Starting phenix.real_space_refine (version: dev) on Mon Dec 19 03:15:45 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yba_10768/12_2022/6yba_10768.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yba_10768/12_2022/6yba_10768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yba_10768/12_2022/6yba_10768.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yba_10768/12_2022/6yba_10768.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yba_10768/12_2022/6yba_10768.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yba_10768/12_2022/6yba_10768.pdb" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.027 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 92": "NH1" <-> "NH2" Residue "A TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 841": "NH1" <-> "NH2" Residue "B TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B ARG 763": "NH1" <-> "NH2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 769": "NH1" <-> "NH2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 421": "NH1" <-> "NH2" Residue "D PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 356": "NH1" <-> "NH2" Residue "F ARG 421": "NH1" <-> "NH2" Residue "F ARG 480": "NH1" <-> "NH2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G ARG 92": "NH1" <-> "NH2" Residue "G ARG 421": "NH1" <-> "NH2" Residue "G ARG 480": "NH1" <-> "NH2" Residue "G ARG 517": "NH1" <-> "NH2" Residue "G ARG 575": "NH1" <-> "NH2" Residue "H TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 73": "NH1" <-> "NH2" Residue "H ARG 845": "NH1" <-> "NH2" Residue "I ARG 46": "NH1" <-> "NH2" Residue "I ARG 92": "NH1" <-> "NH2" Residue "I ARG 421": "NH1" <-> "NH2" Residue "I ARG 519": "NH1" <-> "NH2" Residue "I ARG 527": "NH1" <-> "NH2" Residue "I PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 46": "NH1" <-> "NH2" Residue "J ARG 92": "NH1" <-> "NH2" Residue "J ARG 421": "NH1" <-> "NH2" Residue "K TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 46": "NH1" <-> "NH2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "K ARG 144": "NH1" <-> "NH2" Residue "K ARG 519": "NH1" <-> "NH2" Residue "L ARG 67": "NH1" <-> "NH2" Residue "L ARG 356": "NH1" <-> "NH2" Residue "L ARG 519": "NH1" <-> "NH2" Residue "L ARG 559": "NH1" <-> "NH2" Residue "M ARG 116": "NH1" <-> "NH2" Residue "M ARG 126": "NH1" <-> "NH2" Residue "M ARG 144": "NH1" <-> "NH2" Residue "M ARG 158": "NH1" <-> "NH2" Residue "N PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 223": "NH1" <-> "NH2" Residue "N ARG 229": "NH1" <-> "NH2" Residue "N ARG 241": "NH1" <-> "NH2" Residue "N ARG 258": "NH1" <-> "NH2" Residue "O ARG 30": "NH1" <-> "NH2" Residue "O ARG 43": "NH1" <-> "NH2" Residue "O ARG 48": "NH1" <-> "NH2" Residue "O ARG 51": "NH1" <-> "NH2" Residue "O ARG 66": "NH1" <-> "NH2" Residue "O ARG 93": "NH1" <-> "NH2" Residue "O ARG 171": "NH1" <-> "NH2" Residue "O ARG 185": "NH1" <-> "NH2" Residue "P ARG 30": "NH1" <-> "NH2" Residue "P ARG 43": "NH1" <-> "NH2" Residue "P ARG 48": "NH1" <-> "NH2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P ARG 66": "NH1" <-> "NH2" Residue "P ARG 93": "NH1" <-> "NH2" Residue "P ARG 171": "NH1" <-> "NH2" Residue "P ARG 185": "NH1" <-> "NH2" Residue "Q ARG 24": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 43": "NH1" <-> "NH2" Residue "R ARG 24": "NH1" <-> "NH2" Residue "R ARG 32": "NH1" <-> "NH2" Residue "R ARG 43": "NH1" <-> "NH2" Residue "S ARG 24": "NH1" <-> "NH2" Residue "S ARG 32": "NH1" <-> "NH2" Residue "S ARG 43": "NH1" <-> "NH2" Residue "T ARG 24": "NH1" <-> "NH2" Residue "T ARG 32": "NH1" <-> "NH2" Residue "T ARG 43": "NH1" <-> "NH2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 98037 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 7244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 912, 7244 Classifications: {'peptide': 912} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 851} Chain breaks: 1 Chain: "B" Number of atoms: 7250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 913, 7250 Classifications: {'peptide': 913} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 852} Chain breaks: 1 Chain: "C" Number of atoms: 7254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7254 Classifications: {'peptide': 914} Link IDs: {'PCIS': 3, 'PTRANS': 58, 'TRANS': 852} Chain breaks: 1 Chain: "D" Number of atoms: 7214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7214 Classifications: {'peptide': 908} Link IDs: {'PCIS': 4, 'PTRANS': 56, 'TRANS': 847} Chain breaks: 1 Chain: "E" Number of atoms: 7273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 917, 7273 Classifications: {'peptide': 917} Link IDs: {'PCIS': 3, 'PTRANS': 58, 'TRANS': 855} Chain breaks: 1 Chain: "F" Number of atoms: 7229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 7229 Classifications: {'peptide': 910} Link IDs: {'PCIS': 4, 'PTRANS': 56, 'TRANS': 849} Chain breaks: 1 Chain: "G" Number of atoms: 7229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 7229 Classifications: {'peptide': 910} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 849} Chain breaks: 1 Chain: "H" Number of atoms: 7262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7262 Classifications: {'peptide': 915} Link IDs: {'PCIS': 4, 'PTRANS': 57, 'TRANS': 853} Chain breaks: 1 Chain: "I" Number of atoms: 7214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7214 Classifications: {'peptide': 908} Link IDs: {'PCIS': 4, 'PTRANS': 56, 'TRANS': 847} Chain breaks: 1 Chain: "J" Number of atoms: 7254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7254 Classifications: {'peptide': 914} Link IDs: {'PCIS': 3, 'PTRANS': 58, 'TRANS': 852} Chain breaks: 1 Chain: "K" Number of atoms: 7242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 912, 7242 Classifications: {'peptide': 912} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 851} Chain breaks: 1 Chain: "L" Number of atoms: 7238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 911, 7238 Classifications: {'peptide': 911} Link IDs: {'PCIS': 3, 'PTRANS': 58, 'TRANS': 849} Chain breaks: 2 Chain: "M" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3609 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 421} Chain breaks: 1 Chain: "N" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2315 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 14, 'TRANS': 283} Chain: "O" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1379 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 161} Chain breaks: 1 Chain: "P" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1379 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 161} Chain breaks: 1 Chain: "Q" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 365 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain: "R" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 365 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain: "S" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 365 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain: "T" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 365 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain: "U" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 2, 'TRANS': 26} Chain: "V" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 2, 'TRANS': 26} Chain: "W" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 37 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "Y" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 2, 'TRANS': 26} Chain: "u" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 2, 'TRANS': 26} Chain: "w" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 83 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Time building chain proxies: 40.35, per 1000 atoms: 0.41 Number of scatterers: 98037 At special positions: 0 Unit cell: (311.44, 208.08, 175.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 469 16.00 O 18672 8.00 N 16658 7.00 C 62238 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 29.30 Conformation dependent library (CDL) restraints added in 11.6 seconds 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23146 Finding SS restraints... Secondary structure from input PDB file: 230 helices and 186 sheets defined 13.2% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... Processing helix chain 'A' and resid 7 through 12 removed outlier: 3.588A pdb=" N SER A 11 " --> pdb=" O MET A 7 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A 12 " --> pdb=" O PRO A 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 7 through 12' Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.862A pdb=" N LEU A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.806A pdb=" N ALA A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 310 Processing helix chain 'A' and resid 341 through 347 removed outlier: 4.122A pdb=" N GLN A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 450 removed outlier: 3.539A pdb=" N TRP A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A 449 " --> pdb=" O PHE A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 480 removed outlier: 3.523A pdb=" N ARG A 480 " --> pdb=" O TYR A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 516 through 524 removed outlier: 3.734A pdb=" N SER A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 522 " --> pdb=" O TYR A 518 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 523 " --> pdb=" O ARG A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 543 removed outlier: 3.533A pdb=" N LYS A 543 " --> pdb=" O PHE A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 565 removed outlier: 3.766A pdb=" N ILE A 565 " --> pdb=" O ASP A 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 561 through 565' Processing helix chain 'A' and resid 596 through 607 removed outlier: 3.581A pdb=" N SER A 601 " --> pdb=" O HIS A 597 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR A 602 " --> pdb=" O ASN A 598 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 603 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 683 removed outlier: 4.214A pdb=" N GLY A 683 " --> pdb=" O PRO A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 701 No H-bonds generated for 'chain 'A' and resid 699 through 701' Processing helix chain 'A' and resid 735 through 740 removed outlier: 3.570A pdb=" N LEU A 740 " --> pdb=" O LYS A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 748 removed outlier: 3.546A pdb=" N HIS A 746 " --> pdb=" O GLN A 742 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 747 " --> pdb=" O MET A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 828 removed outlier: 4.198A pdb=" N THR A 827 " --> pdb=" O ILE A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 864 removed outlier: 3.598A pdb=" N ASN A 864 " --> pdb=" O ASP A 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 25 through 33 removed outlier: 3.539A pdb=" N GLN B 30 " --> pdb=" O PRO B 26 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 341 through 346 Processing helix chain 'B' and resid 349 through 354 Processing helix chain 'B' and resid 436 through 448 removed outlier: 4.146A pdb=" N ASN B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 480 removed outlier: 3.674A pdb=" N MET B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 480 " --> pdb=" O TYR B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 524 removed outlier: 3.556A pdb=" N SER B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET B 521 " --> pdb=" O ARG B 517 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 522 " --> pdb=" O TYR B 518 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 523 " --> pdb=" O ARG B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 removed outlier: 4.332A pdb=" N ASN B 544 " --> pdb=" O PHE B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 Processing helix chain 'B' and resid 699 through 701 No H-bonds generated for 'chain 'B' and resid 699 through 701' Processing helix chain 'B' and resid 735 through 748 removed outlier: 3.586A pdb=" N LEU B 740 " --> pdb=" O LYS B 736 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET B 743 " --> pdb=" O PHE B 739 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU B 744 " --> pdb=" O LEU B 740 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER B 745 " --> pdb=" O ILE B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 795 removed outlier: 3.739A pdb=" N GLN B 795 " --> pdb=" O LEU B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 866 removed outlier: 4.075A pdb=" N ASN B 864 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 866 " --> pdb=" O GLN B 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 13 removed outlier: 3.512A pdb=" N MET C 13 " --> pdb=" O GLN C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.664A pdb=" N PHE C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.634A pdb=" N LYS C 44 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE C 45 " --> pdb=" O GLY C 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 41 through 45' Processing helix chain 'C' and resid 287 through 292 Processing helix chain 'C' and resid 307 through 310 Processing helix chain 'C' and resid 341 through 354 removed outlier: 3.672A pdb=" N SER C 345 " --> pdb=" O ASN C 341 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN C 347 " --> pdb=" O GLU C 343 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ASP C 351 " --> pdb=" O GLN C 347 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 376 removed outlier: 3.888A pdb=" N ARG C 375 " --> pdb=" O ASP C 371 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 376 " --> pdb=" O PRO C 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 371 through 376' Processing helix chain 'C' and resid 440 through 449 removed outlier: 3.570A pdb=" N PHE C 445 " --> pdb=" O LEU C 441 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN C 449 " --> pdb=" O PHE C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 480 removed outlier: 3.510A pdb=" N GLY C 479 " --> pdb=" O ALA C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 487 removed outlier: 3.610A pdb=" N ALA C 486 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 505 removed outlier: 4.119A pdb=" N ASN C 504 " --> pdb=" O PRO C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 608 removed outlier: 4.356A pdb=" N MET C 606 " --> pdb=" O THR C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 661 No H-bonds generated for 'chain 'C' and resid 659 through 661' Processing helix chain 'C' and resid 735 through 748 removed outlier: 4.407A pdb=" N ILE C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER C 745 " --> pdb=" O ILE C 741 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS C 746 " --> pdb=" O GLN C 742 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR C 747 " --> pdb=" O MET C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 795 removed outlier: 3.903A pdb=" N GLN C 795 " --> pdb=" O LEU C 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 13 removed outlier: 3.535A pdb=" N MET D 13 " --> pdb=" O GLN D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 removed outlier: 3.721A pdb=" N LEU D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 35 removed outlier: 3.832A pdb=" N ALA D 34 " --> pdb=" O GLN D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 310 Processing helix chain 'D' and resid 342 through 347 removed outlier: 3.502A pdb=" N GLN D 347 " --> pdb=" O GLU D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 450 removed outlier: 3.790A pdb=" N ARG D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 454 removed outlier: 3.700A pdb=" N LEU D 454 " --> pdb=" O ALA D 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 451 through 454' Processing helix chain 'D' and resid 473 through 480 removed outlier: 3.743A pdb=" N MET D 477 " --> pdb=" O THR D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 503 Processing helix chain 'D' and resid 515 through 522 removed outlier: 4.003A pdb=" N MET D 521 " --> pdb=" O ARG D 517 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU D 522 " --> pdb=" O TYR D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 565 Processing helix chain 'D' and resid 598 through 607 Processing helix chain 'D' and resid 678 through 682 Processing helix chain 'D' and resid 728 through 732 removed outlier: 3.777A pdb=" N GLN D 731 " --> pdb=" O ASN D 728 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS D 732 " --> pdb=" O VAL D 729 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 728 through 732' Processing helix chain 'D' and resid 735 through 748 removed outlier: 4.168A pdb=" N ILE D 741 " --> pdb=" O ASP D 737 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU D 744 " --> pdb=" O LEU D 740 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER D 745 " --> pdb=" O ILE D 741 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS D 746 " --> pdb=" O GLN D 742 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR D 747 " --> pdb=" O MET D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 769 No H-bonds generated for 'chain 'D' and resid 767 through 769' Processing helix chain 'D' and resid 798 through 802 removed outlier: 3.866A pdb=" N PHE D 801 " --> pdb=" O ASN D 798 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL D 802 " --> pdb=" O SER D 799 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 798 through 802' Processing helix chain 'E' and resid 6 through 12 Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.681A pdb=" N VAL E 29 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN E 30 " --> pdb=" O PRO E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 292 removed outlier: 4.228A pdb=" N THR E 292 " --> pdb=" O ASP E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 310 Processing helix chain 'E' and resid 436 through 448 removed outlier: 3.874A pdb=" N PHE E 445 " --> pdb=" O LEU E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 478 Processing helix chain 'E' and resid 603 through 608 Processing helix chain 'E' and resid 678 through 683 Processing helix chain 'E' and resid 687 through 689 No H-bonds generated for 'chain 'E' and resid 687 through 689' Processing helix chain 'E' and resid 735 through 740 removed outlier: 3.718A pdb=" N LEU E 740 " --> pdb=" O LYS E 736 " (cutoff:3.500A) Processing helix chain 'E' and resid 742 through 748 Processing helix chain 'E' and resid 767 through 769 No H-bonds generated for 'chain 'E' and resid 767 through 769' Processing helix chain 'E' and resid 860 through 863 removed outlier: 3.878A pdb=" N GLN E 863 " --> pdb=" O ASP E 860 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 860 through 863' Processing helix chain 'E' and resid 864 through 869 removed outlier: 3.802A pdb=" N ASN E 869 " --> pdb=" O MET E 865 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 14 removed outlier: 3.523A pdb=" N SER F 11 " --> pdb=" O MET F 7 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR F 12 " --> pdb=" O PRO F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 35 removed outlier: 3.560A pdb=" N ARG F 33 " --> pdb=" O VAL F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 310 Processing helix chain 'F' and resid 438 through 441 Processing helix chain 'F' and resid 442 through 448 removed outlier: 3.764A pdb=" N SER F 448 " --> pdb=" O SER F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 480 Processing helix chain 'F' and resid 484 through 487 Processing helix chain 'F' and resid 513 through 520 removed outlier: 3.989A pdb=" N TYR F 518 " --> pdb=" O ALA F 514 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER F 520 " --> pdb=" O LEU F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 543 removed outlier: 3.507A pdb=" N LYS F 543 " --> pdb=" O PHE F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 565 Processing helix chain 'F' and resid 596 through 605 removed outlier: 4.550A pdb=" N THR F 602 " --> pdb=" O ASN F 598 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA F 605 " --> pdb=" O SER F 601 " (cutoff:3.500A) Processing helix chain 'F' and resid 606 through 608 No H-bonds generated for 'chain 'F' and resid 606 through 608' Processing helix chain 'F' and resid 678 through 683 removed outlier: 3.718A pdb=" N GLY F 683 " --> pdb=" O PRO F 679 " (cutoff:3.500A) Processing helix chain 'F' and resid 697 through 701 removed outlier: 3.679A pdb=" N SER F 701 " --> pdb=" O PHE F 698 " (cutoff:3.500A) Processing helix chain 'F' and resid 736 through 746 removed outlier: 3.731A pdb=" N LEU F 740 " --> pdb=" O LYS F 736 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE F 741 " --> pdb=" O ASP F 737 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU F 744 " --> pdb=" O LEU F 740 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS F 746 " --> pdb=" O GLN F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 766 through 770 removed outlier: 4.068A pdb=" N ASN F 770 " --> pdb=" O SER F 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 766 through 770' Processing helix chain 'F' and resid 791 through 795 removed outlier: 3.702A pdb=" N GLN F 795 " --> pdb=" O LEU F 792 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 14 removed outlier: 4.059A pdb=" N TYR G 12 " --> pdb=" O PRO G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 33 removed outlier: 3.815A pdb=" N GLN G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 293 removed outlier: 3.749A pdb=" N LEU G 291 " --> pdb=" O ALA G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 310 Processing helix chain 'G' and resid 342 through 346 removed outlier: 4.003A pdb=" N TYR G 346 " --> pdb=" O GLU G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 436 through 450 removed outlier: 4.086A pdb=" N SER G 444 " --> pdb=" O ASN G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 473 through 480 Processing helix chain 'G' and resid 513 through 521 removed outlier: 3.639A pdb=" N TYR G 518 " --> pdb=" O ALA G 514 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG G 519 " --> pdb=" O GLY G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 596 through 606 removed outlier: 3.813A pdb=" N THR G 602 " --> pdb=" O ASN G 598 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA G 605 " --> pdb=" O SER G 601 " (cutoff:3.500A) Processing helix chain 'G' and resid 697 through 701 removed outlier: 4.171A pdb=" N SER G 700 " --> pdb=" O MET G 697 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER G 701 " --> pdb=" O PHE G 698 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 697 through 701' Processing helix chain 'G' and resid 735 through 746 removed outlier: 3.589A pdb=" N LEU G 740 " --> pdb=" O LYS G 736 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU G 744 " --> pdb=" O LEU G 740 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS G 746 " --> pdb=" O GLN G 742 " (cutoff:3.500A) Processing helix chain 'G' and resid 767 through 769 No H-bonds generated for 'chain 'G' and resid 767 through 769' Processing helix chain 'G' and resid 791 through 795 Processing helix chain 'G' and resid 864 through 868 removed outlier: 3.778A pdb=" N ALA G 868 " --> pdb=" O MET G 865 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 14 removed outlier: 3.782A pdb=" N TYR H 12 " --> pdb=" O PRO H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 24 removed outlier: 3.624A pdb=" N TYR H 23 " --> pdb=" O ASP H 19 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 19 through 24' Processing helix chain 'H' and resid 25 through 35 removed outlier: 3.735A pdb=" N VAL H 29 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN H 30 " --> pdb=" O PRO H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 99 No H-bonds generated for 'chain 'H' and resid 97 through 99' Processing helix chain 'H' and resid 307 through 310 Processing helix chain 'H' and resid 348 through 353 removed outlier: 3.660A pdb=" N ALA H 352 " --> pdb=" O LEU H 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 436 through 448 removed outlier: 3.686A pdb=" N TRP H 442 " --> pdb=" O ALA H 438 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER H 444 " --> pdb=" O ASN H 440 " (cutoff:3.500A) Processing helix chain 'H' and resid 450 through 454 removed outlier: 4.056A pdb=" N LEU H 454 " --> pdb=" O ALA H 451 " (cutoff:3.500A) Processing helix chain 'H' and resid 473 through 480 removed outlier: 4.047A pdb=" N MET H 477 " --> pdb=" O THR H 473 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY H 479 " --> pdb=" O ALA H 475 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG H 480 " --> pdb=" O TYR H 476 " (cutoff:3.500A) Processing helix chain 'H' and resid 499 through 504 removed outlier: 4.492A pdb=" N ASN H 504 " --> pdb=" O ASP H 500 " (cutoff:3.500A) Processing helix chain 'H' and resid 515 through 520 Processing helix chain 'H' and resid 539 through 543 Processing helix chain 'H' and resid 599 through 606 Processing helix chain 'H' and resid 659 through 661 No H-bonds generated for 'chain 'H' and resid 659 through 661' Processing helix chain 'H' and resid 678 through 683 Processing helix chain 'H' and resid 699 through 701 No H-bonds generated for 'chain 'H' and resid 699 through 701' Processing helix chain 'H' and resid 736 through 748 removed outlier: 3.589A pdb=" N ILE H 741 " --> pdb=" O ASP H 737 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER H 745 " --> pdb=" O ILE H 741 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS H 746 " --> pdb=" O GLN H 742 " (cutoff:3.500A) Processing helix chain 'H' and resid 849 through 853 removed outlier: 3.856A pdb=" N PHE H 852 " --> pdb=" O SER H 849 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N MET H 853 " --> pdb=" O SER H 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 849 through 853' Processing helix chain 'I' and resid 27 through 35 removed outlier: 3.534A pdb=" N ARG I 33 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 306 through 310 removed outlier: 3.728A pdb=" N PHE I 309 " --> pdb=" O ARG I 306 " (cutoff:3.500A) Processing helix chain 'I' and resid 348 through 352 removed outlier: 3.871A pdb=" N ASP I 351 " --> pdb=" O LEU I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 442 through 448 Processing helix chain 'I' and resid 473 through 480 removed outlier: 3.728A pdb=" N MET I 477 " --> pdb=" O THR I 473 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY I 479 " --> pdb=" O ALA I 475 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG I 480 " --> pdb=" O TYR I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 539 through 543 Processing helix chain 'I' and resid 573 through 578 Processing helix chain 'I' and resid 596 through 607 removed outlier: 3.746A pdb=" N SER I 601 " --> pdb=" O HIS I 597 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR I 602 " --> pdb=" O ASN I 598 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU I 603 " --> pdb=" O THR I 599 " (cutoff:3.500A) Processing helix chain 'I' and resid 659 through 661 No H-bonds generated for 'chain 'I' and resid 659 through 661' Processing helix chain 'I' and resid 678 through 683 Processing helix chain 'I' and resid 686 through 689 removed outlier: 4.416A pdb=" N HIS I 689 " --> pdb=" O TYR I 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 686 through 689' Processing helix chain 'I' and resid 735 through 740 Processing helix chain 'I' and resid 742 through 748 removed outlier: 3.570A pdb=" N HIS I 746 " --> pdb=" O GLN I 742 " (cutoff:3.500A) Processing helix chain 'I' and resid 767 through 771 Processing helix chain 'J' and resid 7 through 12 removed outlier: 3.677A pdb=" N SER J 11 " --> pdb=" O MET J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 24 removed outlier: 4.088A pdb=" N LEU J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 33 removed outlier: 3.661A pdb=" N VAL J 29 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE J 31 " --> pdb=" O GLY J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 292 removed outlier: 3.602A pdb=" N LEU J 291 " --> pdb=" O ALA J 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR J 292 " --> pdb=" O ASP J 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 288 through 292' Processing helix chain 'J' and resid 306 through 310 Processing helix chain 'J' and resid 341 through 347 removed outlier: 4.086A pdb=" N GLN J 347 " --> pdb=" O GLU J 343 " (cutoff:3.500A) Processing helix chain 'J' and resid 348 through 354 Processing helix chain 'J' and resid 436 through 450 removed outlier: 3.930A pdb=" N ARG J 443 " --> pdb=" O ALA J 439 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 480 removed outlier: 3.583A pdb=" N MET J 477 " --> pdb=" O THR J 473 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY J 479 " --> pdb=" O ALA J 475 " (cutoff:3.500A) Processing helix chain 'J' and resid 499 through 504 removed outlier: 4.329A pdb=" N ASN J 504 " --> pdb=" O ASP J 500 " (cutoff:3.500A) Processing helix chain 'J' and resid 516 through 522 removed outlier: 3.793A pdb=" N SER J 520 " --> pdb=" O LEU J 516 " (cutoff:3.500A) Processing helix chain 'J' and resid 539 through 543 removed outlier: 3.616A pdb=" N LYS J 543 " --> pdb=" O PHE J 540 " (cutoff:3.500A) Processing helix chain 'J' and resid 561 through 566 Processing helix chain 'J' and resid 573 through 578 removed outlier: 3.594A pdb=" N ASP J 577 " --> pdb=" O ASP J 573 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY J 578 " --> pdb=" O LEU J 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 573 through 578' Processing helix chain 'J' and resid 597 through 605 removed outlier: 3.622A pdb=" N THR J 602 " --> pdb=" O ASN J 598 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU J 603 " --> pdb=" O THR J 599 " (cutoff:3.500A) Processing helix chain 'J' and resid 686 through 689 removed outlier: 4.274A pdb=" N HIS J 689 " --> pdb=" O TYR J 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 686 through 689' Processing helix chain 'J' and resid 735 through 748 removed outlier: 3.527A pdb=" N MET J 743 " --> pdb=" O PHE J 739 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU J 744 " --> pdb=" O LEU J 740 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS J 746 " --> pdb=" O GLN J 742 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 35 removed outlier: 3.622A pdb=" N VAL K 29 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN K 30 " --> pdb=" O PRO K 26 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA K 34 " --> pdb=" O GLN K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 310 Processing helix chain 'K' and resid 342 through 348 removed outlier: 3.925A pdb=" N GLN K 347 " --> pdb=" O GLU K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 349 through 354 removed outlier: 3.972A pdb=" N GLY K 354 " --> pdb=" O LEU K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 371 through 376 Processing helix chain 'K' and resid 436 through 449 Processing helix chain 'K' and resid 473 through 480 Processing helix chain 'K' and resid 499 through 504 removed outlier: 3.726A pdb=" N ASP K 503 " --> pdb=" O ASP K 500 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN K 504 " --> pdb=" O PRO K 501 " (cutoff:3.500A) Processing helix chain 'K' and resid 513 through 520 removed outlier: 3.833A pdb=" N ARG K 517 " --> pdb=" O ASN K 513 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR K 518 " --> pdb=" O ALA K 514 " (cutoff:3.500A) Processing helix chain 'K' and resid 539 through 543 removed outlier: 3.507A pdb=" N ILE K 542 " --> pdb=" O PHE K 539 " (cutoff:3.500A) Processing helix chain 'K' and resid 561 through 565 removed outlier: 3.532A pdb=" N ILE K 565 " --> pdb=" O ASP K 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 561 through 565' Processing helix chain 'K' and resid 596 through 605 removed outlier: 3.639A pdb=" N SER K 601 " --> pdb=" O HIS K 597 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR K 602 " --> pdb=" O ASN K 598 " (cutoff:3.500A) Processing helix chain 'K' and resid 657 through 661 removed outlier: 3.539A pdb=" N THR K 661 " --> pdb=" O THR K 658 " (cutoff:3.500A) Processing helix chain 'K' and resid 678 through 683 Processing helix chain 'K' and resid 699 through 701 No H-bonds generated for 'chain 'K' and resid 699 through 701' Processing helix chain 'K' and resid 736 through 740 Processing helix chain 'K' and resid 742 through 748 Processing helix chain 'K' and resid 791 through 795 removed outlier: 4.117A pdb=" N GLN K 795 " --> pdb=" O LEU K 792 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 12 removed outlier: 3.641A pdb=" N TYR L 12 " --> pdb=" O PRO L 8 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 35 removed outlier: 3.555A pdb=" N ALA L 34 " --> pdb=" O GLN L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 310 Processing helix chain 'L' and resid 349 through 354 removed outlier: 3.639A pdb=" N LEU L 353 " --> pdb=" O MET L 349 " (cutoff:3.500A) Processing helix chain 'L' and resid 440 through 448 Processing helix chain 'L' and resid 450 through 454 removed outlier: 3.825A pdb=" N LEU L 454 " --> pdb=" O ALA L 451 " (cutoff:3.500A) Processing helix chain 'L' and resid 473 through 478 removed outlier: 3.665A pdb=" N MET L 477 " --> pdb=" O THR L 473 " (cutoff:3.500A) Processing helix chain 'L' and resid 499 through 503 removed outlier: 3.553A pdb=" N ASP L 503 " --> pdb=" O ASP L 500 " (cutoff:3.500A) Processing helix chain 'L' and resid 515 through 520 removed outlier: 3.556A pdb=" N SER L 520 " --> pdb=" O LEU L 516 " (cutoff:3.500A) Processing helix chain 'L' and resid 561 through 565 removed outlier: 3.819A pdb=" N ILE L 565 " --> pdb=" O ASP L 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 561 through 565' Processing helix chain 'L' and resid 599 through 604 removed outlier: 3.628A pdb=" N GLU L 604 " --> pdb=" O ALA L 600 " (cutoff:3.500A) Processing helix chain 'L' and resid 659 through 661 No H-bonds generated for 'chain 'L' and resid 659 through 661' Processing helix chain 'L' and resid 678 through 683 Processing helix chain 'L' and resid 728 through 732 removed outlier: 4.077A pdb=" N GLN L 731 " --> pdb=" O ASN L 728 " (cutoff:3.500A) Processing helix chain 'L' and resid 735 through 740 Processing helix chain 'L' and resid 743 through 748 removed outlier: 3.736A pdb=" N TYR L 747 " --> pdb=" O MET L 743 " (cutoff:3.500A) Processing helix chain 'L' and resid 863 through 868 removed outlier: 3.871A pdb=" N TYR L 867 " --> pdb=" O GLN L 863 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA L 868 " --> pdb=" O ASN L 864 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 863 through 868' Processing helix chain 'M' and resid 71 through 76 removed outlier: 3.852A pdb=" N ALA M 75 " --> pdb=" O ASN M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 172 through 180 removed outlier: 3.663A pdb=" N ILE M 177 " --> pdb=" O GLU M 173 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 183 No H-bonds generated for 'chain 'M' and resid 181 through 183' Processing helix chain 'M' and resid 192 through 196 removed outlier: 3.774A pdb=" N GLY M 196 " --> pdb=" O ARG M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 198 through 202 removed outlier: 4.068A pdb=" N ILE M 202 " --> pdb=" O GLU M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 251 through 256 removed outlier: 3.535A pdb=" N LEU M 255 " --> pdb=" O LEU M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 289 Processing helix chain 'M' and resid 343 through 348 removed outlier: 3.513A pdb=" N ASN M 348 " --> pdb=" O PHE M 344 " (cutoff:3.500A) Processing helix chain 'M' and resid 355 through 359 Processing helix chain 'M' and resid 393 through 397 removed outlier: 4.034A pdb=" N TYR M 397 " --> pdb=" O VAL M 394 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 427 removed outlier: 3.992A pdb=" N LEU M 422 " --> pdb=" O VAL M 418 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 24 Processing helix chain 'N' and resid 34 through 43 removed outlier: 3.759A pdb=" N ASP N 40 " --> pdb=" O ALA N 36 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG N 41 " --> pdb=" O ALA N 37 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE N 42 " --> pdb=" O ALA N 38 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU N 43 " --> pdb=" O MET N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 70 removed outlier: 3.798A pdb=" N PHE N 62 " --> pdb=" O GLN N 58 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA N 64 " --> pdb=" O ASN N 60 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU N 66 " --> pdb=" O PHE N 62 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU N 67 " --> pdb=" O SER N 63 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL N 69 " --> pdb=" O ILE N 65 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL N 70 " --> pdb=" O LEU N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 81 removed outlier: 3.712A pdb=" N VAL N 81 " --> pdb=" O THR N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 91 removed outlier: 4.082A pdb=" N ALA N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER N 91 " --> pdb=" O ALA N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 97 No H-bonds generated for 'chain 'N' and resid 95 through 97' Processing helix chain 'N' and resid 98 through 113 removed outlier: 3.826A pdb=" N ASN N 104 " --> pdb=" O GLY N 100 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU N 108 " --> pdb=" O ASN N 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 126 removed outlier: 3.756A pdb=" N GLN N 119 " --> pdb=" O SER N 115 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP N 123 " --> pdb=" O GLN N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 133 through 139 removed outlier: 3.588A pdb=" N GLU N 137 " --> pdb=" O VAL N 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 178 removed outlier: 3.775A pdb=" N TYR N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL N 170 " --> pdb=" O GLN N 166 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE N 173 " --> pdb=" O TYR N 169 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER N 174 " --> pdb=" O VAL N 170 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU N 178 " --> pdb=" O SER N 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 209 through 217 removed outlier: 4.193A pdb=" N ASN N 215 " --> pdb=" O GLN N 211 " (cutoff:3.500A) Processing helix chain 'N' and resid 239 through 247 removed outlier: 3.606A pdb=" N LEU N 245 " --> pdb=" O ARG N 241 " (cutoff:3.500A) Processing helix chain 'N' and resid 265 through 287 removed outlier: 3.601A pdb=" N THR N 276 " --> pdb=" O ALA N 272 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL N 278 " --> pdb=" O GLY N 274 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLN N 281 " --> pdb=" O GLN N 277 " (cutoff:3.500A) Processing helix chain 'N' and resid 289 through 294 removed outlier: 3.644A pdb=" N LEU N 293 " --> pdb=" O VAL N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 297 through 300 removed outlier: 3.539A pdb=" N SER N 300 " --> pdb=" O ASP N 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 297 through 300' Processing helix chain 'N' and resid 301 through 309 removed outlier: 3.604A pdb=" N ASN N 306 " --> pdb=" O GLU N 302 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE N 307 " --> pdb=" O ALA N 303 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU N 308 " --> pdb=" O THR N 304 " (cutoff:3.500A) Processing helix chain 'O' and resid 33 through 36 Processing helix chain 'O' and resid 37 through 59 removed outlier: 3.529A pdb=" N GLY O 42 " --> pdb=" O PRO O 38 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARG O 43 " --> pdb=" O HIS O 39 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN O 45 " --> pdb=" O ILE O 41 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY O 46 " --> pdb=" O GLY O 42 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR O 50 " --> pdb=" O GLY O 46 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN O 53 " --> pdb=" O ALA O 49 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU O 55 " --> pdb=" O ARG O 51 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU O 56 " --> pdb=" O ASN O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 105 removed outlier: 3.502A pdb=" N THR O 102 " --> pdb=" O GLU O 98 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY O 105 " --> pdb=" O MET O 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 190 through 197 Processing helix chain 'O' and resid 215 through 219 removed outlier: 3.527A pdb=" N PHE O 218 " --> pdb=" O PRO O 215 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE O 219 " --> pdb=" O ASP O 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 215 through 219' Processing helix chain 'P' and resid 32 through 36 removed outlier: 3.956A pdb=" N SER P 35 " --> pdb=" O ASN P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 59 removed outlier: 3.530A pdb=" N GLY P 42 " --> pdb=" O PRO P 38 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG P 43 " --> pdb=" O HIS P 39 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN P 45 " --> pdb=" O ILE P 41 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY P 46 " --> pdb=" O GLY P 42 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR P 50 " --> pdb=" O GLY P 46 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN P 53 " --> pdb=" O ALA P 49 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU P 56 " --> pdb=" O ASN P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 105 removed outlier: 3.502A pdb=" N THR P 102 " --> pdb=" O GLU P 98 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY P 105 " --> pdb=" O MET P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 190 through 197 Processing helix chain 'P' and resid 215 through 219 removed outlier: 3.525A pdb=" N PHE P 218 " --> pdb=" O PRO P 215 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE P 219 " --> pdb=" O ASP P 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 215 through 219' Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 3.672A pdb=" N ASP A 102 " --> pdb=" O ASN A 587 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A 587 " --> pdb=" O ASP A 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 135 removed outlier: 3.570A pdb=" N ARG A 144 " --> pdb=" O CYS A 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 155 removed outlier: 3.607A pdb=" N GLY A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.215A pdb=" N GLU A 255 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 249 " --> pdb=" O GLU A 255 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N PHE A 247 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL A 259 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN A 245 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE A 246 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 229 through 230 removed outlier: 4.014A pdb=" N THR A 239 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 305 removed outlier: 3.592A pdb=" N GLY A 304 " --> pdb=" O GLN A 567 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 388 through 389 removed outlier: 4.261A pdb=" N ASN A 388 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 406 through 407 Processing sheet with id=AB3, first strand: chain 'A' and resid 426 through 427 removed outlier: 6.846A pdb=" N GLU A 426 " --> pdb=" O ALA C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 615 through 616 Processing sheet with id=AB5, first strand: chain 'A' and resid 622 through 629 removed outlier: 3.678A pdb=" N PHE A 893 " --> pdb=" O ALA A 623 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A 625 " --> pdb=" O VAL A 891 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 891 " --> pdb=" O MET A 625 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 887 " --> pdb=" O ILE A 629 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 638 through 643 removed outlier: 5.517A pdb=" N SER A 639 " --> pdb=" O MET A 876 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N MET A 876 " --> pdb=" O SER A 639 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU A 874 " --> pdb=" O PRO A 641 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A 643 " --> pdb=" O HIS A 872 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 650 through 651 Processing sheet with id=AB8, first strand: chain 'A' and resid 697 through 698 Processing sheet with id=AB9, first strand: chain 'A' and resid 774 through 779 removed outlier: 3.757A pdb=" N LYS A 836 " --> pdb=" O MET A 774 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 834 " --> pdb=" O ARG A 776 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 71 through 75 removed outlier: 3.747A pdb=" N VAL B 71 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG B 83 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG B 73 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LYS B 81 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASP B 75 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N SER B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 85 through 88 Processing sheet with id=AC3, first strand: chain 'B' and resid 103 through 107 removed outlier: 3.668A pdb=" N GLY B 105 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 144 through 147 Processing sheet with id=AC5, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.561A pdb=" N PHE B 149 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AC7, first strand: chain 'B' and resid 229 through 230 Processing sheet with id=AC8, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.666A pdb=" N ALA B 248 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 615 through 617 Processing sheet with id=AD1, first strand: chain 'B' and resid 627 through 629 Processing sheet with id=AD2, first strand: chain 'B' and resid 635 through 636 removed outlier: 3.854A pdb=" N PHE B 878 " --> pdb=" O VAL B 636 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 697 through 698 Processing sheet with id=AD4, first strand: chain 'B' and resid 771 through 776 removed outlier: 3.779A pdb=" N LYS B 836 " --> pdb=" O MET B 774 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN B 834 " --> pdb=" O ARG B 776 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 79 through 88 removed outlier: 4.173A pdb=" N VAL C 88 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 533 through 535 removed outlier: 3.743A pdb=" N ASN C 587 " --> pdb=" O ASP C 102 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 106 through 107 Processing sheet with id=AD8, first strand: chain 'C' and resid 134 through 136 Processing sheet with id=AD9, first strand: chain 'C' and resid 149 through 151 removed outlier: 3.719A pdb=" N GLY C 200 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR C 261 " --> pdb=" O GLY C 200 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 263 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE C 247 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 154 through 155 removed outlier: 7.177A pdb=" N ILE C 171 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 229 through 230 removed outlier: 3.897A pdb=" N THR C 239 " --> pdb=" O ILE C 230 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 304 through 305 removed outlier: 3.509A pdb=" N GLY C 304 " --> pdb=" O GLN C 567 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 407 through 408 removed outlier: 3.635A pdb=" N THR C 411 " --> pdb=" O ASN C 408 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 623 through 624 removed outlier: 3.809A pdb=" N ALA C 623 " --> pdb=" O PHE C 893 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 627 through 629 removed outlier: 3.530A pdb=" N TYR C 627 " --> pdb=" O LEU C 889 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 635 through 636 removed outlier: 3.505A pdb=" N LYS C 693 " --> pdb=" O GLU C 879 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AE9, first strand: chain 'C' and resid 774 through 776 removed outlier: 3.584A pdb=" N MET C 774 " --> pdb=" O LYS C 836 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS C 836 " --> pdb=" O MET C 774 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN C 834 " --> pdb=" O ARG C 776 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 901 through 905 removed outlier: 5.641A pdb=" N GLN C 903 " --> pdb=" O GLU C 910 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLU C 910 " --> pdb=" O GLN C 903 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS C 905 " --> pdb=" O VAL C 908 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 74 through 75 removed outlier: 3.827A pdb=" N LYS D 81 " --> pdb=" O GLU D 74 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR D 80 " --> pdb=" O PHE D 558 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 86 through 88 removed outlier: 3.975A pdb=" N VAL D 88 " --> pdb=" O GLY D 550 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU D 555 " --> pdb=" O VAL D 323 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 534 through 535 removed outlier: 3.739A pdb=" N PHE D 101 " --> pdb=" O VAL D 535 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN D 587 " --> pdb=" O ASP D 102 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 105 through 106 removed outlier: 3.582A pdb=" N GLY D 105 " --> pdb=" O PHE D 531 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 133 through 135 removed outlier: 3.630A pdb=" N CYS D 133 " --> pdb=" O ARG D 144 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 149 through 151 Processing sheet with id=AF8, first strand: chain 'D' and resid 161 through 164 Processing sheet with id=AF9, first strand: chain 'D' and resid 216 through 217 Processing sheet with id=AG1, first strand: chain 'D' and resid 304 through 305 removed outlier: 3.708A pdb=" N GLY D 304 " --> pdb=" O GLN D 567 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 389 through 390 removed outlier: 3.589A pdb=" N ASN F 388 " --> pdb=" O ILE F 435 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS F 390 " --> pdb=" O MET F 433 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 423 through 425 removed outlier: 3.528A pdb=" N TYR D 402 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 425 " --> pdb=" O ASP D 400 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN F 245 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU F 260 " --> pdb=" O GLN F 245 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL F 198 " --> pdb=" O VAL F 259 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N TYR F 261 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLY F 200 " --> pdb=" O TYR F 261 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N GLU F 263 " --> pdb=" O GLY F 200 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL F 202 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 614 through 615 Processing sheet with id=AG5, first strand: chain 'D' and resid 623 through 627 removed outlier: 3.543A pdb=" N PHE D 893 " --> pdb=" O ALA D 623 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP D 844 " --> pdb=" O PHE D 653 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 638 through 640 Processing sheet with id=AG7, first strand: chain 'D' and resid 691 through 694 removed outlier: 6.624A pdb=" N GLU D 879 " --> pdb=" O LYS D 692 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 771 through 773 Processing sheet with id=AG9, first strand: chain 'D' and resid 776 through 779 Processing sheet with id=AH1, first strand: chain 'E' and resid 79 through 87 Processing sheet with id=AH2, first strand: chain 'E' and resid 529 through 534 removed outlier: 6.675A pdb=" N TYR E 100 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU E 588 " --> pdb=" O TYR E 100 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASP E 102 " --> pdb=" O ILE E 586 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE E 586 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG E 104 " --> pdb=" O ASP E 584 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 161 through 164 removed outlier: 7.481A pdb=" N ILE E 171 " --> pdb=" O ILE E 162 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.636A pdb=" N VAL E 202 " --> pdb=" O GLU E 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'E' and resid 258 through 259 removed outlier: 4.008A pdb=" N PHE E 246 " --> pdb=" O ILE F 405 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR F 413 " --> pdb=" O LYS F 406 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 304 through 305 Processing sheet with id=AH7, first strand: chain 'E' and resid 388 through 389 Processing sheet with id=AH8, first strand: chain 'E' and resid 406 through 408 removed outlier: 5.636A pdb=" N LYS E 406 " --> pdb=" O THR E 413 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR E 411 " --> pdb=" O ASN E 408 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'E' and resid 622 through 624 removed outlier: 3.513A pdb=" N PHE E 893 " --> pdb=" O ALA E 623 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 627 through 629 Processing sheet with id=AI2, first strand: chain 'E' and resid 635 through 639 removed outlier: 7.409A pdb=" N ASP E 875 " --> pdb=" O ILE E 696 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ILE E 696 " --> pdb=" O ASP E 875 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR E 877 " --> pdb=" O VAL E 694 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL E 694 " --> pdb=" O THR E 877 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU E 879 " --> pdb=" O LYS E 692 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 635 through 639 removed outlier: 7.409A pdb=" N ASP E 875 " --> pdb=" O ILE E 696 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ILE E 696 " --> pdb=" O ASP E 875 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR E 877 " --> pdb=" O VAL E 694 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL E 694 " --> pdb=" O THR E 877 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU E 879 " --> pdb=" O LYS E 692 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 771 through 772 Processing sheet with id=AI5, first strand: chain 'E' and resid 775 through 776 removed outlier: 3.632A pdb=" N GLN E 834 " --> pdb=" O ARG E 776 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 901 through 902 Processing sheet with id=AI7, first strand: chain 'F' and resid 71 through 75 removed outlier: 5.383A pdb=" N ASP F 72 " --> pdb=" O ARG F 83 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG F 83 " --> pdb=" O ASP F 72 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'F' and resid 529 through 535 removed outlier: 3.589A pdb=" N GLY F 105 " --> pdb=" O PHE F 531 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 134 through 136 Processing sheet with id=AJ1, first strand: chain 'F' and resid 161 through 164 removed outlier: 6.497A pdb=" N ILE F 171 " --> pdb=" O ILE F 162 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'F' and resid 229 through 230 Processing sheet with id=AJ3, first strand: chain 'F' and resid 304 through 305 Processing sheet with id=AJ4, first strand: chain 'F' and resid 323 through 324 removed outlier: 3.888A pdb=" N VAL F 323 " --> pdb=" O GLU F 555 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'F' and resid 377 through 378 removed outlier: 3.763A pdb=" N ILE F 377 " --> pdb=" O TRP F 497 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 459 through 460 removed outlier: 3.682A pdb=" N ILE F 460 " --> pdb=" O VAL F 481 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL F 481 " --> pdb=" O ILE F 460 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ6 Processing sheet with id=AJ7, first strand: chain 'F' and resid 614 through 617 removed outlier: 3.945A pdb=" N GLN F 614 " --> pdb=" O ILE F 901 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE F 901 " --> pdb=" O GLN F 614 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'F' and resid 635 through 637 removed outlier: 3.533A pdb=" N SER F 695 " --> pdb=" O THR F 877 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'F' and resid 844 through 847 Processing sheet with id=AK1, first strand: chain 'F' and resid 844 through 847 Processing sheet with id=AK2, first strand: chain 'F' and resid 728 through 729 removed outlier: 4.784A pdb=" N MET F 734 " --> pdb=" O VAL F 729 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'F' and resid 771 through 777 Processing sheet with id=AK4, first strand: chain 'G' and resid 65 through 68 removed outlier: 3.979A pdb=" N LEU G 66 " --> pdb=" O ALA G 590 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA G 590 " --> pdb=" O LEU G 66 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR G 100 " --> pdb=" O TYR G 589 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE G 101 " --> pdb=" O VAL G 535 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY G 105 " --> pdb=" O PHE G 531 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'G' and resid 74 through 75 removed outlier: 3.668A pdb=" N TYR G 80 " --> pdb=" O PHE G 558 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'G' and resid 133 through 136 removed outlier: 3.681A pdb=" N CYS G 133 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG G 144 " --> pdb=" O CYS G 133 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TRP G 135 " --> pdb=" O LYS G 142 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS G 142 " --> pdb=" O TRP G 135 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY G 145 " --> pdb=" O GLU H 424 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'G' and resid 201 through 203 removed outlier: 6.594A pdb=" N VAL G 202 " --> pdb=" O GLU G 263 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA G 258 " --> pdb=" O PHE G 247 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU G 260 " --> pdb=" O GLN G 245 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN G 245 " --> pdb=" O LEU G 260 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'G' and resid 433 through 434 removed outlier: 3.969A pdb=" N ASN H 388 " --> pdb=" O ILE H 435 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'G' and resid 405 through 407 Processing sheet with id=AL1, first strand: chain 'G' and resid 627 through 628 removed outlier: 3.503A pdb=" N LEU G 656 " --> pdb=" O LEU G 888 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'G' and resid 650 through 651 Processing sheet with id=AL3, first strand: chain 'G' and resid 771 through 779 removed outlier: 3.628A pdb=" N LYS G 836 " --> pdb=" O MET G 774 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'G' and resid 900 through 902 removed outlier: 3.547A pdb=" N HIS G 902 " --> pdb=" O GLU G 910 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU G 910 " --> pdb=" O HIS G 902 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'H' and resid 71 through 75 removed outlier: 4.289A pdb=" N ARG H 73 " --> pdb=" O LYS H 81 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS H 81 " --> pdb=" O ARG H 73 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASP H 75 " --> pdb=" O SER H 79 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER H 79 " --> pdb=" O ASP H 75 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR H 80 " --> pdb=" O PHE H 558 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'H' and resid 94 through 95 Processing sheet with id=AL7, first strand: chain 'H' and resid 529 through 535 removed outlier: 3.583A pdb=" N GLY H 105 " --> pdb=" O PHE H 531 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP H 102 " --> pdb=" O ILE H 586 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE H 586 " --> pdb=" O ASP H 102 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG H 104 " --> pdb=" O ASP H 584 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'H' and resid 133 through 136 Processing sheet with id=AL9, first strand: chain 'H' and resid 149 through 151 removed outlier: 3.520A pdb=" N GLY H 200 " --> pdb=" O VAL H 259 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE H 246 " --> pdb=" O ILE I 405 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA H 248 " --> pdb=" O SER I 403 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR I 402 " --> pdb=" O ALA I 423 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA I 423 " --> pdb=" O TYR I 402 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'H' and resid 163 through 164 removed outlier: 3.952A pdb=" N GLY H 163 " --> pdb=" O ILE H 171 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'H' and resid 216 through 217 Processing sheet with id=AM3, first strand: chain 'H' and resid 229 through 230 Processing sheet with id=AM4, first strand: chain 'H' and resid 272 through 275 Processing sheet with id=AM5, first strand: chain 'H' and resid 304 through 305 Processing sheet with id=AM6, first strand: chain 'H' and resid 325 through 326 Processing sheet with id=AM7, first strand: chain 'H' and resid 614 through 617 Processing sheet with id=AM8, first strand: chain 'H' and resid 628 through 629 removed outlier: 3.819A pdb=" N THR H 887 " --> pdb=" O ILE H 629 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP H 844 " --> pdb=" O PHE H 653 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'H' and resid 635 through 639 Processing sheet with id=AN1, first strand: chain 'H' and resid 696 through 698 removed outlier: 4.147A pdb=" N ILE H 696 " --> pdb=" O TRP H 704 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'H' and resid 728 through 729 removed outlier: 4.339A pdb=" N MET H 734 " --> pdb=" O VAL H 729 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'H' and resid 772 through 773 removed outlier: 3.874A pdb=" N GLN H 772 " --> pdb=" O LEU H 838 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU H 838 " --> pdb=" O GLN H 772 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN3 Processing sheet with id=AN4, first strand: chain 'H' and resid 778 through 779 Processing sheet with id=AN5, first strand: chain 'I' and resid 67 through 68 removed outlier: 3.585A pdb=" N LEU I 588 " --> pdb=" O PHE I 68 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN I 587 " --> pdb=" O ASP I 102 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR I 100 " --> pdb=" O TYR I 589 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE I 103 " --> pdb=" O ILE I 533 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE I 533 " --> pdb=" O ILE I 103 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'I' and resid 81 through 82 Processing sheet with id=AN7, first strand: chain 'I' and resid 85 through 86 Processing sheet with id=AN8, first strand: chain 'I' and resid 106 through 107 Processing sheet with id=AN9, first strand: chain 'I' and resid 201 through 203 removed outlier: 3.770A pdb=" N GLU I 263 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE I 247 " --> pdb=" O LYS I 257 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL I 259 " --> pdb=" O GLN I 245 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN I 245 " --> pdb=" O VAL I 259 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'I' and resid 388 through 390 Processing sheet with id=AO2, first strand: chain 'I' and resid 459 through 460 Processing sheet with id=AO3, first strand: chain 'I' and resid 615 through 617 removed outlier: 3.575A pdb=" N LEU I 914 " --> pdb=" O VAL I 898 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR I 913 " --> pdb=" O GLN P 107 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'I' and resid 624 through 628 removed outlier: 4.729A pdb=" N GLY I 650 " --> pdb=" O GLU I 894 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'I' and resid 624 through 628 Processing sheet with id=AO6, first strand: chain 'I' and resid 635 through 636 removed outlier: 3.591A pdb=" N VAL I 636 " --> pdb=" O PHE I 878 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA I 873 " --> pdb=" O PHE I 698 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE I 698 " --> pdb=" O ALA I 873 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ASP I 875 " --> pdb=" O ILE I 696 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ILE I 696 " --> pdb=" O ASP I 875 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR I 877 " --> pdb=" O VAL I 694 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N VAL I 694 " --> pdb=" O THR I 877 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU I 879 " --> pdb=" O LYS I 692 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'I' and resid 639 through 643 removed outlier: 4.374A pdb=" N SER I 642 " --> pdb=" O HIS I 872 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N HIS I 872 " --> pdb=" O SER I 642 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA I 873 " --> pdb=" O PHE I 698 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE I 698 " --> pdb=" O ALA I 873 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ASP I 875 " --> pdb=" O ILE I 696 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ILE I 696 " --> pdb=" O ASP I 875 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR I 877 " --> pdb=" O VAL I 694 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N VAL I 694 " --> pdb=" O THR I 877 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU I 879 " --> pdb=" O LYS I 692 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'I' and resid 776 through 779 Processing sheet with id=AO9, first strand: chain 'J' and resid 74 through 75 Processing sheet with id=AP1, first strand: chain 'J' and resid 532 through 535 Processing sheet with id=AP2, first strand: chain 'J' and resid 134 through 136 Processing sheet with id=AP3, first strand: chain 'J' and resid 216 through 217 Processing sheet with id=AP4, first strand: chain 'J' and resid 229 through 230 Processing sheet with id=AP5, first strand: chain 'J' and resid 377 through 378 removed outlier: 3.745A pdb=" N ILE J 377 " --> pdb=" O TRP J 497 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP J 497 " --> pdb=" O ILE J 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP5 Processing sheet with id=AP6, first strand: chain 'J' and resid 388 through 389 removed outlier: 3.791A pdb=" N ASN J 388 " --> pdb=" O ILE J 435 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASN L 388 " --> pdb=" O ILE L 435 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS L 390 " --> pdb=" O MET L 433 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N MET L 433 " --> pdb=" O CYS L 390 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN K 388 " --> pdb=" O ILE K 435 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'J' and resid 400 through 401 removed outlier: 3.574A pdb=" N ASP J 400 " --> pdb=" O ILE J 425 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLU J 424 " --> pdb=" O GLY L 145 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS L 142 " --> pdb=" O TRP L 135 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TRP L 135 " --> pdb=" O LYS L 142 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'J' and resid 459 through 460 removed outlier: 3.626A pdb=" N VAL J 481 " --> pdb=" O ILE J 460 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'J' and resid 616 through 617 removed outlier: 3.564A pdb=" N PHE J 616 " --> pdb=" O VAL J 899 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL J 899 " --> pdb=" O PHE J 616 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL J 912 " --> pdb=" O ARG J 900 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'J' and resid 623 through 624 removed outlier: 3.829A pdb=" N LEU J 888 " --> pdb=" O LEU J 656 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'J' and resid 635 through 643 removed outlier: 4.160A pdb=" N PHE J 878 " --> pdb=" O VAL J 636 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU J 874 " --> pdb=" O ILE J 640 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER J 642 " --> pdb=" O HIS J 872 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N HIS J 872 " --> pdb=" O SER J 642 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'J' and resid 635 through 643 removed outlier: 4.160A pdb=" N PHE J 878 " --> pdb=" O VAL J 636 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU J 874 " --> pdb=" O ILE J 640 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER J 642 " --> pdb=" O HIS J 872 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N HIS J 872 " --> pdb=" O SER J 642 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'K' and resid 65 through 66 removed outlier: 3.814A pdb=" N LEU K 66 " --> pdb=" O ALA K 590 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA K 590 " --> pdb=" O LEU K 66 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER K 585 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG K 104 " --> pdb=" O SER K 585 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'K' and resid 71 through 75 removed outlier: 5.382A pdb=" N ASP K 72 " --> pdb=" O ARG K 83 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG K 83 " --> pdb=" O ASP K 72 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU K 74 " --> pdb=" O LYS K 81 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'K' and resid 134 through 136 removed outlier: 3.504A pdb=" N TRP K 135 " --> pdb=" O LYS K 142 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N GLU L 424 " --> pdb=" O ILE K 141 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL K 143 " --> pdb=" O GLU L 424 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'K' and resid 161 through 164 removed outlier: 3.697A pdb=" N GLY K 163 " --> pdb=" O ILE K 171 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'K' and resid 245 through 248 removed outlier: 7.356A pdb=" N GLN K 245 " --> pdb=" O VAL K 259 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL K 259 " --> pdb=" O GLN K 245 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE K 247 " --> pdb=" O LYS K 257 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS K 257 " --> pdb=" O PHE K 247 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ8 Processing sheet with id=AQ9, first strand: chain 'K' and resid 304 through 305 Processing sheet with id=AR1, first strand: chain 'K' and resid 400 through 401 Processing sheet with id=AR2, first strand: chain 'K' and resid 637 through 640 removed outlier: 6.762A pdb=" N THR K 877 " --> pdb=" O VAL K 694 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL K 694 " --> pdb=" O THR K 877 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU K 879 " --> pdb=" O LYS K 692 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'K' and resid 844 through 847 removed outlier: 3.571A pdb=" N TRP K 844 " --> pdb=" O PHE K 653 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'K' and resid 697 through 698 Processing sheet with id=AR5, first strand: chain 'K' and resid 728 through 729 removed outlier: 4.031A pdb=" N MET K 734 " --> pdb=" O VAL K 729 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'K' and resid 772 through 779 removed outlier: 3.611A pdb=" N LYS K 836 " --> pdb=" O MET K 774 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN K 834 " --> pdb=" O ARG K 776 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'K' and resid 896 through 898 removed outlier: 3.588A pdb=" N PHE K 896 " --> pdb=" O THR K 916 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU K 914 " --> pdb=" O VAL K 898 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'K' and resid 901 through 902 Processing sheet with id=AR9, first strand: chain 'L' and resid 65 through 68 removed outlier: 3.950A pdb=" N LEU L 588 " --> pdb=" O PHE L 68 " (cutoff:3.500A) Processing sheet with id=AS1, first strand: chain 'L' and resid 74 through 75 removed outlier: 3.662A pdb=" N LYS L 81 " --> pdb=" O GLU L 74 " (cutoff:3.500A) Processing sheet with id=AS2, first strand: chain 'L' and resid 105 through 106 Processing sheet with id=AS3, first strand: chain 'L' and resid 149 through 150 Processing sheet with id=AS4, first strand: chain 'L' and resid 161 through 164 removed outlier: 4.085A pdb=" N GLY L 163 " --> pdb=" O ILE L 171 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE L 171 " --> pdb=" O GLY L 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AS4 Processing sheet with id=AS5, first strand: chain 'L' and resid 243 through 247 removed outlier: 5.533A pdb=" N ASN L 243 " --> pdb=" O TYR L 261 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR L 261 " --> pdb=" O ASN L 243 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN L 245 " --> pdb=" O VAL L 259 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N VAL L 259 " --> pdb=" O GLN L 245 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE L 247 " --> pdb=" O LYS L 257 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'L' and resid 304 through 305 Processing sheet with id=AS7, first strand: chain 'L' and resid 614 through 616 removed outlier: 3.509A pdb=" N GLU L 910 " --> pdb=" O HIS L 902 " (cutoff:3.500A) Processing sheet with id=AS8, first strand: chain 'L' and resid 623 through 624 removed outlier: 3.719A pdb=" N THR L 887 " --> pdb=" O ILE L 629 " (cutoff:3.500A) Processing sheet with id=AS9, first strand: chain 'L' and resid 623 through 624 removed outlier: 3.773A pdb=" N TRP L 844 " --> pdb=" O PHE L 653 " (cutoff:3.500A) Processing sheet with id=AT1, first strand: chain 'L' and resid 635 through 640 removed outlier: 3.901A pdb=" N ILE L 640 " --> pdb=" O LEU L 874 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU L 874 " --> pdb=" O ILE L 640 " (cutoff:3.500A) Processing sheet with id=AT2, first strand: chain 'L' and resid 635 through 640 removed outlier: 3.901A pdb=" N ILE L 640 " --> pdb=" O LEU L 874 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU L 874 " --> pdb=" O ILE L 640 " (cutoff:3.500A) Processing sheet with id=AT3, first strand: chain 'L' and resid 778 through 779 Processing sheet with id=AT4, first strand: chain 'M' and resid 61 through 62 Processing sheet with id=AT5, first strand: chain 'M' and resid 67 through 69 removed outlier: 3.561A pdb=" N LEU M 495 " --> pdb=" O ILE M 124 " (cutoff:3.500A) Processing sheet with id=AT6, first strand: chain 'M' and resid 89 through 92 Processing sheet with id=AT7, first strand: chain 'M' and resid 466 through 467 removed outlier: 6.929A pdb=" N ARG M 116 " --> pdb=" O LEU M 503 " (cutoff:3.500A) Processing sheet with id=AT8, first strand: chain 'M' and resid 141 through 148 removed outlier: 6.341A pdb=" N LYS M 142 " --> pdb=" O PHE M 164 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE M 164 " --> pdb=" O LYS M 142 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ARG M 144 " --> pdb=" O PHE M 162 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE M 162 " --> pdb=" O ARG M 144 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N MET M 146 " --> pdb=" O GLU M 160 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLU M 160 " --> pdb=" O MET M 146 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU M 148 " --> pdb=" O ARG M 158 " (cutoff:3.500A) Processing sheet with id=AT9, first strand: chain 'M' and resid 204 through 208 removed outlier: 5.488A pdb=" N TYR M 340 " --> pdb=" O ILE M 279 " (cutoff:3.500A) Processing sheet with id=AU1, first strand: chain 'M' and resid 407 through 413 Processing sheet with id=AU2, first strand: chain 'N' and resid 187 through 191 removed outlier: 3.712A pdb=" N TYR N 189 " --> pdb=" O PHE N 196 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER N 191 " --> pdb=" O ASP N 194 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP N 194 " --> pdb=" O SER N 191 " (cutoff:3.500A) Processing sheet with id=AU3, first strand: chain 'O' and resid 9 through 10 Processing sheet with id=AU4, first strand: chain 'O' and resid 87 through 89 removed outlier: 3.518A pdb=" N LEU O 177 " --> pdb=" O THR O 87 " (cutoff:3.500A) Processing sheet with id=AU5, first strand: chain 'P' and resid 9 through 10 Processing sheet with id=AU6, first strand: chain 'P' and resid 87 through 89 removed outlier: 3.519A pdb=" N LEU P 177 " --> pdb=" O THR P 87 " (cutoff:3.500A) 1350 hydrogen bonds defined for protein. 3240 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: 39.46 Time building geometry restraints manager: 31.95 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: 26660 1.33 - 1.45: 22131 1.45 - 1.58: 51052 1.58 - 1.70: 0 1.70 - 1.82: 863 Bond restraints: 100706 Sorted by residual: bond pdb=" CG1 ILE D 565 " pdb=" CD1 ILE D 565 " ideal model delta sigma weight residual 1.513 1.404 0.109 3.90e-02 6.57e+02 7.79e+00 bond pdb=" CB LEU H 312 " pdb=" CG LEU H 312 " ideal model delta sigma weight residual 1.530 1.474 0.056 2.00e-02 2.50e+03 7.72e+00 bond pdb=" CG1 ILE I 533 " pdb=" CD1 ILE I 533 " ideal model delta sigma weight residual 1.513 1.405 0.108 3.90e-02 6.57e+02 7.65e+00 bond pdb=" CB TRP A 556 " pdb=" CG TRP A 556 " ideal model delta sigma weight residual 1.498 1.413 0.085 3.10e-02 1.04e+03 7.46e+00 bond pdb=" C PRO I 820 " pdb=" N TYR I 821 " ideal model delta sigma weight residual 1.331 1.275 0.056 2.07e-02 2.33e+03 7.30e+00 ... (remaining 100701 not shown) Histogram of bond angle deviations from ideal: 94.30 - 103.16: 1336 103.16 - 112.01: 44706 112.01 - 120.86: 56058 120.86 - 129.71: 34471 129.71 - 138.57: 675 Bond angle restraints: 137246 Sorted by residual: angle pdb=" N ASN I 139 " pdb=" CA ASN I 139 " pdb=" C ASN I 139 " ideal model delta sigma weight residual 114.62 105.05 9.57 1.14e+00 7.69e-01 7.04e+01 angle pdb=" N VAL N 133 " pdb=" CA VAL N 133 " pdb=" C VAL N 133 " ideal model delta sigma weight residual 112.29 105.37 6.92 9.40e-01 1.13e+00 5.42e+01 angle pdb=" N VAL H 576 " pdb=" CA VAL H 576 " pdb=" C VAL H 576 " ideal model delta sigma weight residual 113.53 106.82 6.71 9.80e-01 1.04e+00 4.69e+01 angle pdb=" N ASP L 95 " pdb=" CA ASP L 95 " pdb=" C ASP L 95 " ideal model delta sigma weight residual 114.56 106.77 7.79 1.27e+00 6.20e-01 3.77e+01 angle pdb=" C PHE C 771 " pdb=" N GLN C 772 " pdb=" CA GLN C 772 " ideal model delta sigma weight residual 122.28 117.07 5.21 8.80e-01 1.29e+00 3.51e+01 ... (remaining 137241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 55742 16.64 - 33.29: 3363 33.29 - 49.93: 506 49.93 - 66.58: 55 66.58 - 83.22: 67 Dihedral angle restraints: 59733 sinusoidal: 23525 harmonic: 36208 Sorted by residual: dihedral pdb=" CA THR B 916 " pdb=" C THR B 916 " pdb=" N PRO B 917 " pdb=" CA PRO B 917 " ideal model delta harmonic sigma weight residual 180.00 108.42 71.58 0 5.00e+00 4.00e-02 2.05e+02 dihedral pdb=" CA THR G 916 " pdb=" C THR G 916 " pdb=" N PRO G 917 " pdb=" CA PRO G 917 " ideal model delta harmonic sigma weight residual -180.00 -109.49 -70.51 0 5.00e+00 4.00e-02 1.99e+02 dihedral pdb=" CA ALA K 288 " pdb=" C ALA K 288 " pdb=" N ASP K 289 " pdb=" CA ASP K 289 " ideal model delta harmonic sigma weight residual -180.00 -124.94 -55.06 0 5.00e+00 4.00e-02 1.21e+02 ... (remaining 59730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 13887 0.126 - 0.252: 753 0.252 - 0.378: 20 0.378 - 0.503: 3 0.503 - 0.629: 1 Chirality restraints: 14664 Sorted by residual: chirality pdb=" CB ILE G 638 " pdb=" CA ILE G 638 " pdb=" CG1 ILE G 638 " pdb=" CG2 ILE G 638 " both_signs ideal model delta sigma weight residual False 2.64 2.02 0.63 2.00e-01 2.50e+01 9.90e+00 chirality pdb=" CB ILE C 425 " pdb=" CA ILE C 425 " pdb=" CG1 ILE C 425 " pdb=" CG2 ILE C 425 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CB ILE F 141 " pdb=" CA ILE F 141 " pdb=" CG1 ILE F 141 " pdb=" CG2 ILE F 141 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 14661 not shown) Planarity restraints: 18133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE K 149 " 0.024 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C PHE K 149 " -0.081 2.00e-02 2.50e+03 pdb=" O PHE K 149 " 0.030 2.00e-02 2.50e+03 pdb=" N ILE K 150 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 916 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO B 917 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO B 917 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 917 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 149 " 0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C PHE E 149 " -0.076 2.00e-02 2.50e+03 pdb=" O PHE E 149 " 0.028 2.00e-02 2.50e+03 pdb=" N ILE E 150 " 0.026 2.00e-02 2.50e+03 ... (remaining 18130 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 14328 2.75 - 3.29: 95233 3.29 - 3.83: 167151 3.83 - 4.36: 197162 4.36 - 4.90: 330224 Nonbonded interactions: 804098 Sorted by model distance: nonbonded pdb=" OH TYR E 315 " pdb=" O THR E 342 " model vdw 2.216 2.440 nonbonded pdb=" O SER B 485 " pdb=" OH TYR B 490 " model vdw 2.219 2.440 nonbonded pdb=" OH TYR N 189 " pdb=" O SER O 208 " model vdw 2.223 2.440 nonbonded pdb=" OH TYR H 314 " pdb=" OD1 ASN H 320 " model vdw 2.230 2.440 nonbonded pdb=" OH TYR D 116 " pdb=" OD2 ASP D 271 " model vdw 2.233 2.440 ... (remaining 804093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 192 or resid 195 through 230 or resid 240 throug \ h 921)) selection = (chain 'B' and (resid 6 through 192 or resid 195 through 230 or resid 240 throug \ h 921)) selection = (chain 'C' and (resid 6 through 192 or resid 195 through 230 or resid 240 throug \ h 921)) selection = (chain 'D' and (resid 6 through 192 or resid 195 through 230 or resid 240 throug \ h 921)) selection = (chain 'E' and (resid 6 through 192 or resid 195 through 230 or resid 240 throug \ h 921)) selection = (chain 'F' and (resid 6 through 192 or resid 195 through 230 or resid 240 throug \ h 921)) selection = (chain 'G' and (resid 6 through 192 or resid 195 through 230 or resid 240 throug \ h 921)) selection = (chain 'H' and (resid 6 through 192 or resid 195 through 230 or resid 240 throug \ h 921)) selection = (chain 'I' and (resid 6 through 192 or resid 195 through 230 or resid 240 throug \ h 921)) selection = (chain 'J' and (resid 6 through 192 or resid 195 through 230 or resid 240 throug \ h 921)) selection = (chain 'K' and (resid 6 through 192 or resid 195 through 230 or resid 240 throug \ h 921)) selection = (chain 'L' and (resid 6 through 230 or resid 240 through 921)) } ncs_group { reference = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'U' selection = chain 'V' selection = chain 'Y' selection = chain 'u' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 469 5.16 5 C 62238 2.51 5 N 16658 2.21 5 O 18672 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 94.550 Check model and map are aligned: 1.080 Convert atoms to be neutral: 0.620 Process input model: 193.090 Find NCS groups from input model: 6.310 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 313.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.007 0.131 100706 Z= 0.490 Angle : 1.212 17.736 137246 Z= 0.633 Chirality : 0.064 0.629 14664 Planarity : 0.009 0.114 18133 Dihedral : 11.328 83.219 36587 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.70 % Favored : 85.16 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.34 % Cis-general : 0.00 % Twisted Proline : 1.21 % Twisted General : 0.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (0.06), residues: 12304 helix: -4.72 (0.05), residues: 1345 sheet: -3.06 (0.11), residues: 1845 loop : -3.20 (0.06), residues: 9114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4019 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 3955 time to evaluate : 8.340 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: 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: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 15 residues processed: 3993 average time/residue: 0.9323 time to fit residues: 6348.1631 Evaluate side-chains 2420 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 2405 time to evaluate : 8.273 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.6672 time to fit residues: 30.9984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 1037 optimal weight: 0.9990 chunk 931 optimal weight: 5.9990 chunk 516 optimal weight: 0.5980 chunk 318 optimal weight: 20.0000 chunk 628 optimal weight: 9.9990 chunk 497 optimal weight: 8.9990 chunk 963 optimal weight: 10.0000 chunk 372 optimal weight: 1.9990 chunk 585 optimal weight: 4.9990 chunk 716 optimal weight: 0.9980 chunk 1116 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN A 146 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN A 338 GLN A 347 GLN A 379 ASN A 408 ASN A 417 ASN A 440 ASN A 449 ASN A 532 HIS ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 ASN ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 728 ASN ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN A 872 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 146 GLN B 153 ASN B 155 ASN B 161 GLN B 293 GLN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN B 408 ASN B 417 ASN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN B 591 ASN B 609 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 728 ASN B 742 GLN B 752 GLN B 770 ASN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 GLN B 834 GLN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 185 GLN C 294 GLN C 308 ASN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 ASN ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 ASN C 532 HIS ** C 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN ** C 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 780 ASN C 813 GLN C 834 GLN C 872 HIS ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN D 155 ASN D 178 GLN D 243 ASN D 264 ASN D 282 GLN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN D 478 ASN ** D 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 612 ASN ** D 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 GLN D 748 ASN D 752 GLN ** D 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 813 GLN D 869 ASN E 14 HIS E 122 ASN ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 ASN E 221 ASN E 232 ASN ** E 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 449 ASN ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 587 ASN ** E 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 609 ASN ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 688 ASN E 742 GLN E 752 GLN E 795 GLN E 834 GLN E 869 ASN F 54 HIS F 62 GLN F 146 GLN F 155 ASN F 168 ASN F 178 GLN F 226 GLN F 243 ASN F 254 ASN F 293 GLN F 294 GLN ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 341 ASN F 417 ASN ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 509 ASN F 537 GLN F 612 ASN F 617 ASN F 688 ASN ** F 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 777 GLN F 834 GLN F 872 HIS G 9 GLN G 47 ASN G 178 GLN ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 308 ASN ** G 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 365 GLN ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 408 ASN ** G 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 470 ASN ** G 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 742 GLN G 772 GLN ** G 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 HIS H 153 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 327 GLN H 338 GLN H 341 ASN H 408 ASN H 472 ASN H 478 ASN H 591 ASN ** H 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 632 ASN H 742 GLN H 770 ASN ** H 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 797 ASN H 798 ASN H 813 GLN H 905 HIS I 161 GLN ** I 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 ASN ** I 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 HIS I 338 GLN I 341 ASN I 347 GLN ** I 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 509 ASN ** I 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 557 ASN I 624 ASN ** I 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 798 ASN I 864 ASN J 54 HIS J 122 ASN J 131 ASN J 158 ASN J 168 ASN ** J 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 245 GLN J 254 ASN ** J 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 ASN J 330 GLN J 341 ASN ** J 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 440 ASN J 470 ASN J 472 ASN ** J 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 509 ASN J 614 GLN ** J 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 624 ASN ** J 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 864 ASN K 18 GLN K 54 HIS K 178 GLN ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 308 ASN ** K 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 347 GLN ** K 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 436 ASN K 472 ASN ** K 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 612 ASN ** K 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 632 ASN ** K 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 864 ASN K 902 HIS ** L 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 HIS L 146 GLN L 169 GLN L 196 GLN L 221 ASN ** L 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 316 ASN L 327 GLN L 332 ASN L 341 ASN L 365 GLN L 449 ASN ** L 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 504 ASN L 612 ASN L 632 ASN L 644 ASN L 746 HIS L 780 ASN ** L 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 798 ASN ** L 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 872 HIS M 51 ASN M 83 GLN M 90 GLN M 110 ASN M 187 ASN M 264 GLN M 337 ASN M 463 HIS M 476 GLN N 49 ASN ** N 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 215 ASN N 306 ASN ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 GLN O 70 ASN ** P 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 ASN Total number of N/Q/H flips: 196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 100706 Z= 0.225 Angle : 0.777 15.707 137246 Z= 0.393 Chirality : 0.048 0.328 14664 Planarity : 0.006 0.095 18133 Dihedral : 7.363 69.935 13679 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.31 % Favored : 88.62 % Rotamer Outliers : 3.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.34 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.07), residues: 12304 helix: -3.94 (0.08), residues: 1411 sheet: -2.71 (0.11), residues: 1981 loop : -2.78 (0.06), residues: 8912 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3079 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 384 poor density : 2695 time to evaluate : 10.174 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: 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 outliers start: 384 outliers final: 196 residues processed: 2909 average time/residue: 0.8619 time to fit residues: 4355.2903 Evaluate side-chains 2434 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 2238 time to evaluate : 8.407 Switching outliers to nearest non-outliers outliers start: 196 outliers final: 0 residues processed: 196 average time/residue: 0.6914 time to fit residues: 269.7947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 620 optimal weight: 1.9990 chunk 346 optimal weight: 9.9990 chunk 928 optimal weight: 0.5980 chunk 759 optimal weight: 7.9990 chunk 307 optimal weight: 0.2980 chunk 1118 optimal weight: 20.0000 chunk 1207 optimal weight: 20.0000 chunk 995 optimal weight: 2.9990 chunk 1108 optimal weight: 7.9990 chunk 381 optimal weight: 0.0470 chunk 896 optimal weight: 8.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 ASN A 742 GLN A 746 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN B 293 GLN B 338 GLN B 417 ASN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN B 509 ASN ** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 GLN B 624 ASN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 818 ASN B 863 GLN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 742 GLN ** C 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 91 ASN D 264 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** D 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN ** D 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 797 ASN D 798 ASN D 869 ASN ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 ASN E 185 GLN ** E 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 ASN ** E 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 GLN F 254 ASN F 273 HIS F 293 GLN F 308 ASN ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 869 ASN ** G 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 472 ASN G 572 ASN ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 644 ASN ** G 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 902 HIS H 14 HIS H 169 GLN H 187 GLN ** H 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 388 ASN H 470 ASN H 478 ASN H 597 HIS ** H 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 327 GLN ** I 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 440 ASN ** I 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 863 GLN J 91 ASN J 122 ASN ** J 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 293 GLN ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 509 ASN J 537 GLN J 617 ASN ** J 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 770 ASN ** J 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 158 ASN ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 245 GLN ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 308 ASN ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 788 GLN ** K 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 HIS ** L 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 GLN ** L 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 746 HIS ** L 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 337 ASN M 439 ASN ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 296 GLN ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 GLN ** P 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 GLN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 100706 Z= 0.194 Angle : 0.730 15.149 137246 Z= 0.364 Chirality : 0.047 0.302 14664 Planarity : 0.005 0.097 18133 Dihedral : 6.713 67.541 13679 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.32 % Favored : 88.61 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.34 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.07), residues: 12304 helix: -3.38 (0.10), residues: 1433 sheet: -2.43 (0.11), residues: 2045 loop : -2.58 (0.06), residues: 8826 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2758 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 2488 time to evaluate : 8.501 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 outliers start: 270 outliers final: 121 residues processed: 2639 average time/residue: 0.8611 time to fit residues: 3963.2860 Evaluate side-chains 2304 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 2183 time to evaluate : 8.279 Switching outliers to nearest non-outliers outliers start: 121 outliers final: 0 residues processed: 121 average time/residue: 0.6880 time to fit residues: 171.0803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 1104 optimal weight: 20.0000 chunk 840 optimal weight: 10.0000 chunk 580 optimal weight: 0.7980 chunk 123 optimal weight: 0.3980 chunk 533 optimal weight: 8.9990 chunk 750 optimal weight: 9.9990 chunk 1122 optimal weight: 10.0000 chunk 1187 optimal weight: 10.0000 chunk 586 optimal weight: 20.0000 chunk 1063 optimal weight: 6.9990 chunk 320 optimal weight: 7.9990 overall best weight: 5.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN B 293 GLN B 365 GLN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 GLN B 905 HIS ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 813 GLN C 902 HIS ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN D 472 ASN D 506 ASN ** D 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN E 330 GLN ** E 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 ASN E 597 HIS ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 707 ASN ** E 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 GLN F 243 ASN ** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN F 293 GLN ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 752 GLN ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 472 ASN ** G 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 788 GLN ** G 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 HIS ** H 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 ASN ** H 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 308 ASN H 316 ASN H 338 GLN H 597 HIS ** H 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 798 ASN I 122 ASN I 146 GLN I 264 ASN ** I 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 308 ASN ** I 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 379 ASN ** I 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 293 GLN ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 ASN ** J 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 742 GLN ** J 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 863 GLN K 161 GLN ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 308 ASN ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 365 GLN K 440 ASN K 509 ASN K 563 ASN ** K 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 HIS ** L 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 GLN L 273 HIS ** L 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 472 ASN ** L 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 GLN ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN N 281 GLN N 296 GLN ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 ASN O 78 GLN O 107 GLN ** P 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 ASN ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 GLN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.089 100706 Z= 0.336 Angle : 0.775 14.803 137246 Z= 0.390 Chirality : 0.049 0.320 14664 Planarity : 0.006 0.102 18133 Dihedral : 6.617 69.254 13679 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.53 % Favored : 87.41 % Rotamer Outliers : 3.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.34 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.07), residues: 12304 helix: -3.14 (0.10), residues: 1470 sheet: -2.36 (0.11), residues: 2072 loop : -2.43 (0.06), residues: 8762 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2811 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 419 poor density : 2392 time to evaluate : 8.565 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: symmetry clash outliers start: 419 outliers final: 242 residues processed: 2633 average time/residue: 0.8626 time to fit residues: 3974.1697 Evaluate side-chains 2394 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 2152 time to evaluate : 8.274 Switching outliers to nearest non-outliers outliers start: 242 outliers final: 0 residues processed: 242 average time/residue: 0.7025 time to fit residues: 336.1615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 989 optimal weight: 0.6980 chunk 674 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 884 optimal weight: 0.8980 chunk 490 optimal weight: 10.0000 chunk 1013 optimal weight: 40.0000 chunk 821 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 606 optimal weight: 6.9990 chunk 1066 optimal weight: 9.9990 chunk 299 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN A 798 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 ASN ** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 612 ASN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 HIS C 264 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 728 ASN ** C 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN D 264 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN ** D 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 752 GLN ** D 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 ASN ** E 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 572 ASN ** E 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 863 GLN ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 GLN F 243 ASN F 254 ASN ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 587 ASN ** F 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 472 ASN ** G 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 GLN H 14 HIS H 169 GLN ** H 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 308 ASN ** H 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 509 ASN ** H 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 440 ASN ** I 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 742 GLN ** I 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 ASN ** J 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 598 ASN ** J 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 308 ASN ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 509 ASN ** K 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 798 ASN ** L 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 449 ASN ** L 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 472 ASN L 772 GLN ** L 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 337 ASN ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 281 GLN ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 GLN ** T 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 100706 Z= 0.223 Angle : 0.718 16.429 137246 Z= 0.357 Chirality : 0.047 0.298 14664 Planarity : 0.005 0.095 18133 Dihedral : 6.313 66.178 13679 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.18 % Favored : 88.78 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.34 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.07), residues: 12304 helix: -2.83 (0.11), residues: 1467 sheet: -2.20 (0.11), residues: 2076 loop : -2.30 (0.06), residues: 8761 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2540 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 2308 time to evaluate : 8.262 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 outliers start: 232 outliers final: 110 residues processed: 2421 average time/residue: 0.8646 time to fit residues: 3666.4994 Evaluate side-chains 2206 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 2096 time to evaluate : 8.381 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 0 residues processed: 110 average time/residue: 0.7081 time to fit residues: 159.3794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 399 optimal weight: 10.0000 chunk 1069 optimal weight: 7.9990 chunk 234 optimal weight: 5.9990 chunk 697 optimal weight: 0.9990 chunk 293 optimal weight: 10.0000 chunk 1189 optimal weight: 4.9990 chunk 987 optimal weight: 0.5980 chunk 550 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 393 optimal weight: 2.9990 chunk 624 optimal weight: 8.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 ASN ** C 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN ** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 863 GLN F 131 ASN F 243 ASN F 254 ASN ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 624 ASN ** F 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN ** G 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 449 ASN ** G 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 510 HIS ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 HIS H 187 GLN ** H 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN H 308 ASN H 338 GLN ** H 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 707 ASN ** H 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 ASN ** J 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 796 HIS ** L 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 772 GLN ** L 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 281 GLN ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 70 ASN Q 33 GLN ** T 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 100706 Z= 0.245 Angle : 0.721 15.676 137246 Z= 0.357 Chirality : 0.047 0.291 14664 Planarity : 0.005 0.097 18133 Dihedral : 6.196 65.906 13679 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.99 % Favored : 87.97 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.34 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.07), residues: 12304 helix: -2.64 (0.12), residues: 1466 sheet: -2.11 (0.11), residues: 2061 loop : -2.25 (0.06), residues: 8777 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2484 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 2221 time to evaluate : 8.425 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 outliers start: 263 outliers final: 159 residues processed: 2354 average time/residue: 0.8787 time to fit residues: 3633.8085 Evaluate side-chains 2237 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 2078 time to evaluate : 8.389 Switching outliers to nearest non-outliers outliers start: 159 outliers final: 0 residues processed: 159 average time/residue: 0.7346 time to fit residues: 232.3419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 1146 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 677 optimal weight: 30.0000 chunk 868 optimal weight: 10.0000 chunk 672 optimal weight: 9.9990 chunk 1000 optimal weight: 7.9990 chunk 664 optimal weight: 10.0000 chunk 1184 optimal weight: 9.9990 chunk 741 optimal weight: 30.0000 chunk 722 optimal weight: 9.9990 chunk 546 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN A 308 ASN A 338 GLN ** A 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 HIS ** B 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 788 GLN E 795 GLN E 796 HIS ** E 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 863 GLN ** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** F 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN ** G 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 472 ASN G 510 HIS ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 GLN ** H 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 308 ASN H 338 GLN H 380 HIS ** H 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 795 GLN ** H 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 872 HIS ** J 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 ASN ** J 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 308 ASN ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 429 ASN ** K 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 563 ASN ** K 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 777 GLN ** L 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 ASN L 365 GLN L 464 ASN L 748 ASN ** L 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 208 ASN N 281 GLN ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 GLN R 39 ASN ** T 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.118 100706 Z= 0.465 Angle : 0.841 15.682 137246 Z= 0.425 Chirality : 0.052 0.359 14664 Planarity : 0.006 0.105 18133 Dihedral : 6.659 69.066 13679 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 14.07 % Favored : 85.89 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.34 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.07), residues: 12304 helix: -2.83 (0.11), residues: 1502 sheet: -2.20 (0.11), residues: 2067 loop : -2.32 (0.06), residues: 8735 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2520 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 2217 time to evaluate : 8.441 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 outliers start: 303 outliers final: 177 residues processed: 2384 average time/residue: 0.8832 time to fit residues: 3698.1984 Evaluate side-chains 2246 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 2069 time to evaluate : 8.434 Switching outliers to nearest non-outliers outliers start: 177 outliers final: 0 residues processed: 177 average time/residue: 0.7443 time to fit residues: 260.0482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 732 optimal weight: 1.9990 chunk 473 optimal weight: 4.9990 chunk 707 optimal weight: 1.9990 chunk 356 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 753 optimal weight: 8.9990 chunk 807 optimal weight: 7.9990 chunk 585 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 931 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 707 ASN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 795 GLN ** B 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 472 ASN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 HIS ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 ASN ** E 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 788 GLN E 863 GLN ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 ASN ** F 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 510 HIS ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 308 ASN ** H 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 338 GLN H 492 ASN H 587 ASN ** H 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 ASN ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 ASN ** J 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 598 ASN ** J 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 GLN ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 308 ASN ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 506 ASN ** K 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 798 ASN ** L 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 281 GLN ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 70 ASN ** P 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 ASN ** T 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 100706 Z= 0.239 Angle : 0.755 16.511 137246 Z= 0.373 Chirality : 0.048 0.368 14664 Planarity : 0.005 0.095 18133 Dihedral : 6.372 64.384 13679 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.35 % Favored : 88.61 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.34 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.07), residues: 12304 helix: -2.58 (0.12), residues: 1496 sheet: -2.04 (0.11), residues: 2042 loop : -2.19 (0.07), residues: 8766 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2371 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 2203 time to evaluate : 8.503 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 outliers start: 168 outliers final: 94 residues processed: 2283 average time/residue: 0.8981 time to fit residues: 3615.7410 Evaluate side-chains 2153 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 2059 time to evaluate : 8.432 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 0 residues processed: 94 average time/residue: 0.7442 time to fit residues: 143.9442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 1077 optimal weight: 10.0000 chunk 1134 optimal weight: 5.9990 chunk 1035 optimal weight: 9.9990 chunk 1103 optimal weight: 10.0000 chunk 664 optimal weight: 0.0570 chunk 480 optimal weight: 20.0000 chunk 866 optimal weight: 2.9990 chunk 338 optimal weight: 10.0000 chunk 997 optimal weight: 9.9990 chunk 1044 optimal weight: 4.9990 chunk 1100 optimal weight: 7.9990 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN ** C 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 572 ASN ** E 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 788 GLN E 863 GLN ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 ASN ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 365 GLN ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 472 ASN G 492 ASN G 510 HIS ** G 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 624 ASN ** G 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 872 HIS ** H 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 338 GLN ** H 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 752 GLN ** I 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 ASN ** J 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 ASN ** M 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 281 GLN ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 205 ASN ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 100706 Z= 0.304 Angle : 0.774 16.740 137246 Z= 0.384 Chirality : 0.049 0.373 14664 Planarity : 0.005 0.100 18133 Dihedral : 6.362 65.639 13679 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.04 % Favored : 86.92 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.34 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.07), residues: 12304 helix: -2.50 (0.12), residues: 1502 sheet: -2.05 (0.11), residues: 2050 loop : -2.18 (0.07), residues: 8752 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2249 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 2133 time to evaluate : 8.362 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 outliers start: 116 outliers final: 68 residues processed: 2188 average time/residue: 0.9321 time to fit residues: 3597.6829 Evaluate side-chains 2124 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 2056 time to evaluate : 8.368 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.7408 time to fit residues: 107.2125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 724 optimal weight: 0.8980 chunk 1167 optimal weight: 0.0970 chunk 712 optimal weight: 9.9990 chunk 553 optimal weight: 10.0000 chunk 811 optimal weight: 9.9990 chunk 1224 optimal weight: 9.9990 chunk 1126 optimal weight: 4.9990 chunk 974 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 753 optimal weight: 8.9990 chunk 597 optimal weight: 6.9990 overall best weight: 2.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN A 320 ASN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN ** C 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 788 GLN E 795 GLN E 863 GLN F 182 GLN ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS ** G 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 320 ASN ** G 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 510 HIS ** G 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 624 ASN ** G 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 308 ASN H 320 ASN H 338 GLN ** H 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 587 ASN ** H 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 281 GLN ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 ASN ** T 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 100706 Z= 0.235 Angle : 0.755 17.072 137246 Z= 0.372 Chirality : 0.048 0.343 14664 Planarity : 0.005 0.094 18133 Dihedral : 6.231 64.092 13679 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.46 % Favored : 88.51 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.34 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.07), residues: 12304 helix: -2.30 (0.12), residues: 1462 sheet: -2.00 (0.11), residues: 2033 loop : -2.11 (0.07), residues: 8809 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24608 Ramachandran restraints generated. 12304 Oldfield, 0 Emsley, 12304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2242 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 2183 time to evaluate : 8.680 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 outliers start: 59 outliers final: 33 residues processed: 2209 average time/residue: 0.8802 time to fit residues: 3420.4260 Evaluate side-chains 2097 residues out of total 10642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 2064 time to evaluate : 8.312 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.7485 time to fit residues: 58.0952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 774 optimal weight: 5.9990 chunk 1038 optimal weight: 9.9990 chunk 298 optimal weight: 8.9990 chunk 899 optimal weight: 20.0000 chunk 143 optimal weight: 7.9990 chunk 270 optimal weight: 10.0000 chunk 976 optimal weight: 7.9990 chunk 408 optimal weight: 5.9990 chunk 1002 optimal weight: 10.0000 chunk 123 optimal weight: 0.0040 chunk 179 optimal weight: 5.9990 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN A 338 GLN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN ** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 612 ASN ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 HIS ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN ** D 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 788 GLN E 863 GLN E 903 GLN ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 472 ASN ** G 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 510 HIS G 624 ASN ** G 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 863 GLN H 131 ASN ** H 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 320 ASN H 338 GLN ** H 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 ASN J 320 ASN J 380 HIS ** J 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 504 ASN ** K 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 281 GLN ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 ASN ** T 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.136535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.121717 restraints weight = 148398.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.123952 restraints weight = 91695.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.125151 restraints weight = 60769.956| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 100706 Z= 0.343 Angle : 0.802 17.138 137246 Z= 0.399 Chirality : 0.050 0.384 14664 Planarity : 0.006 0.103 18133 Dihedral : 6.382 66.098 13679 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.39 % Favored : 86.57 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.34 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.07), residues: 12304 helix: -2.34 (0.12), residues: 1475 sheet: -2.01 (0.11), residues: 2076 loop : -2.13 (0.07), residues: 8753