Starting phenix.real_space_refine on Sat Dec 9 18:48:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgb_30354/12_2023/7cgb_30354.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgb_30354/12_2023/7cgb_30354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgb_30354/12_2023/7cgb_30354.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgb_30354/12_2023/7cgb_30354.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgb_30354/12_2023/7cgb_30354.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgb_30354/12_2023/7cgb_30354.pdb" } resolution = 3.4 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= 0.040 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: 4 Type Number sf(0) Gaussians S 176 5.16 5 C 39908 2.51 5 N 11154 2.21 5 O 13596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "DP PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EA PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EF ARG 380": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 64834 Number of models: 1 Model: "" Number of chains: 22 Chain: "DL" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DM" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DN" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DO" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DP" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DQ" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DR" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DS" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DT" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DU" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DV" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DW" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DX" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DY" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "DZ" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "EA" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "EB" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "EC" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "ED" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "EE" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "EF" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Chain: "EG" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2947 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 388} Time building chain proxies: 23.95, per 1000 atoms: 0.37 Number of scatterers: 64834 At special positions: 0 Unit cell: (190.822, 201.278, 222.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 176 16.00 O 13596 8.00 N 11154 7.00 C 39908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.14 Conformation dependent library (CDL) restraints added in 9.0 seconds 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15928 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 224 sheets defined 15.7% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.78 Creating SS restraints... Processing helix chain 'DL' and resid 3 through 26 Processing helix chain 'DL' and resid 27 through 29 No H-bonds generated for 'chain 'DL' and resid 27 through 29' Processing helix chain 'DL' and resid 174 through 178 Processing helix chain 'DL' and resid 368 through 387 Processing helix chain 'DL' and resid 389 through 401 removed outlier: 4.235A pdb=" N ILEDL 395 " --> pdb=" O THRDL 391 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEUDL 396 " --> pdb=" O GLNDL 392 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VALDL 400 " --> pdb=" O LEUDL 396 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASNDL 401 " --> pdb=" O ASNDL 397 " (cutoff:3.500A) Processing helix chain 'DM' and resid 3 through 26 Processing helix chain 'DM' and resid 27 through 29 No H-bonds generated for 'chain 'DM' and resid 27 through 29' Processing helix chain 'DM' and resid 174 through 178 removed outlier: 3.716A pdb=" N TYRDM 178 " --> pdb=" O ALADM 175 " (cutoff:3.500A) Processing helix chain 'DM' and resid 367 through 402 Processing helix chain 'DN' and resid 3 through 23 removed outlier: 3.846A pdb=" N LEUDN 10 " --> pdb=" O ALADN 6 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASNDN 22 " --> pdb=" O ASPDN 18 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASNDN 23 " --> pdb=" O VALDN 19 " (cutoff:3.500A) Processing helix chain 'DN' and resid 24 through 28 removed outlier: 4.417A pdb=" N ALADN 28 " --> pdb=" O ALADN 25 " (cutoff:3.500A) Processing helix chain 'DN' and resid 174 through 178 removed outlier: 3.576A pdb=" N SERDN 177 " --> pdb=" O ASPDN 174 " (cutoff:3.500A) Processing helix chain 'DN' and resid 368 through 402 removed outlier: 3.705A pdb=" N VALDN 373 " --> pdb=" O SERDN 369 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASNDN 374 " --> pdb=" O LYSDN 370 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILEDN 376 " --> pdb=" O LEUDN 372 " (cutoff:3.500A) Processing helix chain 'DO' and resid 3 through 26 removed outlier: 3.663A pdb=" N ALADO 25 " --> pdb=" O GLYDO 21 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASNDO 26 " --> pdb=" O ASNDO 22 " (cutoff:3.500A) Processing helix chain 'DO' and resid 174 through 178 Processing helix chain 'DO' and resid 250 through 254 removed outlier: 3.584A pdb=" N GLYDO 253 " --> pdb=" O THRDO 250 " (cutoff:3.500A) Processing helix chain 'DO' and resid 367 through 402 removed outlier: 4.374A pdb=" N VALDO 373 " --> pdb=" O SERDO 369 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASNDO 374 " --> pdb=" O LYSDO 370 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THRDO 388 " --> pdb=" O SERDO 384 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILEDO 395 " --> pdb=" O THRDO 391 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEUDO 396 " --> pdb=" O GLNDO 392 " (cutoff:3.500A) Processing helix chain 'DP' and resid 3 through 26 removed outlier: 3.932A pdb=" N SERDP 8 " --> pdb=" O SERDP 4 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLYDP 9 " --> pdb=" O GLNDP 5 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILEDP 20 " --> pdb=" O ASNDP 16 " (cutoff:3.500A) Processing helix chain 'DP' and resid 174 through 178 removed outlier: 3.842A pdb=" N SERDP 177 " --> pdb=" O ASPDP 174 " (cutoff:3.500A) Processing helix chain 'DP' and resid 367 through 402 removed outlier: 3.788A pdb=" N GLUDP 371 " --> pdb=" O ASPDP 367 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VALDP 373 " --> pdb=" O SERDP 369 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASNDP 374 " --> pdb=" O LYSDP 370 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILEDP 376 " --> pdb=" O LEUDP 372 " (cutoff:3.500A) Processing helix chain 'DQ' and resid 3 through 26 Processing helix chain 'DQ' and resid 174 through 178 removed outlier: 3.720A pdb=" N TYRDQ 178 " --> pdb=" O ALADQ 175 " (cutoff:3.500A) Processing helix chain 'DQ' and resid 367 through 402 removed outlier: 4.119A pdb=" N GLUDQ 371 " --> pdb=" O ASPDQ 367 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VALDQ 373 " --> pdb=" O SERDQ 369 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILEDQ 376 " --> pdb=" O LEUDQ 372 " (cutoff:3.500A) Processing helix chain 'DR' and resid 3 through 26 removed outlier: 3.532A pdb=" N THRDR 15 " --> pdb=" O ASNDR 11 " (cutoff:3.500A) Processing helix chain 'DR' and resid 27 through 29 No H-bonds generated for 'chain 'DR' and resid 27 through 29' Processing helix chain 'DR' and resid 367 through 402 removed outlier: 3.762A pdb=" N VALDR 373 " --> pdb=" O SERDR 369 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASNDR 374 " --> pdb=" O LYSDR 370 " (cutoff:3.500A) Processing helix chain 'DS' and resid 3 through 26 removed outlier: 3.934A pdb=" N SERDS 8 " --> pdb=" O SERDS 4 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLYDS 9 " --> pdb=" O GLNDS 5 " (cutoff:3.500A) Processing helix chain 'DS' and resid 174 through 178 Processing helix chain 'DS' and resid 367 through 402 removed outlier: 4.373A pdb=" N GLUDS 371 " --> pdb=" O ASPDS 367 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VALDS 373 " --> pdb=" O SERDS 369 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASNDS 374 " --> pdb=" O LYSDS 370 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N METDS 375 " --> pdb=" O GLUDS 371 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILEDS 376 " --> pdb=" O LEUDS 372 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THRDS 388 " --> pdb=" O SERDS 384 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILEDS 389 " --> pdb=" O ASNDS 385 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYSDS 390 " --> pdb=" O ALADS 386 " (cutoff:3.500A) Processing helix chain 'DT' and resid 3 through 26 removed outlier: 4.042A pdb=" N SERDT 8 " --> pdb=" O SERDT 4 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLYDT 9 " --> pdb=" O GLNDT 5 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THRDT 15 " --> pdb=" O ASNDT 11 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASNDT 16 " --> pdb=" O ALADT 12 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEUDT 17 " --> pdb=" O ALADT 13 " (cutoff:3.500A) Processing helix chain 'DT' and resid 174 through 178 removed outlier: 3.683A pdb=" N SERDT 177 " --> pdb=" O ASPDT 174 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYRDT 178 " --> pdb=" O ALADT 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'DT' and resid 174 through 178' Processing helix chain 'DT' and resid 367 through 402 removed outlier: 3.587A pdb=" N GLUDT 371 " --> pdb=" O ASPDT 367 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VALDT 373 " --> pdb=" O SERDT 369 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEUDT 402 " --> pdb=" O THRDT 398 " (cutoff:3.500A) Processing helix chain 'DU' and resid 3 through 26 removed outlier: 3.669A pdb=" N SERDU 8 " --> pdb=" O SERDU 4 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLYDU 9 " --> pdb=" O GLNDU 5 " (cutoff:3.500A) Processing helix chain 'DU' and resid 367 through 401 removed outlier: 3.522A pdb=" N GLUDU 371 " --> pdb=" O ASPDU 367 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VALDU 373 " --> pdb=" O SERDU 369 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASNDU 374 " --> pdb=" O LYSDU 370 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILEDU 376 " --> pdb=" O LEUDU 372 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VALDU 377 " --> pdb=" O VALDU 373 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THRDU 388 " --> pdb=" O SERDU 384 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILEDU 389 " --> pdb=" O ASNDU 385 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYSDU 390 " --> pdb=" O ALADU 386 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THRDU 391 " --> pdb=" O GLNDU 387 " (cutoff:3.500A) Processing helix chain 'DV' and resid 3 through 26 Processing helix chain 'DV' and resid 367 through 398 removed outlier: 3.962A pdb=" N GLUDV 371 " --> pdb=" O ASPDV 367 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VALDV 373 " --> pdb=" O SERDV 369 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASNDV 374 " --> pdb=" O LYSDV 370 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILEDV 376 " --> pdb=" O LEUDV 372 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEUDV 396 " --> pdb=" O GLNDV 392 " (cutoff:3.500A) Processing helix chain 'DW' and resid 3 through 26 Processing helix chain 'DW' and resid 27 through 29 No H-bonds generated for 'chain 'DW' and resid 27 through 29' Processing helix chain 'DW' and resid 367 through 401 removed outlier: 3.549A pdb=" N GLUDW 371 " --> pdb=" O ASPDW 367 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VALDW 373 " --> pdb=" O SERDW 369 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILEDW 376 " --> pdb=" O LEUDW 372 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THRDW 388 " --> pdb=" O SERDW 384 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILEDW 389 " --> pdb=" O ASNDW 385 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASNDW 401 " --> pdb=" O ASNDW 397 " (cutoff:3.500A) Processing helix chain 'DX' and resid 3 through 26 Processing helix chain 'DX' and resid 174 through 178 removed outlier: 3.529A pdb=" N TYRDX 178 " --> pdb=" O ALADX 175 " (cutoff:3.500A) Processing helix chain 'DX' and resid 369 through 401 removed outlier: 3.523A pdb=" N VALDX 373 " --> pdb=" O SERDX 369 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASNDX 374 " --> pdb=" O LYSDX 370 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N METDX 375 " --> pdb=" O GLUDX 371 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILEDX 376 " --> pdb=" O LEUDX 372 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THRDX 388 " --> pdb=" O SERDX 384 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILEDX 389 " --> pdb=" O ASNDX 385 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYSDX 390 " --> pdb=" O ALADX 386 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEUDX 399 " --> pdb=" O ILEDX 395 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASNDX 401 " --> pdb=" O ASNDX 397 " (cutoff:3.500A) Processing helix chain 'DY' and resid 3 through 26 removed outlier: 3.834A pdb=" N GLYDY 9 " --> pdb=" O GLNDY 5 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALADY 14 " --> pdb=" O LEUDY 10 " (cutoff:3.500A) Processing helix chain 'DY' and resid 174 through 178 removed outlier: 3.809A pdb=" N TYRDY 178 " --> pdb=" O ALADY 175 " (cutoff:3.500A) Processing helix chain 'DY' and resid 368 through 401 removed outlier: 3.696A pdb=" N ILEDY 376 " --> pdb=" O LEUDY 372 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THRDY 388 " --> pdb=" O SERDY 384 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILEDY 389 " --> pdb=" O ASNDY 385 " (cutoff:3.500A) Processing helix chain 'DZ' and resid 3 through 26 removed outlier: 3.644A pdb=" N THRDZ 15 " --> pdb=" O ASNDZ 11 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILEDZ 20 " --> pdb=" O ASNDZ 16 " (cutoff:3.500A) Processing helix chain 'DZ' and resid 367 through 401 removed outlier: 3.605A pdb=" N GLUDZ 371 " --> pdb=" O ASPDZ 367 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VALDZ 373 " --> pdb=" O SERDZ 369 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEUDZ 399 " --> pdb=" O ILEDZ 395 " (cutoff:3.500A) Processing helix chain 'EA' and resid 3 through 26 Processing helix chain 'EA' and resid 174 through 178 removed outlier: 3.534A pdb=" N TYREA 178 " --> pdb=" O ALAEA 175 " (cutoff:3.500A) Processing helix chain 'EA' and resid 367 through 401 removed outlier: 3.568A pdb=" N ASNEA 374 " --> pdb=" O LYSEA 370 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILEEA 376 " --> pdb=" O LEUEA 372 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VALEA 377 " --> pdb=" O VALEA 373 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEUEA 399 " --> pdb=" O ILEEA 395 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASNEA 401 " --> pdb=" O ASNEA 397 " (cutoff:3.500A) Processing helix chain 'EB' and resid 3 through 26 Processing helix chain 'EB' and resid 174 through 178 Processing helix chain 'EB' and resid 369 through 401 removed outlier: 3.715A pdb=" N VALEB 373 " --> pdb=" O SEREB 369 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASNEB 374 " --> pdb=" O LYSEB 370 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N METEB 375 " --> pdb=" O GLUEB 371 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILEEB 376 " --> pdb=" O LEUEB 372 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VALEB 377 " --> pdb=" O VALEB 373 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THREB 388 " --> pdb=" O SEREB 384 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILEEB 389 " --> pdb=" O ASNEB 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEUEB 399 " --> pdb=" O ILEEB 395 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASNEB 401 " --> pdb=" O ASNEB 397 " (cutoff:3.500A) Processing helix chain 'EC' and resid 3 through 26 Processing helix chain 'EC' and resid 174 through 178 Processing helix chain 'EC' and resid 368 through 401 removed outlier: 3.920A pdb=" N VALEC 373 " --> pdb=" O SEREC 369 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASNEC 374 " --> pdb=" O LYSEC 370 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THREC 388 " --> pdb=" O SEREC 384 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILEEC 389 " --> pdb=" O ASNEC 385 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYSEC 390 " --> pdb=" O ALAEC 386 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASNEC 401 " --> pdb=" O ASNEC 397 " (cutoff:3.500A) Processing helix chain 'ED' and resid 3 through 26 removed outlier: 4.062A pdb=" N ILEED 20 " --> pdb=" O ASNED 16 " (cutoff:3.500A) Processing helix chain 'ED' and resid 367 through 401 removed outlier: 3.603A pdb=" N GLUED 371 " --> pdb=" O ASPED 367 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THRED 388 " --> pdb=" O SERED 384 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILEED 389 " --> pdb=" O ASNED 385 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYSED 390 " --> pdb=" O ALAED 386 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEUED 399 " --> pdb=" O ILEED 395 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASNED 401 " --> pdb=" O ASNED 397 " (cutoff:3.500A) Processing helix chain 'EE' and resid 3 through 26 Processing helix chain 'EE' and resid 367 through 401 removed outlier: 3.732A pdb=" N VALEE 373 " --> pdb=" O SEREE 369 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASNEE 374 " --> pdb=" O LYSEE 370 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N METEE 375 " --> pdb=" O GLUEE 371 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILEEE 376 " --> pdb=" O LEUEE 372 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASNEE 401 " --> pdb=" O ASNEE 397 " (cutoff:3.500A) Processing helix chain 'EF' and resid 3 through 26 removed outlier: 3.689A pdb=" N GLYEF 9 " --> pdb=" O GLNEF 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILEEF 20 " --> pdb=" O ASNEF 16 " (cutoff:3.500A) Processing helix chain 'EF' and resid 174 through 178 removed outlier: 3.522A pdb=" N SEREF 177 " --> pdb=" O ASPEF 174 " (cutoff:3.500A) Processing helix chain 'EF' and resid 367 through 402 removed outlier: 3.827A pdb=" N VALEF 373 " --> pdb=" O SEREF 369 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASNEF 374 " --> pdb=" O LYSEF 370 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILEEF 376 " --> pdb=" O LEUEF 372 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VALEF 377 " --> pdb=" O VALEF 373 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THREF 388 " --> pdb=" O SEREF 384 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILEEF 389 " --> pdb=" O ASNEF 385 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASNEF 401 " --> pdb=" O ASNEF 397 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEUEF 402 " --> pdb=" O THREF 398 " (cutoff:3.500A) Processing helix chain 'EG' and resid 3 through 26 Processing helix chain 'EG' and resid 367 through 401 removed outlier: 3.758A pdb=" N GLUEG 371 " --> pdb=" O ASPEG 367 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VALEG 373 " --> pdb=" O SEREG 369 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASNEG 374 " --> pdb=" O LYSEG 370 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILEEG 376 " --> pdb=" O LEUEG 372 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VALEG 377 " --> pdb=" O VALEG 373 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEUEG 396 " --> pdb=" O GLNEG 392 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASNEG 401 " --> pdb=" O ASNEG 397 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'DL' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'DL' and resid 40 through 41 Processing sheet with id=AA3, first strand: chain 'DL' and resid 75 through 77 Processing sheet with id=AA4, first strand: chain 'DL' and resid 92 through 95 removed outlier: 5.727A pdb=" N ARGDL 84 " --> pdb=" O THRDL 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'DL' and resid 92 through 95 removed outlier: 5.727A pdb=" N ARGDL 84 " --> pdb=" O THRDL 117 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEUDL 312 " --> pdb=" O VALDL 300 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VALDL 300 " --> pdb=" O LEUDL 312 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'DL' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'DL' and resid 121 through 122 Processing sheet with id=AA8, first strand: chain 'DL' and resid 267 through 268 removed outlier: 4.008A pdb=" N METDL 267 " --> pdb=" O ILEDL 156 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SERDL 153 " --> pdb=" O THRDL 279 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THRDL 279 " --> pdb=" O SERDL 153 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLNDL 155 " --> pdb=" O VALDL 277 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASNDL 275 " --> pdb=" O ASNDL 157 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'DL' and resid 180 through 187 removed outlier: 7.269A pdb=" N GLUDL 207 " --> pdb=" O THRDL 203 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYSDL 231 " --> pdb=" O GLUDL 239 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'DL' and resid 243 through 247 Processing sheet with id=AB2, first strand: chain 'DL' and resid 327 through 328 removed outlier: 3.509A pdb=" N ALADL 327 " --> pdb=" O ALADL 335 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'DM' and resid 35 through 40 removed outlier: 6.432A pdb=" N THRDM 36 " --> pdb=" O ILEDM 57 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILEDM 57 " --> pdb=" O THRDM 36 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N SERDM 38 " --> pdb=" O ALADM 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'DM' and resid 66 through 68 Processing sheet with id=AB5, first strand: chain 'DM' and resid 75 through 77 Processing sheet with id=AB6, first strand: chain 'DM' and resid 92 through 95 removed outlier: 16.279A pdb=" N PHEDM 82 " --> pdb=" O TYRDM 119 " (cutoff:3.500A) removed outlier: 11.422A pdb=" N TYRDM 119 " --> pdb=" O PHEDM 82 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ARGDM 84 " --> pdb=" O THRDM 117 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLYDM 313 " --> pdb=" O VALDM 300 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'DM' and resid 135 through 136 removed outlier: 5.742A pdb=" N ARGDM 84 " --> pdb=" O THRDM 117 " (cutoff:3.500A) removed outlier: 11.422A pdb=" N TYRDM 119 " --> pdb=" O PHEDM 82 " (cutoff:3.500A) removed outlier: 16.279A pdb=" N PHEDM 82 " --> pdb=" O TYRDM 119 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'DM' and resid 121 through 122 removed outlier: 3.574A pdb=" N THRDM 122 " --> pdb=" O THRDM 127 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'DM' and resid 143 through 144 removed outlier: 3.527A pdb=" N GLYDM 287 " --> pdb=" O METDM 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'DM' and resid 243 through 247 Processing sheet with id=AC2, first strand: chain 'DM' and resid 243 through 247 removed outlier: 7.198A pdb=" N THRDM 151 " --> pdb=" O GLNDM 281 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLNDM 281 " --> pdb=" O THRDM 151 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N SERDM 153 " --> pdb=" O THRDM 279 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THRDM 279 " --> pdb=" O SERDM 153 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLNDM 155 " --> pdb=" O VALDM 277 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'DM' and resid 180 through 187 removed outlier: 7.343A pdb=" N GLUDM 207 " --> pdb=" O THRDM 203 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYSDM 231 " --> pdb=" O GLUDM 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'DN' and resid 35 through 38 Processing sheet with id=AC5, first strand: chain 'DN' and resid 92 through 95 Processing sheet with id=AC6, first strand: chain 'DN' and resid 121 through 122 Processing sheet with id=AC7, first strand: chain 'DN' and resid 243 through 246 removed outlier: 6.863A pdb=" N THRDN 151 " --> pdb=" O GLNDN 281 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLNDN 281 " --> pdb=" O THRDN 151 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SERDN 153 " --> pdb=" O THRDN 279 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THRDN 279 " --> pdb=" O SERDN 153 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLNDN 155 " --> pdb=" O VALDN 277 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'DN' and resid 180 through 186 removed outlier: 6.897A pdb=" N GLUDN 207 " --> pdb=" O THRDN 203 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LYSDN 231 " --> pdb=" O GLUDN 239 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'DN' and resid 289 through 294 removed outlier: 7.070A pdb=" N ASNDN 303 " --> pdb=" O VALDN 290 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N TYRDN 292 " --> pdb=" O VALDN 301 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VALDN 301 " --> pdb=" O TYRDN 292 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ILEDN 294 " --> pdb=" O THRDN 299 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THRDN 299 " --> pdb=" O ILEDN 294 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VALDN 300 " --> pdb=" O LEUDN 312 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'DN' and resid 317 through 318 Processing sheet with id=AD2, first strand: chain 'DN' and resid 327 through 328 Processing sheet with id=AD3, first strand: chain 'DO' and resid 35 through 38 Processing sheet with id=AD4, first strand: chain 'DO' and resid 66 through 67 removed outlier: 3.582A pdb=" N LEUDO 361 " --> pdb=" O THRDO 67 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'DO' and resid 75 through 77 Processing sheet with id=AD6, first strand: chain 'DO' and resid 135 through 136 removed outlier: 6.028A pdb=" N VALDO 300 " --> pdb=" O LEUDO 312 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'DO' and resid 135 through 136 removed outlier: 3.766A pdb=" N GLNDO 115 " --> pdb=" O VALDO 86 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VALDO 86 " --> pdb=" O GLNDO 115 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ARGDO 84 " --> pdb=" O THRDO 117 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALADO 327 " --> pdb=" O ALADO 335 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'DO' and resid 100 through 102 Processing sheet with id=AD9, first strand: chain 'DO' and resid 121 through 122 Processing sheet with id=AE1, first strand: chain 'DO' and resid 243 through 247 removed outlier: 3.947A pdb=" N ALADO 278 " --> pdb=" O GLNDO 155 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASNDO 157 " --> pdb=" O ILEDO 276 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILEDO 276 " --> pdb=" O ASNDO 157 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'DO' and resid 180 through 186 removed outlier: 4.048A pdb=" N THRDO 203 " --> pdb=" O GLUDO 207 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N GLUDO 207 " --> pdb=" O THRDO 203 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYSDO 231 " --> pdb=" O GLUDO 239 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'DO' and resid 317 through 318 Processing sheet with id=AE4, first strand: chain 'DP' and resid 35 through 43 removed outlier: 5.913A pdb=" N ALADP 40 " --> pdb=" O VALDP 54 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VALDP 54 " --> pdb=" O ALADP 40 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N METDP 42 " --> pdb=" O VALDP 52 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VALDP 52 " --> pdb=" O METDP 42 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'DP' and resid 67 through 68 Processing sheet with id=AE6, first strand: chain 'DP' and resid 75 through 77 Processing sheet with id=AE7, first strand: chain 'DP' and resid 92 through 95 removed outlier: 5.040A pdb=" N ARGDP 84 " --> pdb=" O THRDP 117 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'DP' and resid 92 through 95 removed outlier: 5.040A pdb=" N ARGDP 84 " --> pdb=" O THRDP 117 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLUDP 309 " --> pdb=" O TYRDP 304 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYRDP 304 " --> pdb=" O GLUDP 309 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VALDP 311 " --> pdb=" O GLYDP 302 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLYDP 302 " --> pdb=" O VALDP 311 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLYDP 313 " --> pdb=" O VALDP 300 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THRDP 299 " --> pdb=" O ILEDP 294 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILEDP 294 " --> pdb=" O THRDP 299 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VALDP 301 " --> pdb=" O TYRDP 292 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYRDP 292 " --> pdb=" O VALDP 301 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASNDP 303 " --> pdb=" O VALDP 290 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'DP' and resid 121 through 122 Processing sheet with id=AF1, first strand: chain 'DP' and resid 243 through 246 Processing sheet with id=AF2, first strand: chain 'DP' and resid 243 through 246 removed outlier: 7.790A pdb=" N THRDP 151 " --> pdb=" O GLNDP 281 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLNDP 281 " --> pdb=" O THRDP 151 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SERDP 153 " --> pdb=" O THRDP 279 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THRDP 279 " --> pdb=" O SERDP 153 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLNDP 155 " --> pdb=" O VALDP 277 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'DP' and resid 180 through 187 removed outlier: 7.263A pdb=" N LYSDP 231 " --> pdb=" O GLUDP 239 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLUDP 239 " --> pdb=" O LYSDP 231 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'DP' and resid 317 through 318 removed outlier: 4.206A pdb=" N GLYDP 346 " --> pdb=" O LEUDP 317 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'DP' and resid 327 through 328 Processing sheet with id=AF6, first strand: chain 'DQ' and resid 34 through 43 removed outlier: 4.478A pdb=" N SERDQ 34 " --> pdb=" O ASPDQ 60 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ALADQ 40 " --> pdb=" O VALDQ 54 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VALDQ 54 " --> pdb=" O ALADQ 40 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N METDQ 42 " --> pdb=" O VALDQ 52 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VALDQ 52 " --> pdb=" O METDQ 42 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'DQ' and resid 66 through 68 Processing sheet with id=AF8, first strand: chain 'DQ' and resid 75 through 77 Processing sheet with id=AF9, first strand: chain 'DQ' and resid 92 through 95 removed outlier: 16.107A pdb=" N PHEDQ 82 " --> pdb=" O TYRDQ 119 " (cutoff:3.500A) removed outlier: 11.164A pdb=" N TYRDQ 119 " --> pdb=" O PHEDQ 82 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARGDQ 84 " --> pdb=" O THRDQ 117 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THRDQ 117 " --> pdb=" O ARGDQ 84 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLNDQ 314 " --> pdb=" O TYRDQ 119 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLUDQ 309 " --> pdb=" O TYRDQ 304 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N TYRDQ 304 " --> pdb=" O GLUDQ 309 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VALDQ 311 " --> pdb=" O GLYDQ 302 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLYDQ 302 " --> pdb=" O VALDQ 311 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLYDQ 313 " --> pdb=" O VALDQ 300 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THRDQ 299 " --> pdb=" O ILEDQ 294 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILEDQ 294 " --> pdb=" O THRDQ 299 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VALDQ 301 " --> pdb=" O TYRDQ 292 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYRDQ 292 " --> pdb=" O VALDQ 301 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASNDQ 303 " --> pdb=" O VALDQ 290 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'DQ' and resid 135 through 136 removed outlier: 3.533A pdb=" N THRDQ 117 " --> pdb=" O ARGDQ 84 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARGDQ 84 " --> pdb=" O THRDQ 117 " (cutoff:3.500A) removed outlier: 11.164A pdb=" N TYRDQ 119 " --> pdb=" O PHEDQ 82 " (cutoff:3.500A) removed outlier: 16.107A pdb=" N PHEDQ 82 " --> pdb=" O TYRDQ 119 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'DQ' and resid 101 through 102 Processing sheet with id=AG3, first strand: chain 'DQ' and resid 121 through 122 Processing sheet with id=AG4, first strand: chain 'DQ' and resid 243 through 246 removed outlier: 3.527A pdb=" N ALADQ 278 " --> pdb=" O GLNDQ 155 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASNDQ 157 " --> pdb=" O ILEDQ 276 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILEDQ 276 " --> pdb=" O ASNDQ 157 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'DQ' and resid 180 through 187 removed outlier: 6.971A pdb=" N GLUDQ 207 " --> pdb=" O THRDQ 203 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LYSDQ 231 " --> pdb=" O GLUDQ 239 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'DQ' and resid 327 through 328 Processing sheet with id=AG7, first strand: chain 'DR' and resid 35 through 41 removed outlier: 5.687A pdb=" N ALADR 40 " --> pdb=" O VALDR 54 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VALDR 54 " --> pdb=" O ALADR 40 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'DR' and resid 66 through 68 Processing sheet with id=AG9, first strand: chain 'DR' and resid 75 through 77 Processing sheet with id=AH1, first strand: chain 'DR' and resid 92 through 95 removed outlier: 16.863A pdb=" N PHEDR 82 " --> pdb=" O TYRDR 119 " (cutoff:3.500A) removed outlier: 12.024A pdb=" N TYRDR 119 " --> pdb=" O PHEDR 82 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ARGDR 84 " --> pdb=" O THRDR 117 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THRDR 117 " --> pdb=" O ARGDR 84 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'DR' and resid 92 through 95 removed outlier: 4.102A pdb=" N ARGDR 84 " --> pdb=" O VALDR 316 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VALDR 316 " --> pdb=" O ARGDR 84 " (cutoff:3.500A) removed outlier: 12.074A pdb=" N VALDR 86 " --> pdb=" O GLNDR 314 " (cutoff:3.500A) removed outlier: 15.896A pdb=" N GLNDR 314 " --> pdb=" O VALDR 86 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'DR' and resid 135 through 136 removed outlier: 17.208A pdb=" N GLNDR 115 " --> pdb=" O ALADR 318 " (cutoff:3.500A) removed outlier: 12.528A pdb=" N ALADR 318 " --> pdb=" O GLNDR 115 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THRDR 117 " --> pdb=" O VALDR 316 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VALDR 316 " --> pdb=" O THRDR 117 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VALDR 300 " --> pdb=" O LEUDR 312 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SERDR 291 " --> pdb=" O ASNDR 303 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'DR' and resid 121 through 122 Processing sheet with id=AH5, first strand: chain 'DR' and resid 244 through 247 removed outlier: 3.562A pdb=" N METDR 154 " --> pdb=" O SERDR 262 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'DR' and resid 244 through 247 removed outlier: 3.562A pdb=" N METDR 154 " --> pdb=" O SERDR 262 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALADR 278 " --> pdb=" O GLNDR 155 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASNDR 157 " --> pdb=" O ILEDR 276 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ILEDR 276 " --> pdb=" O ASNDR 157 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'DR' and resid 180 through 187 removed outlier: 6.991A pdb=" N GLUDR 207 " --> pdb=" O THRDR 203 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'DR' and resid 327 through 328 removed outlier: 3.749A pdb=" N ALADR 327 " --> pdb=" O ALADR 335 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'DS' and resid 35 through 42 removed outlier: 5.824A pdb=" N THRDS 36 " --> pdb=" O ILEDS 57 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILEDS 57 " --> pdb=" O THRDS 36 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SERDS 38 " --> pdb=" O ALADS 55 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLYDS 51 " --> pdb=" O METDS 42 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'DS' and resid 66 through 68 Processing sheet with id=AI2, first strand: chain 'DS' and resid 75 through 77 Processing sheet with id=AI3, first strand: chain 'DS' and resid 92 through 95 removed outlier: 6.114A pdb=" N ARGDS 84 " --> pdb=" O THRDS 117 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'DS' and resid 92 through 95 Processing sheet with id=AI5, first strand: chain 'DS' and resid 101 through 102 Processing sheet with id=AI6, first strand: chain 'DS' and resid 121 through 122 Processing sheet with id=AI7, first strand: chain 'DS' and resid 243 through 247 removed outlier: 3.649A pdb=" N SERDS 262 " --> pdb=" O ALADS 152 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N METDS 267 " --> pdb=" O ILEDS 156 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'DS' and resid 243 through 247 removed outlier: 3.649A pdb=" N SERDS 262 " --> pdb=" O ALADS 152 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALADS 278 " --> pdb=" O GLNDS 155 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASNDS 157 " --> pdb=" O ILEDS 276 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILEDS 276 " --> pdb=" O ASNDS 157 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'DS' and resid 180 through 187 removed outlier: 7.058A pdb=" N GLUDS 207 " --> pdb=" O THRDS 203 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'DS' and resid 289 through 294 removed outlier: 5.978A pdb=" N VALDS 300 " --> pdb=" O LEUDS 312 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'DS' and resid 327 through 328 Processing sheet with id=AJ3, first strand: chain 'DT' and resid 35 through 42 removed outlier: 6.326A pdb=" N THRDT 36 " --> pdb=" O ILEDT 57 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILEDT 57 " --> pdb=" O THRDT 36 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SERDT 38 " --> pdb=" O ALADT 55 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLYDT 51 " --> pdb=" O METDT 42 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'DT' and resid 67 through 68 Processing sheet with id=AJ5, first strand: chain 'DT' and resid 76 through 77 removed outlier: 3.520A pdb=" N ALADT 76 " --> pdb=" O THRDT 357 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'DT' and resid 327 through 328 removed outlier: 3.655A pdb=" N ALADT 327 " --> pdb=" O ALADT 335 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ARGDT 84 " --> pdb=" O THRDT 117 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'DT' and resid 327 through 328 removed outlier: 3.655A pdb=" N ALADT 327 " --> pdb=" O ALADT 335 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARGDT 84 " --> pdb=" O VALDT 316 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VALDT 316 " --> pdb=" O ARGDT 84 " (cutoff:3.500A) removed outlier: 12.162A pdb=" N VALDT 86 " --> pdb=" O GLNDT 314 " (cutoff:3.500A) removed outlier: 16.149A pdb=" N GLNDT 314 " --> pdb=" O VALDT 86 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'DT' and resid 135 through 136 removed outlier: 16.074A pdb=" N GLNDT 115 " --> pdb=" O ALADT 318 " (cutoff:3.500A) removed outlier: 12.623A pdb=" N ALADT 318 " --> pdb=" O GLNDT 115 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THRDT 117 " --> pdb=" O VALDT 316 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VALDT 316 " --> pdb=" O THRDT 117 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLNDT 308 " --> pdb=" O TYRDT 304 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VALDT 300 " --> pdb=" O LEUDT 312 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'DT' and resid 100 through 102 Processing sheet with id=AK1, first strand: chain 'DT' and resid 121 through 122 Processing sheet with id=AK2, first strand: chain 'DT' and resid 243 through 247 removed outlier: 8.614A pdb=" N METDT 267 " --> pdb=" O METDT 154 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILEDT 156 " --> pdb=" O METDT 267 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'DT' and resid 243 through 247 removed outlier: 6.559A pdb=" N THRDT 151 " --> pdb=" O GLNDT 281 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLNDT 281 " --> pdb=" O THRDT 151 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SERDT 153 " --> pdb=" O THRDT 279 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THRDT 279 " --> pdb=" O SERDT 153 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLNDT 155 " --> pdb=" O VALDT 277 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASNDT 157 " --> pdb=" O ASNDT 275 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASNDT 275 " --> pdb=" O ASNDT 157 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'DT' and resid 180 through 187 removed outlier: 7.079A pdb=" N GLUDT 207 " --> pdb=" O THRDT 203 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LYSDT 231 " --> pdb=" O GLUDT 239 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'DU' and resid 35 through 43 removed outlier: 5.939A pdb=" N ALADU 40 " --> pdb=" O VALDU 54 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VALDU 54 " --> pdb=" O ALADU 40 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N METDU 42 " --> pdb=" O VALDU 52 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VALDU 52 " --> pdb=" O METDU 42 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'DU' and resid 75 through 77 Processing sheet with id=AK7, first strand: chain 'DU' and resid 135 through 136 Processing sheet with id=AK8, first strand: chain 'DU' and resid 135 through 136 removed outlier: 5.225A pdb=" N ARGDU 84 " --> pdb=" O THRDU 117 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'DU' and resid 121 through 122 Processing sheet with id=AL1, first strand: chain 'DU' and resid 243 through 247 removed outlier: 6.734A pdb=" N ALADU 152 " --> pdb=" O SERDU 262 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASNDU 157 " --> pdb=" O ILEDU 276 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILEDU 276 " --> pdb=" O ASNDU 157 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'DU' and resid 180 through 187 removed outlier: 7.214A pdb=" N GLUDU 207 " --> pdb=" O THRDU 203 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYSDU 231 " --> pdb=" O GLUDU 239 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'DU' and resid 289 through 294 removed outlier: 6.883A pdb=" N ASNDU 303 " --> pdb=" O VALDU 290 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYRDU 292 " --> pdb=" O VALDU 301 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VALDU 301 " --> pdb=" O TYRDU 292 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'DU' and resid 317 through 318 Processing sheet with id=AL5, first strand: chain 'DV' and resid 35 through 43 removed outlier: 6.292A pdb=" N THRDV 36 " --> pdb=" O ILEDV 57 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILEDV 57 " --> pdb=" O THRDV 36 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SERDV 38 " --> pdb=" O ALADV 55 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALADV 40 " --> pdb=" O LYSDV 53 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLYDV 51 " --> pdb=" O METDV 42 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'DV' and resid 66 through 68 Processing sheet with id=AL7, first strand: chain 'DV' and resid 135 through 136 removed outlier: 5.599A pdb=" N ARGDV 84 " --> pdb=" O THRDV 117 " (cutoff:3.500A) removed outlier: 11.145A pdb=" N TYRDV 119 " --> pdb=" O PHEDV 82 " (cutoff:3.500A) removed outlier: 15.983A pdb=" N PHEDV 82 " --> pdb=" O TYRDV 119 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'DV' and resid 289 through 294 removed outlier: 5.773A pdb=" N VALDV 300 " --> pdb=" O LEUDV 312 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ARGDV 84 " --> pdb=" O THRDV 117 " (cutoff:3.500A) removed outlier: 11.145A pdb=" N TYRDV 119 " --> pdb=" O PHEDV 82 " (cutoff:3.500A) removed outlier: 15.983A pdb=" N PHEDV 82 " --> pdb=" O TYRDV 119 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEUDV 317 " --> pdb=" O GLYDV 346 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'DV' and resid 100 through 103 Processing sheet with id=AM1, first strand: chain 'DV' and resid 121 through 122 Processing sheet with id=AM2, first strand: chain 'DV' and resid 243 through 246 Processing sheet with id=AM3, first strand: chain 'DV' and resid 243 through 246 removed outlier: 6.145A pdb=" N ASNDV 157 " --> pdb=" O ILEDV 276 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILEDV 276 " --> pdb=" O ASNDV 157 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'DV' and resid 180 through 187 removed outlier: 7.037A pdb=" N GLUDV 207 " --> pdb=" O THRDV 203 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYSDV 231 " --> pdb=" O GLUDV 239 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'DW' and resid 35 through 36 Processing sheet with id=AM6, first strand: chain 'DW' and resid 39 through 41 Processing sheet with id=AM7, first strand: chain 'DW' and resid 75 through 77 Processing sheet with id=AM8, first strand: chain 'DW' and resid 92 through 95 removed outlier: 16.316A pdb=" N PHEDW 82 " --> pdb=" O TYRDW 119 " (cutoff:3.500A) removed outlier: 11.494A pdb=" N TYRDW 119 " --> pdb=" O PHEDW 82 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ARGDW 84 " --> pdb=" O THRDW 117 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VALDW 300 " --> pdb=" O LEUDW 312 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'DW' and resid 135 through 136 removed outlier: 5.967A pdb=" N ARGDW 84 " --> pdb=" O THRDW 117 " (cutoff:3.500A) removed outlier: 11.494A pdb=" N TYRDW 119 " --> pdb=" O PHEDW 82 " (cutoff:3.500A) removed outlier: 16.316A pdb=" N PHEDW 82 " --> pdb=" O TYRDW 119 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'DW' and resid 121 through 122 Processing sheet with id=AN2, first strand: chain 'DW' and resid 243 through 246 removed outlier: 3.692A pdb=" N SERDW 262 " --> pdb=" O ALADW 152 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N METDW 154 " --> pdb=" O SERDW 262 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N METDW 267 " --> pdb=" O ILEDW 156 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'DW' and resid 243 through 246 removed outlier: 3.692A pdb=" N SERDW 262 " --> pdb=" O ALADW 152 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N METDW 154 " --> pdb=" O SERDW 262 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALADW 278 " --> pdb=" O GLNDW 155 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASNDW 157 " --> pdb=" O ILEDW 276 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILEDW 276 " --> pdb=" O ASNDW 157 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'DW' and resid 180 through 187 removed outlier: 7.104A pdb=" N GLUDW 207 " --> pdb=" O THRDW 203 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYSDW 231 " --> pdb=" O GLUDW 239 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'DW' and resid 327 through 328 Processing sheet with id=AN6, first strand: chain 'DX' and resid 34 through 41 removed outlier: 7.005A pdb=" N SERDX 34 " --> pdb=" O GLNDX 59 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLNDX 59 " --> pdb=" O SERDX 34 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THRDX 36 " --> pdb=" O ILEDX 57 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILEDX 57 " --> pdb=" O THRDX 36 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N SERDX 38 " --> pdb=" O ALADX 55 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'DX' and resid 66 through 68 Processing sheet with id=AN8, first strand: chain 'DX' and resid 92 through 95 removed outlier: 5.494A pdb=" N ARGDX 84 " --> pdb=" O THRDX 117 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'DX' and resid 92 through 95 removed outlier: 5.494A pdb=" N ARGDX 84 " --> pdb=" O THRDX 117 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLNDX 314 " --> pdb=" O TYRDX 119 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLUDX 309 " --> pdb=" O TYRDX 304 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N TYRDX 304 " --> pdb=" O GLUDX 309 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N VALDX 311 " --> pdb=" O GLYDX 302 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLYDX 302 " --> pdb=" O VALDX 311 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLYDX 313 " --> pdb=" O VALDX 300 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'DX' and resid 101 through 102 Processing sheet with id=AO2, first strand: chain 'DX' and resid 121 through 122 Processing sheet with id=AO3, first strand: chain 'DX' and resid 244 through 246 removed outlier: 4.036A pdb=" N SERDX 262 " --> pdb=" O ALADX 152 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N METDX 154 " --> pdb=" O SERDX 262 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'DX' and resid 180 through 187 removed outlier: 7.097A pdb=" N GLUDX 207 " --> pdb=" O THRDX 203 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYSDX 231 " --> pdb=" O GLUDX 239 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'DX' and resid 317 through 318 Processing sheet with id=AO6, first strand: chain 'DY' and resid 37 through 42 removed outlier: 6.987A pdb=" N SERDY 38 " --> pdb=" O ALADY 55 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLYDY 51 " --> pdb=" O METDY 42 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'DY' and resid 75 through 77 Processing sheet with id=AO8, first strand: chain 'DY' and resid 92 through 95 Processing sheet with id=AO9, first strand: chain 'DY' and resid 101 through 102 Processing sheet with id=AP1, first strand: chain 'DY' and resid 118 through 119 removed outlier: 5.494A pdb=" N VALDY 300 " --> pdb=" O LEUDY 312 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'DY' and resid 243 through 247 removed outlier: 6.379A pdb=" N ASNDY 157 " --> pdb=" O ILEDY 276 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILEDY 276 " --> pdb=" O ASNDY 157 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'DY' and resid 180 through 187 removed outlier: 6.937A pdb=" N GLUDY 207 " --> pdb=" O THRDY 203 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'DY' and resid 326 through 328 Processing sheet with id=AP5, first strand: chain 'DZ' and resid 35 through 43 removed outlier: 5.866A pdb=" N THRDZ 36 " --> pdb=" O ILEDZ 57 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILEDZ 57 " --> pdb=" O THRDZ 36 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SERDZ 38 " --> pdb=" O ALADZ 55 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N METDZ 42 " --> pdb=" O GLYDZ 51 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLYDZ 51 " --> pdb=" O METDZ 42 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'DZ' and resid 66 through 67 Processing sheet with id=AP7, first strand: chain 'DZ' and resid 75 through 77 Processing sheet with id=AP8, first strand: chain 'DZ' and resid 135 through 136 removed outlier: 6.474A pdb=" N VALDZ 300 " --> pdb=" O LEUDZ 312 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'DZ' and resid 135 through 136 removed outlier: 5.456A pdb=" N ARGDZ 84 " --> pdb=" O THRDZ 117 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'DZ' and resid 100 through 103 Processing sheet with id=AQ2, first strand: chain 'DZ' and resid 121 through 122 Processing sheet with id=AQ3, first strand: chain 'DZ' and resid 244 through 246 removed outlier: 6.668A pdb=" N ALADZ 152 " --> pdb=" O SERDZ 262 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'DZ' and resid 244 through 246 removed outlier: 6.668A pdb=" N ALADZ 152 " --> pdb=" O SERDZ 262 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASNDZ 157 " --> pdb=" O ILEDZ 276 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILEDZ 276 " --> pdb=" O ASNDZ 157 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'DZ' and resid 180 through 187 removed outlier: 7.132A pdb=" N GLUDZ 207 " --> pdb=" O THRDZ 203 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'DZ' and resid 317 through 318 removed outlier: 3.504A pdb=" N LEUDZ 317 " --> pdb=" O GLYDZ 346 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLYDZ 346 " --> pdb=" O LEUDZ 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ6 Processing sheet with id=AQ7, first strand: chain 'EA' and resid 35 through 43 removed outlier: 6.031A pdb=" N THREA 36 " --> pdb=" O ILEEA 57 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILEEA 57 " --> pdb=" O THREA 36 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SEREA 38 " --> pdb=" O ALAEA 55 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLYEA 51 " --> pdb=" O METEA 42 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'EA' and resid 66 through 68 Processing sheet with id=AQ9, first strand: chain 'EA' and resid 75 through 77 Processing sheet with id=AR1, first strand: chain 'EA' and resid 92 through 95 removed outlier: 16.160A pdb=" N PHEEA 82 " --> pdb=" O TYREA 119 " (cutoff:3.500A) removed outlier: 11.139A pdb=" N TYREA 119 " --> pdb=" O PHEEA 82 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARGEA 84 " --> pdb=" O THREA 117 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLUEA 309 " --> pdb=" O TYREA 304 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N TYREA 304 " --> pdb=" O GLUEA 309 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VALEA 311 " --> pdb=" O GLYEA 302 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLYEA 302 " --> pdb=" O VALEA 311 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLYEA 313 " --> pdb=" O VALEA 300 " (cutoff:3.500A) Processing sheet with id=AR2, first strand: chain 'EA' and resid 135 through 136 removed outlier: 5.688A pdb=" N ARGEA 84 " --> pdb=" O THREA 117 " (cutoff:3.500A) removed outlier: 11.139A pdb=" N TYREA 119 " --> pdb=" O PHEEA 82 " (cutoff:3.500A) removed outlier: 16.160A pdb=" N PHEEA 82 " --> pdb=" O TYREA 119 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'EA' and resid 100 through 102 removed outlier: 3.686A pdb=" N VALEA 109 " --> pdb=" O LYSEA 101 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'EA' and resid 121 through 122 Processing sheet with id=AR5, first strand: chain 'EA' and resid 244 through 246 removed outlier: 7.170A pdb=" N ALAEA 152 " --> pdb=" O SEREA 262 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N METEA 267 " --> pdb=" O ILEEA 156 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'EA' and resid 244 through 246 removed outlier: 7.170A pdb=" N ALAEA 152 " --> pdb=" O SEREA 262 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N SEREA 153 " --> pdb=" O THREA 279 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THREA 279 " --> pdb=" O SEREA 153 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLNEA 155 " --> pdb=" O VALEA 277 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'EA' and resid 180 through 187 removed outlier: 3.986A pdb=" N THREA 203 " --> pdb=" O GLUEA 207 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLUEA 207 " --> pdb=" O THREA 203 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYSEA 231 " --> pdb=" O GLUEA 239 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'EB' and resid 35 through 36 Processing sheet with id=AR9, first strand: chain 'EB' and resid 39 through 41 Processing sheet with id=AS1, first strand: chain 'EB' and resid 66 through 68 Processing sheet with id=AS2, first strand: chain 'EB' and resid 75 through 77 Processing sheet with id=AS3, first strand: chain 'EB' and resid 93 through 95 Processing sheet with id=AS4, first strand: chain 'EB' and resid 127 through 128 Processing sheet with id=AS5, first strand: chain 'EB' and resid 127 through 128 removed outlier: 3.814A pdb=" N GLNEB 314 " --> pdb=" O TYREB 119 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALAEB 121 " --> pdb=" O LEUEB 312 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEUEB 312 " --> pdb=" O ALAEB 121 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLUEB 309 " --> pdb=" O TYREB 304 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N TYREB 304 " --> pdb=" O GLUEB 309 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VALEB 311 " --> pdb=" O GLYEB 302 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLYEB 302 " --> pdb=" O VALEB 311 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLYEB 313 " --> pdb=" O VALEB 300 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'EB' and resid 245 through 247 Processing sheet with id=AS7, first strand: chain 'EB' and resid 245 through 247 removed outlier: 7.274A pdb=" N THREB 151 " --> pdb=" O GLNEB 281 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLNEB 281 " --> pdb=" O THREB 151 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N SEREB 153 " --> pdb=" O THREB 279 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N THREB 279 " --> pdb=" O SEREB 153 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLNEB 155 " --> pdb=" O VALEB 277 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VALEB 277 " --> pdb=" O GLNEB 155 " (cutoff:3.500A) Processing sheet with id=AS8, first strand: chain 'EB' and resid 180 through 187 removed outlier: 6.963A pdb=" N GLUEB 207 " --> pdb=" O THREB 203 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SEREB 240 " --> pdb=" O LYSEB 231 " (cutoff:3.500A) Processing sheet with id=AS9, first strand: chain 'EB' and resid 327 through 328 Processing sheet with id=AT1, first strand: chain 'EC' and resid 35 through 36 Processing sheet with id=AT2, first strand: chain 'EC' and resid 39 through 41 Processing sheet with id=AT3, first strand: chain 'EC' and resid 66 through 68 Processing sheet with id=AT4, first strand: chain 'EC' and resid 135 through 136 removed outlier: 5.905A pdb=" N VALEC 311 " --> pdb=" O GLYEC 302 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLYEC 302 " --> pdb=" O VALEC 311 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLYEC 313 " --> pdb=" O VALEC 300 " (cutoff:3.500A) Processing sheet with id=AT5, first strand: chain 'EC' and resid 135 through 136 removed outlier: 3.529A pdb=" N THREC 117 " --> pdb=" O ARGEC 84 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ARGEC 84 " --> pdb=" O THREC 117 " (cutoff:3.500A) Processing sheet with id=AT6, first strand: chain 'EC' and resid 121 through 122 Processing sheet with id=AT7, first strand: chain 'EC' and resid 243 through 246 Processing sheet with id=AT8, first strand: chain 'EC' and resid 157 through 158 Processing sheet with id=AT9, first strand: chain 'EC' and resid 180 through 187 removed outlier: 3.639A pdb=" N THREC 203 " --> pdb=" O GLUEC 207 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLUEC 207 " --> pdb=" O THREC 203 " (cutoff:3.500A) Processing sheet with id=AU1, first strand: chain 'EC' and resid 317 through 318 removed outlier: 3.508A pdb=" N LEUEC 317 " --> pdb=" O GLYEC 346 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLYEC 346 " --> pdb=" O LEUEC 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AU1 Processing sheet with id=AU2, first strand: chain 'ED' and resid 35 through 41 removed outlier: 3.598A pdb=" N GLYED 56 " --> pdb=" O SERED 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALAED 40 " --> pdb=" O VALED 54 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VALED 54 " --> pdb=" O ALAED 40 " (cutoff:3.500A) Processing sheet with id=AU3, first strand: chain 'ED' and resid 66 through 68 Processing sheet with id=AU4, first strand: chain 'ED' and resid 75 through 77 Processing sheet with id=AU5, first strand: chain 'ED' and resid 92 through 95 removed outlier: 5.209A pdb=" N ARGED 84 " --> pdb=" O THRED 117 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VALED 86 " --> pdb=" O GLNED 115 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLNED 115 " --> pdb=" O VALED 86 " (cutoff:3.500A) Processing sheet with id=AU6, first strand: chain 'ED' and resid 92 through 95 removed outlier: 5.209A pdb=" N ARGED 84 " --> pdb=" O THRED 117 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VALED 86 " --> pdb=" O GLNED 115 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLNED 115 " --> pdb=" O VALED 86 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VALED 311 " --> pdb=" O GLYED 302 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLYED 302 " --> pdb=" O VALED 311 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLYED 313 " --> pdb=" O VALED 300 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THRED 299 " --> pdb=" O ILEED 294 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ILEED 294 " --> pdb=" O THRED 299 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VALED 301 " --> pdb=" O TYRED 292 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYRED 292 " --> pdb=" O VALED 301 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASNED 303 " --> pdb=" O VALED 290 " (cutoff:3.500A) Processing sheet with id=AU7, first strand: chain 'ED' and resid 100 through 101 Processing sheet with id=AU8, first strand: chain 'ED' and resid 121 through 122 Processing sheet with id=AU9, first strand: chain 'ED' and resid 152 through 153 removed outlier: 6.782A pdb=" N ALAED 152 " --> pdb=" O SERED 262 " (cutoff:3.500A) Processing sheet with id=AV1, first strand: chain 'ED' and resid 156 through 157 Processing sheet with id=AV2, first strand: chain 'ED' and resid 180 through 187 removed outlier: 7.110A pdb=" N GLUED 207 " --> pdb=" O THRED 203 " (cutoff:3.500A) Processing sheet with id=AV3, first strand: chain 'ED' and resid 317 through 318 Processing sheet with id=AV4, first strand: chain 'ED' and resid 327 through 328 Processing sheet with id=AV5, first strand: chain 'EE' and resid 35 through 36 Processing sheet with id=AV6, first strand: chain 'EE' and resid 39 through 41 Processing sheet with id=AV7, first strand: chain 'EE' and resid 66 through 67 Processing sheet with id=AV8, first strand: chain 'EE' and resid 92 through 95 Processing sheet with id=AV9, first strand: chain 'EE' and resid 100 through 102 Processing sheet with id=AW1, first strand: chain 'EE' and resid 121 through 122 Processing sheet with id=AW2, first strand: chain 'EE' and resid 243 through 247 removed outlier: 6.237A pdb=" N ALAEE 152 " --> pdb=" O SEREE 262 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAEE 278 " --> pdb=" O GLNEE 155 " (cutoff:3.500A) Processing sheet with id=AW3, first strand: chain 'EE' and resid 180 through 187 removed outlier: 7.054A pdb=" N GLUEE 207 " --> pdb=" O THREE 203 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LYSEE 231 " --> pdb=" O GLUEE 239 " (cutoff:3.500A) Processing sheet with id=AW4, first strand: chain 'EE' and resid 289 through 294 removed outlier: 6.133A pdb=" N VALEE 300 " --> pdb=" O LEUEE 312 " (cutoff:3.500A) Processing sheet with id=AW5, first strand: chain 'EE' and resid 317 through 318 Processing sheet with id=AW6, first strand: chain 'EE' and resid 327 through 328 removed outlier: 3.535A pdb=" N ALAEE 327 " --> pdb=" O ALAEE 335 " (cutoff:3.500A) Processing sheet with id=AW7, first strand: chain 'EF' and resid 35 through 43 removed outlier: 5.760A pdb=" N THREF 36 " --> pdb=" O ILEEF 57 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILEEF 57 " --> pdb=" O THREF 36 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SEREF 38 " --> pdb=" O ALAEF 55 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLYEF 51 " --> pdb=" O METEF 42 " (cutoff:3.500A) Processing sheet with id=AW8, first strand: chain 'EF' and resid 66 through 67 Processing sheet with id=AW9, first strand: chain 'EF' and resid 92 through 95 removed outlier: 5.723A pdb=" N ARGEF 84 " --> pdb=" O THREF 117 " (cutoff:3.500A) Processing sheet with id=AX1, first strand: chain 'EF' and resid 92 through 95 removed outlier: 5.723A pdb=" N ARGEF 84 " --> pdb=" O THREF 117 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLUEF 309 " --> pdb=" O TYREF 304 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYREF 304 " --> pdb=" O GLUEF 309 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N VALEF 311 " --> pdb=" O GLYEF 302 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLYEF 302 " --> pdb=" O VALEF 311 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLYEF 313 " --> pdb=" O VALEF 300 " (cutoff:3.500A) Processing sheet with id=AX2, first strand: chain 'EF' and resid 101 through 102 Processing sheet with id=AX3, first strand: chain 'EF' and resid 121 through 122 Processing sheet with id=AX4, first strand: chain 'EF' and resid 243 through 247 removed outlier: 6.605A pdb=" N ALAEF 152 " --> pdb=" O SEREF 262 " (cutoff:3.500A) Processing sheet with id=AX5, first strand: chain 'EF' and resid 180 through 187 removed outlier: 7.042A pdb=" N GLUEF 207 " --> pdb=" O THREF 203 " (cutoff:3.500A) Processing sheet with id=AX6, first strand: chain 'EF' and resid 327 through 328 removed outlier: 3.954A pdb=" N ALAEF 327 " --> pdb=" O ALAEF 335 " (cutoff:3.500A) Processing sheet with id=AX7, first strand: chain 'EG' and resid 35 through 43 removed outlier: 6.309A pdb=" N THREG 36 " --> pdb=" O ILEEG 57 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILEEG 57 " --> pdb=" O THREG 36 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N SEREG 38 " --> pdb=" O ALAEG 55 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLYEG 51 " --> pdb=" O METEG 42 " (cutoff:3.500A) Processing sheet with id=AX8, first strand: chain 'EG' and resid 66 through 68 Processing sheet with id=AX9, first strand: chain 'EG' and resid 75 through 77 removed outlier: 4.025A pdb=" N ALAEG 76 " --> pdb=" O THREG 357 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THREG 357 " --> pdb=" O ALAEG 76 " (cutoff:3.500A) No H-bonds generated for sheet with id=AX9 Processing sheet with id=AY1, first strand: chain 'EG' and resid 92 through 95 removed outlier: 15.937A pdb=" N PHEEG 82 " --> pdb=" O TYREG 119 " (cutoff:3.500A) removed outlier: 11.034A pdb=" N TYREG 119 " --> pdb=" O PHEEG 82 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ARGEG 84 " --> pdb=" O THREG 117 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THREG 117 " --> pdb=" O ARGEG 84 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VALEG 300 " --> pdb=" O LEUEG 312 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SEREG 291 " --> pdb=" O ASNEG 303 " (cutoff:3.500A) Processing sheet with id=AY2, first strand: chain 'EG' and resid 135 through 136 removed outlier: 3.761A pdb=" N THREG 117 " --> pdb=" O ARGEG 84 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ARGEG 84 " --> pdb=" O THREG 117 " (cutoff:3.500A) removed outlier: 11.034A pdb=" N TYREG 119 " --> pdb=" O PHEEG 82 " (cutoff:3.500A) removed outlier: 15.937A pdb=" N PHEEG 82 " --> pdb=" O TYREG 119 " (cutoff:3.500A) Processing sheet with id=AY3, first strand: chain 'EG' and resid 100 through 102 Processing sheet with id=AY4, first strand: chain 'EG' and resid 121 through 122 removed outlier: 3.518A pdb=" N THREG 122 " --> pdb=" O THREG 127 " (cutoff:3.500A) Processing sheet with id=AY5, first strand: chain 'EG' and resid 152 through 157 removed outlier: 6.785A pdb=" N ASNEG 157 " --> pdb=" O ILEEG 276 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILEEG 276 " --> pdb=" O ASNEG 157 " (cutoff:3.500A) Processing sheet with id=AY6, first strand: chain 'EG' and resid 180 through 187 removed outlier: 7.051A pdb=" N GLUEG 207 " --> pdb=" O THREG 203 " (cutoff:3.500A) Processing sheet with id=AY7, first strand: chain 'EG' and resid 244 through 247 Processing sheet with id=AY8, first strand: chain 'EG' and resid 327 through 329 removed outlier: 4.262A pdb=" N VALEG 333 " --> pdb=" O GLNEG 329 " (cutoff:3.500A) 2391 hydrogen bonds defined for protein. 6393 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: 28.15 Time building geometry restraints manager: 20.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 11637 1.29 - 1.42: 15845 1.42 - 1.56: 37967 1.56 - 1.69: 1 1.69 - 1.82: 352 Bond restraints: 65802 Sorted by residual: bond pdb=" C LYSDQ 285 " pdb=" N PRODQ 286 " ideal model delta sigma weight residual 1.331 1.504 -0.173 1.27e-02 6.20e+03 1.85e+02 bond pdb=" C ASNDL 133 " pdb=" N PRODL 134 " ideal model delta sigma weight residual 1.332 1.504 -0.172 1.34e-02 5.57e+03 1.65e+02 bond pdb=" C GLNDL 379 " pdb=" O GLNDL 379 " ideal model delta sigma weight residual 1.237 1.160 0.077 1.17e-02 7.31e+03 4.29e+01 bond pdb=" C ASNDL 397 " pdb=" O ASNDL 397 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.22e-02 6.72e+03 3.83e+01 bond pdb=" C THRDL 391 " pdb=" O THRDL 391 " ideal model delta sigma weight residual 1.235 1.158 0.077 1.26e-02 6.30e+03 3.75e+01 ... (remaining 65797 not shown) Histogram of bond angle deviations from ideal: 97.51 - 105.84: 1160 105.84 - 114.17: 38308 114.17 - 122.50: 39394 122.50 - 130.84: 10710 130.84 - 139.17: 100 Bond angle restraints: 89672 Sorted by residual: angle pdb=" C LYSDQ 285 " pdb=" N PRODQ 286 " pdb=" CA PRODQ 286 " ideal model delta sigma weight residual 119.90 134.59 -14.69 1.02e+00 9.61e-01 2.07e+02 angle pdb=" C ASNDL 133 " pdb=" N PRODL 134 " pdb=" CA PRODL 134 " ideal model delta sigma weight residual 119.78 134.17 -14.39 1.03e+00 9.43e-01 1.95e+02 angle pdb=" CA GLYDN 49 " pdb=" C GLYDN 49 " pdb=" O GLYDN 49 " ideal model delta sigma weight residual 122.23 114.83 7.40 6.90e-01 2.10e+00 1.15e+02 angle pdb=" C TYRDW 284 " pdb=" N LYSDW 285 " pdb=" CA LYSDW 285 " ideal model delta sigma weight residual 120.94 139.17 -18.23 1.90e+00 2.77e-01 9.20e+01 angle pdb=" N LYSDP 390 " pdb=" CA LYSDP 390 " pdb=" C LYSDP 390 " ideal model delta sigma weight residual 111.40 100.52 10.88 1.22e+00 6.72e-01 7.95e+01 ... (remaining 89667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 35925 18.00 - 35.99: 2441 35.99 - 53.99: 363 53.99 - 71.98: 111 71.98 - 89.98: 56 Dihedral angle restraints: 38896 sinusoidal: 13926 harmonic: 24970 Sorted by residual: dihedral pdb=" C LYSDP 390 " pdb=" N LYSDP 390 " pdb=" CA LYSDP 390 " pdb=" CB LYSDP 390 " ideal model delta harmonic sigma weight residual -122.60 -104.18 -18.42 0 2.50e+00 1.60e-01 5.43e+01 dihedral pdb=" C ASNDU 401 " pdb=" N ASNDU 401 " pdb=" CA ASNDU 401 " pdb=" CB ASNDU 401 " ideal model delta harmonic sigma weight residual -122.60 -140.68 18.08 0 2.50e+00 1.60e-01 5.23e+01 dihedral pdb=" C ASNDQ 401 " pdb=" N ASNDQ 401 " pdb=" CA ASNDQ 401 " pdb=" CB ASNDQ 401 " ideal model delta harmonic sigma weight residual -122.60 -138.21 15.61 0 2.50e+00 1.60e-01 3.90e+01 ... (remaining 38893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 10266 0.123 - 0.245: 226 0.245 - 0.368: 37 0.368 - 0.491: 7 0.491 - 0.613: 2 Chirality restraints: 10538 Sorted by residual: chirality pdb=" CA ASNDU 401 " pdb=" N ASNDU 401 " pdb=" C ASNDU 401 " pdb=" CB ASNDU 401 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.40e+00 chirality pdb=" CA ASNDQ 401 " pdb=" N ASNDQ 401 " pdb=" C ASNDQ 401 " pdb=" CB ASNDQ 401 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.11e+00 chirality pdb=" CA GLUDM 324 " pdb=" N GLUDM 324 " pdb=" C GLUDM 324 " pdb=" CB GLUDM 324 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.69e+00 ... (remaining 10535 not shown) Planarity restraints: 12034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THRDP 388 " 0.025 2.00e-02 2.50e+03 5.36e-02 2.87e+01 pdb=" C THRDP 388 " -0.093 2.00e-02 2.50e+03 pdb=" O THRDP 388 " 0.037 2.00e-02 2.50e+03 pdb=" N ILEDP 389 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALADL 132 " -0.025 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C ALADL 132 " 0.087 2.00e-02 2.50e+03 pdb=" O ALADL 132 " -0.033 2.00e-02 2.50e+03 pdb=" N ASNDL 133 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILEDP 389 " 0.024 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C ILEDP 389 " -0.081 2.00e-02 2.50e+03 pdb=" O ILEDP 389 " 0.029 2.00e-02 2.50e+03 pdb=" N LYSDP 390 " 0.028 2.00e-02 2.50e+03 ... (remaining 12031 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 1269 2.61 - 3.18: 61121 3.18 - 3.75: 101450 3.75 - 4.33: 137157 4.33 - 4.90: 224082 Nonbonded interactions: 525079 Sorted by model distance: nonbonded pdb=" CB ALADN 146 " pdb=" O SERDN 189 " model vdw 2.035 3.460 nonbonded pdb=" O ASNDW 385 " pdb=" OG1 THRDW 388 " model vdw 2.063 2.440 nonbonded pdb=" O GLNDO 392 " pdb=" NE2 GLNDO 392 " model vdw 2.064 2.520 nonbonded pdb=" N GLNDL 5 " pdb=" OE1 GLNDL 5 " model vdw 2.083 2.520 nonbonded pdb=" NH1 ARGDW 106 " pdb=" O ILEDW 139 " model vdw 2.124 2.520 ... (remaining 525074 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'DL' selection = chain 'DM' selection = chain 'DN' selection = chain 'DO' selection = chain 'DP' selection = chain 'DQ' selection = chain 'DR' selection = chain 'DS' selection = chain 'DT' selection = chain 'DU' selection = chain 'DV' selection = chain 'DW' selection = chain 'DX' selection = chain 'DY' selection = chain 'DZ' selection = chain 'EA' selection = chain 'EB' selection = chain 'EC' selection = chain 'ED' selection = chain 'EE' selection = chain 'EF' selection = chain 'EG' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.120 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: 0.040 Extract box with map and model: 27.070 Check model and map are aligned: 0.730 Set scattering table: 0.450 Process input model: 132.440 Find NCS groups from input model: 4.050 Set up NCS constraints: 0.530 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: 0.020 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 173.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.004 0.173 65802 Z= 0.269 Angle : 0.790 18.227 89672 Z= 0.495 Chirality : 0.051 0.613 10538 Planarity : 0.004 0.060 12034 Dihedral : 13.097 89.978 22968 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.24 % Favored : 94.62 % Rotamer: Outliers : 1.60 % Allowed : 0.79 % Favored : 97.61 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: -1.64 (0.09), residues: 8778 helix: 1.32 (0.15), residues: 1221 sheet: -1.10 (0.11), residues: 2308 loop : -1.73 (0.08), residues: 5249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPDW 208 HIS 0.004 0.001 HISDR 194 PHE 0.023 0.001 PHEDN 43 TYR 0.045 0.001 TYRDX 382 ARG 0.009 0.001 ARGEC 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1245 time to evaluate : 5.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 34 residues processed: 1305 average time/residue: 0.5829 time to fit residues: 1314.7368 Evaluate side-chains 963 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 929 time to evaluate : 5.367 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.4569 time to fit residues: 36.3858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 743 optimal weight: 8.9990 chunk 666 optimal weight: 6.9990 chunk 370 optimal weight: 3.9990 chunk 227 optimal weight: 10.0000 chunk 449 optimal weight: 4.9990 chunk 356 optimal weight: 10.0000 chunk 689 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 419 optimal weight: 9.9990 chunk 513 optimal weight: 0.2980 chunk 799 optimal weight: 0.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DL 23 ASN ** DL 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DM 197 ASN ** DM 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DN 392 GLN DO 5 GLN DO 97 ASN ** DO 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DO 275 ASN DO 310 GLN DO 401 ASN ** DP 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DP 308 GLN DP 379 GLN ** DQ 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DQ 190 GLN ** DQ 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DQ 296 ASN ** DQ 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DR 23 ASN ** DR 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DR 206 ASN DR 252 ASN ** DR 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DS 16 ASN ** DS 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DT 99 GLN ** DT 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DT 374 ASN ** DT 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DU 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DU 293 GLN DU 295 ASN ** DU 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DU 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DU 401 ASN ** DV 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DW 374 ASN ** DW 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 379 GLN DX 381 ASN DY 107 ASN ** DY 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DY 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DZ 303 ASN ** DZ 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DZ 385 ASN DZ 387 GLN ** EA 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 394 GLN EC 99 GLN ** EC 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EC 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EC 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EC 310 GLN ** EC 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ED 401 ASN ** EE 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EF 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EF 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EG 133 ASN ** EG 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 65802 Z= 0.388 Angle : 0.680 12.803 89672 Z= 0.366 Chirality : 0.044 0.208 10538 Planarity : 0.004 0.056 12034 Dihedral : 4.826 25.367 9152 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.61 % Favored : 92.34 % Rotamer: Outliers : 2.45 % Allowed : 11.51 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: -1.73 (0.09), residues: 8778 helix: 1.44 (0.14), residues: 1231 sheet: -1.27 (0.11), residues: 2313 loop : -1.79 (0.08), residues: 5234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPDM 208 HIS 0.008 0.002 HISEE 213 PHE 0.023 0.002 PHEDO 43 TYR 0.052 0.002 TYRDN 382 ARG 0.007 0.001 ARGED 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 964 time to evaluate : 5.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 173 outliers final: 136 residues processed: 1064 average time/residue: 0.5883 time to fit residues: 1093.9685 Evaluate side-chains 1013 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 877 time to evaluate : 5.402 Switching outliers to nearest non-outliers outliers start: 136 outliers final: 0 residues processed: 136 average time/residue: 0.4684 time to fit residues: 129.0837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 444 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 665 optimal weight: 10.0000 chunk 544 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 chunk 800 optimal weight: 0.5980 chunk 864 optimal weight: 4.9990 chunk 712 optimal weight: 4.9990 chunk 793 optimal weight: 6.9990 chunk 272 optimal weight: 1.9990 chunk 642 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** DL 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DL 192 ASN DL 310 GLN ** DL 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DM 79 GLN ** DM 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DN 332 ASN DN 392 GLN ** DO 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DO 275 ASN ** DP 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DP 379 GLN ** DQ 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DQ 194 HIS ** DQ 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DR 206 ASN ** DR 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DS 141 ASN ** DS 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DT 379 GLN DT 394 GLN ** DU 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DU 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DU 293 GLN DU 295 ASN ** DU 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DW 112 GLN ** DW 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DW 332 ASN ** DW 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 99 GLN DX 155 GLN ** DY 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DY 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 397 ASN EC 99 GLN ** EC 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EC 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EC 310 GLN EC 385 ASN ** ED 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ED 401 ASN EE 329 GLN EF 105 ASN ** EF 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EF 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EF 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EG 97 ASN ** EG 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 65802 Z= 0.238 Angle : 0.585 11.530 89672 Z= 0.313 Chirality : 0.042 0.183 10538 Planarity : 0.003 0.050 12034 Dihedral : 4.618 23.725 9152 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.35 % Favored : 93.61 % Rotamer: Outliers : 1.44 % Allowed : 15.19 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: -1.53 (0.09), residues: 8778 helix: 1.76 (0.14), residues: 1243 sheet: -1.17 (0.11), residues: 2266 loop : -1.69 (0.08), residues: 5269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPDM 208 HIS 0.009 0.001 HISEE 213 PHE 0.015 0.001 PHEDO 43 TYR 0.027 0.001 TYRDN 382 ARG 0.006 0.000 ARGEF 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 982 time to evaluate : 5.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 57 residues processed: 1053 average time/residue: 0.5804 time to fit residues: 1060.5243 Evaluate side-chains 947 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 890 time to evaluate : 5.404 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.4762 time to fit residues: 57.6921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 790 optimal weight: 4.9990 chunk 601 optimal weight: 0.9990 chunk 415 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 382 optimal weight: 10.0000 chunk 537 optimal weight: 8.9990 chunk 803 optimal weight: 2.9990 chunk 850 optimal weight: 1.9990 chunk 419 optimal weight: 9.9990 chunk 761 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** DL 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DN 385 ASN DN 392 GLN ** DO 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DO 141 ASN ** DO 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DO 275 ASN DO 401 ASN ** DP 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DR 206 ASN ** DR 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DR 383 GLN ** DS 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DU 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DU 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DU 293 GLN DU 295 ASN ** DU 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DW 323 ASN ** DW 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 296 ASN ** DY 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DZ 141 ASN ** DZ 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 394 GLN EC 99 GLN EC 115 GLN ** EC 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EC 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EC 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EE 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EF 157 ASN ** EF 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EF 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EF 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EG 26 ASN ** EG 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 65802 Z= 0.299 Angle : 0.609 11.832 89672 Z= 0.327 Chirality : 0.042 0.314 10538 Planarity : 0.003 0.050 12034 Dihedral : 4.707 24.496 9152 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.80 % Favored : 92.15 % Rotamer: Outliers : 2.31 % Allowed : 17.13 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: -1.59 (0.09), residues: 8778 helix: 1.67 (0.14), residues: 1243 sheet: -1.21 (0.11), residues: 2232 loop : -1.72 (0.08), residues: 5303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPDM 208 HIS 0.008 0.001 HISEE 213 PHE 0.016 0.002 PHEDT 353 TYR 0.031 0.002 TYRDV 382 ARG 0.007 0.001 ARGEF 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 948 time to evaluate : 5.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 163 outliers final: 103 residues processed: 1044 average time/residue: 0.5761 time to fit residues: 1047.3739 Evaluate side-chains 995 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 892 time to evaluate : 5.428 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 0 residues processed: 103 average time/residue: 0.4697 time to fit residues: 99.4126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 708 optimal weight: 2.9990 chunk 482 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 633 optimal weight: 0.9990 chunk 350 optimal weight: 4.9990 chunk 725 optimal weight: 0.8980 chunk 587 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 434 optimal weight: 9.9990 chunk 763 optimal weight: 5.9990 chunk 214 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** DL 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DL 383 GLN ** DL 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DN 5 GLN ** DN 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DO 141 ASN DO 192 ASN DO 252 ASN ** DO 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DO 275 ASN ** DO 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DO 310 GLN ** DO 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DP 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DP 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DR 206 ASN ** DR 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DS 141 ASN ** DS 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DU 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DU 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DU 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DU 385 ASN ** DV 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 233 ASN ** DX 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 296 ASN DY 274 ASN ** DZ 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 155 GLN EA 235 ASN ** EA 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 397 ASN ** EB 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 332 ASN ** EC 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EC 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EC 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EF 157 ASN EF 265 ASN ** EF 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EF 379 GLN ** EF 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EG 394 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 65802 Z= 0.228 Angle : 0.586 13.833 89672 Z= 0.311 Chirality : 0.042 0.349 10538 Planarity : 0.003 0.049 12034 Dihedral : 4.559 25.021 9152 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.56 % Favored : 93.40 % Rotamer: Outliers : 1.43 % Allowed : 18.69 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: -1.45 (0.09), residues: 8778 helix: 1.88 (0.14), residues: 1243 sheet: -1.13 (0.11), residues: 2223 loop : -1.65 (0.08), residues: 5312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPEC 334 HIS 0.008 0.001 HISEE 213 PHE 0.014 0.001 PHEDO 43 TYR 0.023 0.001 TYRDV 382 ARG 0.006 0.000 ARGEF 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 969 time to evaluate : 5.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 54 residues processed: 1040 average time/residue: 0.5907 time to fit residues: 1067.0525 Evaluate side-chains 952 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 898 time to evaluate : 5.467 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.4902 time to fit residues: 57.1024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 286 optimal weight: 10.0000 chunk 766 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 499 optimal weight: 8.9990 chunk 209 optimal weight: 1.9990 chunk 851 optimal weight: 2.9990 chunk 706 optimal weight: 0.9980 chunk 394 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 281 optimal weight: 0.9980 chunk 446 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** DL 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DL 383 GLN ** DL 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DO 275 ASN ** DO 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DP 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DP 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DP 383 GLN ** DQ 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DS 79 GLN ** DS 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DS 397 ASN DT 59 GLN ** DT 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DT 314 GLN DT 319 ASN ** DT 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DU 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DU 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 296 ASN DX 314 GLN DY 274 ASN ** DZ 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DZ 141 ASN ** DZ 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 99 GLN EA 155 GLN ** EA 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EC 99 GLN ** EC 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EC 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EC 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EE 5 GLN ** EF 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EF 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EF 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EG 394 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 65802 Z= 0.232 Angle : 0.596 15.159 89672 Z= 0.314 Chirality : 0.042 0.356 10538 Planarity : 0.003 0.049 12034 Dihedral : 4.496 25.077 9152 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.04 % Favored : 92.91 % Rotamer: Outliers : 1.59 % Allowed : 19.65 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: -1.40 (0.09), residues: 8778 helix: 1.90 (0.14), residues: 1244 sheet: -1.07 (0.11), residues: 2221 loop : -1.63 (0.08), residues: 5313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPDM 208 HIS 0.009 0.001 HISEE 213 PHE 0.023 0.001 PHEDS 43 TYR 0.039 0.001 TYRDS 382 ARG 0.006 0.000 ARGEF 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 941 time to evaluate : 5.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 68 residues processed: 1009 average time/residue: 0.5792 time to fit residues: 1013.8231 Evaluate side-chains 962 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 894 time to evaluate : 5.411 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.4704 time to fit residues: 67.5306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 820 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 485 optimal weight: 0.0470 chunk 621 optimal weight: 3.9990 chunk 481 optimal weight: 0.7980 chunk 716 optimal weight: 0.9980 chunk 475 optimal weight: 6.9990 chunk 848 optimal weight: 1.9990 chunk 530 optimal weight: 2.9990 chunk 517 optimal weight: 1.9990 chunk 391 optimal weight: 3.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** DL 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DO 197 ASN DO 275 ASN DO 293 GLN DO 374 ASN ** DO 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DP 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DP 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DR 322 ASN ** DR 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DT 397 ASN ** DU 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DU 97 ASN DU 401 ASN ** DV 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 296 ASN DX 314 GLN DY 274 ASN ** DY 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 26 ASN ** EA 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 394 GLN EC 99 GLN ** EC 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EC 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EC 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ED 268 GLN ** ED 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EF 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EG 394 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 65802 Z= 0.189 Angle : 0.594 15.816 89672 Z= 0.310 Chirality : 0.042 0.377 10538 Planarity : 0.003 0.051 12034 Dihedral : 4.334 22.096 9152 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.99 % Favored : 93.97 % Rotamer: Outliers : 1.08 % Allowed : 20.69 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: -1.26 (0.09), residues: 8778 helix: 2.03 (0.15), residues: 1246 sheet: -0.96 (0.11), residues: 2200 loop : -1.54 (0.08), residues: 5332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPEC 334 HIS 0.011 0.001 HISEE 213 PHE 0.018 0.001 PHEDW 43 TYR 0.044 0.001 TYRDS 382 ARG 0.006 0.000 ARGEF 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 963 time to evaluate : 5.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 37 residues processed: 1015 average time/residue: 0.5788 time to fit residues: 1034.7331 Evaluate side-chains 941 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 904 time to evaluate : 5.513 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.4568 time to fit residues: 40.5488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 524 optimal weight: 2.9990 chunk 338 optimal weight: 7.9990 chunk 506 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 539 optimal weight: 9.9990 chunk 577 optimal weight: 5.9990 chunk 419 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 666 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** DL 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DL 107 ASN DL 268 GLN ** DL 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DL 365 ASN ** DL 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DO 23 ASN DO 197 ASN DO 275 ASN DO 310 GLN ** DO 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DO 374 ASN ** DO 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DP 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DP 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DP 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DR 206 ASN ** DR 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DR 295 ASN DR 314 GLN DR 322 ASN ** DR 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DR 383 GLN DR 385 ASN ** DS 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DU 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DU 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DU 401 ASN ** DV 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DV 269 GLN ** DV 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DW 308 GLN ** DX 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 394 GLN DY 274 ASN DY 381 ASN ** DY 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DZ 268 GLN ** DZ 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 233 ASN ** EA 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 385 ASN EB 129 GLN ** EB 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EC 99 GLN ** EC 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EC 213 HIS ** EC 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EF 5 GLN ** EF 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EF 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EF 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EF 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EF 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EG 310 GLN ** EG 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EG 394 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.121 65802 Z= 0.474 Angle : 0.752 17.159 89672 Z= 0.399 Chirality : 0.045 0.325 10538 Planarity : 0.004 0.051 12034 Dihedral : 5.108 24.408 9152 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 23.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.61 % Favored : 90.34 % Rotamer: Outliers : 2.15 % Allowed : 20.94 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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 (0.09), residues: 8778 helix: 1.30 (0.14), residues: 1244 sheet: -1.25 (0.11), residues: 2163 loop : -1.79 (0.08), residues: 5371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPDM 208 HIS 0.009 0.002 HISEE 213 PHE 0.023 0.002 PHEDM 39 TYR 0.075 0.002 TYRDS 382 ARG 0.007 0.001 ARGDL 380 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1019 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 867 time to evaluate : 5.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 152 outliers final: 100 residues processed: 955 average time/residue: 0.5979 time to fit residues: 992.5705 Evaluate side-chains 928 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 828 time to evaluate : 5.519 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 0 residues processed: 100 average time/residue: 0.4734 time to fit residues: 96.6986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 771 optimal weight: 0.7980 chunk 812 optimal weight: 0.7980 chunk 741 optimal weight: 10.0000 chunk 790 optimal weight: 0.0980 chunk 475 optimal weight: 3.9990 chunk 344 optimal weight: 5.9990 chunk 620 optimal weight: 4.9990 chunk 242 optimal weight: 0.7980 chunk 714 optimal weight: 3.9990 chunk 747 optimal weight: 7.9990 chunk 787 optimal weight: 9.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** DL 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DL 107 ASN DL 268 GLN ** DL 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DO 197 ASN DO 275 ASN ** DO 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DO 310 GLN ** DO 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DP 206 ASN ** DP 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DQ 129 GLN ** DQ 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DR 206 ASN DR 295 ASN DR 314 GLN ** DR 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DR 383 GLN ** DS 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DT 112 GLN ** DT 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DU 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DU 401 ASN DV 213 HIS ** DV 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DV 269 GLN ** DV 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DV 296 ASN ** DV 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DY 274 ASN ** DZ 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DZ 141 ASN ** DZ 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DZ 385 ASN EA 233 ASN ** EA 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 397 ASN EC 99 GLN ** EC 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EC 206 ASN ** EC 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EC 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ED 394 GLN ** EE 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EF 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EF 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EG 310 GLN ** EG 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 65802 Z= 0.211 Angle : 0.648 17.500 89672 Z= 0.335 Chirality : 0.043 0.363 10538 Planarity : 0.003 0.055 12034 Dihedral : 4.632 23.761 9152 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.84 % Favored : 94.12 % Rotamer: Outliers : 0.71 % Allowed : 21.67 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: -1.44 (0.09), residues: 8778 helix: 1.70 (0.14), residues: 1241 sheet: -1.08 (0.11), residues: 2187 loop : -1.60 (0.08), residues: 5350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPEC 334 HIS 0.010 0.001 HISEE 213 PHE 0.022 0.001 PHEDN 43 TYR 0.058 0.002 TYRDS 382 ARG 0.007 0.000 ARGDL 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 947 time to evaluate : 5.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 24 residues processed: 978 average time/residue: 0.5957 time to fit residues: 1012.8394 Evaluate side-chains 920 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 896 time to evaluate : 5.505 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4853 time to fit residues: 29.1338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 519 optimal weight: 0.9980 chunk 835 optimal weight: 5.9990 chunk 510 optimal weight: 0.9990 chunk 396 optimal weight: 0.9980 chunk 581 optimal weight: 0.0060 chunk 876 optimal weight: 0.6980 chunk 806 optimal weight: 4.9990 chunk 698 optimal weight: 0.6980 chunk 72 optimal weight: 0.0870 chunk 539 optimal weight: 0.6980 chunk 428 optimal weight: 0.0980 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** DL 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DM 26 ASN ** DM 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DN 80 ASN ** DN 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DO 141 ASN DO 275 ASN ** DO 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DO 310 GLN DO 374 ASN ** DO 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DP 268 GLN ** DP 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DR 206 ASN ** DR 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DR 322 ASN ** DR 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DS 379 GLN ** DS 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DT 99 GLN ** DT 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DT 379 GLN ** DU 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DU 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DV 274 ASN ** DV 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DW 99 GLN ** DW 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 296 ASN DX 394 GLN DY 274 ASN DY 358 ASN ** DZ 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DZ 157 ASN ** DZ 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DZ 310 GLN ** EA 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EC 99 GLN ** EC 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EC 252 ASN ** ED 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EE 5 GLN EE 79 GLN ** EE 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EF 197 ASN ** EF 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EF 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 65802 Z= 0.174 Angle : 0.642 19.477 89672 Z= 0.326 Chirality : 0.042 0.269 10538 Planarity : 0.003 0.052 12034 Dihedral : 4.232 23.263 9152 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.86 % Favored : 94.13 % Rotamer: Outliers : 0.42 % Allowed : 22.66 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: -1.19 (0.09), residues: 8778 helix: 1.89 (0.15), residues: 1244 sheet: -0.86 (0.11), residues: 2177 loop : -1.47 (0.08), residues: 5357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPEC 334 HIS 0.012 0.001 HISEE 213 PHE 0.025 0.001 PHEDS 43 TYR 0.060 0.001 TYRDS 382 ARG 0.009 0.000 ARGEF 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 984 time to evaluate : 5.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 1001 average time/residue: 0.5935 time to fit residues: 1031.5577 Evaluate side-chains 941 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 923 time to evaluate : 5.427 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4679 time to fit residues: 23.2299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 554 optimal weight: 6.9990 chunk 743 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 643 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 chunk 699 optimal weight: 9.9990 chunk 292 optimal weight: 9.9990 chunk 718 optimal weight: 0.7980 chunk 88 optimal weight: 0.0070 chunk 128 optimal weight: 3.9990 overall best weight: 1.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** DL 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DL 107 ASN ** DL 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DL 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DN 323 ASN ** DN 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DN 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DO 275 ASN ** DO 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DP 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DQ 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DR 314 GLN DR 322 ASN ** DR 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DS 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DU 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DU 141 ASN ** DU 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DW 293 GLN ** DW 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DZ 141 ASN ** DZ 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EC 99 GLN ** EC 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EC 252 ASN ** EC 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ED 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EE 5 GLN ** EE 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EE 80 ASN EF 157 ASN ** EF 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EF 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EF 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EG 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EG 385 ASN EG 394 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.086050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.071140 restraints weight = 269867.037| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 4.79 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 65802 Z= 0.238 Angle : 0.649 17.264 89672 Z= 0.333 Chirality : 0.042 0.328 10538 Planarity : 0.003 0.053 12034 Dihedral : 4.295 23.300 9152 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.29 % Favored : 93.68 % Rotamer: Outliers : 0.40 % Allowed : 23.31 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: -1.21 (0.09), residues: 8778 helix: 1.85 (0.15), residues: 1244 sheet: -0.90 (0.11), residues: 2213 loop : -1.46 (0.08), residues: 5321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPDM 208 HIS 0.012 0.001 HISEE 213 PHE 0.019 0.001 PHEED 263 TYR 0.043 0.002 TYRDS 382 ARG 0.007 0.000 ARGDL 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16881.33 seconds wall clock time: 297 minutes 54.10 seconds (17874.10 seconds total)