Starting phenix.real_space_refine on Sun Dec 29 10:48:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yn5_10849/12_2024/6yn5_10849.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yn5_10849/12_2024/6yn5_10849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6yn5_10849/12_2024/6yn5_10849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yn5_10849/12_2024/6yn5_10849.map" model { file = "/net/cci-nas-00/data/ceres_data/6yn5_10849/12_2024/6yn5_10849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yn5_10849/12_2024/6yn5_10849.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.335 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 370 5.16 5 C 36466 2.51 5 N 9500 2.21 5 O 10648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 160 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 56994 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 5697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 5703 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 5832 Chain: "D" Number of atoms: 5703 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 5832 Chain: "E" Number of atoms: 5697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 5697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 5697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 5703 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 5832 Chain: "I" Number of atoms: 5703 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 5832 Chain: "J" Number of atoms: 5697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 32.08, per 1000 atoms: 0.56 Number of scatterers: 56994 At special positions: 0 Unit cell: (197.784, 192.96, 104.922, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 370 16.00 P 10 15.00 O 10648 8.00 N 9500 7.00 C 36466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.02 Conformation dependent library (CDL) restraints added in 7.9 seconds 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13348 Finding SS restraints... Secondary structure from input PDB file: 302 helices and 70 sheets defined 49.6% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.66 Creating SS restraints... Processing helix chain 'A' and resid 12 through 28 Proline residue: A 18 - end of helix Processing helix chain 'A' and resid 38 through 49 Processing helix chain 'A' and resid 59 through 74 removed outlier: 5.887A pdb=" N LEU A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLU A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'A' and resid 172 through 178 removed outlier: 3.741A pdb=" N MET A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 removed outlier: 3.566A pdb=" N LEU A 187 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 209 Processing helix chain 'A' and resid 218 through 232 removed outlier: 3.730A pdb=" N THR A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 255 removed outlier: 3.707A pdb=" N THR A 249 " --> pdb=" O HIS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 336 through 344 removed outlier: 4.157A pdb=" N SER A 340 " --> pdb=" O THR A 337 " (cutoff:3.500A) Proline residue: A 341 - end of helix removed outlier: 3.559A pdb=" N GLU A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 385 through 395 Processing helix chain 'A' and resid 402 through 416 Processing helix chain 'A' and resid 417 through 446 removed outlier: 3.780A pdb=" N GLY A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 521 removed outlier: 3.808A pdb=" N VAL A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 562 Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 570 through 577 removed outlier: 3.684A pdb=" N ASP A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 601 Processing helix chain 'A' and resid 601 through 610 removed outlier: 3.689A pdb=" N PHE A 610 " --> pdb=" O MET A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 629 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 669 through 683 removed outlier: 3.981A pdb=" N LEU A 673 " --> pdb=" O SER A 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 29 Proline residue: B 18 - end of helix Processing helix chain 'B' and resid 38 through 49 Processing helix chain 'B' and resid 59 through 74 removed outlier: 6.093A pdb=" N LEU B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLU B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 109 through 129 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 157 through 160 removed outlier: 3.555A pdb=" N LYS B 160 " --> pdb=" O ALA B 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 160' Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 172 through 178 removed outlier: 3.584A pdb=" N MET B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 188 removed outlier: 3.625A pdb=" N LEU B 187 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 188 " --> pdb=" O SER B 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 184 through 188' Processing helix chain 'B' and resid 195 through 209 Processing helix chain 'B' and resid 218 through 232 removed outlier: 3.774A pdb=" N THR B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 255 removed outlier: 3.687A pdb=" N THR B 249 " --> pdb=" O HIS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 280 Processing helix chain 'B' and resid 281 through 292 Processing helix chain 'B' and resid 314 through 322 Processing helix chain 'B' and resid 336 through 344 removed outlier: 4.131A pdb=" N SER B 340 " --> pdb=" O THR B 337 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.609A pdb=" N GLU B 344 " --> pdb=" O PRO B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 385 through 395 Processing helix chain 'B' and resid 402 through 416 Processing helix chain 'B' and resid 417 through 446 removed outlier: 3.856A pdb=" N GLY B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 521 removed outlier: 3.799A pdb=" N VAL B 514 " --> pdb=" O PRO B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 562 Processing helix chain 'B' and resid 565 through 570 Processing helix chain 'B' and resid 570 through 577 removed outlier: 3.704A pdb=" N ASP B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 601 Processing helix chain 'B' and resid 601 through 611 removed outlier: 3.630A pdb=" N PHE B 610 " --> pdb=" O MET B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 629 Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 669 through 683 removed outlier: 3.967A pdb=" N LEU B 673 " --> pdb=" O SER B 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 29 Proline residue: C 18 - end of helix Processing helix chain 'C' and resid 38 through 49 Processing helix chain 'C' and resid 59 through 72 removed outlier: 6.063A pdb=" N LEU C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLU C 65 " --> pdb=" O LYS C 61 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLU C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 109 through 129 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 157 through 160 removed outlier: 3.546A pdb=" N LYS C 160 " --> pdb=" O ALA C 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 157 through 160' Processing helix chain 'C' and resid 161 through 172 Processing helix chain 'C' and resid 172 through 178 removed outlier: 3.552A pdb=" N MET C 176 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 188 removed outlier: 3.522A pdb=" N LEU C 187 " --> pdb=" O VAL C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 209 Processing helix chain 'C' and resid 218 through 232 removed outlier: 3.614A pdb=" N THR C 222 " --> pdb=" O ASN C 218 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 255 Processing helix chain 'C' and resid 276 through 280 Processing helix chain 'C' and resid 281 through 292 Processing helix chain 'C' and resid 314 through 322 Processing helix chain 'C' and resid 340 through 344 removed outlier: 3.695A pdb=" N GLU C 344 " --> pdb=" O PRO C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 385 through 395 Processing helix chain 'C' and resid 402 through 416 removed outlier: 3.648A pdb=" N ALA C 413 " --> pdb=" O THR C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 446 Processing helix chain 'C' and resid 510 through 521 removed outlier: 3.831A pdb=" N VAL C 514 " --> pdb=" O PRO C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 562 Processing helix chain 'C' and resid 565 through 570 Processing helix chain 'C' and resid 570 through 577 removed outlier: 3.679A pdb=" N ASP C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 601 Processing helix chain 'C' and resid 601 through 612 removed outlier: 3.896A pdb=" N VAL C 612 " --> pdb=" O ARG C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 629 Processing helix chain 'C' and resid 638 through 640 No H-bonds generated for 'chain 'C' and resid 638 through 640' Processing helix chain 'C' and resid 669 through 683 removed outlier: 4.041A pdb=" N LEU C 673 " --> pdb=" O SER C 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 29 Proline residue: D 18 - end of helix Processing helix chain 'D' and resid 38 through 49 Processing helix chain 'D' and resid 59 through 74 removed outlier: 5.865A pdb=" N LEU D 64 " --> pdb=" O ASP D 60 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLU D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLU D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLU D 69 " --> pdb=" O GLU D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 130 through 143 Processing helix chain 'D' and resid 157 through 160 removed outlier: 3.536A pdb=" N LYS D 160 " --> pdb=" O ALA D 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 157 through 160' Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 172 through 178 removed outlier: 3.662A pdb=" N MET D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 188 Processing helix chain 'D' and resid 195 through 209 Processing helix chain 'D' and resid 218 through 232 removed outlier: 3.719A pdb=" N THR D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS D 225 " --> pdb=" O SER D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 254 Processing helix chain 'D' and resid 276 through 280 Processing helix chain 'D' and resid 281 through 292 Processing helix chain 'D' and resid 314 through 322 Processing helix chain 'D' and resid 336 through 344 removed outlier: 4.045A pdb=" N SER D 340 " --> pdb=" O THR D 337 " (cutoff:3.500A) Proline residue: D 341 - end of helix removed outlier: 3.584A pdb=" N GLU D 344 " --> pdb=" O PRO D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 369 Processing helix chain 'D' and resid 385 through 395 Processing helix chain 'D' and resid 402 through 416 removed outlier: 3.650A pdb=" N ALA D 413 " --> pdb=" O THR D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 446 Processing helix chain 'D' and resid 510 through 521 removed outlier: 3.714A pdb=" N VAL D 514 " --> pdb=" O PRO D 510 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS D 521 " --> pdb=" O TYR D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 562 Processing helix chain 'D' and resid 565 through 570 Processing helix chain 'D' and resid 570 through 577 removed outlier: 3.636A pdb=" N ASP D 577 " --> pdb=" O LEU D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 601 Processing helix chain 'D' and resid 601 through 611 Processing helix chain 'D' and resid 619 through 629 Processing helix chain 'D' and resid 638 through 641 removed outlier: 4.622A pdb=" N VAL D 641 " --> pdb=" O ASP D 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 638 through 641' Processing helix chain 'D' and resid 669 through 683 removed outlier: 3.997A pdb=" N LEU D 673 " --> pdb=" O SER D 669 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU D 676 " --> pdb=" O VAL D 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 29 Proline residue: E 18 - end of helix Processing helix chain 'E' and resid 38 through 49 Processing helix chain 'E' and resid 59 through 74 removed outlier: 6.011A pdb=" N LEU E 64 " --> pdb=" O ASP E 60 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLU E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 130 through 143 Processing helix chain 'E' and resid 161 through 172 Processing helix chain 'E' and resid 172 through 178 removed outlier: 3.597A pdb=" N MET E 176 " --> pdb=" O GLY E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 188 Processing helix chain 'E' and resid 195 through 209 Processing helix chain 'E' and resid 218 through 232 removed outlier: 3.730A pdb=" N THR E 222 " --> pdb=" O ASN E 218 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS E 225 " --> pdb=" O SER E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 255 removed outlier: 3.586A pdb=" N THR E 249 " --> pdb=" O HIS E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 280 Processing helix chain 'E' and resid 281 through 292 Processing helix chain 'E' and resid 314 through 322 Processing helix chain 'E' and resid 340 through 344 removed outlier: 3.542A pdb=" N GLU E 344 " --> pdb=" O PRO E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 369 Processing helix chain 'E' and resid 385 through 397 removed outlier: 3.728A pdb=" N HIS E 396 " --> pdb=" O ALA E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 416 removed outlier: 3.712A pdb=" N ALA E 413 " --> pdb=" O THR E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 446 Processing helix chain 'E' and resid 510 through 521 removed outlier: 3.773A pdb=" N VAL E 514 " --> pdb=" O PRO E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 562 Processing helix chain 'E' and resid 565 through 570 Processing helix chain 'E' and resid 570 through 577 removed outlier: 3.612A pdb=" N ASP E 577 " --> pdb=" O LEU E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 601 Processing helix chain 'E' and resid 601 through 611 Processing helix chain 'E' and resid 619 through 629 Processing helix chain 'E' and resid 638 through 640 No H-bonds generated for 'chain 'E' and resid 638 through 640' Processing helix chain 'E' and resid 669 through 683 removed outlier: 3.975A pdb=" N LEU E 673 " --> pdb=" O SER E 669 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 28 Proline residue: F 18 - end of helix Processing helix chain 'F' and resid 38 through 49 Processing helix chain 'F' and resid 59 through 74 removed outlier: 5.882A pdb=" N LEU F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N GLU F 65 " --> pdb=" O LYS F 61 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLU F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLU F 69 " --> pdb=" O GLU F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 130 through 143 Processing helix chain 'F' and resid 157 through 160 Processing helix chain 'F' and resid 161 through 178 Proline residue: F 173 - end of helix removed outlier: 3.640A pdb=" N MET F 176 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 188 removed outlier: 3.563A pdb=" N LEU F 187 " --> pdb=" O VAL F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 209 Processing helix chain 'F' and resid 218 through 232 removed outlier: 3.736A pdb=" N THR F 222 " --> pdb=" O ASN F 218 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS F 225 " --> pdb=" O SER F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 255 removed outlier: 3.683A pdb=" N THR F 249 " --> pdb=" O HIS F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 280 Processing helix chain 'F' and resid 281 through 291 Processing helix chain 'F' and resid 314 through 322 Processing helix chain 'F' and resid 336 through 344 removed outlier: 4.157A pdb=" N SER F 340 " --> pdb=" O THR F 337 " (cutoff:3.500A) Proline residue: F 341 - end of helix removed outlier: 3.560A pdb=" N GLU F 344 " --> pdb=" O PRO F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 369 Processing helix chain 'F' and resid 385 through 395 Processing helix chain 'F' and resid 402 through 416 Processing helix chain 'F' and resid 417 through 446 removed outlier: 3.813A pdb=" N GLY F 421 " --> pdb=" O LYS F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 521 removed outlier: 3.819A pdb=" N VAL F 514 " --> pdb=" O PRO F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 562 Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 570 through 577 removed outlier: 3.647A pdb=" N ASP F 577 " --> pdb=" O LEU F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 585 through 601 Processing helix chain 'F' and resid 601 through 610 removed outlier: 3.639A pdb=" N PHE F 610 " --> pdb=" O MET F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 629 Processing helix chain 'F' and resid 638 through 640 No H-bonds generated for 'chain 'F' and resid 638 through 640' Processing helix chain 'F' and resid 666 through 668 No H-bonds generated for 'chain 'F' and resid 666 through 668' Processing helix chain 'F' and resid 669 through 683 removed outlier: 4.039A pdb=" N LEU F 673 " --> pdb=" O SER F 669 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 29 Proline residue: G 18 - end of helix Processing helix chain 'G' and resid 38 through 49 Processing helix chain 'G' and resid 59 through 74 removed outlier: 6.094A pdb=" N LEU G 64 " --> pdb=" O ASP G 60 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLU G 65 " --> pdb=" O LYS G 61 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLU G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLU G 69 " --> pdb=" O GLU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 94 Processing helix chain 'G' and resid 109 through 129 Processing helix chain 'G' and resid 130 through 143 Processing helix chain 'G' and resid 157 through 160 removed outlier: 3.604A pdb=" N LYS G 160 " --> pdb=" O ALA G 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 157 through 160' Processing helix chain 'G' and resid 161 through 172 Processing helix chain 'G' and resid 172 through 178 removed outlier: 3.556A pdb=" N MET G 176 " --> pdb=" O GLY G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 188 removed outlier: 3.655A pdb=" N LEU G 187 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY G 188 " --> pdb=" O SER G 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 184 through 188' Processing helix chain 'G' and resid 195 through 209 Processing helix chain 'G' and resid 218 through 232 removed outlier: 3.701A pdb=" N THR G 222 " --> pdb=" O ASN G 218 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS G 225 " --> pdb=" O SER G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 255 removed outlier: 3.561A pdb=" N THR G 249 " --> pdb=" O HIS G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 280 Processing helix chain 'G' and resid 281 through 292 Processing helix chain 'G' and resid 314 through 322 Processing helix chain 'G' and resid 336 through 344 removed outlier: 4.133A pdb=" N SER G 340 " --> pdb=" O THR G 337 " (cutoff:3.500A) Proline residue: G 341 - end of helix removed outlier: 3.609A pdb=" N GLU G 344 " --> pdb=" O PRO G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 369 Processing helix chain 'G' and resid 385 through 395 Processing helix chain 'G' and resid 402 through 416 Processing helix chain 'G' and resid 418 through 446 Processing helix chain 'G' and resid 510 through 521 removed outlier: 3.800A pdb=" N VAL G 514 " --> pdb=" O PRO G 510 " (cutoff:3.500A) Processing helix chain 'G' and resid 542 through 562 Processing helix chain 'G' and resid 565 through 570 Processing helix chain 'G' and resid 570 through 577 removed outlier: 3.717A pdb=" N ASP G 577 " --> pdb=" O LEU G 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 585 through 601 Processing helix chain 'G' and resid 601 through 611 removed outlier: 3.646A pdb=" N PHE G 610 " --> pdb=" O MET G 606 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 629 Processing helix chain 'G' and resid 638 through 640 No H-bonds generated for 'chain 'G' and resid 638 through 640' Processing helix chain 'G' and resid 666 through 668 No H-bonds generated for 'chain 'G' and resid 666 through 668' Processing helix chain 'G' and resid 669 through 683 removed outlier: 3.969A pdb=" N LEU G 673 " --> pdb=" O SER G 669 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 29 Proline residue: H 18 - end of helix Processing helix chain 'H' and resid 38 through 49 Processing helix chain 'H' and resid 59 through 72 removed outlier: 6.063A pdb=" N LEU H 64 " --> pdb=" O ASP H 60 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLU H 65 " --> pdb=" O LYS H 61 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLU H 68 " --> pdb=" O LEU H 64 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLU H 69 " --> pdb=" O GLU H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 109 through 129 Processing helix chain 'H' and resid 130 through 143 Processing helix chain 'H' and resid 157 through 160 removed outlier: 3.568A pdb=" N LYS H 160 " --> pdb=" O ALA H 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 157 through 160' Processing helix chain 'H' and resid 161 through 172 Processing helix chain 'H' and resid 172 through 178 removed outlier: 3.553A pdb=" N MET H 176 " --> pdb=" O GLY H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 188 removed outlier: 3.522A pdb=" N LEU H 187 " --> pdb=" O VAL H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 209 Processing helix chain 'H' and resid 218 through 232 removed outlier: 3.653A pdb=" N THR H 222 " --> pdb=" O ASN H 218 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS H 225 " --> pdb=" O SER H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 255 Processing helix chain 'H' and resid 276 through 280 Processing helix chain 'H' and resid 281 through 292 Processing helix chain 'H' and resid 314 through 322 Processing helix chain 'H' and resid 340 through 344 removed outlier: 3.695A pdb=" N GLU H 344 " --> pdb=" O PRO H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 369 Processing helix chain 'H' and resid 385 through 395 Processing helix chain 'H' and resid 402 through 416 removed outlier: 3.645A pdb=" N ALA H 413 " --> pdb=" O THR H 409 " (cutoff:3.500A) Processing helix chain 'H' and resid 418 through 446 Processing helix chain 'H' and resid 510 through 521 removed outlier: 3.835A pdb=" N VAL H 514 " --> pdb=" O PRO H 510 " (cutoff:3.500A) Processing helix chain 'H' and resid 542 through 562 Processing helix chain 'H' and resid 565 through 570 Processing helix chain 'H' and resid 570 through 577 removed outlier: 3.680A pdb=" N ASP H 577 " --> pdb=" O LEU H 573 " (cutoff:3.500A) Processing helix chain 'H' and resid 585 through 601 Processing helix chain 'H' and resid 601 through 611 Processing helix chain 'H' and resid 619 through 629 Processing helix chain 'H' and resid 638 through 640 No H-bonds generated for 'chain 'H' and resid 638 through 640' Processing helix chain 'H' and resid 666 through 668 No H-bonds generated for 'chain 'H' and resid 666 through 668' Processing helix chain 'H' and resid 669 through 683 removed outlier: 4.044A pdb=" N LEU H 673 " --> pdb=" O SER H 669 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 29 Proline residue: I 18 - end of helix Processing helix chain 'I' and resid 38 through 49 Processing helix chain 'I' and resid 59 through 74 removed outlier: 5.837A pdb=" N LEU I 64 " --> pdb=" O ASP I 60 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLU I 65 " --> pdb=" O LYS I 61 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLU I 68 " --> pdb=" O LEU I 64 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLU I 69 " --> pdb=" O GLU I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 94 Processing helix chain 'I' and resid 109 through 129 Processing helix chain 'I' and resid 130 through 143 Processing helix chain 'I' and resid 157 through 160 removed outlier: 3.530A pdb=" N LYS I 160 " --> pdb=" O ALA I 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 157 through 160' Processing helix chain 'I' and resid 161 through 172 Processing helix chain 'I' and resid 172 through 178 removed outlier: 3.611A pdb=" N MET I 176 " --> pdb=" O GLY I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 188 Processing helix chain 'I' and resid 195 through 209 Processing helix chain 'I' and resid 218 through 232 removed outlier: 3.718A pdb=" N THR I 222 " --> pdb=" O ASN I 218 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS I 225 " --> pdb=" O SER I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 245 through 254 removed outlier: 3.507A pdb=" N THR I 249 " --> pdb=" O HIS I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 276 through 280 Processing helix chain 'I' and resid 281 through 292 Processing helix chain 'I' and resid 314 through 322 Processing helix chain 'I' and resid 336 through 344 removed outlier: 4.044A pdb=" N SER I 340 " --> pdb=" O THR I 337 " (cutoff:3.500A) Proline residue: I 341 - end of helix removed outlier: 3.583A pdb=" N GLU I 344 " --> pdb=" O PRO I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 369 Processing helix chain 'I' and resid 385 through 395 Processing helix chain 'I' and resid 402 through 416 removed outlier: 3.651A pdb=" N ALA I 413 " --> pdb=" O THR I 409 " (cutoff:3.500A) Processing helix chain 'I' and resid 418 through 446 Processing helix chain 'I' and resid 510 through 521 removed outlier: 3.714A pdb=" N VAL I 514 " --> pdb=" O PRO I 510 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS I 521 " --> pdb=" O TYR I 517 " (cutoff:3.500A) Processing helix chain 'I' and resid 542 through 562 Processing helix chain 'I' and resid 565 through 570 Processing helix chain 'I' and resid 570 through 577 removed outlier: 3.748A pdb=" N ASP I 577 " --> pdb=" O LEU I 573 " (cutoff:3.500A) Processing helix chain 'I' and resid 585 through 601 Processing helix chain 'I' and resid 601 through 611 Processing helix chain 'I' and resid 619 through 629 Processing helix chain 'I' and resid 638 through 640 No H-bonds generated for 'chain 'I' and resid 638 through 640' Processing helix chain 'I' and resid 669 through 683 removed outlier: 3.999A pdb=" N LEU I 673 " --> pdb=" O SER I 669 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU I 676 " --> pdb=" O VAL I 672 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 29 Proline residue: J 18 - end of helix Processing helix chain 'J' and resid 38 through 49 Processing helix chain 'J' and resid 59 through 72 removed outlier: 6.053A pdb=" N LEU J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLU J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU J 68 " --> pdb=" O LEU J 64 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLU J 69 " --> pdb=" O GLU J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 94 Processing helix chain 'J' and resid 109 through 129 Processing helix chain 'J' and resid 130 through 143 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 172 through 178 removed outlier: 3.597A pdb=" N MET J 176 " --> pdb=" O GLY J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 188 Processing helix chain 'J' and resid 195 through 209 Processing helix chain 'J' and resid 218 through 232 removed outlier: 3.730A pdb=" N THR J 222 " --> pdb=" O ASN J 218 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS J 225 " --> pdb=" O SER J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 245 through 255 removed outlier: 3.596A pdb=" N THR J 249 " --> pdb=" O HIS J 245 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 280 Processing helix chain 'J' and resid 281 through 292 Processing helix chain 'J' and resid 314 through 322 Processing helix chain 'J' and resid 340 through 344 removed outlier: 3.541A pdb=" N GLU J 344 " --> pdb=" O PRO J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 369 Processing helix chain 'J' and resid 385 through 395 Processing helix chain 'J' and resid 402 through 416 removed outlier: 3.714A pdb=" N ALA J 413 " --> pdb=" O THR J 409 " (cutoff:3.500A) Processing helix chain 'J' and resid 418 through 446 Processing helix chain 'J' and resid 510 through 521 removed outlier: 3.770A pdb=" N VAL J 514 " --> pdb=" O PRO J 510 " (cutoff:3.500A) Processing helix chain 'J' and resid 542 through 562 Processing helix chain 'J' and resid 565 through 570 Processing helix chain 'J' and resid 570 through 577 removed outlier: 3.678A pdb=" N ASP J 577 " --> pdb=" O LEU J 573 " (cutoff:3.500A) Processing helix chain 'J' and resid 585 through 601 Processing helix chain 'J' and resid 601 through 611 Processing helix chain 'J' and resid 619 through 629 Processing helix chain 'J' and resid 638 through 640 No H-bonds generated for 'chain 'J' and resid 638 through 640' Processing helix chain 'J' and resid 669 through 683 removed outlier: 3.965A pdb=" N LEU J 673 " --> pdb=" O SER J 669 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.868A pdb=" N VAL A 3 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ILE A 56 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA A 5 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N ASP A 58 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU A 7 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N CYS A 53 " --> pdb=" O PRO A 78 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N TYR A 80 " --> pdb=" O CYS A 53 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A 55 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE A 82 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE A 57 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 212 through 216 removed outlier: 6.226A pdb=" N ALA A 301 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ASP A 330 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE A 303 " --> pdb=" O ASP A 330 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N HIS A 300 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE A 238 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE A 262 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE A 240 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 453 removed outlier: 4.050A pdb=" N LYS A 527 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 615 through 616 Processing sheet with id=AA6, first strand: chain 'A' and resid 632 through 636 Processing sheet with id=AA7, first strand: chain 'A' and resid 650 through 652 removed outlier: 4.513A pdb=" N ASP A 692 " --> pdb=" O TYR A 652 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 32 through 34 removed outlier: 6.917A pdb=" N VAL B 3 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ILE B 56 " --> pdb=" O VAL B 3 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA B 5 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ASP B 58 " --> pdb=" O ALA B 5 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N LEU B 7 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS B 53 " --> pdb=" O PRO B 78 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N TYR B 80 " --> pdb=" O CYS B 53 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL B 55 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N PHE B 82 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N PHE B 57 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 212 through 216 removed outlier: 6.261A pdb=" N ALA B 301 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASP B 330 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE B 303 " --> pdb=" O ASP B 330 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR B 237 " --> pdb=" O HIS B 300 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N VAL B 302 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU B 239 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N THR B 304 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ASP B 241 " --> pdb=" O THR B 304 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE B 238 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N PHE B 262 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE B 240 " --> pdb=" O PHE B 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 311 through 313 Processing sheet with id=AB2, first strand: chain 'B' and resid 452 through 453 removed outlier: 4.001A pdb=" N LYS B 527 " --> pdb=" O LEU B 534 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 615 through 616 Processing sheet with id=AB4, first strand: chain 'B' and resid 632 through 636 Processing sheet with id=AB5, first strand: chain 'B' and resid 650 through 652 removed outlier: 4.505A pdb=" N ASP B 692 " --> pdb=" O TYR B 652 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.955A pdb=" N VAL C 3 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N ILE C 56 " --> pdb=" O VAL C 3 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA C 5 " --> pdb=" O ILE C 56 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N ASP C 58 " --> pdb=" O ALA C 5 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N LEU C 7 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS C 53 " --> pdb=" O PRO C 78 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N TYR C 80 " --> pdb=" O CYS C 53 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL C 55 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N PHE C 82 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE C 57 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 212 through 216 removed outlier: 6.268A pdb=" N ALA C 301 " --> pdb=" O HIS C 328 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ASP C 330 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE C 303 " --> pdb=" O ASP C 330 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR C 237 " --> pdb=" O HIS C 300 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N VAL C 302 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU C 239 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N THR C 304 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N ASP C 241 " --> pdb=" O THR C 304 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE C 238 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N PHE C 262 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE C 240 " --> pdb=" O PHE C 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 311 through 313 Processing sheet with id=AB9, first strand: chain 'C' and resid 452 through 453 removed outlier: 3.950A pdb=" N LYS C 527 " --> pdb=" O LEU C 534 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 615 through 616 Processing sheet with id=AC2, first strand: chain 'C' and resid 632 through 636 Processing sheet with id=AC3, first strand: chain 'C' and resid 650 through 652 removed outlier: 4.477A pdb=" N ASP C 692 " --> pdb=" O TYR C 652 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 32 through 34 removed outlier: 6.945A pdb=" N VAL D 3 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ILE D 56 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA D 5 " --> pdb=" O ILE D 56 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N ASP D 58 " --> pdb=" O ALA D 5 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N LEU D 7 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N CYS D 53 " --> pdb=" O PRO D 78 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N TYR D 80 " --> pdb=" O CYS D 53 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL D 55 " --> pdb=" O TYR D 80 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N PHE D 82 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE D 57 " --> pdb=" O PHE D 82 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 212 through 216 removed outlier: 6.217A pdb=" N ALA D 301 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP D 330 " --> pdb=" O ALA D 301 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE D 303 " --> pdb=" O ASP D 330 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS D 300 " --> pdb=" O THR D 237 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE D 238 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE D 262 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE D 240 " --> pdb=" O PHE D 262 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 311 through 313 Processing sheet with id=AC7, first strand: chain 'D' and resid 452 through 453 removed outlier: 3.930A pdb=" N LYS D 527 " --> pdb=" O LEU D 534 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 615 through 616 Processing sheet with id=AC9, first strand: chain 'D' and resid 632 through 636 Processing sheet with id=AD1, first strand: chain 'D' and resid 650 through 652 removed outlier: 4.584A pdb=" N ASP D 692 " --> pdb=" O TYR D 652 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 32 through 34 removed outlier: 6.913A pdb=" N VAL E 3 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE E 56 " --> pdb=" O VAL E 3 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA E 5 " --> pdb=" O ILE E 56 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ASP E 58 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N LEU E 7 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N CYS E 53 " --> pdb=" O PRO E 78 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N TYR E 80 " --> pdb=" O CYS E 53 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL E 55 " --> pdb=" O TYR E 80 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N PHE E 82 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N PHE E 57 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 212 through 216 removed outlier: 6.259A pdb=" N ALA E 301 " --> pdb=" O HIS E 328 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASP E 330 " --> pdb=" O ALA E 301 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE E 303 " --> pdb=" O ASP E 330 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS E 300 " --> pdb=" O THR E 237 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE E 238 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE E 262 " --> pdb=" O ILE E 238 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE E 240 " --> pdb=" O PHE E 262 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 311 through 313 Processing sheet with id=AD5, first strand: chain 'E' and resid 452 through 453 removed outlier: 3.990A pdb=" N LYS E 527 " --> pdb=" O LEU E 534 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 615 through 616 Processing sheet with id=AD7, first strand: chain 'E' and resid 632 through 636 Processing sheet with id=AD8, first strand: chain 'E' and resid 650 through 652 removed outlier: 4.542A pdb=" N ASP E 692 " --> pdb=" O TYR E 652 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 32 through 34 removed outlier: 6.872A pdb=" N VAL F 3 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ILE F 56 " --> pdb=" O VAL F 3 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA F 5 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N ASP F 58 " --> pdb=" O ALA F 5 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N LEU F 7 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N CYS F 53 " --> pdb=" O PRO F 78 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N TYR F 80 " --> pdb=" O CYS F 53 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL F 55 " --> pdb=" O TYR F 80 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N PHE F 82 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE F 57 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 212 through 216 removed outlier: 6.227A pdb=" N ALA F 301 " --> pdb=" O HIS F 328 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ASP F 330 " --> pdb=" O ALA F 301 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE F 303 " --> pdb=" O ASP F 330 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS F 300 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR F 304 " --> pdb=" O ASP F 241 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE F 238 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE F 262 " --> pdb=" O ILE F 238 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE F 240 " --> pdb=" O PHE F 262 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 311 through 312 Processing sheet with id=AE3, first strand: chain 'F' and resid 452 through 453 removed outlier: 4.008A pdb=" N LYS F 527 " --> pdb=" O LEU F 534 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 615 through 616 Processing sheet with id=AE5, first strand: chain 'F' and resid 632 through 636 Processing sheet with id=AE6, first strand: chain 'F' and resid 650 through 652 removed outlier: 4.451A pdb=" N ASP F 692 " --> pdb=" O TYR F 652 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 32 through 34 removed outlier: 6.914A pdb=" N VAL G 3 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ILE G 56 " --> pdb=" O VAL G 3 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA G 5 " --> pdb=" O ILE G 56 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ASP G 58 " --> pdb=" O ALA G 5 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N LEU G 7 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N CYS G 53 " --> pdb=" O PRO G 78 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N TYR G 80 " --> pdb=" O CYS G 53 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL G 55 " --> pdb=" O TYR G 80 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N PHE G 82 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE G 57 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 212 through 216 removed outlier: 6.262A pdb=" N ALA G 301 " --> pdb=" O HIS G 328 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ASP G 330 " --> pdb=" O ALA G 301 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE G 303 " --> pdb=" O ASP G 330 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR G 237 " --> pdb=" O HIS G 300 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N VAL G 302 " --> pdb=" O THR G 237 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU G 239 " --> pdb=" O VAL G 302 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N THR G 304 " --> pdb=" O LEU G 239 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ASP G 241 " --> pdb=" O THR G 304 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE G 238 " --> pdb=" O ILE G 260 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N PHE G 262 " --> pdb=" O ILE G 238 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE G 240 " --> pdb=" O PHE G 262 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 311 through 313 Processing sheet with id=AF1, first strand: chain 'G' and resid 452 through 453 removed outlier: 4.000A pdb=" N LYS G 527 " --> pdb=" O LEU G 534 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 615 through 616 Processing sheet with id=AF3, first strand: chain 'G' and resid 632 through 636 Processing sheet with id=AF4, first strand: chain 'G' and resid 650 through 652 removed outlier: 4.500A pdb=" N ASP G 692 " --> pdb=" O TYR G 652 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 32 through 34 removed outlier: 6.955A pdb=" N VAL H 3 " --> pdb=" O GLY H 54 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N ILE H 56 " --> pdb=" O VAL H 3 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA H 5 " --> pdb=" O ILE H 56 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N ASP H 58 " --> pdb=" O ALA H 5 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N LEU H 7 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS H 53 " --> pdb=" O PRO H 78 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N TYR H 80 " --> pdb=" O CYS H 53 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL H 55 " --> pdb=" O TYR H 80 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N PHE H 82 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE H 57 " --> pdb=" O PHE H 82 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 212 through 216 removed outlier: 6.252A pdb=" N ALA H 301 " --> pdb=" O HIS H 328 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP H 330 " --> pdb=" O ALA H 301 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE H 303 " --> pdb=" O ASP H 330 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR H 237 " --> pdb=" O HIS H 300 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N VAL H 302 " --> pdb=" O THR H 237 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU H 239 " --> pdb=" O VAL H 302 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N THR H 304 " --> pdb=" O LEU H 239 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ASP H 241 " --> pdb=" O THR H 304 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE H 238 " --> pdb=" O ILE H 260 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE H 262 " --> pdb=" O ILE H 238 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE H 240 " --> pdb=" O PHE H 262 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 311 through 313 Processing sheet with id=AF8, first strand: chain 'H' and resid 452 through 453 removed outlier: 3.951A pdb=" N LYS H 527 " --> pdb=" O LEU H 534 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 615 through 616 Processing sheet with id=AG1, first strand: chain 'H' and resid 632 through 636 Processing sheet with id=AG2, first strand: chain 'H' and resid 650 through 652 removed outlier: 4.473A pdb=" N ASP H 692 " --> pdb=" O TYR H 652 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 32 through 34 removed outlier: 6.937A pdb=" N VAL I 3 " --> pdb=" O GLY I 54 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ILE I 56 " --> pdb=" O VAL I 3 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA I 5 " --> pdb=" O ILE I 56 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ASP I 58 " --> pdb=" O ALA I 5 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N LEU I 7 " --> pdb=" O ASP I 58 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N CYS I 53 " --> pdb=" O PRO I 78 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N TYR I 80 " --> pdb=" O CYS I 53 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL I 55 " --> pdb=" O TYR I 80 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N PHE I 82 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N PHE I 57 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 212 through 216 removed outlier: 6.212A pdb=" N ALA I 301 " --> pdb=" O HIS I 328 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASP I 330 " --> pdb=" O ALA I 301 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE I 303 " --> pdb=" O ASP I 330 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N HIS I 300 " --> pdb=" O THR I 237 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE I 238 " --> pdb=" O ILE I 260 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE I 262 " --> pdb=" O ILE I 238 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE I 240 " --> pdb=" O PHE I 262 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 311 through 313 Processing sheet with id=AG6, first strand: chain 'I' and resid 452 through 453 removed outlier: 3.929A pdb=" N LYS I 527 " --> pdb=" O LEU I 534 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 615 through 616 Processing sheet with id=AG8, first strand: chain 'I' and resid 632 through 636 Processing sheet with id=AG9, first strand: chain 'I' and resid 650 through 652 removed outlier: 4.542A pdb=" N ASP I 692 " --> pdb=" O TYR I 652 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 32 through 34 removed outlier: 6.914A pdb=" N VAL J 3 " --> pdb=" O GLY J 54 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ILE J 56 " --> pdb=" O VAL J 3 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA J 5 " --> pdb=" O ILE J 56 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ASP J 58 " --> pdb=" O ALA J 5 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N LEU J 7 " --> pdb=" O ASP J 58 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N CYS J 53 " --> pdb=" O PRO J 78 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N TYR J 80 " --> pdb=" O CYS J 53 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL J 55 " --> pdb=" O TYR J 80 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N PHE J 82 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N PHE J 57 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 212 through 216 removed outlier: 6.257A pdb=" N ALA J 301 " --> pdb=" O HIS J 328 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASP J 330 " --> pdb=" O ALA J 301 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE J 303 " --> pdb=" O ASP J 330 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS J 300 " --> pdb=" O THR J 237 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE J 238 " --> pdb=" O ILE J 260 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N PHE J 262 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE J 240 " --> pdb=" O PHE J 262 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 311 through 313 Processing sheet with id=AH4, first strand: chain 'J' and resid 452 through 453 removed outlier: 3.958A pdb=" N LYS J 527 " --> pdb=" O LEU J 534 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 615 through 616 Processing sheet with id=AH6, first strand: chain 'J' and resid 632 through 636 Processing sheet with id=AH7, first strand: chain 'J' and resid 650 through 652 removed outlier: 4.560A pdb=" N ASP J 692 " --> pdb=" O TYR J 652 " (cutoff:3.500A) 2646 hydrogen bonds defined for protein. 7544 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: 27.18 Time building geometry restraints manager: 13.03 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: 16077 1.33 - 1.45: 10428 1.45 - 1.57: 31233 1.57 - 1.69: 10 1.69 - 1.81: 670 Bond restraints: 58418 Sorted by residual: bond pdb=" OP4 LLP I 367 " pdb=" P LLP I 367 " ideal model delta sigma weight residual 1.726 1.530 0.196 2.00e-02 2.50e+03 9.58e+01 bond pdb=" OP4 LLP D 367 " pdb=" P LLP D 367 " ideal model delta sigma weight residual 1.726 1.531 0.195 2.00e-02 2.50e+03 9.55e+01 bond pdb=" OP4 LLP B 367 " pdb=" P LLP B 367 " ideal model delta sigma weight residual 1.726 1.532 0.194 2.00e-02 2.50e+03 9.39e+01 bond pdb=" OP4 LLP C 367 " pdb=" P LLP C 367 " ideal model delta sigma weight residual 1.726 1.532 0.194 2.00e-02 2.50e+03 9.38e+01 bond pdb=" OP4 LLP G 367 " pdb=" P LLP G 367 " ideal model delta sigma weight residual 1.726 1.533 0.193 2.00e-02 2.50e+03 9.30e+01 ... (remaining 58413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 77982 2.64 - 5.28: 1051 5.28 - 7.93: 131 7.93 - 10.57: 30 10.57 - 13.21: 20 Bond angle restraints: 79214 Sorted by residual: angle pdb=" C CYS E 148 " pdb=" N THR E 149 " pdb=" CA THR E 149 " ideal model delta sigma weight residual 122.48 135.69 -13.21 1.77e+00 3.19e-01 5.57e+01 angle pdb=" C CYS J 148 " pdb=" N THR J 149 " pdb=" CA THR J 149 " ideal model delta sigma weight residual 122.48 135.52 -13.04 1.77e+00 3.19e-01 5.43e+01 angle pdb=" N ASN A 8 " pdb=" CA ASN A 8 " pdb=" C ASN A 8 " ideal model delta sigma weight residual 107.73 118.99 -11.26 1.61e+00 3.86e-01 4.89e+01 angle pdb=" C CYS H 148 " pdb=" N THR H 149 " pdb=" CA THR H 149 " ideal model delta sigma weight residual 122.48 134.76 -12.28 1.77e+00 3.19e-01 4.81e+01 angle pdb=" N ASN D 8 " pdb=" CA ASN D 8 " pdb=" C ASN D 8 " ideal model delta sigma weight residual 108.07 118.81 -10.74 1.59e+00 3.96e-01 4.56e+01 ... (remaining 79209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.96: 34443 32.96 - 65.91: 485 65.91 - 98.87: 18 98.87 - 131.82: 0 131.82 - 164.78: 2 Dihedral angle restraints: 34948 sinusoidal: 14152 harmonic: 20796 Sorted by residual: dihedral pdb=" CA ASN J 8 " pdb=" C ASN J 8 " pdb=" N HIS J 9 " pdb=" CA HIS J 9 " ideal model delta harmonic sigma weight residual 180.00 140.51 39.49 0 5.00e+00 4.00e-02 6.24e+01 dihedral pdb=" CA LEU I 7 " pdb=" C LEU I 7 " pdb=" N ASN I 8 " pdb=" CA ASN I 8 " ideal model delta harmonic sigma weight residual 180.00 140.70 39.30 0 5.00e+00 4.00e-02 6.18e+01 dihedral pdb=" CA ASN E 8 " pdb=" C ASN E 8 " pdb=" N HIS E 9 " pdb=" CA HIS E 9 " ideal model delta harmonic sigma weight residual 180.00 141.83 38.17 0 5.00e+00 4.00e-02 5.83e+01 ... (remaining 34945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 5951 0.050 - 0.100: 2167 0.100 - 0.150: 523 0.150 - 0.200: 31 0.200 - 0.250: 2 Chirality restraints: 8674 Sorted by residual: chirality pdb=" CB THR I 492 " pdb=" CA THR I 492 " pdb=" OG1 THR I 492 " pdb=" CG2 THR I 492 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB THR D 492 " pdb=" CA THR D 492 " pdb=" OG1 THR D 492 " pdb=" CG2 THR D 492 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ASN A 8 " pdb=" N ASN A 8 " pdb=" C ASN A 8 " pdb=" CB ASN A 8 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.63e-01 ... (remaining 8671 not shown) Planarity restraints: 10168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP G 367 " 0.197 2.00e-02 2.50e+03 3.34e-01 1.12e+03 pdb=" NZ LLP G 367 " -0.495 2.00e-02 2.50e+03 pdb=" C4 LLP G 367 " -0.095 2.00e-02 2.50e+03 pdb=" C4' LLP G 367 " 0.393 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 367 " -0.197 2.00e-02 2.50e+03 3.34e-01 1.12e+03 pdb=" NZ LLP B 367 " 0.494 2.00e-02 2.50e+03 pdb=" C4 LLP B 367 " 0.095 2.00e-02 2.50e+03 pdb=" C4' LLP B 367 " -0.392 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP H 367 " 0.204 2.00e-02 2.50e+03 3.33e-01 1.11e+03 pdb=" NZ LLP H 367 " -0.497 2.00e-02 2.50e+03 pdb=" C4 LLP H 367 " -0.088 2.00e-02 2.50e+03 pdb=" C4' LLP H 367 " 0.382 2.00e-02 2.50e+03 ... (remaining 10165 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 12091 2.78 - 3.31: 51006 3.31 - 3.84: 101394 3.84 - 4.37: 124425 4.37 - 4.90: 209556 Nonbonded interactions: 498472 Sorted by model distance: nonbonded pdb=" O MET I 215 " pdb=" OH TYR I 393 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR F 574 " pdb=" OE1 GLU F 582 " model vdw 2.250 3.040 nonbonded pdb=" O MET D 215 " pdb=" OH TYR D 393 " model vdw 2.257 3.040 nonbonded pdb=" OH TYR A 574 " pdb=" OE1 GLU A 582 " model vdw 2.258 3.040 nonbonded pdb=" O MET G 215 " pdb=" OH TYR G 393 " model vdw 2.263 3.040 ... (remaining 498467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 610 or resid 612 through 711)) selection = (chain 'B' and (resid 1 through 610 or resid 612 through 711)) selection = (chain 'C' and (resid 1 through 610 or resid 612 through 711)) selection = (chain 'D' and (resid 1 through 610 or resid 612 through 711)) selection = (chain 'E' and (resid 1 through 610 or resid 612 through 711)) selection = (chain 'F' and (resid 1 through 610 or resid 612 through 711)) selection = (chain 'G' and (resid 1 through 610 or resid 612 through 711)) selection = (chain 'H' and (resid 1 through 610 or resid 612 through 711)) selection = (chain 'I' and (resid 1 through 610 or resid 612 through 711)) selection = (chain 'J' and (resid 1 through 610 or resid 612 through 711)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.760 Check model and map are aligned: 0.350 Set scattering table: 0.400 Process input model: 116.260 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 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 : 0.008 0.196 58418 Z= 0.521 Angle : 0.845 13.209 79214 Z= 0.463 Chirality : 0.052 0.250 8674 Planarity : 0.012 0.334 10168 Dihedral : 11.703 164.780 21600 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.03 % Allowed : 0.21 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.33 (0.10), residues: 7064 helix: -0.08 (0.09), residues: 2980 sheet: -0.10 (0.16), residues: 1070 loop : -0.21 (0.11), residues: 3014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 333 HIS 0.018 0.002 HIS D 599 PHE 0.071 0.003 PHE C 82 TYR 0.035 0.003 TYR H 531 ARG 0.016 0.001 ARG I 263 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 650 time to evaluate : 5.064 Fit side-chains revert: symmetry clash REVERT: A 664 MET cc_start: 0.8571 (ttm) cc_final: 0.8219 (ttp) REVERT: B 569 MET cc_start: 0.8877 (ttt) cc_final: 0.8169 (ttp) REVERT: C 122 ASP cc_start: 0.8175 (m-30) cc_final: 0.7925 (m-30) REVERT: D 122 ASP cc_start: 0.8162 (m-30) cc_final: 0.7881 (m-30) REVERT: E 122 ASP cc_start: 0.8132 (m-30) cc_final: 0.7861 (m-30) REVERT: E 664 MET cc_start: 0.8587 (ttm) cc_final: 0.8278 (ttm) REVERT: G 569 MET cc_start: 0.8877 (ttt) cc_final: 0.8166 (ttp) REVERT: G 618 MET cc_start: 0.8866 (ptp) cc_final: 0.8511 (ptp) REVERT: G 631 MET cc_start: 0.7932 (mmm) cc_final: 0.7526 (mmm) REVERT: H 122 ASP cc_start: 0.8181 (m-30) cc_final: 0.7933 (m-30) REVERT: I 122 ASP cc_start: 0.8170 (m-30) cc_final: 0.7901 (m-30) REVERT: I 660 MET cc_start: 0.9041 (mmt) cc_final: 0.8621 (mmm) REVERT: J 39 ARG cc_start: 0.8527 (tmm-80) cc_final: 0.8284 (tmm-80) REVERT: J 122 ASP cc_start: 0.8138 (m-30) cc_final: 0.7880 (m-30) outliers start: 0 outliers final: 0 residues processed: 650 average time/residue: 1.6350 time to fit residues: 1304.5610 Evaluate side-chains 538 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 538 time to evaluate : 5.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 599 optimal weight: 5.9990 chunk 538 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 363 optimal weight: 6.9990 chunk 287 optimal weight: 4.9990 chunk 556 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 338 optimal weight: 1.9990 chunk 414 optimal weight: 7.9990 chunk 644 optimal weight: 2.9990 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 281 GLN B 9 HIS B 385 ASN C 174 ASN C 591 GLN D 9 HIS D 23 HIS D 174 ASN D 385 ASN ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 ASN E 76 ASN E 385 ASN ** E 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN F 281 GLN F 282 HIS G 9 HIS G 385 ASN H 591 GLN I 23 HIS I 174 ASN I 645 ASN ** J 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 694 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 58418 Z= 0.207 Angle : 0.526 11.049 79214 Z= 0.279 Chirality : 0.043 0.149 8674 Planarity : 0.005 0.056 10168 Dihedral : 5.999 77.777 7818 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.68 % Allowed : 4.67 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.75 (0.10), residues: 7064 helix: 1.07 (0.09), residues: 2970 sheet: 0.30 (0.17), residues: 970 loop : 0.15 (0.12), residues: 3124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 454 HIS 0.009 0.001 HIS G 9 PHE 0.029 0.002 PHE H 82 TYR 0.020 0.002 TYR C 531 ARG 0.005 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 595 time to evaluate : 5.230 Fit side-chains REVERT: B 1 MET cc_start: 0.8681 (ttm) cc_final: 0.8442 (ttp) REVERT: B 73 MET cc_start: 0.8742 (mtm) cc_final: 0.8532 (mtm) REVERT: B 569 MET cc_start: 0.8861 (ttt) cc_final: 0.8096 (ttp) REVERT: C 122 ASP cc_start: 0.8154 (m-30) cc_final: 0.7910 (m-30) REVERT: C 637 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8903 (tm) REVERT: C 668 GLU cc_start: 0.7600 (mp0) cc_final: 0.7347 (mp0) REVERT: D 122 ASP cc_start: 0.8141 (m-30) cc_final: 0.7861 (m-30) REVERT: E 1 MET cc_start: 0.8354 (tpp) cc_final: 0.8119 (tpp) REVERT: E 122 ASP cc_start: 0.8131 (m-30) cc_final: 0.7882 (m-30) REVERT: E 664 MET cc_start: 0.8610 (ttm) cc_final: 0.8388 (ttm) REVERT: G 1 MET cc_start: 0.8685 (ttm) cc_final: 0.8445 (ttp) REVERT: G 73 MET cc_start: 0.8778 (mtm) cc_final: 0.8516 (mtm) REVERT: G 631 MET cc_start: 0.7882 (mmm) cc_final: 0.7462 (mmm) REVERT: H 122 ASP cc_start: 0.8157 (m-30) cc_final: 0.7912 (m-30) REVERT: I 122 ASP cc_start: 0.8079 (m-30) cc_final: 0.7783 (m-30) REVERT: I 246 LYS cc_start: 0.7911 (ttpp) cc_final: 0.7553 (tptm) REVERT: I 660 MET cc_start: 0.9045 (mmt) cc_final: 0.8845 (mpp) REVERT: J 1 MET cc_start: 0.8349 (tpp) cc_final: 0.8136 (tpp) REVERT: J 122 ASP cc_start: 0.8139 (m-30) cc_final: 0.7894 (m-30) outliers start: 39 outliers final: 16 residues processed: 607 average time/residue: 1.6168 time to fit residues: 1211.8933 Evaluate side-chains 543 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 526 time to evaluate : 5.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 660 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 638 ASP Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain G residue 416 MET Chi-restraints excluded: chain G residue 638 ASP Chi-restraints excluded: chain H residue 637 LEU Chi-restraints excluded: chain H residue 638 ASP Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain J residue 149 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 358 optimal weight: 1.9990 chunk 200 optimal weight: 0.4980 chunk 536 optimal weight: 8.9990 chunk 439 optimal weight: 0.9990 chunk 177 optimal weight: 10.0000 chunk 645 optimal weight: 5.9990 chunk 697 optimal weight: 9.9990 chunk 575 optimal weight: 0.6980 chunk 640 optimal weight: 4.9990 chunk 220 optimal weight: 10.0000 chunk 518 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 HIS A 115 ASN ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** E 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 694 HIS H 250 HIS H 338 ASN I 338 ASN I 645 ASN J 76 ASN J 591 GLN ** J 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 58418 Z= 0.157 Angle : 0.478 10.630 79214 Z= 0.251 Chirality : 0.041 0.137 8674 Planarity : 0.005 0.055 10168 Dihedral : 5.698 79.803 7818 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.76 % Allowed : 6.53 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.22 (0.10), residues: 7064 helix: 1.57 (0.09), residues: 2970 sheet: 0.37 (0.17), residues: 950 loop : 0.34 (0.12), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 297 HIS 0.007 0.001 HIS D 599 PHE 0.018 0.001 PHE H 82 TYR 0.014 0.001 TYR E 139 ARG 0.007 0.000 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 593 time to evaluate : 5.176 Fit side-chains REVERT: A 246 LYS cc_start: 0.8401 (pttm) cc_final: 0.8179 (pttp) REVERT: A 678 MET cc_start: 0.8937 (tmm) cc_final: 0.8727 (tmt) REVERT: B 1 MET cc_start: 0.8677 (ttm) cc_final: 0.8456 (ttp) REVERT: B 377 MET cc_start: 0.8271 (mtt) cc_final: 0.7935 (mtt) REVERT: C 122 ASP cc_start: 0.8146 (m-30) cc_final: 0.7895 (m-30) REVERT: C 637 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8918 (tm) REVERT: D 122 ASP cc_start: 0.8133 (m-30) cc_final: 0.7846 (m-30) REVERT: E 122 ASP cc_start: 0.8118 (m-30) cc_final: 0.7871 (m-30) REVERT: E 153 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7808 (mtt) REVERT: E 489 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8957 (pt) REVERT: E 664 MET cc_start: 0.8616 (ttm) cc_final: 0.8400 (ttp) REVERT: G 1 MET cc_start: 0.8676 (ttm) cc_final: 0.8459 (ttp) REVERT: G 73 MET cc_start: 0.8756 (mtm) cc_final: 0.8495 (mtm) REVERT: G 569 MET cc_start: 0.8740 (ttt) cc_final: 0.7930 (mtp) REVERT: G 618 MET cc_start: 0.8914 (ptm) cc_final: 0.8628 (ptp) REVERT: G 631 MET cc_start: 0.7866 (mmm) cc_final: 0.7500 (mmm) REVERT: H 122 ASP cc_start: 0.8161 (m-30) cc_final: 0.7912 (m-30) REVERT: I 122 ASP cc_start: 0.8140 (m-30) cc_final: 0.7847 (m-30) REVERT: J 122 ASP cc_start: 0.8123 (m-30) cc_final: 0.7881 (m-30) REVERT: J 153 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7825 (mtt) REVERT: J 387 GLU cc_start: 0.7871 (mp0) cc_final: 0.7624 (mp0) REVERT: J 489 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8971 (pt) outliers start: 44 outliers final: 16 residues processed: 616 average time/residue: 1.5547 time to fit residues: 1193.3688 Evaluate side-chains 546 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 525 time to evaluate : 7.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain G residue 254 MET Chi-restraints excluded: chain G residue 572 SER Chi-restraints excluded: chain G residue 638 ASP Chi-restraints excluded: chain H residue 287 LYS Chi-restraints excluded: chain H residue 637 LEU Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 153 MET Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 489 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 638 optimal weight: 10.0000 chunk 485 optimal weight: 10.0000 chunk 335 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 308 optimal weight: 10.0000 chunk 433 optimal weight: 7.9990 chunk 648 optimal weight: 0.9980 chunk 686 optimal weight: 9.9990 chunk 338 optimal weight: 0.9990 chunk 614 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 HIS A 694 HIS B 328 HIS B 645 ASN ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 HIS C 694 HIS D 599 HIS E 591 GLN ** E 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 694 HIS F 9 HIS G 328 HIS G 645 ASN ** H 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 ASN H 338 ASN H 599 HIS H 694 HIS I 338 ASN I 599 HIS J 599 HIS ** J 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 58418 Z= 0.384 Angle : 0.588 9.893 79214 Z= 0.309 Chirality : 0.046 0.189 8674 Planarity : 0.005 0.054 10168 Dihedral : 6.069 80.554 7818 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.34 % Allowed : 7.16 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.02 (0.10), residues: 7064 helix: 1.33 (0.09), residues: 2970 sheet: 0.21 (0.17), residues: 970 loop : 0.35 (0.12), residues: 3124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 454 HIS 0.013 0.002 HIS I 599 PHE 0.039 0.002 PHE C 82 TYR 0.024 0.002 TYR C 531 ARG 0.006 0.001 ARG G 263 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 530 time to evaluate : 5.273 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7910 (mtt) REVERT: A 668 GLU cc_start: 0.7571 (mp0) cc_final: 0.7360 (mp0) REVERT: B 1 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8518 (ttp) REVERT: B 16 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7502 (mt-10) REVERT: B 65 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7401 (mm-30) REVERT: B 153 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7303 (mtm) REVERT: B 395 MET cc_start: 0.8702 (mtt) cc_final: 0.8289 (mtt) REVERT: C 122 ASP cc_start: 0.8168 (m-30) cc_final: 0.7935 (m-30) REVERT: C 668 GLU cc_start: 0.7609 (mp0) cc_final: 0.7314 (mp0) REVERT: D 122 ASP cc_start: 0.8174 (m-30) cc_final: 0.7884 (m-30) REVERT: D 246 LYS cc_start: 0.8129 (mmtm) cc_final: 0.7838 (ptmm) REVERT: E 39 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8170 (tmm-80) REVERT: E 122 ASP cc_start: 0.8134 (m-30) cc_final: 0.7877 (m-30) REVERT: E 385 ASN cc_start: 0.8594 (t0) cc_final: 0.8380 (t0) REVERT: E 489 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.8975 (pt) REVERT: E 664 MET cc_start: 0.8693 (ttm) cc_final: 0.8474 (ttm) REVERT: G 1 MET cc_start: 0.8735 (ttm) cc_final: 0.8524 (ttp) REVERT: G 65 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7386 (mm-30) REVERT: G 72 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8475 (mtpt) REVERT: G 73 MET cc_start: 0.8850 (mtm) cc_final: 0.8621 (mtm) REVERT: G 153 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7318 (mtm) REVERT: G 248 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.8936 (mm) REVERT: G 631 MET cc_start: 0.7872 (mmm) cc_final: 0.7448 (mmm) REVERT: H 122 ASP cc_start: 0.8169 (m-30) cc_final: 0.7931 (m-30) REVERT: H 272 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8697 (mp) REVERT: H 668 GLU cc_start: 0.7721 (mp0) cc_final: 0.7468 (mp0) REVERT: I 122 ASP cc_start: 0.8176 (m-30) cc_final: 0.7871 (m-30) REVERT: I 660 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8908 (mpp) REVERT: J 97 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7916 (ttt90) REVERT: J 122 ASP cc_start: 0.8137 (m-30) cc_final: 0.7881 (m-30) REVERT: J 387 GLU cc_start: 0.7901 (mp0) cc_final: 0.7626 (mp0) REVERT: J 489 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.8990 (pt) outliers start: 80 outliers final: 31 residues processed: 580 average time/residue: 1.5274 time to fit residues: 1117.2090 Evaluate side-chains 559 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 513 time to evaluate : 5.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain E residue 572 SER Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 638 ASP Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 664 MET Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 72 LYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 638 ASP Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 287 LYS Chi-restraints excluded: chain H residue 637 LEU Chi-restraints excluded: chain H residue 638 ASP Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 660 MET Chi-restraints excluded: chain J residue 97 ARG Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 365 THR Chi-restraints excluded: chain J residue 489 ILE Chi-restraints excluded: chain J residue 498 MET Chi-restraints excluded: chain J residue 528 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 571 optimal weight: 1.9990 chunk 389 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 510 optimal weight: 0.9980 chunk 283 optimal weight: 6.9990 chunk 585 optimal weight: 3.9990 chunk 474 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 350 optimal weight: 8.9990 chunk 615 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 HIS ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 HIS E 37 ASN E 599 HIS E 645 ASN ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 599 HIS J 9 HIS J 599 HIS J 645 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 58418 Z= 0.324 Angle : 0.558 10.013 79214 Z= 0.293 Chirality : 0.045 0.171 8674 Planarity : 0.005 0.054 10168 Dihedral : 6.014 80.789 7818 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.32 % Allowed : 7.88 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.06 (0.10), residues: 7064 helix: 1.38 (0.09), residues: 2970 sheet: 0.17 (0.17), residues: 970 loop : 0.37 (0.12), residues: 3124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 454 HIS 0.011 0.001 HIS E 599 PHE 0.034 0.002 PHE H 82 TYR 0.021 0.002 TYR C 531 ARG 0.006 0.000 ARG E 703 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 534 time to evaluate : 5.292 Fit side-chains revert: symmetry clash REVERT: A 265 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8174 (p) REVERT: A 678 MET cc_start: 0.8817 (tmt) cc_final: 0.8613 (ttp) REVERT: B 1 MET cc_start: 0.8686 (ttm) cc_final: 0.8457 (ttp) REVERT: B 65 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7378 (mm-30) REVERT: B 153 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7365 (mtm) REVERT: B 395 MET cc_start: 0.8505 (mtt) cc_final: 0.7943 (mtt) REVERT: B 569 MET cc_start: 0.8727 (ttt) cc_final: 0.8192 (mtp) REVERT: C 122 ASP cc_start: 0.8166 (m-30) cc_final: 0.7929 (m-30) REVERT: C 668 GLU cc_start: 0.7614 (mp0) cc_final: 0.7373 (mp0) REVERT: D 122 ASP cc_start: 0.8166 (m-30) cc_final: 0.7877 (m-30) REVERT: D 246 LYS cc_start: 0.8053 (mmtm) cc_final: 0.7702 (ptmm) REVERT: E 27 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7792 (mt-10) REVERT: E 39 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8164 (tmm-80) REVERT: E 122 ASP cc_start: 0.8196 (m-30) cc_final: 0.7950 (m-30) REVERT: E 153 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8102 (mtm) REVERT: E 385 ASN cc_start: 0.8614 (t0) cc_final: 0.8395 (t0) REVERT: E 489 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.8990 (pt) REVERT: E 664 MET cc_start: 0.8692 (ttm) cc_final: 0.8486 (ttm) REVERT: F 678 MET cc_start: 0.8941 (tmm) cc_final: 0.8720 (tmt) REVERT: G 1 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8462 (ttp) REVERT: G 65 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7370 (mm-30) REVERT: G 72 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8475 (mtpt) REVERT: G 73 MET cc_start: 0.8820 (mtm) cc_final: 0.8565 (mtm) REVERT: G 153 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7322 (mtm) REVERT: G 248 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.8970 (mm) REVERT: G 386 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: G 569 MET cc_start: 0.8626 (ttt) cc_final: 0.8234 (ttp) REVERT: G 631 MET cc_start: 0.7870 (mmm) cc_final: 0.7449 (mmm) REVERT: H 122 ASP cc_start: 0.8169 (m-30) cc_final: 0.7931 (m-30) REVERT: I 122 ASP cc_start: 0.8169 (m-30) cc_final: 0.7864 (m-30) REVERT: I 246 LYS cc_start: 0.8067 (ttpt) cc_final: 0.7805 (tptm) REVERT: I 660 MET cc_start: 0.9233 (mpp) cc_final: 0.9013 (mpp) REVERT: J 122 ASP cc_start: 0.8200 (m-30) cc_final: 0.7958 (m-30) REVERT: J 153 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8026 (mtm) REVERT: J 387 GLU cc_start: 0.7897 (mp0) cc_final: 0.7634 (mp0) REVERT: J 489 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9004 (pt) outliers start: 79 outliers final: 44 residues processed: 580 average time/residue: 1.5215 time to fit residues: 1104.7529 Evaluate side-chains 578 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 520 time to evaluate : 5.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 498 MET Chi-restraints excluded: chain E residue 572 SER Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 503 THR Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 638 ASP Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 664 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 72 LYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 254 MET Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 416 MET Chi-restraints excluded: chain G residue 572 SER Chi-restraints excluded: chain G residue 638 ASP Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 287 LYS Chi-restraints excluded: chain H residue 572 SER Chi-restraints excluded: chain H residue 637 LEU Chi-restraints excluded: chain H residue 638 ASP Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 153 MET Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 365 THR Chi-restraints excluded: chain J residue 489 ILE Chi-restraints excluded: chain J residue 498 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 230 optimal weight: 4.9990 chunk 618 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 402 optimal weight: 0.0770 chunk 169 optimal weight: 6.9990 chunk 686 optimal weight: 9.9990 chunk 570 optimal weight: 0.9990 chunk 318 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 227 optimal weight: 0.9980 chunk 360 optimal weight: 7.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 HIS ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 HIS ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 HIS ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 599 HIS I 599 HIS J 9 HIS J 599 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 58418 Z= 0.169 Angle : 0.483 10.158 79214 Z= 0.253 Chirality : 0.042 0.133 8674 Planarity : 0.004 0.055 10168 Dihedral : 5.697 80.465 7818 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.50 % Allowed : 8.19 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.36 (0.10), residues: 7064 helix: 1.75 (0.09), residues: 2970 sheet: 0.23 (0.17), residues: 970 loop : 0.43 (0.12), residues: 3124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 297 HIS 0.011 0.001 HIS I 599 PHE 0.018 0.001 PHE H 82 TYR 0.015 0.001 TYR E 139 ARG 0.006 0.000 ARG E 703 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 553 time to evaluate : 5.254 Fit side-chains REVERT: A 246 LYS cc_start: 0.8438 (pttm) cc_final: 0.8189 (pttp) REVERT: A 678 MET cc_start: 0.8866 (tmt) cc_final: 0.8631 (ttp) REVERT: B 1 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8383 (ttp) REVERT: B 65 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7464 (mm-30) REVERT: B 153 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7397 (mtm) REVERT: B 395 MET cc_start: 0.8560 (mtt) cc_final: 0.8011 (mtt) REVERT: B 569 MET cc_start: 0.8742 (ttt) cc_final: 0.8236 (ttp) REVERT: C 122 ASP cc_start: 0.8148 (m-30) cc_final: 0.7929 (m-30) REVERT: D 122 ASP cc_start: 0.8141 (m-30) cc_final: 0.7853 (m-30) REVERT: E 27 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7897 (mt-10) REVERT: E 39 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8148 (tmm-80) REVERT: E 122 ASP cc_start: 0.8172 (m-30) cc_final: 0.7931 (m-30) REVERT: E 153 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7629 (mtm) REVERT: E 489 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8960 (pt) REVERT: E 664 MET cc_start: 0.8680 (ttm) cc_final: 0.8449 (ttm) REVERT: F 678 MET cc_start: 0.8941 (tmm) cc_final: 0.8727 (tmt) REVERT: G 1 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8406 (ttp) REVERT: G 65 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7478 (mm-30) REVERT: G 72 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8439 (mtpt) REVERT: G 73 MET cc_start: 0.8758 (mtm) cc_final: 0.8533 (mtm) REVERT: G 153 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7411 (mtm) REVERT: G 248 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.8962 (mm) REVERT: G 569 MET cc_start: 0.8703 (ttt) cc_final: 0.8209 (mtp) REVERT: G 631 MET cc_start: 0.7880 (mmm) cc_final: 0.7510 (mmm) REVERT: H 122 ASP cc_start: 0.8155 (m-30) cc_final: 0.7930 (m-30) REVERT: I 122 ASP cc_start: 0.8153 (m-30) cc_final: 0.7847 (m-30) REVERT: I 660 MET cc_start: 0.9200 (mpp) cc_final: 0.8918 (mpp) REVERT: J 122 ASP cc_start: 0.8181 (m-30) cc_final: 0.7941 (m-30) REVERT: J 153 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7624 (mtm) REVERT: J 387 GLU cc_start: 0.7839 (mp0) cc_final: 0.7576 (mp0) REVERT: J 489 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8972 (pt) outliers start: 90 outliers final: 34 residues processed: 603 average time/residue: 1.5379 time to fit residues: 1158.7484 Evaluate side-chains 580 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 533 time to evaluate : 5.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 498 MET Chi-restraints excluded: chain E residue 572 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 664 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 72 LYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 254 MET Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 572 SER Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 287 LYS Chi-restraints excluded: chain H residue 637 LEU Chi-restraints excluded: chain H residue 638 ASP Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 153 MET Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 365 THR Chi-restraints excluded: chain J residue 489 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 662 optimal weight: 10.0000 chunk 77 optimal weight: 0.5980 chunk 391 optimal weight: 0.5980 chunk 501 optimal weight: 1.9990 chunk 388 optimal weight: 3.9990 chunk 578 optimal weight: 0.9990 chunk 383 optimal weight: 9.9990 chunk 684 optimal weight: 6.9990 chunk 428 optimal weight: 0.0970 chunk 417 optimal weight: 2.9990 chunk 315 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN C 338 ASN C 599 HIS ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 HIS D 645 ASN E 599 HIS G 591 GLN H 8 ASN H 338 ASN H 599 HIS I 599 HIS J 599 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 58418 Z= 0.134 Angle : 0.457 10.208 79214 Z= 0.239 Chirality : 0.041 0.134 8674 Planarity : 0.004 0.055 10168 Dihedral : 5.519 81.130 7818 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.16 % Allowed : 8.82 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.63 (0.10), residues: 7064 helix: 2.02 (0.09), residues: 2984 sheet: 0.33 (0.17), residues: 950 loop : 0.53 (0.12), residues: 3130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 449 HIS 0.012 0.001 HIS I 599 PHE 0.011 0.001 PHE H 82 TYR 0.013 0.001 TYR G 203 ARG 0.007 0.000 ARG E 468 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 571 time to evaluate : 5.227 Fit side-chains REVERT: A 503 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8403 (p) REVERT: A 678 MET cc_start: 0.8841 (tmt) cc_final: 0.8624 (ttp) REVERT: B 1 MET cc_start: 0.8617 (ttm) cc_final: 0.8351 (ttp) REVERT: B 122 ASP cc_start: 0.7984 (m-30) cc_final: 0.7744 (m-30) REVERT: B 153 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7432 (mtm) REVERT: B 395 MET cc_start: 0.8310 (mtt) cc_final: 0.7911 (mtt) REVERT: B 569 MET cc_start: 0.8772 (ttt) cc_final: 0.8303 (ttp) REVERT: C 122 ASP cc_start: 0.8142 (m-30) cc_final: 0.7914 (m-30) REVERT: C 637 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8964 (tm) REVERT: D 122 ASP cc_start: 0.8130 (m-30) cc_final: 0.7843 (m-30) REVERT: E 122 ASP cc_start: 0.8161 (m-30) cc_final: 0.7919 (m-30) REVERT: E 153 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7716 (mtt) REVERT: E 489 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8915 (pt) REVERT: F 664 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8456 (ptp) REVERT: F 678 MET cc_start: 0.8939 (tmm) cc_final: 0.8733 (tmt) REVERT: G 1 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8421 (ttp) REVERT: G 122 ASP cc_start: 0.7929 (m-30) cc_final: 0.7688 (m-30) REVERT: G 153 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7438 (mtm) REVERT: G 248 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.8911 (mm) REVERT: G 569 MET cc_start: 0.8747 (ttt) cc_final: 0.8294 (ttp) REVERT: G 631 MET cc_start: 0.7883 (mmm) cc_final: 0.7511 (mmm) REVERT: H 122 ASP cc_start: 0.8146 (m-30) cc_final: 0.7923 (m-30) REVERT: H 246 LYS cc_start: 0.7312 (mmpt) cc_final: 0.6957 (mppt) REVERT: H 668 GLU cc_start: 0.7682 (mp0) cc_final: 0.7417 (mp0) REVERT: I 122 ASP cc_start: 0.8151 (m-30) cc_final: 0.7851 (m-30) REVERT: I 377 MET cc_start: 0.8490 (mtt) cc_final: 0.7848 (mtt) REVERT: J 122 ASP cc_start: 0.8166 (m-30) cc_final: 0.7930 (m-30) REVERT: J 153 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7707 (mtt) REVERT: J 489 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8923 (pt) outliers start: 69 outliers final: 21 residues processed: 614 average time/residue: 1.5500 time to fit residues: 1194.4804 Evaluate side-chains 568 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 536 time to evaluate : 5.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 664 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain G residue 572 SER Chi-restraints excluded: chain H residue 637 LEU Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 153 MET Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 365 THR Chi-restraints excluded: chain J residue 489 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 423 optimal weight: 0.0170 chunk 273 optimal weight: 0.9990 chunk 408 optimal weight: 8.9990 chunk 206 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 435 optimal weight: 0.9980 chunk 466 optimal weight: 4.9990 chunk 338 optimal weight: 5.9990 chunk 63 optimal weight: 0.0970 chunk 537 optimal weight: 2.9990 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN C 599 HIS ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 HIS E 599 HIS F 591 GLN G 591 GLN H 599 HIS I 599 HIS J 599 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 58418 Z= 0.144 Angle : 0.465 10.101 79214 Z= 0.242 Chirality : 0.041 0.131 8674 Planarity : 0.004 0.055 10168 Dihedral : 5.501 81.244 7818 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.18 % Allowed : 9.20 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.75 (0.10), residues: 7064 helix: 2.16 (0.09), residues: 2970 sheet: 0.35 (0.17), residues: 950 loop : 0.57 (0.12), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 449 HIS 0.013 0.001 HIS D 599 PHE 0.012 0.001 PHE C 82 TYR 0.013 0.001 TYR J 139 ARG 0.008 0.000 ARG B 468 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 546 time to evaluate : 5.392 Fit side-chains REVERT: A 503 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8380 (p) REVERT: A 678 MET cc_start: 0.8847 (tmt) cc_final: 0.8626 (ttp) REVERT: B 1 MET cc_start: 0.8619 (ttm) cc_final: 0.8355 (ttp) REVERT: B 122 ASP cc_start: 0.7981 (m-30) cc_final: 0.7737 (m-30) REVERT: B 153 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7472 (mtm) REVERT: B 290 LYS cc_start: 0.8343 (mtpt) cc_final: 0.8088 (mtpm) REVERT: B 395 MET cc_start: 0.8302 (mtt) cc_final: 0.8058 (mtt) REVERT: B 569 MET cc_start: 0.8781 (ttt) cc_final: 0.8334 (ttp) REVERT: B 618 MET cc_start: 0.8851 (ptp) cc_final: 0.8563 (ptp) REVERT: C 122 ASP cc_start: 0.8144 (m-30) cc_final: 0.7912 (m-30) REVERT: C 246 LYS cc_start: 0.7675 (mppt) cc_final: 0.7454 (mmtt) REVERT: C 668 GLU cc_start: 0.7690 (mp0) cc_final: 0.7396 (mp0) REVERT: D 122 ASP cc_start: 0.8131 (m-30) cc_final: 0.7852 (m-30) REVERT: D 660 MET cc_start: 0.8915 (tpp) cc_final: 0.8680 (mmm) REVERT: E 1 MET cc_start: 0.8786 (ttm) cc_final: 0.8352 (tpp) REVERT: E 122 ASP cc_start: 0.8153 (m-30) cc_final: 0.7914 (m-30) REVERT: E 153 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7713 (mtt) REVERT: E 489 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.8929 (pt) REVERT: G 1 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8373 (ttp) REVERT: G 72 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8390 (mtpt) REVERT: G 122 ASP cc_start: 0.7987 (m-30) cc_final: 0.7746 (m-30) REVERT: G 153 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7482 (mtm) REVERT: G 248 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.8975 (mm) REVERT: G 290 LYS cc_start: 0.8369 (mtpt) cc_final: 0.8131 (mtpm) REVERT: G 569 MET cc_start: 0.8756 (ttt) cc_final: 0.8330 (ttp) REVERT: G 631 MET cc_start: 0.7882 (mmm) cc_final: 0.7513 (mmm) REVERT: H 122 ASP cc_start: 0.8152 (m-30) cc_final: 0.7927 (m-30) REVERT: H 246 LYS cc_start: 0.7344 (mmpt) cc_final: 0.6983 (mppt) REVERT: H 668 GLU cc_start: 0.7656 (mp0) cc_final: 0.7413 (mp0) REVERT: I 122 ASP cc_start: 0.8153 (m-30) cc_final: 0.7851 (m-30) REVERT: I 246 LYS cc_start: 0.7639 (ttpt) cc_final: 0.7298 (tttp) REVERT: J 1 MET cc_start: 0.8804 (ttm) cc_final: 0.8405 (tpp) REVERT: J 122 ASP cc_start: 0.8161 (m-30) cc_final: 0.7927 (m-30) REVERT: J 153 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7741 (mtt) REVERT: J 387 GLU cc_start: 0.7864 (mp0) cc_final: 0.7647 (mp0) REVERT: J 489 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.8919 (pt) outliers start: 70 outliers final: 30 residues processed: 589 average time/residue: 1.5178 time to fit residues: 1125.8477 Evaluate side-chains 577 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 537 time to evaluate : 5.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 664 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 72 LYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain G residue 572 SER Chi-restraints excluded: chain H residue 572 SER Chi-restraints excluded: chain H residue 637 LEU Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 153 MET Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 365 THR Chi-restraints excluded: chain J residue 489 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 622 optimal weight: 0.9990 chunk 655 optimal weight: 0.9990 chunk 598 optimal weight: 1.9990 chunk 637 optimal weight: 10.0000 chunk 383 optimal weight: 9.9990 chunk 277 optimal weight: 10.0000 chunk 500 optimal weight: 0.0000 chunk 195 optimal weight: 4.9990 chunk 576 optimal weight: 6.9990 chunk 603 optimal weight: 0.0040 chunk 635 optimal weight: 0.9990 overall best weight: 0.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN C 521 HIS C 599 HIS ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 ASN D 599 HIS E 591 GLN E 599 HIS F 591 GLN G 591 GLN H 250 HIS H 521 HIS H 599 HIS I 338 ASN I 599 HIS J 591 GLN J 599 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 58418 Z= 0.122 Angle : 0.449 10.196 79214 Z= 0.233 Chirality : 0.040 0.132 8674 Planarity : 0.004 0.056 10168 Dihedral : 5.391 81.868 7818 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.76 % Allowed : 9.83 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.88 (0.10), residues: 7064 helix: 2.31 (0.09), residues: 2970 sheet: 0.39 (0.17), residues: 950 loop : 0.61 (0.12), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 465 HIS 0.013 0.001 HIS D 599 PHE 0.012 0.001 PHE J 624 TYR 0.012 0.001 TYR B 203 ARG 0.007 0.000 ARG B 468 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 578 time to evaluate : 5.145 Fit side-chains revert: symmetry clash REVERT: A 503 THR cc_start: 0.8615 (m) cc_final: 0.8308 (p) REVERT: A 678 MET cc_start: 0.8857 (tmt) cc_final: 0.8630 (ttp) REVERT: B 1 MET cc_start: 0.8579 (ttm) cc_final: 0.8332 (ttp) REVERT: B 122 ASP cc_start: 0.7963 (m-30) cc_final: 0.7744 (m-30) REVERT: B 290 LYS cc_start: 0.8327 (mtpt) cc_final: 0.8077 (mtpm) REVERT: B 377 MET cc_start: 0.8146 (mtt) cc_final: 0.7701 (mtt) REVERT: B 569 MET cc_start: 0.8799 (ttt) cc_final: 0.8519 (ttt) REVERT: B 618 MET cc_start: 0.8883 (ptp) cc_final: 0.8554 (ptp) REVERT: C 122 ASP cc_start: 0.8136 (m-30) cc_final: 0.7911 (m-30) REVERT: C 668 GLU cc_start: 0.7669 (mp0) cc_final: 0.7384 (mp0) REVERT: D 122 ASP cc_start: 0.8121 (m-30) cc_final: 0.7834 (m-30) REVERT: D 156 THR cc_start: 0.9017 (m) cc_final: 0.8767 (m) REVERT: D 246 LYS cc_start: 0.7146 (mppt) cc_final: 0.6925 (mmmt) REVERT: D 660 MET cc_start: 0.8960 (tpp) cc_final: 0.8733 (mmm) REVERT: E 1 MET cc_start: 0.8731 (ttm) cc_final: 0.8278 (tpp) REVERT: E 39 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8422 (tmm-80) REVERT: E 122 ASP cc_start: 0.8142 (m-30) cc_final: 0.7902 (m-30) REVERT: E 489 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8909 (pt) REVERT: G 1 MET cc_start: 0.8607 (ttm) cc_final: 0.8373 (ttp) REVERT: G 122 ASP cc_start: 0.7939 (m-30) cc_final: 0.7730 (m-30) REVERT: G 290 LYS cc_start: 0.8336 (mtpt) cc_final: 0.8088 (mtpm) REVERT: G 569 MET cc_start: 0.8778 (ttt) cc_final: 0.8518 (ttt) REVERT: G 631 MET cc_start: 0.7874 (mmm) cc_final: 0.7525 (mmm) REVERT: H 122 ASP cc_start: 0.8143 (m-30) cc_final: 0.7918 (m-30) REVERT: H 246 LYS cc_start: 0.7204 (mmpt) cc_final: 0.6878 (mppt) REVERT: H 668 GLU cc_start: 0.7660 (mp0) cc_final: 0.7414 (mp0) REVERT: I 122 ASP cc_start: 0.8151 (m-30) cc_final: 0.7845 (m-30) REVERT: I 156 THR cc_start: 0.9035 (m) cc_final: 0.8792 (m) REVERT: I 377 MET cc_start: 0.8438 (mtt) cc_final: 0.7829 (mtt) REVERT: J 1 MET cc_start: 0.8758 (ttm) cc_final: 0.8474 (tpp) REVERT: J 122 ASP cc_start: 0.8153 (m-30) cc_final: 0.7918 (m-30) REVERT: J 387 GLU cc_start: 0.7860 (mp0) cc_final: 0.7636 (mp0) REVERT: J 489 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8916 (pt) outliers start: 44 outliers final: 18 residues processed: 603 average time/residue: 1.5371 time to fit residues: 1163.5277 Evaluate side-chains 559 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 538 time to evaluate : 5.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 664 MET Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain H residue 637 LEU Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 365 THR Chi-restraints excluded: chain J residue 489 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 418 optimal weight: 1.9990 chunk 674 optimal weight: 8.9990 chunk 411 optimal weight: 5.9990 chunk 319 optimal weight: 7.9990 chunk 468 optimal weight: 9.9990 chunk 707 optimal weight: 4.9990 chunk 651 optimal weight: 1.9990 chunk 563 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 435 optimal weight: 6.9990 chunk 345 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN ** B 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN C 338 ASN C 599 HIS ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 ASN D 599 HIS E 599 HIS F 591 GLN ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 250 HIS G 591 GLN H 599 HIS I 294 ASN I 338 ASN I 599 HIS J 599 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 58418 Z= 0.235 Angle : 0.518 9.922 79214 Z= 0.268 Chirality : 0.043 0.153 8674 Planarity : 0.004 0.055 10168 Dihedral : 5.677 81.150 7818 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.82 % Allowed : 9.95 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.68 (0.10), residues: 7064 helix: 2.03 (0.09), residues: 2980 sheet: 0.31 (0.17), residues: 950 loop : 0.61 (0.12), residues: 3134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 454 HIS 0.013 0.001 HIS D 599 PHE 0.021 0.002 PHE H 82 TYR 0.016 0.002 TYR J 139 ARG 0.008 0.000 ARG D 263 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 540 time to evaluate : 5.302 Fit side-chains revert: symmetry clash REVERT: A 678 MET cc_start: 0.8853 (tmt) cc_final: 0.8641 (ttp) REVERT: B 1 MET cc_start: 0.8661 (ttm) cc_final: 0.8441 (ttp) REVERT: B 153 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7436 (mtm) REVERT: B 290 LYS cc_start: 0.8369 (mtpt) cc_final: 0.8119 (mtpm) REVERT: B 377 MET cc_start: 0.8499 (mtt) cc_final: 0.8026 (mtt) REVERT: B 395 MET cc_start: 0.8481 (mmm) cc_final: 0.7876 (mtm) REVERT: C 122 ASP cc_start: 0.8156 (m-30) cc_final: 0.7934 (m-30) REVERT: C 668 GLU cc_start: 0.7669 (mp0) cc_final: 0.7397 (mp0) REVERT: D 122 ASP cc_start: 0.8150 (m-30) cc_final: 0.7856 (m-30) REVERT: D 660 MET cc_start: 0.8945 (tpp) cc_final: 0.8733 (mmm) REVERT: E 1 MET cc_start: 0.8767 (ttm) cc_final: 0.8330 (tpp) REVERT: E 39 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8172 (tmm-80) REVERT: E 122 ASP cc_start: 0.8172 (m-30) cc_final: 0.7931 (m-30) REVERT: E 153 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7666 (mtt) REVERT: E 489 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8943 (pt) REVERT: F 16 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7560 (mt-10) REVERT: F 668 GLU cc_start: 0.7656 (mp0) cc_final: 0.7440 (mp0) REVERT: G 1 MET cc_start: 0.8664 (ttm) cc_final: 0.8449 (ttp) REVERT: G 72 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8408 (mtpt) REVERT: G 122 ASP cc_start: 0.7950 (m-30) cc_final: 0.7725 (m-30) REVERT: G 290 LYS cc_start: 0.8379 (mtpt) cc_final: 0.8125 (mtpm) REVERT: G 377 MET cc_start: 0.8503 (mtt) cc_final: 0.8292 (mtt) REVERT: G 631 MET cc_start: 0.7879 (mmm) cc_final: 0.7494 (mmm) REVERT: H 122 ASP cc_start: 0.8159 (m-30) cc_final: 0.7934 (m-30) REVERT: H 246 LYS cc_start: 0.7604 (mmpt) cc_final: 0.7193 (mppt) REVERT: H 668 GLU cc_start: 0.7675 (mp0) cc_final: 0.7435 (mp0) REVERT: I 122 ASP cc_start: 0.8178 (m-30) cc_final: 0.7881 (m-30) REVERT: J 1 MET cc_start: 0.8778 (ttm) cc_final: 0.8326 (tpp) REVERT: J 97 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7862 (ttt90) REVERT: J 122 ASP cc_start: 0.8182 (m-30) cc_final: 0.7942 (m-30) REVERT: J 153 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7673 (mtt) REVERT: J 387 GLU cc_start: 0.7870 (mp0) cc_final: 0.7604 (mp0) REVERT: J 489 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8950 (pt) outliers start: 48 outliers final: 25 residues processed: 573 average time/residue: 1.5214 time to fit residues: 1097.5718 Evaluate side-chains 562 residues out of total 6196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 528 time to evaluate : 5.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 664 MET Chi-restraints excluded: chain G residue 72 LYS Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain G residue 572 SER Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain H residue 637 LEU Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain J residue 97 ARG Chi-restraints excluded: chain J residue 153 MET Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 365 THR Chi-restraints excluded: chain J residue 489 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 447 optimal weight: 7.9990 chunk 600 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 519 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 564 optimal weight: 0.8980 chunk 236 optimal weight: 9.9990 chunk 579 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN ** B 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN C 599 HIS ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 HIS E 599 HIS F 591 GLN ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 591 GLN H 250 HIS H 338 ASN H 599 HIS I 599 HIS J 599 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.098432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.082830 restraints weight = 112360.799| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.79 r_work: 0.2824 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 58418 Z= 0.338 Angle : 0.581 10.555 79214 Z= 0.301 Chirality : 0.045 0.188 8674 Planarity : 0.005 0.053 10168 Dihedral : 5.944 80.868 7818 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.00 % Allowed : 9.96 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.38 (0.10), residues: 7064 helix: 1.71 (0.09), residues: 2970 sheet: 0.17 (0.17), residues: 970 loop : 0.53 (0.12), residues: 3124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 454 HIS 0.014 0.001 HIS I 599 PHE 0.034 0.002 PHE C 82 TYR 0.019 0.002 TYR I 139 ARG 0.007 0.001 ARG J 468 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16607.53 seconds wall clock time: 290 minutes 13.44 seconds (17413.44 seconds total)