final: 0.7707 (tpp) REVERT: E 593 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7701 (mmt180) REVERT: E 623 LEU cc_start: 0.8096 (tp) cc_final: 0.7868 (tm) REVERT: E 627 ILE cc_start: 0.8024 (pt) cc_final: 0.7577 (pp) REVERT: E 646 ARG cc_start: 0.7681 (mtt90) cc_final: 0.6979 (mmp80) REVERT: E 659 ASN cc_start: 0.7845 (m-40) cc_final: 0.7550 (t0) REVERT: F 184 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8302 (pp20) REVERT: F 309 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6630 (tmtt) REVERT: F 379 MET cc_start: 0.7676 (mmm) cc_final: 0.7247 (mtt) REVERT: F 415 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.7119 (ptp) REVERT: F 496 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8347 (t) REVERT: F 640 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: F 711 ASN cc_start: 0.8023 (p0) cc_final: 0.7238 (p0) REVERT: G 74 MET cc_start: 0.7705 (ttt) cc_final: 0.7340 (mtp) REVERT: G 87 MET cc_start: 0.6220 (mmt) cc_final: 0.5968 (mmm) REVERT: G 196 ASP cc_start: 0.7730 (m-30) cc_final: 0.7429 (m-30) REVERT: G 202 THR cc_start: 0.6734 (t) cc_final: 0.6491 (p) REVERT: G 207 ARG cc_start: 0.7079 (mpp80) cc_final: 0.6466 (mtm-85) REVERT: H 35 LYS cc_start: 0.9074 (tptm) cc_final: 0.8428 (mttt) REVERT: H 64 GLU cc_start: 0.8070 (tt0) cc_final: 0.7715 (tt0) REVERT: H 70 ARG cc_start: 0.6544 (ttp-170) cc_final: 0.6156 (ttp-110) REVERT: H 144 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: H 190 THR cc_start: 0.8039 (m) cc_final: 0.7786 (p) REVERT: I 35 LYS cc_start: 0.8625 (tptm) cc_final: 0.8293 (mptt) REVERT: I 144 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8174 (mp-120) REVERT: K 42 ILE cc_start: 0.7870 (mt) cc_final: 0.7414 (mm) REVERT: K 97 ARG cc_start: 0.6625 (mtm180) cc_final: 0.5332 (mmp-170) REVERT: K 125 MET cc_start: 0.7302 (mpp) cc_final: 0.6929 (mpp) REVERT: K 129 ASN cc_start: 0.8480 (m-40) cc_final: 0.8236 (m-40) REVERT: L 35 LYS cc_start: 0.8715 (tptm) cc_final: 0.8432 (tptt) REVERT: L 39 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6818 (mt-10) REVERT: L 57 MET cc_start: 0.7302 (mtt) cc_final: 0.7004 (mtt) REVERT: L 125 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6669 (mtm) REVERT: L 165 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: L 201 ASP cc_start: 0.7687 (m-30) cc_final: 0.7303 (m-30) REVERT: M 95 TYR cc_start: 0.7540 (t80) cc_final: 0.7271 (t80) REVERT: M 105 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7311 (mm) REVERT: M 125 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6534 (ptp) REVERT: M 190 THR cc_start: 0.6548 (m) cc_final: 0.6327 (p) REVERT: M 201 ASP cc_start: 0.6930 (m-30) cc_final: 0.6409 (m-30) REVERT: N 58 LYS cc_start: 0.9121 (mtmm) cc_final: 0.8877 (mttt) REVERT: N 168 ASP cc_start: 0.8870 (m-30) cc_final: 0.8567 (m-30) REVERT: O 55 ASP cc_start: 0.8504 (t0) cc_final: 0.8130 (t0) REVERT: P 35 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8219 (tp30) REVERT: P 58 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8697 (mttp) REVERT: Q 22 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8090 (tm-30) REVERT: Q 192 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6231 (mpp80) REVERT: R 58 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8897 (mtmm) REVERT: S 59 ASP cc_start: 0.8662 (m-30) cc_final: 0.8219 (m-30) REVERT: S 109 LYS cc_start: 0.9093 (mmmm) cc_final: 0.8877 (tppt) REVERT: S 111 LYS cc_start: 0.9050 (mttt) cc_final: 0.8799 (mttt) REVERT: S 182 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7942 (tm-30) outliers start: 161 outliers final: 67 residues processed: 853 average time/residue: 0.4993 time to fit residues: 525.5988 Evaluate side-chains 795 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 703 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 653 ARG Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 589 PHE Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 675 LYS Chi-restraints excluded: chain C residue 706 ARG Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 637 SER Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 510 MET Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 593 ARG Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain F residue 483 GLN Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 640 GLN Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 144 GLN 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 44 LEU Chi-restraints excluded: chain L residue 125 MET Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 165 GLU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 143 ILE Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain O residue 86 CYS Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 58 LYS Chi-restraints excluded: chain P residue 98 SER Chi-restraints excluded: chain P residue 192 ARG Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 192 ARG Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 98 SER Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain S residue 182 GLU Chi-restraints excluded: chain S residue 190 ILE Chi-restraints excluded: chain T residue 163 GLU Chi-restraints excluded: chain T residue 190 ILE Chi-restraints excluded: chain U residue 4 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 418 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 151 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 369 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 chunk 273 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 341 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS A 391 ASN ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 GLN ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 720 HIS ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 HIS E 640 GLN ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 741 GLN G 34 ASN G 129 ASN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 GLN J 34 ASN K 135 HIS L 129 ASN M 59 GLN M 129 ASN M 136 GLN O 42 ASN ** O 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** 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 = 0.3885 r_free = 0.3885 target = 0.117705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.088679 restraints weight = 74807.746| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.88 r_work: 0.3295 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 47153 Z= 0.179 Angle : 0.623 9.948 63608 Z= 0.310 Chirality : 0.044 0.249 7268 Planarity : 0.004 0.075 8230 Dihedral : 9.896 125.121 6966 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.37 % Favored : 95.58 % Rotamer: Outliers : 3.38 % Allowed : 16.56 % Favored : 80.06 % 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: -0.17 (0.11), residues: 5812 helix: 0.77 (0.09), residues: 3161 sheet: -2.09 (0.19), residues: 547 loop : -0.77 (0.14), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 692 TYR 0.022 0.001 TYR C 366 PHE 0.023 0.001 PHE F 394 TRP 0.014 0.001 TRP B 807 HIS 0.012 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00408 (47121) covalent geometry : angle 0.62315 (63608) hydrogen bonds : bond 0.03471 ( 2189) hydrogen bonds : angle 4.64234 ( 6636) Misc. bond : bond 0.00190 ( 32) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 732 time to evaluate : 1.175 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: A 261 TYR cc_start: 0.8445 (m-80) cc_final: 0.8231 (m-80) REVERT: A 267 GLU cc_start: 0.8346 (tp30) cc_final: 0.7698 (tm-30) REVERT: A 327 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7584 (mt-10) REVERT: A 330 LYS cc_start: 0.8565 (mtpm) cc_final: 0.8348 (mtmt) REVERT: A 509 ARG cc_start: 0.8017 (mtm110) cc_final: 0.7674 (ptp90) REVERT: A 543 LYS cc_start: 0.8450 (mtmt) cc_final: 0.8246 (mtmm) REVERT: A 639 LEU cc_start: 0.8753 (tt) cc_final: 0.8553 (tp) REVERT: A 653 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7759 (ttm170) REVERT: A 692 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8237 (ttp-110) REVERT: A 708 GLU cc_start: 0.8352 (tt0) cc_final: 0.8067 (tp30) REVERT: A 734 MET cc_start: 0.9235 (mtt) cc_final: 0.8864 (mtt) REVERT: A 780 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8176 (mt-10) REVERT: B 371 ARG cc_start: 0.8845 (mpp80) cc_final: 0.8578 (mtm110) REVERT: B 413 ARG cc_start: 0.8028 (mpt-90) cc_final: 0.7645 (mpt-90) REVERT: B 672 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7690 (p0) REVERT: B 695 GLN cc_start: 0.8357 (mm110) cc_final: 0.7884 (mp10) REVERT: B 696 LYS cc_start: 0.8783 (tppt) cc_final: 0.8393 (tptm) REVERT: B 767 VAL cc_start: 0.9070 (m) cc_final: 0.8724 (t) REVERT: C 195 LYS cc_start: 0.8929 (mtmm) cc_final: 0.8671 (mtpp) REVERT: C 217 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8318 (mm-30) REVERT: C 523 ASP cc_start: 0.8674 (m-30) cc_final: 0.8348 (p0) REVERT: C 573 ASP cc_start: 0.8454 (t0) cc_final: 0.8212 (t0) REVERT: C 588 ARG cc_start: 0.8593 (ptp-110) cc_final: 0.8201 (ttp80) REVERT: C 606 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7529 (mp0) REVERT: D 658 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8651 (mttp) REVERT: D 725 GLU cc_start: 0.8395 (mp0) cc_final: 0.8131 (pm20) REVERT: E 260 ARG cc_start: 0.8039 (ptp-110) cc_final: 0.7611 (ptt-90) REVERT: E 324 THR cc_start: 0.8980 (m) cc_final: 0.8236 (p) REVERT: E 326 ASP cc_start: 0.8427 (p0) cc_final: 0.8157 (p0) REVERT: E 327 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7329 (mt-10) REVERT: E 330 LYS cc_start: 0.9449 (ttpp) cc_final: 0.9148 (ttpt) REVERT: E 507 LEU cc_start: 0.8838 (mt) cc_final: 0.8284 (mp) REVERT: E 509 ARG cc_start: 0.7985 (pmt-80) cc_final: 0.7631 (ppt90) REVERT: E 510 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7660 (tmm) REVERT: E 533 ARG cc_start: 0.7778 (mtm180) cc_final: 0.7402 (mtt-85) REVERT: E 548 SER cc_start: 0.8084 (t) cc_final: 0.7660 (t) REVERT: E 582 MET cc_start: 0.8037 (tpp) cc_final: 0.7702 (tpp) REVERT: E 623 LEU cc_start: 0.8175 (tp) cc_final: 0.7937 (tm) REVERT: E 627 ILE cc_start: 0.7971 (pt) cc_final: 0.7524 (pp) REVERT: E 646 ARG cc_start: 0.7639 (mtt90) cc_final: 0.6905 (mmp80) REVERT: E 659 ASN cc_start: 0.7814 (m-40) cc_final: 0.7496 (t0) REVERT: F 184 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8337 (pp20) REVERT: F 309 LYS cc_start: 0.7001 (OUTLIER) cc_final: 0.6743 (tmtt) REVERT: F 379 MET cc_start: 0.7821 (mmm) cc_final: 0.7315 (mtt) REVERT: F 496 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8380 (t) REVERT: F 640 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: F 711 ASN cc_start: 0.8034 (p0) cc_final: 0.7309 (p0) REVERT: G 74 MET cc_start: 0.7671 (ttt) cc_final: 0.7282 (mtp) REVERT: G 87 MET cc_start: 0.6090 (mmt) cc_final: 0.5876 (mmm) REVERT: G 202 THR cc_start: 0.6702 (t) cc_final: 0.6408 (p) REVERT: G 207 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6361 (mtm-85) REVERT: H 35 LYS cc_start: 0.9034 (tptm) cc_final: 0.8533 (mttt) REVERT: H 64 GLU cc_start: 0.8084 (tt0) cc_final: 0.7699 (tt0) REVERT: H 144 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8071 (mp10) REVERT: H 181 LYS cc_start: 0.8967 (mtpp) cc_final: 0.8667 (mtmp) REVERT: H 190 THR cc_start: 0.8015 (m) cc_final: 0.7751 (p) REVERT: I 35 LYS cc_start: 0.8675 (tptm) cc_final: 0.8333 (mptt) REVERT: I 144 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8624 (mp10) REVERT: I 170 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8057 (ptt180) REVERT: K 42 ILE cc_start: 0.7818 (mt) cc_final: 0.7381 (mm) REVERT: K 125 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6916 (mpp) REVERT: K 129 ASN cc_start: 0.8448 (m-40) cc_final: 0.8207 (m-40) REVERT: L 129 ASN cc_start: 0.7522 (m-40) cc_final: 0.7321 (m110) REVERT: L 165 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7704 (mt-10) REVERT: L 201 ASP cc_start: 0.7676 (m-30) cc_final: 0.7265 (m-30) REVERT: M 95 TYR cc_start: 0.7481 (t80) cc_final: 0.7217 (t80) REVERT: M 105 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7270 (mm) REVERT: M 144 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8243 (mp10) REVERT: N 58 LYS cc_start: 0.9133 (mtmm) cc_final: 0.8915 (mttt) REVERT: N 168 ASP cc_start: 0.8889 (m-30) cc_final: 0.8607 (m-30) REVERT: O 55 ASP cc_start: 0.8516 (t0) cc_final: 0.8102 (t0) REVERT: P 35 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8281 (tp30) REVERT: P 58 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8692 (mttp) REVERT: Q 22 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8090 (tm-30) REVERT: R 55 ASP cc_start: 0.8505 (t0) cc_final: 0.8264 (t0) REVERT: R 58 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8803 (mtmm) REVERT: S 55 ASP cc_start: 0.8600 (t0) cc_final: 0.8374 (t0) REVERT: S 59 ASP cc_start: 0.8709 (m-30) cc_final: 0.8320 (m-30) REVERT: S 182 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: U 16 ARG cc_start: 0.8310 (ptp90) cc_final: 0.8052 (pmm150) REVERT: U 19 GLU cc_start: 0.8332 (pm20) cc_final: 0.7880 (pm20) outliers start: 163 outliers final: 74 residues processed: 822 average time/residue: 0.5058 time to fit residues: 512.4800 Evaluate side-chains 790 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 695 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 653 ARG Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 589 PHE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 675 LYS Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 799 VAL Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 637 SER Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 510 MET Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 593 ARG Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 483 GLN Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 640 GLN Chi-restraints excluded: chain F residue 697 VAL Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 207 ARG Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 102 THR 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 142 VAL Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 143 ILE Chi-restraints excluded: chain M residue 144 GLN Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain O residue 86 CYS Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 58 LYS Chi-restraints excluded: chain P residue 98 SER Chi-restraints excluded: chain P residue 192 ARG Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 192 ARG Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 98 SER Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain S residue 182 GLU Chi-restraints excluded: chain S residue 190 ILE Chi-restraints excluded: chain U residue 4 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 285 optimal weight: 0.7980 chunk 186 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 324 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 269 optimal weight: 5.9990 chunk 22 optimal weight: 0.0770 chunk 338 optimal weight: 10.0000 chunk 496 optimal weight: 0.6980 chunk 399 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 GLN ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 720 HIS ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 HIS ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 483 GLN F 741 GLN F 806 ASN G 31 ASN G 34 ASN G 129 ASN H 135 HIS I 144 GLN M 59 GLN M 129 ASN O 42 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.119495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.090783 restraints weight = 74697.014| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.92 r_work: 0.3319 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 47153 Z= 0.139 Angle : 0.606 11.297 63608 Z= 0.301 Chirality : 0.043 0.236 7268 Planarity : 0.004 0.067 8230 Dihedral : 9.825 126.851 6966 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.70 % Rotamer: Outliers : 3.09 % Allowed : 17.31 % Favored : 79.60 % 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: 0.01 (0.11), residues: 5812 helix: 0.93 (0.09), residues: 3163 sheet: -2.08 (0.19), residues: 547 loop : -0.70 (0.14), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 692 TYR 0.014 0.001 TYR C 366 PHE 0.026 0.001 PHE E 709 TRP 0.013 0.001 TRP B 807 HIS 0.013 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00312 (47121) covalent geometry : angle 0.60622 (63608) hydrogen bonds : bond 0.03228 ( 2189) hydrogen bonds : angle 4.55203 ( 6636) Misc. bond : bond 0.00166 ( 32) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 742 time to evaluate : 0.960 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: A 262 ARG cc_start: 0.6891 (mtt90) cc_final: 0.5776 (ptp-110) REVERT: A 267 GLU cc_start: 0.8322 (tp30) cc_final: 0.7550 (tm-30) REVERT: A 271 LYS cc_start: 0.8827 (mttt) cc_final: 0.8512 (ttmm) REVERT: A 327 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7583 (mt-10) REVERT: A 329 ARG cc_start: 0.8020 (mtm180) cc_final: 0.7713 (mpt180) REVERT: A 330 LYS cc_start: 0.8587 (mtpm) cc_final: 0.8358 (mtmt) REVERT: A 509 ARG cc_start: 0.7957 (mtm110) cc_final: 0.7616 (ptp90) REVERT: A 543 LYS cc_start: 0.8498 (mtmt) cc_final: 0.8255 (mtmm) REVERT: A 653 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7779 (ttm170) REVERT: A 692 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8243 (ttp-110) REVERT: A 708 GLU cc_start: 0.8255 (tt0) cc_final: 0.7902 (tp30) REVERT: A 734 MET cc_start: 0.9198 (mtt) cc_final: 0.8929 (mtt) REVERT: A 780 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8077 (mt-10) REVERT: B 371 ARG cc_start: 0.8890 (mpp80) cc_final: 0.8583 (mtm110) REVERT: B 413 ARG cc_start: 0.8076 (mpt-90) cc_final: 0.7865 (mmt90) REVERT: B 672 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7799 (p0) REVERT: B 695 GLN cc_start: 0.8384 (mm110) cc_final: 0.7841 (mp10) REVERT: C 195 LYS cc_start: 0.8911 (mtmm) cc_final: 0.8649 (mtpp) REVERT: C 503 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7712 (mp0) REVERT: C 523 ASP cc_start: 0.8610 (m-30) cc_final: 0.8313 (p0) REVERT: C 588 ARG cc_start: 0.8532 (ptp-110) cc_final: 0.8139 (ttp80) REVERT: C 606 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7516 (mp0) REVERT: C 711 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8654 (t0) REVERT: D 658 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8578 (mttp) REVERT: D 725 GLU cc_start: 0.8454 (mp0) cc_final: 0.8180 (pm20) REVERT: E 260 ARG cc_start: 0.8086 (ptp-110) cc_final: 0.7593 (ptt-90) REVERT: E 324 THR cc_start: 0.8932 (m) cc_final: 0.8159 (p) REVERT: E 326 ASP cc_start: 0.8408 (p0) cc_final: 0.8144 (p0) REVERT: E 327 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7244 (mt-10) REVERT: E 330 LYS cc_start: 0.9393 (ttpp) cc_final: 0.9074 (ttpp) REVERT: E 334 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8485 (tppp) REVERT: E 507 LEU cc_start: 0.8886 (mt) cc_final: 0.8437 (mp) REVERT: E 509 ARG cc_start: 0.7998 (pmt-80) cc_final: 0.7617 (ppt90) REVERT: E 510 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7780 (tmm) REVERT: E 533 ARG cc_start: 0.7777 (mtm180) cc_final: 0.7394 (mtt-85) REVERT: E 582 MET cc_start: 0.7990 (tpp) cc_final: 0.7626 (tpp) REVERT: E 593 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.6849 (tpm170) REVERT: E 627 ILE cc_start: 0.7826 (pt) cc_final: 0.7381 (pp) REVERT: E 646 ARG cc_start: 0.7630 (mtt90) cc_final: 0.6880 (mmp80) REVERT: E 659 ASN cc_start: 0.7732 (m-40) cc_final: 0.7402 (t0) REVERT: F 339 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7881 (tm-30) REVERT: F 379 MET cc_start: 0.7777 (mmm) cc_final: 0.7556 (mtt) REVERT: F 496 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8409 (t) REVERT: F 640 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: F 711 ASN cc_start: 0.8125 (p0) cc_final: 0.7450 (p0) REVERT: G 42 ILE cc_start: 0.8794 (pp) cc_final: 0.8459 (pp) REVERT: G 74 MET cc_start: 0.7587 (ttt) cc_final: 0.7086 (ttt) REVERT: G 93 MET cc_start: 0.6560 (ptm) cc_final: 0.6285 (mtm) REVERT: G 202 THR cc_start: 0.6670 (t) cc_final: 0.6380 (p) REVERT: G 207 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6399 (mtm-85) REVERT: H 35 LYS cc_start: 0.9078 (tptm) cc_final: 0.8466 (mttt) REVERT: H 64 GLU cc_start: 0.8067 (tt0) cc_final: 0.7652 (tt0) REVERT: H 144 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8025 (mp10) REVERT: H 181 LYS cc_start: 0.9024 (mtpp) cc_final: 0.8716 (mtmp) REVERT: I 34 ASN cc_start: 0.8099 (m-40) cc_final: 0.7744 (m-40) REVERT: J 125 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.7076 (mmm) REVERT: J 165 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8099 (mt-10) REVERT: K 42 ILE cc_start: 0.7796 (mt) cc_final: 0.7337 (mm) REVERT: K 97 ARG cc_start: 0.6737 (mtm180) cc_final: 0.6385 (mtm180) REVERT: K 125 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6939 (mpp) REVERT: K 129 ASN cc_start: 0.8447 (m-40) cc_final: 0.8228 (m-40) REVERT: L 40 ARG cc_start: 0.5997 (mtp85) cc_final: 0.5593 (mtp85) REVERT: L 57 MET cc_start: 0.7242 (mtt) cc_final: 0.6942 (mtp) REVERT: L 165 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: L 201 ASP cc_start: 0.7608 (m-30) cc_final: 0.7215 (m-30) REVERT: M 95 TYR cc_start: 0.7394 (t80) cc_final: 0.7129 (t80) REVERT: M 105 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7205 (mm) REVERT: M 125 MET cc_start: 0.6628 (OUTLIER) cc_final: 0.6351 (ptp) REVERT: M 201 ASP cc_start: 0.6820 (m-30) cc_final: 0.6288 (m-30) REVERT: N 58 LYS cc_start: 0.9115 (mtmm) cc_final: 0.8859 (mttt) REVERT: N 59 ASP cc_start: 0.8825 (m-30) cc_final: 0.8464 (m-30) REVERT: N 168 ASP cc_start: 0.8887 (m-30) cc_final: 0.8582 (m-30) REVERT: O 55 ASP cc_start: 0.8507 (t0) cc_final: 0.8069 (t0) REVERT: P 35 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8160 (tp30) REVERT: P 58 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8658 (mttp) REVERT: P 59 ASP cc_start: 0.8592 (m-30) cc_final: 0.8338 (m-30) REVERT: Q 22 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8027 (tm-30) REVERT: Q 58 LYS cc_start: 0.8989 (mtpp) cc_final: 0.8671 (mtpm) REVERT: Q 192 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6269 (mpp80) REVERT: R 58 LYS cc_start: 0.9091 (mtmm) cc_final: 0.8803 (mtmm) REVERT: S 55 ASP cc_start: 0.8527 (t0) cc_final: 0.8293 (t0) REVERT: S 59 ASP cc_start: 0.8606 (m-30) cc_final: 0.8361 (m-30) REVERT: S 182 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: U 16 ARG cc_start: 0.8255 (ptp90) cc_final: 0.8023 (pmm150) REVERT: U 19 GLU cc_start: 0.8244 (pm20) cc_final: 0.7821 (pm20) outliers start: 149 outliers final: 70 residues processed: 826 average time/residue: 0.4607 time to fit residues: 470.0704 Evaluate side-chains 776 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 685 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 653 ARG Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain C residue 675 LYS Chi-restraints excluded: chain C residue 706 ARG Chi-restraints excluded: chain C residue 711 ASN Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 799 VAL Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 637 SER Chi-restraints excluded: chain D residue 655 VAL Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 510 MET Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 593 ARG Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 483 GLN Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 640 GLN Chi-restraints excluded: chain F residue 697 VAL Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 207 ARG Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 125 MET 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 142 VAL Chi-restraints excluded: chain L residue 165 GLU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 143 ILE Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain O residue 86 CYS Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 190 ILE Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 58 LYS Chi-restraints excluded: chain P residue 192 ARG Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 192 ARG Chi-restraints excluded: chain R residue 98 SER Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain S residue 182 GLU Chi-restraints excluded: chain S residue 190 ILE Chi-restraints excluded: chain T residue 99 MET Chi-restraints excluded: chain T residue 190 ILE Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 9 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 370 optimal weight: 4.9990 chunk 471 optimal weight: 0.5980 chunk 338 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 205 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 390 optimal weight: 0.7980 chunk 532 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 27 optimal weight: 0.0570 chunk 571 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 GLN ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 720 HIS D 784 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 HIS ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 741 GLN G 34 ASN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN I 144 GLN L 107 GLN M 59 GLN M 129 ASN O 42 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.120330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.091512 restraints weight = 74539.976| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.96 r_work: 0.3335 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 47153 Z= 0.129 Angle : 0.601 11.260 63608 Z= 0.298 Chirality : 0.043 0.240 7268 Planarity : 0.004 0.050 8230 Dihedral : 9.608 127.192 6961 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.32 % Favored : 95.63 % Rotamer: Outliers : 2.74 % Allowed : 17.85 % Favored : 79.41 % 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: 0.17 (0.11), residues: 5812 helix: 1.05 (0.09), residues: 3178 sheet: -1.99 (0.20), residues: 529 loop : -0.64 (0.14), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 692 TYR 0.021 0.001 TYR M 90 PHE 0.020 0.001 PHE F 394 TRP 0.013 0.001 TRP B 807 HIS 0.011 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00291 (47121) covalent geometry : angle 0.60144 (63608) hydrogen bonds : bond 0.03132 ( 2189) hydrogen bonds : angle 4.47861 ( 6636) Misc. bond : bond 0.00161 ( 32) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 713 time to evaluate : 1.220 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 267 GLU cc_start: 0.8336 (tp30) cc_final: 0.7592 (tm-30) REVERT: A 271 LYS cc_start: 0.8827 (mttt) cc_final: 0.8527 (ttmm) REVERT: A 327 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7549 (mt-10) REVERT: A 329 ARG cc_start: 0.8038 (mtm180) cc_final: 0.7728 (mpt180) REVERT: A 330 LYS cc_start: 0.8633 (mtpm) cc_final: 0.8415 (mtmt) REVERT: A 509 ARG cc_start: 0.7965 (mtm110) cc_final: 0.7644 (ptp90) REVERT: A 543 LYS cc_start: 0.8410 (mtmt) cc_final: 0.8186 (mtmm) REVERT: A 605 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7835 (pm20) REVERT: A 646 ARG cc_start: 0.8234 (mtp-110) cc_final: 0.7738 (mtm110) REVERT: A 653 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7835 (ttm170) REVERT: A 692 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8178 (ttp-110) REVERT: A 708 GLU cc_start: 0.8217 (tt0) cc_final: 0.7841 (tp30) REVERT: A 734 MET cc_start: 0.9206 (mtt) cc_final: 0.8934 (mtt) REVERT: B 371 ARG cc_start: 0.8848 (mpp80) cc_final: 0.8564 (mtm110) REVERT: B 672 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7696 (p0) REVERT: B 695 GLN cc_start: 0.8283 (mm110) cc_final: 0.7798 (mp10) REVERT: B 794 VAL cc_start: 0.8711 (m) cc_final: 0.8502 (t) REVERT: C 195 LYS cc_start: 0.8947 (mtmm) cc_final: 0.8679 (mtpp) REVERT: C 523 ASP cc_start: 0.8623 (m-30) cc_final: 0.8296 (p0) REVERT: C 588 ARG cc_start: 0.8499 (ptp-110) cc_final: 0.8109 (ttp80) REVERT: C 606 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7536 (mp0) REVERT: C 711 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8687 (t0) REVERT: D 176 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.7703 (ptp90) REVERT: D 658 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8523 (mttp) REVERT: D 700 GLU cc_start: 0.8396 (tt0) cc_final: 0.8063 (tt0) REVERT: D 704 HIS cc_start: 0.8812 (t-90) cc_final: 0.8491 (t-90) REVERT: D 725 GLU cc_start: 0.8431 (mp0) cc_final: 0.8152 (pm20) REVERT: D 785 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7783 (mt) REVERT: E 260 ARG cc_start: 0.8035 (ptp-110) cc_final: 0.7719 (ptt-90) REVERT: E 324 THR cc_start: 0.8944 (m) cc_final: 0.8119 (p) REVERT: E 326 ASP cc_start: 0.8399 (p0) cc_final: 0.8148 (p0) REVERT: E 327 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7249 (mt-10) REVERT: E 330 LYS cc_start: 0.9400 (ttpp) cc_final: 0.9114 (ttpp) REVERT: E 334 LYS cc_start: 0.8796 (mmmt) cc_final: 0.8465 (tppp) REVERT: E 507 LEU cc_start: 0.8882 (mt) cc_final: 0.8423 (mp) REVERT: E 509 ARG cc_start: 0.7961 (pmt-80) cc_final: 0.7621 (ppt90) REVERT: E 510 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7700 (tmm) REVERT: E 533 ARG cc_start: 0.7738 (mtm180) cc_final: 0.7367 (mtt-85) REVERT: E 582 MET cc_start: 0.8039 (tpp) cc_final: 0.7636 (tpp) REVERT: E 593 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.6796 (tpm170) REVERT: E 627 ILE cc_start: 0.7796 (pt) cc_final: 0.7337 (pp) REVERT: E 646 ARG cc_start: 0.7650 (mtt90) cc_final: 0.6895 (mmp80) REVERT: E 659 ASN cc_start: 0.7755 (m-40) cc_final: 0.7412 (t0) REVERT: F 339 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7879 (tm-30) REVERT: F 379 MET cc_start: 0.7809 (mmm) cc_final: 0.7563 (mtt) REVERT: F 483 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7036 (mp10) REVERT: F 496 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8431 (t) REVERT: F 640 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7861 (tm-30) REVERT: F 711 ASN cc_start: 0.8152 (p0) cc_final: 0.7532 (p0) REVERT: G 70 ARG cc_start: 0.6448 (mmm-85) cc_final: 0.5589 (mtp-110) REVERT: G 74 MET cc_start: 0.7558 (ttt) cc_final: 0.7120 (mtp) REVERT: G 93 MET cc_start: 0.6550 (ptm) cc_final: 0.6326 (mtm) REVERT: G 97 ARG cc_start: 0.4639 (ttt180) cc_final: 0.3687 (tmt170) REVERT: G 202 THR cc_start: 0.6646 (t) cc_final: 0.6368 (p) REVERT: G 207 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6373 (mtm-85) REVERT: H 35 LYS cc_start: 0.8972 (tptm) cc_final: 0.8518 (mttt) REVERT: H 64 GLU cc_start: 0.8037 (tt0) cc_final: 0.7660 (tt0) REVERT: H 144 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.7984 (mp10) REVERT: H 181 LYS cc_start: 0.8984 (mtpp) cc_final: 0.8680 (mtmp) REVERT: I 35 LYS cc_start: 0.5774 (mptt) cc_final: 0.5407 (mmtt) REVERT: I 144 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8125 (mp-120) REVERT: J 125 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.7040 (mmm) REVERT: J 165 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8089 (mt-10) REVERT: K 42 ILE cc_start: 0.7832 (mt) cc_final: 0.7355 (mm) REVERT: K 94 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7561 (mm-40) REVERT: K 125 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6900 (mpp) REVERT: K 129 ASN cc_start: 0.8458 (m-40) cc_final: 0.8221 (m-40) REVERT: L 39 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6748 (mt-10) REVERT: L 57 MET cc_start: 0.7258 (mtt) cc_final: 0.6741 (mtp) REVERT: L 97 ARG cc_start: 0.5587 (ttt180) cc_final: 0.5144 (mmm160) REVERT: L 165 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: L 201 ASP cc_start: 0.7577 (m-30) cc_final: 0.7194 (m-30) REVERT: M 105 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7243 (mm) REVERT: M 125 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6379 (ptp) REVERT: N 58 LYS cc_start: 0.9112 (mtmm) cc_final: 0.8842 (mttt) REVERT: N 168 ASP cc_start: 0.8897 (m-30) cc_final: 0.8593 (m-30) REVERT: O 22 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8242 (tm-30) REVERT: O 55 ASP cc_start: 0.8504 (t0) cc_final: 0.8113 (t0) REVERT: P 58 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8652 (mttp) REVERT: Q 22 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8014 (tm-30) REVERT: Q 58 LYS cc_start: 0.8934 (mtpp) cc_final: 0.8672 (mtpm) REVERT: Q 164 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8478 (ttt180) REVERT: Q 192 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6227 (mpp80) REVERT: S 55 ASP cc_start: 0.8466 (t0) cc_final: 0.8228 (t0) REVERT: S 59 ASP cc_start: 0.8607 (m-30) cc_final: 0.8246 (m-30) REVERT: S 182 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: T 22 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8184 (tm-30) REVERT: T 58 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8649 (mtpt) REVERT: U 19 GLU cc_start: 0.8224 (pm20) cc_final: 0.7871 (pm20) outliers start: 132 outliers final: 64 residues processed: 784 average time/residue: 0.4707 time to fit residues: 453.8423 Evaluate side-chains 783 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 693 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 653 ARG Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain C residue 675 LYS Chi-restraints excluded: chain C residue 711 ASN Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 637 SER Chi-restraints excluded: chain D residue 655 VAL Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 510 MET Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 593 ARG Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 483 GLN Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 640 GLN Chi-restraints excluded: chain F residue 697 VAL Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 207 ARG Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 125 MET 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 L residue 44 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 165 GLU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 143 ILE Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain O residue 22 GLU Chi-restraints excluded: chain O residue 86 CYS Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 190 ILE Chi-restraints excluded: chain P residue 58 LYS Chi-restraints excluded: chain P residue 192 ARG Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 164 ARG Chi-restraints excluded: chain Q residue 192 ARG Chi-restraints excluded: chain R residue 98 SER Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain S residue 182 GLU Chi-restraints excluded: chain S residue 190 ILE Chi-restraints excluded: chain T residue 58 LYS Chi-restraints excluded: chain T residue 99 MET Chi-restraints excluded: chain T residue 190 ILE Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 9 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 525 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 410 optimal weight: 0.0770 chunk 555 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 413 optimal weight: 2.9990 chunk 355 optimal weight: 1.9990 chunk 444 optimal weight: 0.7980 chunk 565 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 720 HIS ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 HIS ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 741 GLN F 806 ASN G 31 ASN G 34 ASN K 144 GLN L 31 ASN M 59 GLN M 129 ASN O 42 ASN ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.119520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.090636 restraints weight = 74022.350| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.83 r_work: 0.3333 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 47153 Z= 0.142 Angle : 0.612 12.240 63608 Z= 0.303 Chirality : 0.043 0.246 7268 Planarity : 0.004 0.057 8230 Dihedral : 9.544 127.467 6961 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.22 % Favored : 95.73 % Rotamer: Outliers : 2.68 % Allowed : 18.45 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.11), residues: 5812 helix: 1.14 (0.09), residues: 3166 sheet: -1.97 (0.20), residues: 520 loop : -0.61 (0.14), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 260 TYR 0.027 0.001 TYR M 90 PHE 0.030 0.001 PHE E 709 TRP 0.013 0.001 TRP B 807 HIS 0.011 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00322 (47121) covalent geometry : angle 0.61191 (63608) hydrogen bonds : bond 0.03184 ( 2189) hydrogen bonds : angle 4.46658 ( 6636) Misc. bond : bond 0.00162 ( 32) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 708 time to evaluate : 0.961 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 247 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8584 (tt) REVERT: A 262 ARG cc_start: 0.6902 (mtt90) cc_final: 0.6496 (mtm180) REVERT: A 267 GLU cc_start: 0.8343 (tp30) cc_final: 0.7587 (tm-30) REVERT: A 271 LYS cc_start: 0.8804 (mttt) cc_final: 0.8531 (ttmm) REVERT: A 327 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7494 (mt-10) REVERT: A 329 ARG cc_start: 0.7995 (mtm180) cc_final: 0.7668 (mpt180) REVERT: A 330 LYS cc_start: 0.8633 (mtpm) cc_final: 0.8408 (mtmt) REVERT: A 509 ARG cc_start: 0.7962 (mtm110) cc_final: 0.7700 (ptp90) REVERT: A 543 LYS cc_start: 0.8502 (mtmt) cc_final: 0.8261 (mtmm) REVERT: A 605 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7878 (pm20) REVERT: A 646 ARG cc_start: 0.8231 (mtp-110) cc_final: 0.7676 (mtm110) REVERT: A 653 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7785 (ttm170) REVERT: A 692 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8114 (ttp-110) REVERT: A 708 GLU cc_start: 0.8289 (tt0) cc_final: 0.7899 (tp30) REVERT: A 734 MET cc_start: 0.9211 (mtt) cc_final: 0.8884 (mtt) REVERT: B 371 ARG cc_start: 0.8879 (mpp80) cc_final: 0.8568 (mtm110) REVERT: B 672 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7692 (p0) REVERT: B 695 GLN cc_start: 0.8309 (mm110) cc_final: 0.7740 (mp10) REVERT: C 195 LYS cc_start: 0.8935 (mtmm) cc_final: 0.8669 (mtpp) REVERT: C 503 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7666 (mp0) REVERT: C 523 ASP cc_start: 0.8553 (m-30) cc_final: 0.8266 (p0) REVERT: C 606 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7554 (mp0) REVERT: C 632 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8400 (mm110) REVERT: C 711 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8654 (t0) REVERT: D 176 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.7717 (ptp90) REVERT: D 658 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8588 (mttp) REVERT: D 704 HIS cc_start: 0.8713 (t-90) cc_final: 0.8216 (t-90) REVERT: D 705 PHE cc_start: 0.7117 (m-80) cc_final: 0.6898 (m-80) REVERT: D 725 GLU cc_start: 0.8479 (mp0) cc_final: 0.8196 (pm20) REVERT: D 737 ARG cc_start: 0.8847 (tmm160) cc_final: 0.8560 (tmm160) REVERT: D 785 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7839 (mt) REVERT: E 260 ARG cc_start: 0.8104 (ptp-110) cc_final: 0.7738 (ptt-90) REVERT: E 324 THR cc_start: 0.8984 (m) cc_final: 0.8236 (p) REVERT: E 326 ASP cc_start: 0.8373 (p0) cc_final: 0.8107 (p0) REVERT: E 327 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7246 (mt-10) REVERT: E 330 LYS cc_start: 0.9367 (ttpp) cc_final: 0.9045 (ttpp) REVERT: E 334 LYS cc_start: 0.8804 (mmmt) cc_final: 0.8468 (tppp) REVERT: E 507 LEU cc_start: 0.8848 (mt) cc_final: 0.8526 (mp) REVERT: E 509 ARG cc_start: 0.7915 (pmt-80) cc_final: 0.7540 (ppt90) REVERT: E 510 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7665 (tmm) REVERT: E 533 ARG cc_start: 0.7780 (mtm180) cc_final: 0.7447 (mtt-85) REVERT: E 568 ASN cc_start: 0.6113 (m-40) cc_final: 0.5800 (m110) REVERT: E 582 MET cc_start: 0.7990 (tpp) cc_final: 0.7690 (tpp) REVERT: E 593 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.6690 (tpm170) REVERT: E 627 ILE cc_start: 0.7878 (pt) cc_final: 0.7422 (pp) REVERT: E 646 ARG cc_start: 0.7685 (mtt90) cc_final: 0.6932 (mmp80) REVERT: E 659 ASN cc_start: 0.7813 (m-40) cc_final: 0.7449 (t0) REVERT: F 339 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7922 (tm-30) REVERT: F 379 MET cc_start: 0.7823 (mmm) cc_final: 0.7556 (mtt) REVERT: F 496 VAL cc_start: 0.8736 (OUTLIER) cc_final: 0.8489 (t) REVERT: F 711 ASN cc_start: 0.8150 (p0) cc_final: 0.7202 (p0) REVERT: G 42 ILE cc_start: 0.8780 (pp) cc_final: 0.8428 (pp) REVERT: G 70 ARG cc_start: 0.6556 (mmm-85) cc_final: 0.5753 (mtp-110) REVERT: G 71 ASP cc_start: 0.6176 (OUTLIER) cc_final: 0.5292 (m-30) REVERT: G 74 MET cc_start: 0.7612 (ttt) cc_final: 0.7040 (ttt) REVERT: G 93 MET cc_start: 0.6611 (ptm) cc_final: 0.6395 (mtm) REVERT: G 97 ARG cc_start: 0.4685 (ttt180) cc_final: 0.4031 (tmt-80) REVERT: G 202 THR cc_start: 0.6706 (t) cc_final: 0.6417 (p) REVERT: G 207 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6350 (mtt180) REVERT: H 35 LYS cc_start: 0.9062 (tptm) cc_final: 0.8480 (mttt) REVERT: H 144 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.7995 (mp10) REVERT: I 34 ASN cc_start: 0.8129 (m-40) cc_final: 0.7799 (m-40) REVERT: I 143 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8032 (tt) REVERT: J 125 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.7048 (mmm) REVERT: J 165 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8065 (mt-10) REVERT: K 42 ILE cc_start: 0.7794 (mt) cc_final: 0.7320 (mm) REVERT: K 94 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7599 (mm-40) REVERT: K 125 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6950 (mpp) REVERT: K 129 ASN cc_start: 0.8514 (m-40) cc_final: 0.8270 (m-40) REVERT: L 57 MET cc_start: 0.7274 (mtt) cc_final: 0.6785 (mtp) REVERT: L 97 ARG cc_start: 0.5569 (ttt180) cc_final: 0.5145 (mmm160) REVERT: L 165 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: L 201 ASP cc_start: 0.7631 (m-30) cc_final: 0.7250 (m-30) REVERT: M 105 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7292 (mm) REVERT: M 125 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6426 (ptp) REVERT: M 144 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8198 (mp10) REVERT: M 201 ASP cc_start: 0.6856 (m-30) cc_final: 0.6327 (m-30) REVERT: N 168 ASP cc_start: 0.8909 (m-30) cc_final: 0.8599 (m-30) REVERT: O 22 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8241 (tm-30) REVERT: O 55 ASP cc_start: 0.8516 (t0) cc_final: 0.8122 (t0) REVERT: P 58 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8638 (mttp) REVERT: Q 22 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8009 (tm-30) REVERT: Q 58 LYS cc_start: 0.8939 (mtpp) cc_final: 0.8703 (mtpm) REVERT: Q 164 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8482 (ttt180) REVERT: Q 192 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6246 (mpp80) REVERT: R 58 LYS cc_start: 0.9133 (mtmm) cc_final: 0.8750 (mtmm) REVERT: S 55 ASP cc_start: 0.8487 (t0) cc_final: 0.8253 (t0) REVERT: S 59 ASP cc_start: 0.8600 (m-30) cc_final: 0.8391 (m-30) REVERT: S 182 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: T 22 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8080 (tm-30) REVERT: T 58 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8662 (mtpt) REVERT: U 19 GLU cc_start: 0.8203 (pm20) cc_final: 0.7988 (pm20) outliers start: 129 outliers final: 65 residues processed: 783 average time/residue: 0.4689 time to fit residues: 451.3742 Evaluate side-chains 766 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 674 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 653 ARG Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 675 LYS Chi-restraints excluded: chain C residue 711 ASN Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 637 SER Chi-restraints excluded: chain D residue 655 VAL Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 510 MET Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 593 ARG Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 207 ARG Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 125 MET 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 L residue 44 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 165 GLU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 143 ILE Chi-restraints excluded: chain M residue 144 GLN Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain O residue 22 GLU Chi-restraints excluded: chain O residue 86 CYS Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 190 ILE Chi-restraints excluded: chain P residue 58 LYS Chi-restraints excluded: chain P residue 192 ARG Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 164 ARG Chi-restraints excluded: chain Q residue 192 ARG Chi-restraints excluded: chain R residue 98 SER Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain S residue 182 GLU Chi-restraints excluded: chain S residue 190 ILE Chi-restraints excluded: chain T residue 58 LYS Chi-restraints excluded: chain T residue 99 MET Chi-restraints excluded: chain T residue 190 ILE Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 9 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 216 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 524 optimal weight: 0.0670 chunk 232 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 720 HIS ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 HIS ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 483 GLN F 741 GLN G 34 ASN I 144 GLN L 107 GLN M 59 GLN O 42 ASN ** O 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.117604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.089008 restraints weight = 74740.204| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.97 r_work: 0.3286 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 47153 Z= 0.184 Angle : 0.649 12.897 63608 Z= 0.321 Chirality : 0.044 0.257 7268 Planarity : 0.004 0.069 8230 Dihedral : 9.691 127.382 6961 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.32 % Favored : 95.63 % Rotamer: Outliers : 2.28 % Allowed : 19.15 % Favored : 78.56 % 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: 0.22 (0.11), residues: 5812 helix: 1.07 (0.09), residues: 3175 sheet: -1.95 (0.20), residues: 522 loop : -0.58 (0.14), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 692 TYR 0.031 0.002 TYR M 90 PHE 0.026 0.001 PHE A 589 TRP 0.014 0.001 TRP B 807 HIS 0.010 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00422 (47121) covalent geometry : angle 0.64949 (63608) hydrogen bonds : bond 0.03428 ( 2189) hydrogen bonds : angle 4.56521 ( 6636) Misc. bond : bond 0.00182 ( 32) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11624 Ramachandran restraints generated. 5812 Oldfield, 0 Emsley, 5812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 686 time to evaluate : 0.961 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: A 247 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8654 (tt) REVERT: A 262 ARG cc_start: 0.6957 (mtt90) cc_final: 0.6484 (mtm110) REVERT: A 267 GLU cc_start: 0.8305 (tp30) cc_final: 0.7576 (tm-30) REVERT: A 271 LYS cc_start: 0.8868 (mttt) cc_final: 0.8594 (ttmm) REVERT: A 327 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7596 (mt-10) REVERT: A 329 ARG cc_start: 0.8007 (mtm180) cc_final: 0.7691 (mpt180) REVERT: A 330 LYS cc_start: 0.8667 (mtpm) cc_final: 0.8442 (mtmt) REVERT: A 509 ARG cc_start: 0.8024 (mtm110) cc_final: 0.7715 (ptp90) REVERT: A 543 LYS cc_start: 0.8469 (mtmt) cc_final: 0.8268 (mtmm) REVERT: A 646 ARG cc_start: 0.8355 (mtp-110) cc_final: 0.8110 (mtm110) REVERT: A 653 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7734 (ttm170) REVERT: A 692 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8208 (ttp-110) REVERT: A 708 GLU cc_start: 0.8303 (tt0) cc_final: 0.7893 (tp30) REVERT: A 734 MET cc_start: 0.9231 (mtt) cc_final: 0.8827 (mtt) REVERT: B 371 ARG cc_start: 0.8934 (mpp80) cc_final: 0.8620 (mtm110) REVERT: B 575 ASP cc_start: 0.8385 (m-30) cc_final: 0.8124 (m-30) REVERT: B 672 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7507 (p0) REVERT: B 695 GLN cc_start: 0.8390 (mm110) cc_final: 0.7816 (mp10) REVERT: B 696 LYS cc_start: 0.8742 (tppt) cc_final: 0.8457 (tptm) REVERT: C 195 LYS cc_start: 0.8935 (mtmm) cc_final: 0.8697 (mtpp) REVERT: C 503 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7754 (mp0) REVERT: C 523 ASP cc_start: 0.8630 (m-30) cc_final: 0.8304 (p0) REVERT: C 606 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7611 (mp0) REVERT: D 176 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.7791 (ptp90) REVERT: D 725 GLU cc_start: 0.8538 (mp0) cc_final: 0.8244 (pm20) REVERT: D 737 ARG cc_start: 0.8841 (tmm160) cc_final: 0.8584 (tmm160) REVERT: E 260 ARG cc_start: 0.8111 (ptp-110) cc_final: 0.7859 (ptt-90) REVERT: E 324 THR cc_start: 0.9052 (m) cc_final: 0.8328 (p) REVERT: E 326 ASP cc_start: 0.8352 (p0) cc_final: 0.8053 (p0) REVERT: E 327 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7288 (mt-10) REVERT: E 330 LYS cc_start: 0.9336 (ttpp) cc_final: 0.9041 (ttpp) REVERT: E 334 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8480 (tppp) REVERT: E 507 LEU cc_start: 0.8857 (mt) cc_final: 0.8429 (mp) REVERT: E 510 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7658 (tmm) REVERT: E 533 ARG cc_start: 0.7788 (mtm180) cc_final: 0.7406 (mtt-85) REVERT: E 593 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.6815 (tpm170) REVERT: E 646 ARG cc_start: 0.7688 (mtt90) cc_final: 0.6936 (mmp80) REVERT: F 339 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7905 (tm-30) REVERT: F 379 MET cc_start: 0.7958 (mmm) cc_final: 0.7622 (mtt) REVERT: F 496 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8529 (t) REVERT: F 510 MET cc_start: 0.5888 (ptp) cc_final: 0.4434 (ptp) REVERT: F 711 ASN cc_start: 0.8162 (p0) cc_final: 0.7589 (p0) REVERT: G 42 ILE cc_start: 0.8825 (pp) cc_final: 0.8409 (pp) REVERT: G 70 ARG cc_start: 0.6524 (mmm-85) cc_final: 0.5683 (mtp-110) REVERT: G 71 ASP cc_start: 0.6227 (OUTLIER) cc_final: 0.5346 (m-30) REVERT: G 74 MET cc_start: 0.7668 (ttt) cc_final: 0.7199 (mtp) REVERT: G 93 MET cc_start: 0.6662 (ptm) cc_final: 0.6426 (mtm) REVERT: G 97 ARG cc_start: 0.4750 (ttt180) cc_final: 0.4081 (tmt-80) REVERT: G 202 THR cc_start: 0.6779 (t) cc_final: 0.6472 (p) REVERT: G 207 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6365 (mtt180) REVERT: H 35 LYS cc_start: 0.9056 (tptm) cc_final: 0.8585 (mttt) REVERT: H 144 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8101 (mp10) REVERT: H 181 LYS cc_start: 0.9035 (mtpp) cc_final: 0.8737 (mtmp) REVERT: J 97 ARG cc_start: 0.6608 (ttt180) cc_final: 0.6327 (mtt90) REVERT: J 125 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7147 (mmm) REVERT: J 127 LEU cc_start: 0.8378 (mm) cc_final: 0.8153 (mt) REVERT: J 165 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8080 (mt-10) REVERT: K 42 ILE cc_start: 0.7852 (mt) cc_final: 0.7394 (mm) REVERT: K 97 ARG cc_start: 0.6787 (mtm180) cc_final: 0.5395 (tpt170) REVERT: K 125 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.6928 (mpp) REVERT: K 129 ASN cc_start: 0.8484 (m-40) cc_final: 0.8234 (m-40) REVERT: K 202 THR cc_start: 0.7933 (t) cc_final: 0.7725 (t) REVERT: L 97 ARG cc_start: 0.5552 (ttt180) cc_final: 0.5150 (mmm160) REVERT: L 165 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: L 201 ASP cc_start: 0.7680 (m-30) cc_final: 0.7252 (m-30) REVERT: M 105 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7293 (mm) REVERT: M 144 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8203 (mp10) REVERT: N 168 ASP cc_start: 0.8923 (m-30) cc_final: 0.8623 (m-30) REVERT: N 192 ARG cc_start: 0.6819 (mtm180) cc_final: 0.6520 (mtp180) REVERT: O 22 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8311 (tm-30) REVERT: O 55 ASP cc_start: 0.8487 (t0) cc_final: 0.8103 (t0) REVERT: P 58 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8661 (mttp) REVERT: Q 22 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8074 (tm-30) REVERT: Q 58 LYS cc_start: 0.9001 (mtpp) cc_final: 0.8760 (mtpm) REVERT: Q 192 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.6236 (mpp80) REVERT: R 58 LYS cc_start: 0.9151 (mtmm) cc_final: 0.8761 (mtmm) REVERT: S 59 ASP cc_start: 0.8667 (m-30) cc_final: 0.8217 (m-30) REVERT: S 111 LYS cc_start: 0.9137 (mttt) cc_final: 0.8828 (mttt) REVERT: T 58 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8700 (mtpt) outliers start: 110 outliers final: 64 residues processed: 747 average time/residue: 0.4745 time to fit residues: 434.8585 Evaluate side-chains 761 residues out of total 4819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 677 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 653 ARG Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 762 ARG Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 675 LYS Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 637 SER Chi-restraints excluded: chain D residue 655 VAL Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 510 MET Chi-restraints excluded: chain E residue 593 ARG Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 207 ARG Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 125 MET 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 L residue 44 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 165 GLU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 143 ILE Chi-restraints excluded: chain M residue 144 GLN Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain O residue 22 GLU Chi-restraints excluded: chain O residue 86 CYS Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 190 ILE Chi-restraints excluded: chain P residue 58 LYS Chi-restraints excluded: chain P residue 98 SER Chi-restraints excluded: chain P residue 192 ARG Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 190 ILE Chi-restraints excluded: chain Q residue 192 ARG Chi-restraints excluded: chain R residue 98 SER Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain S residue 190 ILE Chi-restraints excluded: chain T residue 58 LYS Chi-restraints excluded: chain T residue 99 MET Chi-restraints excluded: chain T residue 190 ILE Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 9 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 559 optimal weight: 0.9980 chunk 508 optimal weight: 1.9990 chunk 571 optimal weight: 2.9990 chunk 369 optimal weight: 0.7980 chunk 244 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 396 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 330 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 ASN ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN ** C 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 720 HIS ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 HIS ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 483 GLN F 741 GLN G 31 ASN G 34 ASN I 144 GLN L 107 GLN ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 59 GLN ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 ASN ** O 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.117749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.088551 restraints weight = 75015.639| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.90 r_work: 0.3285 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 47153 Z= 0.163 Angle : 0.638 11.826 63608 Z= 0.317 Chirality : 0.044 0.256 7268 Planarity : 0.004 0.060 8230 Dihedral : 9.596 127.606 6961 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.73 % Rotamer: Outliers : 2.18 % Allowed : 19.30 % Favored : 78.52 % 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: 0.26 (0.11), residues: 5812 helix: 1.10 (0.09), residues: 3179 sheet: -1.95 (0.20), residues: 522 loop : -0.57 (0.14), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 692 TYR 0.027 0.001 TYR M 90 PHE 0.031 0.001 PHE E 709 TRP 0.014 0.001 TRP B 807 HIS 0.010 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00373 (47121) covalent geometry : angle 0.63836 (63608) hydrogen bonds : bond 0.03309 ( 2189) hydrogen bonds : angle 4.53922 ( 6636) Misc. bond : bond 0.00170 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19694.37 seconds wall clock time: 333 minutes 12.68 seconds (19992.68 seconds total)