Starting phenix.real_space_refine on Tue Dec 31 05:16:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7n_29817/12_2024/8g7n_29817.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7n_29817/12_2024/8g7n_29817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g7n_29817/12_2024/8g7n_29817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7n_29817/12_2024/8g7n_29817.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7n_29817/12_2024/8g7n_29817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7n_29817/12_2024/8g7n_29817.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.169 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 14 8.98 5 P 42 5.49 5 Mg 14 5.21 5 S 210 5.16 5 C 41468 2.51 5 N 11242 2.21 5 O 13118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 182 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 66108 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "G" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "F" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "E" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "D" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "C" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "B" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "J" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "I" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "H" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "N" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "Y" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "L" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "K" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3932 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "O" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "U" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "T" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "R" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "Q" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "P" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "X" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "W" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "V" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "2" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "1" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "Z" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "M" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 26.85, per 1000 atoms: 0.41 Number of scatterers: 66108 At special positions: 0 Unit cell: (160.371, 157.59, 264.195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 14 19.00 S 210 16.00 P 42 15.00 Mg 14 11.99 O 13118 8.00 N 11242 7.00 C 41468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.37 Conformation dependent library (CDL) restraints added in 6.9 seconds 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15876 Finding SS restraints... Secondary structure from input PDB file: 322 helices and 98 sheets defined 50.7% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.52 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 removed outlier: 3.911A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 57 removed outlier: 3.548A pdb=" N SER A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 84 removed outlier: 3.991A pdb=" N GLY A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 104 removed outlier: 3.575A pdb=" N LYS A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 133 Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.510A pdb=" N ILE A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 removed outlier: 3.532A pdb=" N GLY A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 227 through 242 removed outlier: 3.629A pdb=" N ILE A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 280 through 295 removed outlier: 3.615A pdb=" N LYS A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.552A pdb=" N ASP A 310 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.565A pdb=" N LEU A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 353 removed outlier: 3.732A pdb=" N ASP A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 373 Processing helix chain 'A' and resid 384 through 408 removed outlier: 3.664A pdb=" N ARG A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 421 through 426 removed outlier: 3.875A pdb=" N LEU A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 421 through 426' Processing helix chain 'A' and resid 432 through 446 Processing helix chain 'A' and resid 447 through 457 Processing helix chain 'A' and resid 460 through 470 Processing helix chain 'A' and resid 487 through 491 Processing helix chain 'A' and resid 496 through 514 removed outlier: 3.811A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 27 removed outlier: 3.911A pdb=" N VAL G 27 " --> pdb=" O ASP G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 57 removed outlier: 3.549A pdb=" N SER G 57 " --> pdb=" O THR G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 84 removed outlier: 3.992A pdb=" N GLY G 68 " --> pdb=" O TYR G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 104 removed outlier: 3.575A pdb=" N LYS G 104 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 133 Processing helix chain 'G' and resid 138 through 150 removed outlier: 3.510A pdb=" N ILE G 142 " --> pdb=" O THR G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 168 removed outlier: 3.532A pdb=" N GLY G 157 " --> pdb=" O ASP G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 203 Processing helix chain 'G' and resid 227 through 242 removed outlier: 3.629A pdb=" N ILE G 231 " --> pdb=" O SER G 227 " (cutoff:3.500A) Proline residue: G 233 - end of helix Processing helix chain 'G' and resid 253 through 268 Processing helix chain 'G' and resid 280 through 295 removed outlier: 3.616A pdb=" N LYS G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 311 removed outlier: 3.552A pdb=" N ASP G 310 " --> pdb=" O ASN G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 316 removed outlier: 3.565A pdb=" N LEU G 316 " --> pdb=" O PRO G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 353 removed outlier: 3.732A pdb=" N ASP G 353 " --> pdb=" O ILE G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 373 Processing helix chain 'G' and resid 384 through 408 removed outlier: 3.664A pdb=" N ARG G 394 " --> pdb=" O GLU G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 420 Processing helix chain 'G' and resid 421 through 426 removed outlier: 3.875A pdb=" N LEU G 425 " --> pdb=" O CYS G 421 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP G 426 " --> pdb=" O ILE G 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 421 through 426' Processing helix chain 'G' and resid 432 through 446 Processing helix chain 'G' and resid 447 through 457 Processing helix chain 'G' and resid 460 through 470 Processing helix chain 'G' and resid 487 through 491 Processing helix chain 'G' and resid 496 through 514 removed outlier: 3.811A pdb=" N LEU G 512 " --> pdb=" O GLY G 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 27 removed outlier: 3.911A pdb=" N VAL F 27 " --> pdb=" O ASP F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 57 removed outlier: 3.548A pdb=" N SER F 57 " --> pdb=" O THR F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 84 removed outlier: 3.991A pdb=" N GLY F 68 " --> pdb=" O TYR F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 104 removed outlier: 3.575A pdb=" N LYS F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 133 Processing helix chain 'F' and resid 138 through 150 removed outlier: 3.511A pdb=" N ILE F 142 " --> pdb=" O THR F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 168 removed outlier: 3.532A pdb=" N GLY F 157 " --> pdb=" O ASP F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 203 Processing helix chain 'F' and resid 227 through 242 removed outlier: 3.629A pdb=" N ILE F 231 " --> pdb=" O SER F 227 " (cutoff:3.500A) Proline residue: F 233 - end of helix Processing helix chain 'F' and resid 253 through 268 Processing helix chain 'F' and resid 280 through 295 removed outlier: 3.616A pdb=" N LYS F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 311 removed outlier: 3.553A pdb=" N ASP F 310 " --> pdb=" O ASN F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 316 removed outlier: 3.564A pdb=" N LEU F 316 " --> pdb=" O PRO F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 355 removed outlier: 3.732A pdb=" N ASP F 353 " --> pdb=" O ILE F 349 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL F 354 " --> pdb=" O GLU F 350 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR F 355 " --> pdb=" O GLN F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 373 Processing helix chain 'F' and resid 384 through 408 removed outlier: 3.665A pdb=" N ARG F 394 " --> pdb=" O GLU F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 Processing helix chain 'F' and resid 421 through 426 removed outlier: 3.875A pdb=" N LEU F 425 " --> pdb=" O CYS F 421 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP F 426 " --> pdb=" O ILE F 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 421 through 426' Processing helix chain 'F' and resid 432 through 446 Processing helix chain 'F' and resid 447 through 457 Processing helix chain 'F' and resid 460 through 470 Processing helix chain 'F' and resid 487 through 491 Processing helix chain 'F' and resid 496 through 514 removed outlier: 3.811A pdb=" N LEU F 512 " --> pdb=" O GLY F 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 27 removed outlier: 3.910A pdb=" N VAL E 27 " --> pdb=" O ASP E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 57 removed outlier: 3.548A pdb=" N SER E 57 " --> pdb=" O THR E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 84 removed outlier: 3.992A pdb=" N GLY E 68 " --> pdb=" O TYR E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 104 removed outlier: 3.574A pdb=" N LYS E 104 " --> pdb=" O GLU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 133 Processing helix chain 'E' and resid 138 through 150 removed outlier: 3.510A pdb=" N ILE E 142 " --> pdb=" O THR E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 168 removed outlier: 3.532A pdb=" N GLY E 157 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 Processing helix chain 'E' and resid 227 through 242 removed outlier: 3.629A pdb=" N ILE E 231 " --> pdb=" O SER E 227 " (cutoff:3.500A) Proline residue: E 233 - end of helix Processing helix chain 'E' and resid 253 through 268 Processing helix chain 'E' and resid 280 through 295 removed outlier: 3.615A pdb=" N LYS E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 311 removed outlier: 3.552A pdb=" N ASP E 310 " --> pdb=" O ASN E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 removed outlier: 3.565A pdb=" N LEU E 316 " --> pdb=" O PRO E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 353 removed outlier: 3.732A pdb=" N ASP E 353 " --> pdb=" O ILE E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 373 Processing helix chain 'E' and resid 384 through 408 removed outlier: 3.664A pdb=" N ARG E 394 " --> pdb=" O GLU E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 420 Processing helix chain 'E' and resid 421 through 426 removed outlier: 3.875A pdb=" N LEU E 425 " --> pdb=" O CYS E 421 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP E 426 " --> pdb=" O ILE E 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 421 through 426' Processing helix chain 'E' and resid 432 through 446 Processing helix chain 'E' and resid 447 through 457 Processing helix chain 'E' and resid 460 through 470 Processing helix chain 'E' and resid 487 through 491 Processing helix chain 'E' and resid 496 through 514 removed outlier: 3.811A pdb=" N LEU E 512 " --> pdb=" O GLY E 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 27 removed outlier: 3.911A pdb=" N VAL D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 57 removed outlier: 3.548A pdb=" N SER D 57 " --> pdb=" O THR D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 84 removed outlier: 3.992A pdb=" N GLY D 68 " --> pdb=" O TYR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 104 removed outlier: 3.574A pdb=" N LYS D 104 " --> pdb=" O GLU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 133 Processing helix chain 'D' and resid 138 through 150 removed outlier: 3.511A pdb=" N ILE D 142 " --> pdb=" O THR D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 168 removed outlier: 3.532A pdb=" N GLY D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 203 Processing helix chain 'D' and resid 227 through 242 removed outlier: 3.629A pdb=" N ILE D 231 " --> pdb=" O SER D 227 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 253 through 268 Processing helix chain 'D' and resid 280 through 295 removed outlier: 3.616A pdb=" N LYS D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 311 removed outlier: 3.552A pdb=" N ASP D 310 " --> pdb=" O ASN D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 316 removed outlier: 3.565A pdb=" N LEU D 316 " --> pdb=" O PRO D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 353 removed outlier: 3.732A pdb=" N ASP D 353 " --> pdb=" O ILE D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 373 Processing helix chain 'D' and resid 384 through 408 removed outlier: 3.663A pdb=" N ARG D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 421 through 426 removed outlier: 3.874A pdb=" N LEU D 425 " --> pdb=" O CYS D 421 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP D 426 " --> pdb=" O ILE D 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 421 through 426' Processing helix chain 'D' and resid 432 through 446 Processing helix chain 'D' and resid 447 through 457 Processing helix chain 'D' and resid 460 through 470 Processing helix chain 'D' and resid 487 through 491 Processing helix chain 'D' and resid 496 through 514 removed outlier: 3.811A pdb=" N LEU D 512 " --> pdb=" O GLY D 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 27 removed outlier: 3.911A pdb=" N VAL C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 57 removed outlier: 3.548A pdb=" N SER C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 84 removed outlier: 3.991A pdb=" N GLY C 68 " --> pdb=" O TYR C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 104 removed outlier: 3.575A pdb=" N LYS C 104 " --> pdb=" O GLU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 133 Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.511A pdb=" N ILE C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 168 removed outlier: 3.532A pdb=" N GLY C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 227 through 242 removed outlier: 3.629A pdb=" N ILE C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 253 through 268 Processing helix chain 'C' and resid 280 through 295 removed outlier: 3.615A pdb=" N LYS C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 311 removed outlier: 3.552A pdb=" N ASP C 310 " --> pdb=" O ASN C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 removed outlier: 3.565A pdb=" N LEU C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 353 removed outlier: 3.733A pdb=" N ASP C 353 " --> pdb=" O ILE C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 373 Processing helix chain 'C' and resid 384 through 408 removed outlier: 3.664A pdb=" N ARG C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 421 through 426 removed outlier: 3.875A pdb=" N LEU C 425 " --> pdb=" O CYS C 421 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP C 426 " --> pdb=" O ILE C 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 421 through 426' Processing helix chain 'C' and resid 432 through 446 Processing helix chain 'C' and resid 447 through 457 Processing helix chain 'C' and resid 460 through 470 Processing helix chain 'C' and resid 487 through 491 Processing helix chain 'C' and resid 496 through 514 removed outlier: 3.811A pdb=" N LEU C 512 " --> pdb=" O GLY C 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 27 removed outlier: 3.911A pdb=" N VAL B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 57 removed outlier: 3.548A pdb=" N SER B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 84 removed outlier: 3.991A pdb=" N GLY B 68 " --> pdb=" O TYR B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 104 removed outlier: 3.575A pdb=" N LYS B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 133 Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.510A pdb=" N ILE B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 168 removed outlier: 3.532A pdb=" N GLY B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 227 through 242 removed outlier: 3.629A pdb=" N ILE B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 280 through 295 removed outlier: 3.615A pdb=" N LYS B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 311 removed outlier: 3.552A pdb=" N ASP B 310 " --> pdb=" O ASN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 removed outlier: 3.565A pdb=" N LEU B 316 " --> pdb=" O PRO B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 355 removed outlier: 3.732A pdb=" N ASP B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR B 355 " --> pdb=" O GLN B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 373 Processing helix chain 'B' and resid 384 through 408 removed outlier: 3.664A pdb=" N ARG B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 421 through 426 removed outlier: 3.875A pdb=" N LEU B 425 " --> pdb=" O CYS B 421 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP B 426 " --> pdb=" O ILE B 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 421 through 426' Processing helix chain 'B' and resid 432 through 446 Processing helix chain 'B' and resid 447 through 457 Processing helix chain 'B' and resid 460 through 470 Processing helix chain 'B' and resid 487 through 491 Processing helix chain 'B' and resid 496 through 514 removed outlier: 3.811A pdb=" N LEU B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 27 removed outlier: 3.911A pdb=" N VAL J 27 " --> pdb=" O ASP J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 57 removed outlier: 3.548A pdb=" N SER J 57 " --> pdb=" O THR J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 84 removed outlier: 3.991A pdb=" N GLY J 68 " --> pdb=" O TYR J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 104 removed outlier: 3.575A pdb=" N LYS J 104 " --> pdb=" O GLU J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 133 Processing helix chain 'J' and resid 138 through 150 removed outlier: 3.510A pdb=" N ILE J 142 " --> pdb=" O THR J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 168 removed outlier: 3.532A pdb=" N GLY J 157 " --> pdb=" O ASP J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 203 Processing helix chain 'J' and resid 227 through 242 removed outlier: 3.629A pdb=" N ILE J 231 " --> pdb=" O SER J 227 " (cutoff:3.500A) Proline residue: J 233 - end of helix Processing helix chain 'J' and resid 253 through 268 Processing helix chain 'J' and resid 280 through 295 removed outlier: 3.615A pdb=" N LYS J 284 " --> pdb=" O GLY J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 311 removed outlier: 3.552A pdb=" N ASP J 310 " --> pdb=" O ASN J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 312 through 316 removed outlier: 3.565A pdb=" N LEU J 316 " --> pdb=" O PRO J 313 " (cutoff:3.500A) Processing helix chain 'J' and resid 337 through 353 removed outlier: 3.732A pdb=" N ASP J 353 " --> pdb=" O ILE J 349 " (cutoff:3.500A) Processing helix chain 'J' and resid 357 through 373 Processing helix chain 'J' and resid 384 through 408 removed outlier: 3.664A pdb=" N ARG J 394 " --> pdb=" O GLU J 390 " (cutoff:3.500A) Processing helix chain 'J' and resid 415 through 420 Processing helix chain 'J' and resid 421 through 426 removed outlier: 3.875A pdb=" N LEU J 425 " --> pdb=" O CYS J 421 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP J 426 " --> pdb=" O ILE J 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 421 through 426' Processing helix chain 'J' and resid 432 through 446 Processing helix chain 'J' and resid 447 through 457 Processing helix chain 'J' and resid 460 through 470 Processing helix chain 'J' and resid 487 through 491 Processing helix chain 'J' and resid 496 through 514 removed outlier: 3.811A pdb=" N LEU J 512 " --> pdb=" O GLY J 508 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 27 removed outlier: 3.911A pdb=" N VAL I 27 " --> pdb=" O ASP I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 57 removed outlier: 3.547A pdb=" N SER I 57 " --> pdb=" O THR I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 84 removed outlier: 3.992A pdb=" N GLY I 68 " --> pdb=" O TYR I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 104 removed outlier: 3.575A pdb=" N LYS I 104 " --> pdb=" O GLU I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 133 Processing helix chain 'I' and resid 138 through 150 removed outlier: 3.511A pdb=" N ILE I 142 " --> pdb=" O THR I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 168 removed outlier: 3.532A pdb=" N GLY I 157 " --> pdb=" O ASP I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 203 Processing helix chain 'I' and resid 227 through 242 removed outlier: 3.630A pdb=" N ILE I 231 " --> pdb=" O SER I 227 " (cutoff:3.500A) Proline residue: I 233 - end of helix Processing helix chain 'I' and resid 253 through 268 Processing helix chain 'I' and resid 280 through 295 removed outlier: 3.615A pdb=" N LYS I 284 " --> pdb=" O GLY I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 311 removed outlier: 3.552A pdb=" N ASP I 310 " --> pdb=" O ASN I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 312 through 316 removed outlier: 3.565A pdb=" N LEU I 316 " --> pdb=" O PRO I 313 " (cutoff:3.500A) Processing helix chain 'I' and resid 337 through 353 removed outlier: 3.732A pdb=" N ASP I 353 " --> pdb=" O ILE I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 357 through 373 Processing helix chain 'I' and resid 384 through 408 removed outlier: 3.664A pdb=" N ARG I 394 " --> pdb=" O GLU I 390 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 420 Processing helix chain 'I' and resid 421 through 426 removed outlier: 3.875A pdb=" N LEU I 425 " --> pdb=" O CYS I 421 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP I 426 " --> pdb=" O ILE I 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 421 through 426' Processing helix chain 'I' and resid 432 through 446 Processing helix chain 'I' and resid 447 through 457 Processing helix chain 'I' and resid 460 through 470 Processing helix chain 'I' and resid 487 through 491 Processing helix chain 'I' and resid 496 through 514 removed outlier: 3.811A pdb=" N LEU I 512 " --> pdb=" O GLY I 508 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 27 removed outlier: 3.911A pdb=" N VAL H 27 " --> pdb=" O ASP H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 57 removed outlier: 3.547A pdb=" N SER H 57 " --> pdb=" O THR H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 84 removed outlier: 3.991A pdb=" N GLY H 68 " --> pdb=" O TYR H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 104 removed outlier: 3.575A pdb=" N LYS H 104 " --> pdb=" O GLU H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 133 Processing helix chain 'H' and resid 138 through 150 removed outlier: 3.510A pdb=" N ILE H 142 " --> pdb=" O THR H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 168 removed outlier: 3.532A pdb=" N GLY H 157 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 203 Processing helix chain 'H' and resid 227 through 242 removed outlier: 3.629A pdb=" N ILE H 231 " --> pdb=" O SER H 227 " (cutoff:3.500A) Proline residue: H 233 - end of helix Processing helix chain 'H' and resid 253 through 268 Processing helix chain 'H' and resid 280 through 295 removed outlier: 3.615A pdb=" N LYS H 284 " --> pdb=" O GLY H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 311 removed outlier: 3.553A pdb=" N ASP H 310 " --> pdb=" O ASN H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 316 removed outlier: 3.564A pdb=" N LEU H 316 " --> pdb=" O PRO H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 355 removed outlier: 3.732A pdb=" N ASP H 353 " --> pdb=" O ILE H 349 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL H 354 " --> pdb=" O GLU H 350 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR H 355 " --> pdb=" O GLN H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 373 Processing helix chain 'H' and resid 384 through 408 removed outlier: 3.664A pdb=" N ARG H 394 " --> pdb=" O GLU H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 420 Processing helix chain 'H' and resid 421 through 426 removed outlier: 3.875A pdb=" N LEU H 425 " --> pdb=" O CYS H 421 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP H 426 " --> pdb=" O ILE H 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 421 through 426' Processing helix chain 'H' and resid 432 through 446 Processing helix chain 'H' and resid 447 through 457 Processing helix chain 'H' and resid 460 through 470 Processing helix chain 'H' and resid 487 through 491 Processing helix chain 'H' and resid 496 through 514 removed outlier: 3.811A pdb=" N LEU H 512 " --> pdb=" O GLY H 508 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 27 removed outlier: 3.910A pdb=" N VAL N 27 " --> pdb=" O ASP N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 57 removed outlier: 3.548A pdb=" N SER N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 84 removed outlier: 3.991A pdb=" N GLY N 68 " --> pdb=" O TYR N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 104 removed outlier: 3.575A pdb=" N LYS N 104 " --> pdb=" O GLU N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 133 Processing helix chain 'N' and resid 138 through 150 removed outlier: 3.510A pdb=" N ILE N 142 " --> pdb=" O THR N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 168 removed outlier: 3.533A pdb=" N GLY N 157 " --> pdb=" O ASP N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 203 Processing helix chain 'N' and resid 227 through 242 removed outlier: 3.628A pdb=" N ILE N 231 " --> pdb=" O SER N 227 " (cutoff:3.500A) Proline residue: N 233 - end of helix Processing helix chain 'N' and resid 253 through 268 Processing helix chain 'N' and resid 280 through 295 removed outlier: 3.615A pdb=" N LYS N 284 " --> pdb=" O GLY N 280 " (cutoff:3.500A) Processing helix chain 'N' and resid 307 through 311 removed outlier: 3.552A pdb=" N ASP N 310 " --> pdb=" O ASN N 307 " (cutoff:3.500A) Processing helix chain 'N' and resid 312 through 316 removed outlier: 3.565A pdb=" N LEU N 316 " --> pdb=" O PRO N 313 " (cutoff:3.500A) Processing helix chain 'N' and resid 337 through 355 removed outlier: 3.732A pdb=" N ASP N 353 " --> pdb=" O ILE N 349 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL N 354 " --> pdb=" O GLU N 350 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR N 355 " --> pdb=" O GLN N 351 " (cutoff:3.500A) Processing helix chain 'N' and resid 357 through 373 Processing helix chain 'N' and resid 384 through 408 removed outlier: 3.663A pdb=" N ARG N 394 " --> pdb=" O GLU N 390 " (cutoff:3.500A) Processing helix chain 'N' and resid 415 through 420 Processing helix chain 'N' and resid 421 through 426 removed outlier: 3.875A pdb=" N LEU N 425 " --> pdb=" O CYS N 421 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP N 426 " --> pdb=" O ILE N 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 421 through 426' Processing helix chain 'N' and resid 432 through 446 Processing helix chain 'N' and resid 447 through 457 Processing helix chain 'N' and resid 460 through 470 Processing helix chain 'N' and resid 487 through 491 Processing helix chain 'N' and resid 496 through 514 removed outlier: 3.811A pdb=" N LEU N 512 " --> pdb=" O GLY N 508 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 27 removed outlier: 3.910A pdb=" N VAL Y 27 " --> pdb=" O ASP Y 23 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 57 removed outlier: 3.548A pdb=" N SER Y 57 " --> pdb=" O THR Y 53 " (cutoff:3.500A) Processing helix chain 'Y' and resid 64 through 84 removed outlier: 3.992A pdb=" N GLY Y 68 " --> pdb=" O TYR Y 64 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 104 removed outlier: 3.574A pdb=" N LYS Y 104 " --> pdb=" O GLU Y 100 " (cutoff:3.500A) Processing helix chain 'Y' and resid 110 through 133 Processing helix chain 'Y' and resid 138 through 150 removed outlier: 3.511A pdb=" N ILE Y 142 " --> pdb=" O THR Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 168 removed outlier: 3.532A pdb=" N GLY Y 157 " --> pdb=" O ASP Y 153 " (cutoff:3.500A) Processing helix chain 'Y' and resid 199 through 203 Processing helix chain 'Y' and resid 227 through 242 removed outlier: 3.628A pdb=" N ILE Y 231 " --> pdb=" O SER Y 227 " (cutoff:3.500A) Proline residue: Y 233 - end of helix Processing helix chain 'Y' and resid 253 through 268 Processing helix chain 'Y' and resid 280 through 295 removed outlier: 3.615A pdb=" N LYS Y 284 " --> pdb=" O GLY Y 280 " (cutoff:3.500A) Processing helix chain 'Y' and resid 307 through 311 removed outlier: 3.552A pdb=" N ASP Y 310 " --> pdb=" O ASN Y 307 " (cutoff:3.500A) Processing helix chain 'Y' and resid 312 through 316 removed outlier: 3.565A pdb=" N LEU Y 316 " --> pdb=" O PRO Y 313 " (cutoff:3.500A) Processing helix chain 'Y' and resid 337 through 355 removed outlier: 3.732A pdb=" N ASP Y 353 " --> pdb=" O ILE Y 349 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL Y 354 " --> pdb=" O GLU Y 350 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR Y 355 " --> pdb=" O GLN Y 351 " (cutoff:3.500A) Processing helix chain 'Y' and resid 357 through 373 Processing helix chain 'Y' and resid 384 through 408 removed outlier: 3.664A pdb=" N ARG Y 394 " --> pdb=" O GLU Y 390 " (cutoff:3.500A) Processing helix chain 'Y' and resid 415 through 420 Processing helix chain 'Y' and resid 421 through 426 removed outlier: 3.875A pdb=" N LEU Y 425 " --> pdb=" O CYS Y 421 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP Y 426 " --> pdb=" O ILE Y 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 421 through 426' Processing helix chain 'Y' and resid 432 through 446 Processing helix chain 'Y' and resid 447 through 457 Processing helix chain 'Y' and resid 460 through 470 Processing helix chain 'Y' and resid 487 through 491 Processing helix chain 'Y' and resid 496 through 514 removed outlier: 3.811A pdb=" N LEU Y 512 " --> pdb=" O GLY Y 508 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 27 removed outlier: 3.910A pdb=" N VAL L 27 " --> pdb=" O ASP L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 57 removed outlier: 3.548A pdb=" N SER L 57 " --> pdb=" O THR L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 84 removed outlier: 3.991A pdb=" N GLY L 68 " --> pdb=" O TYR L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 104 removed outlier: 3.575A pdb=" N LYS L 104 " --> pdb=" O GLU L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 133 Processing helix chain 'L' and resid 138 through 150 removed outlier: 3.510A pdb=" N ILE L 142 " --> pdb=" O THR L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 153 through 168 removed outlier: 3.532A pdb=" N GLY L 157 " --> pdb=" O ASP L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 199 through 203 Processing helix chain 'L' and resid 227 through 242 removed outlier: 3.630A pdb=" N ILE L 231 " --> pdb=" O SER L 227 " (cutoff:3.500A) Proline residue: L 233 - end of helix Processing helix chain 'L' and resid 253 through 268 Processing helix chain 'L' and resid 280 through 295 removed outlier: 3.615A pdb=" N LYS L 284 " --> pdb=" O GLY L 280 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 311 removed outlier: 3.552A pdb=" N ASP L 310 " --> pdb=" O ASN L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 312 through 316 removed outlier: 3.564A pdb=" N LEU L 316 " --> pdb=" O PRO L 313 " (cutoff:3.500A) Processing helix chain 'L' and resid 337 through 353 removed outlier: 3.733A pdb=" N ASP L 353 " --> pdb=" O ILE L 349 " (cutoff:3.500A) Processing helix chain 'L' and resid 357 through 373 Processing helix chain 'L' and resid 384 through 408 removed outlier: 3.664A pdb=" N ARG L 394 " --> pdb=" O GLU L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 415 through 420 Processing helix chain 'L' and resid 421 through 426 removed outlier: 3.875A pdb=" N LEU L 425 " --> pdb=" O CYS L 421 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP L 426 " --> pdb=" O ILE L 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 421 through 426' Processing helix chain 'L' and resid 432 through 446 Processing helix chain 'L' and resid 447 through 457 Processing helix chain 'L' and resid 460 through 470 Processing helix chain 'L' and resid 487 through 491 Processing helix chain 'L' and resid 496 through 514 removed outlier: 3.811A pdb=" N LEU L 512 " --> pdb=" O GLY L 508 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 27 removed outlier: 3.910A pdb=" N VAL K 27 " --> pdb=" O ASP K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 57 removed outlier: 3.548A pdb=" N SER K 57 " --> pdb=" O THR K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 84 removed outlier: 3.992A pdb=" N GLY K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 104 removed outlier: 3.575A pdb=" N LYS K 104 " --> pdb=" O GLU K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 133 Processing helix chain 'K' and resid 138 through 150 removed outlier: 3.510A pdb=" N ILE K 142 " --> pdb=" O THR K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 168 removed outlier: 3.532A pdb=" N GLY K 157 " --> pdb=" O ASP K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 203 Processing helix chain 'K' and resid 227 through 242 removed outlier: 3.629A pdb=" N ILE K 231 " --> pdb=" O SER K 227 " (cutoff:3.500A) Proline residue: K 233 - end of helix Processing helix chain 'K' and resid 253 through 268 Processing helix chain 'K' and resid 280 through 295 removed outlier: 3.615A pdb=" N LYS K 284 " --> pdb=" O GLY K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 311 removed outlier: 3.553A pdb=" N ASP K 310 " --> pdb=" O ASN K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 312 through 316 removed outlier: 3.565A pdb=" N LEU K 316 " --> pdb=" O PRO K 313 " (cutoff:3.500A) Processing helix chain 'K' and resid 337 through 353 removed outlier: 3.732A pdb=" N ASP K 353 " --> pdb=" O ILE K 349 " (cutoff:3.500A) Processing helix chain 'K' and resid 357 through 373 Processing helix chain 'K' and resid 384 through 408 removed outlier: 3.664A pdb=" N ARG K 394 " --> pdb=" O GLU K 390 " (cutoff:3.500A) Processing helix chain 'K' and resid 415 through 420 Processing helix chain 'K' and resid 421 through 426 removed outlier: 3.875A pdb=" N LEU K 425 " --> pdb=" O CYS K 421 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP K 426 " --> pdb=" O ILE K 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 421 through 426' Processing helix chain 'K' and resid 432 through 446 Processing helix chain 'K' and resid 447 through 457 Processing helix chain 'K' and resid 460 through 470 Processing helix chain 'K' and resid 487 through 491 Processing helix chain 'K' and resid 496 through 514 removed outlier: 3.811A pdb=" N LEU K 512 " --> pdb=" O GLY K 508 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 removed outlier: 4.581A pdb=" N ALA A 516 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE B 37 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 518 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 48 removed outlier: 5.656A pdb=" N THR A 35 " --> pdb=" O ALA G 516 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL G 518 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 6.573A pdb=" N VAL A 172 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU A 378 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR A 174 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL A 380 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS A 176 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU A 331 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS A 318 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR A 217 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 320 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU A 245 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL A 274 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE A 247 " --> pdb=" O VAL A 274 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU A 331 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS A 318 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR A 217 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 320 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N PHE A 299 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU A 220 " --> pdb=" O PHE A 299 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 475 through 478 Processing sheet with id=AA8, first strand: chain 'G' and resid 46 through 48 removed outlier: 5.660A pdb=" N THR G 35 " --> pdb=" O ALA F 516 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL F 518 " --> pdb=" O THR G 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 172 through 177 removed outlier: 6.573A pdb=" N VAL G 172 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU G 378 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR G 174 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL G 380 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS G 176 " --> pdb=" O VAL G 380 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU G 331 " --> pdb=" O MET G 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS G 318 " --> pdb=" O TYR G 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR G 217 " --> pdb=" O LYS G 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY G 320 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU G 245 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL G 274 " --> pdb=" O LEU G 245 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE G 247 " --> pdb=" O VAL G 274 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU G 331 " --> pdb=" O MET G 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS G 318 " --> pdb=" O TYR G 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR G 217 " --> pdb=" O LYS G 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY G 320 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N PHE G 299 " --> pdb=" O VAL G 218 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU G 220 " --> pdb=" O PHE G 299 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 410 through 412 Processing sheet with id=AB4, first strand: chain 'G' and resid 475 through 478 Processing sheet with id=AB5, first strand: chain 'F' and resid 46 through 48 removed outlier: 5.669A pdb=" N THR F 35 " --> pdb=" O ALA E 516 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 518 " --> pdb=" O THR F 35 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 172 through 177 removed outlier: 6.574A pdb=" N VAL F 172 " --> pdb=" O ALA F 376 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU F 378 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR F 174 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL F 380 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS F 176 " --> pdb=" O VAL F 380 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU F 331 " --> pdb=" O MET F 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS F 318 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR F 217 " --> pdb=" O LYS F 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY F 320 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU F 245 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL F 274 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE F 247 " --> pdb=" O VAL F 274 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU F 331 " --> pdb=" O MET F 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS F 318 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR F 217 " --> pdb=" O LYS F 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY F 320 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N PHE F 299 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU F 220 " --> pdb=" O PHE F 299 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 410 through 412 Processing sheet with id=AC1, first strand: chain 'F' and resid 475 through 478 Processing sheet with id=AC2, first strand: chain 'E' and resid 46 through 48 removed outlier: 5.662A pdb=" N THR E 35 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL D 518 " --> pdb=" O THR E 35 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 172 through 177 removed outlier: 6.573A pdb=" N VAL E 172 " --> pdb=" O ALA E 376 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU E 378 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR E 174 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL E 380 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LYS E 176 " --> pdb=" O VAL E 380 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU E 331 " --> pdb=" O MET E 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS E 318 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR E 217 " --> pdb=" O LYS E 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY E 320 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU E 245 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL E 274 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE E 247 " --> pdb=" O VAL E 274 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU E 331 " --> pdb=" O MET E 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS E 318 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR E 217 " --> pdb=" O LYS E 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY E 320 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N PHE E 299 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU E 220 " --> pdb=" O PHE E 299 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 410 through 412 Processing sheet with id=AC7, first strand: chain 'E' and resid 475 through 478 Processing sheet with id=AC8, first strand: chain 'D' and resid 46 through 48 removed outlier: 5.674A pdb=" N THR D 35 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL C 518 " --> pdb=" O THR D 35 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 172 through 177 Processing sheet with id=AD1, first strand: chain 'D' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU D 331 " --> pdb=" O MET D 191 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS D 318 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR D 217 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY D 320 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU D 245 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL D 274 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE D 247 " --> pdb=" O VAL D 274 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU D 331 " --> pdb=" O MET D 191 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS D 318 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR D 217 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY D 320 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N PHE D 299 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU D 220 " --> pdb=" O PHE D 299 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AD4, first strand: chain 'D' and resid 475 through 478 Processing sheet with id=AD5, first strand: chain 'C' and resid 46 through 48 removed outlier: 5.663A pdb=" N THR C 35 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 518 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 172 through 177 removed outlier: 6.574A pdb=" N VAL C 172 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU C 378 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR C 174 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL C 380 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS C 176 " --> pdb=" O VAL C 380 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU C 331 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS C 318 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR C 217 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY C 320 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU C 245 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL C 274 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE C 247 " --> pdb=" O VAL C 274 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU C 331 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS C 318 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR C 217 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY C 320 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N PHE C 299 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU C 220 " --> pdb=" O PHE C 299 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AE1, first strand: chain 'C' and resid 475 through 478 Processing sheet with id=AE2, first strand: chain 'B' and resid 172 through 177 removed outlier: 6.573A pdb=" N VAL B 172 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU B 378 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR B 174 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL B 380 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS B 176 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU B 331 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS B 318 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR B 217 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 320 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU B 245 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL B 274 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE B 247 " --> pdb=" O VAL B 274 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU B 331 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS B 318 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR B 217 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 320 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N PHE B 299 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU B 220 " --> pdb=" O PHE B 299 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AE6, first strand: chain 'B' and resid 475 through 478 Processing sheet with id=AE7, first strand: chain 'J' and resid 2 through 6 removed outlier: 4.594A pdb=" N ALA J 516 " --> pdb=" O THR K 35 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE K 37 " --> pdb=" O ALA J 516 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL J 518 " --> pdb=" O ILE K 37 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 46 through 48 removed outlier: 5.661A pdb=" N THR J 35 " --> pdb=" O ALA I 516 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL I 518 " --> pdb=" O THR J 35 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 172 through 177 removed outlier: 6.573A pdb=" N VAL J 172 " --> pdb=" O ALA J 376 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU J 378 " --> pdb=" O VAL J 172 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR J 174 " --> pdb=" O LEU J 378 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL J 380 " --> pdb=" O THR J 174 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS J 176 " --> pdb=" O VAL J 380 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU J 331 " --> pdb=" O MET J 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS J 318 " --> pdb=" O TYR J 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR J 217 " --> pdb=" O LYS J 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY J 320 " --> pdb=" O ASP J 215 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU J 245 " --> pdb=" O VAL J 272 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL J 274 " --> pdb=" O LEU J 245 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE J 247 " --> pdb=" O VAL J 274 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU J 331 " --> pdb=" O MET J 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS J 318 " --> pdb=" O TYR J 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR J 217 " --> pdb=" O LYS J 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY J 320 " --> pdb=" O ASP J 215 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N PHE J 299 " --> pdb=" O VAL J 218 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU J 220 " --> pdb=" O PHE J 299 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 410 through 412 Processing sheet with id=AF4, first strand: chain 'J' and resid 475 through 478 Processing sheet with id=AF5, first strand: chain 'I' and resid 46 through 48 removed outlier: 5.666A pdb=" N THR I 35 " --> pdb=" O ALA H 516 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL H 518 " --> pdb=" O THR I 35 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 172 through 177 removed outlier: 6.573A pdb=" N VAL I 172 " --> pdb=" O ALA I 376 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU I 378 " --> pdb=" O VAL I 172 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR I 174 " --> pdb=" O LEU I 378 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL I 380 " --> pdb=" O THR I 174 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS I 176 " --> pdb=" O VAL I 380 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU I 331 " --> pdb=" O MET I 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS I 318 " --> pdb=" O TYR I 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR I 217 " --> pdb=" O LYS I 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY I 320 " --> pdb=" O ASP I 215 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU I 245 " --> pdb=" O VAL I 272 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL I 274 " --> pdb=" O LEU I 245 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE I 247 " --> pdb=" O VAL I 274 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU I 331 " --> pdb=" O MET I 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS I 318 " --> pdb=" O TYR I 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR I 217 " --> pdb=" O LYS I 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY I 320 " --> pdb=" O ASP I 215 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N PHE I 299 " --> pdb=" O VAL I 218 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU I 220 " --> pdb=" O PHE I 299 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 410 through 412 Processing sheet with id=AG1, first strand: chain 'I' and resid 475 through 478 Processing sheet with id=AG2, first strand: chain 'H' and resid 46 through 48 removed outlier: 5.678A pdb=" N THR H 35 " --> pdb=" O ALA N 516 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL N 518 " --> pdb=" O THR H 35 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 172 through 177 removed outlier: 6.573A pdb=" N VAL H 172 " --> pdb=" O ALA H 376 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU H 378 " --> pdb=" O VAL H 172 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR H 174 " --> pdb=" O LEU H 378 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL H 380 " --> pdb=" O THR H 174 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS H 176 " --> pdb=" O VAL H 380 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 191 through 192 removed outlier: 3.576A pdb=" N LEU H 331 " --> pdb=" O MET H 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS H 318 " --> pdb=" O TYR H 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR H 217 " --> pdb=" O LYS H 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY H 320 " --> pdb=" O ASP H 215 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU H 245 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL H 274 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE H 247 " --> pdb=" O VAL H 274 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 191 through 192 removed outlier: 3.576A pdb=" N LEU H 331 " --> pdb=" O MET H 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS H 318 " --> pdb=" O TYR H 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR H 217 " --> pdb=" O LYS H 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY H 320 " --> pdb=" O ASP H 215 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N PHE H 299 " --> pdb=" O VAL H 218 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU H 220 " --> pdb=" O PHE H 299 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 410 through 412 Processing sheet with id=AG7, first strand: chain 'H' and resid 475 through 478 Processing sheet with id=AG8, first strand: chain 'N' and resid 46 through 48 removed outlier: 5.663A pdb=" N THR N 35 " --> pdb=" O ALA Y 516 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL Y 518 " --> pdb=" O THR N 35 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 172 through 177 removed outlier: 6.573A pdb=" N VAL N 172 " --> pdb=" O ALA N 376 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU N 378 " --> pdb=" O VAL N 172 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR N 174 " --> pdb=" O LEU N 378 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL N 380 " --> pdb=" O THR N 174 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LYS N 176 " --> pdb=" O VAL N 380 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU N 331 " --> pdb=" O MET N 191 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS N 318 " --> pdb=" O TYR N 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR N 217 " --> pdb=" O LYS N 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY N 320 " --> pdb=" O ASP N 215 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU N 245 " --> pdb=" O VAL N 272 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL N 274 " --> pdb=" O LEU N 245 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE N 247 " --> pdb=" O VAL N 274 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 191 through 192 removed outlier: 3.577A pdb=" N LEU N 331 " --> pdb=" O MET N 191 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS N 318 " --> pdb=" O TYR N 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR N 217 " --> pdb=" O LYS N 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY N 320 " --> pdb=" O ASP N 215 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N PHE N 299 " --> pdb=" O VAL N 218 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU N 220 " --> pdb=" O PHE N 299 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 410 through 412 Processing sheet with id=AH4, first strand: chain 'N' and resid 475 through 478 Processing sheet with id=AH5, first strand: chain 'Y' and resid 46 through 48 removed outlier: 5.656A pdb=" N THR Y 35 " --> pdb=" O ALA L 516 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL L 518 " --> pdb=" O THR Y 35 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Y' and resid 172 through 177 removed outlier: 6.573A pdb=" N VAL Y 172 " --> pdb=" O ALA Y 376 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU Y 378 " --> pdb=" O VAL Y 172 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR Y 174 " --> pdb=" O LEU Y 378 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL Y 380 " --> pdb=" O THR Y 174 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS Y 176 " --> pdb=" O VAL Y 380 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Y' and resid 191 through 192 removed outlier: 3.576A pdb=" N LEU Y 331 " --> pdb=" O MET Y 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS Y 318 " --> pdb=" O TYR Y 217 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR Y 217 " --> pdb=" O LYS Y 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY Y 320 " --> pdb=" O ASP Y 215 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU Y 245 " --> pdb=" O VAL Y 272 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL Y 274 " --> pdb=" O LEU Y 245 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE Y 247 " --> pdb=" O VAL Y 274 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Y' and resid 191 through 192 removed outlier: 3.576A pdb=" N LEU Y 331 " --> pdb=" O MET Y 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS Y 318 " --> pdb=" O TYR Y 217 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR Y 217 " --> pdb=" O LYS Y 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY Y 320 " --> pdb=" O ASP Y 215 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N PHE Y 299 " --> pdb=" O VAL Y 218 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU Y 220 " --> pdb=" O PHE Y 299 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Y' and resid 410 through 412 Processing sheet with id=AI1, first strand: chain 'Y' and resid 475 through 478 Processing sheet with id=AI2, first strand: chain 'L' and resid 46 through 48 removed outlier: 5.660A pdb=" N THR L 35 " --> pdb=" O ALA K 516 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL K 518 " --> pdb=" O THR L 35 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 172 through 177 removed outlier: 6.573A pdb=" N VAL L 172 " --> pdb=" O ALA L 376 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU L 378 " --> pdb=" O VAL L 172 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR L 174 " --> pdb=" O LEU L 378 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL L 380 " --> pdb=" O THR L 174 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS L 176 " --> pdb=" O VAL L 380 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'L' and resid 191 through 192 removed outlier: 3.576A pdb=" N LEU L 331 " --> pdb=" O MET L 191 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS L 318 " --> pdb=" O TYR L 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR L 217 " --> pdb=" O LYS L 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY L 320 " --> pdb=" O ASP L 215 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU L 245 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL L 274 " --> pdb=" O LEU L 245 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE L 247 " --> pdb=" O VAL L 274 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'L' and resid 191 through 192 removed outlier: 3.576A pdb=" N LEU L 331 " --> pdb=" O MET L 191 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS L 318 " --> pdb=" O TYR L 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR L 217 " --> pdb=" O LYS L 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY L 320 " --> pdb=" O ASP L 215 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N PHE L 299 " --> pdb=" O VAL L 218 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU L 220 " --> pdb=" O PHE L 299 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'L' and resid 410 through 412 Processing sheet with id=AI7, first strand: chain 'L' and resid 475 through 478 Processing sheet with id=AI8, first strand: chain 'K' and resid 172 through 177 removed outlier: 6.574A pdb=" N VAL K 172 " --> pdb=" O ALA K 376 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU K 378 " --> pdb=" O VAL K 172 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR K 174 " --> pdb=" O LEU K 378 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL K 380 " --> pdb=" O THR K 174 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LYS K 176 " --> pdb=" O VAL K 380 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'K' and resid 191 through 192 removed outlier: 3.578A pdb=" N LEU K 331 " --> pdb=" O MET K 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS K 318 " --> pdb=" O TYR K 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR K 217 " --> pdb=" O LYS K 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY K 320 " --> pdb=" O ASP K 215 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU K 245 " --> pdb=" O VAL K 272 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL K 274 " --> pdb=" O LEU K 245 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE K 247 " --> pdb=" O VAL K 274 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 191 through 192 removed outlier: 3.578A pdb=" N LEU K 331 " --> pdb=" O MET K 191 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS K 318 " --> pdb=" O TYR K 217 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR K 217 " --> pdb=" O LYS K 318 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY K 320 " --> pdb=" O ASP K 215 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N PHE K 299 " --> pdb=" O VAL K 218 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU K 220 " --> pdb=" O PHE K 299 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'K' and resid 410 through 412 Processing sheet with id=AJ3, first strand: chain 'K' and resid 475 through 478 Processing sheet with id=AJ4, first strand: chain 'O' and resid 9 through 11 removed outlier: 4.746A pdb=" N LYS U 70 " --> pdb=" O TYR U 100 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU U 17 " --> pdb=" O VAL U 47 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL U 49 " --> pdb=" O ARG U 15 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG U 15 " --> pdb=" O VAL U 49 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG U 20 " --> pdb=" O ASP U 87 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ASP U 87 " --> pdb=" O ARG U 20 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'O' and resid 79 through 83 removed outlier: 8.392A pdb=" N ASP O 87 " --> pdb=" O ARG O 20 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG O 20 " --> pdb=" O ASP O 87 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG O 15 " --> pdb=" O VAL O 49 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL O 49 " --> pdb=" O ARG O 15 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU O 17 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS O 70 " --> pdb=" O TYR O 100 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'U' and resid 9 through 11 removed outlier: 4.746A pdb=" N LYS T 70 " --> pdb=" O TYR T 100 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU T 17 " --> pdb=" O VAL T 47 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL T 49 " --> pdb=" O ARG T 15 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG T 15 " --> pdb=" O VAL T 49 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG T 20 " --> pdb=" O ASP T 87 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ASP T 87 " --> pdb=" O ARG T 20 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'T' and resid 9 through 11 removed outlier: 4.745A pdb=" N LYS S 70 " --> pdb=" O TYR S 100 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU S 17 " --> pdb=" O VAL S 47 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL S 49 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG S 15 " --> pdb=" O VAL S 49 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG S 20 " --> pdb=" O ASP S 87 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ASP S 87 " --> pdb=" O ARG S 20 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'S' and resid 9 through 11 removed outlier: 4.745A pdb=" N LYS R 70 " --> pdb=" O TYR R 100 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU R 17 " --> pdb=" O VAL R 47 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL R 49 " --> pdb=" O ARG R 15 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG R 15 " --> pdb=" O VAL R 49 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG R 20 " --> pdb=" O ASP R 87 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ASP R 87 " --> pdb=" O ARG R 20 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'R' and resid 9 through 11 removed outlier: 4.746A pdb=" N LYS Q 70 " --> pdb=" O TYR Q 100 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU Q 17 " --> pdb=" O VAL Q 47 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL Q 49 " --> pdb=" O ARG Q 15 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARG Q 15 " --> pdb=" O VAL Q 49 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ARG Q 20 " --> pdb=" O ASP Q 87 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ASP Q 87 " --> pdb=" O ARG Q 20 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Q' and resid 9 through 11 removed outlier: 4.746A pdb=" N LYS P 70 " --> pdb=" O TYR P 100 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU P 17 " --> pdb=" O VAL P 47 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL P 49 " --> pdb=" O ARG P 15 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG P 15 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG P 20 " --> pdb=" O ASP P 87 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASP P 87 " --> pdb=" O ARG P 20 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'X' and resid 9 through 11 removed outlier: 4.746A pdb=" N LYS W 70 " --> pdb=" O TYR W 100 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU W 17 " --> pdb=" O VAL W 47 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL W 49 " --> pdb=" O ARG W 15 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG W 15 " --> pdb=" O VAL W 49 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG W 20 " --> pdb=" O ASP W 87 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ASP W 87 " --> pdb=" O ARG W 20 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'X' and resid 79 through 83 removed outlier: 8.392A pdb=" N ASP X 87 " --> pdb=" O ARG X 20 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG X 20 " --> pdb=" O ASP X 87 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG X 15 " --> pdb=" O VAL X 49 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL X 49 " --> pdb=" O ARG X 15 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU X 17 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS X 70 " --> pdb=" O TYR X 100 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'W' and resid 9 through 11 removed outlier: 4.745A pdb=" N LYS V 70 " --> pdb=" O TYR V 100 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU V 17 " --> pdb=" O VAL V 47 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL V 49 " --> pdb=" O ARG V 15 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG V 15 " --> pdb=" O VAL V 49 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG V 20 " --> pdb=" O ASP V 87 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ASP V 87 " --> pdb=" O ARG V 20 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'V' and resid 9 through 11 removed outlier: 4.745A pdb=" N LYS 2 70 " --> pdb=" O TYR 2 100 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU 2 17 " --> pdb=" O VAL 2 47 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N VAL 2 49 " --> pdb=" O ARG 2 15 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG 2 15 " --> pdb=" O VAL 2 49 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG 2 20 " --> pdb=" O ASP 2 87 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ASP 2 87 " --> pdb=" O ARG 2 20 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain '2' and resid 9 through 11 removed outlier: 4.745A pdb=" N LYS 1 70 " --> pdb=" O TYR 1 100 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU 1 17 " --> pdb=" O VAL 1 47 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL 1 49 " --> pdb=" O ARG 1 15 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG 1 15 " --> pdb=" O VAL 1 49 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG 1 20 " --> pdb=" O ASP 1 87 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ASP 1 87 " --> pdb=" O ARG 1 20 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain '1' and resid 9 through 11 removed outlier: 4.746A pdb=" N LYS Z 70 " --> pdb=" O TYR Z 100 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU Z 17 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL Z 49 " --> pdb=" O ARG Z 15 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG Z 15 " --> pdb=" O VAL Z 49 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ARG Z 20 " --> pdb=" O ASP Z 87 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ASP Z 87 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'Z' and resid 9 through 11 removed outlier: 4.745A pdb=" N LYS M 70 " --> pdb=" O TYR M 100 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU M 17 " --> pdb=" O VAL M 47 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL M 49 " --> pdb=" O ARG M 15 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG M 15 " --> pdb=" O VAL M 49 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ARG M 20 " --> pdb=" O ASP M 87 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ASP M 87 " --> pdb=" O ARG M 20 " (cutoff:3.500A) 3809 hydrogen bonds defined for protein. 10797 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: 34.38 Time building geometry restraints manager: 15.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 22188 1.34 - 1.46: 8777 1.46 - 1.57: 35297 1.57 - 1.69: 70 1.69 - 1.81: 378 Bond restraints: 66710 Sorted by residual: bond pdb=" CD GLN K 286 " pdb=" OE1 GLN K 286 " ideal model delta sigma weight residual 1.231 1.327 -0.096 1.90e-02 2.77e+03 2.55e+01 bond pdb=" CD GLN E 286 " pdb=" OE1 GLN E 286 " ideal model delta sigma weight residual 1.231 1.327 -0.096 1.90e-02 2.77e+03 2.54e+01 bond pdb=" CD GLN F 286 " pdb=" OE1 GLN F 286 " ideal model delta sigma weight residual 1.231 1.327 -0.096 1.90e-02 2.77e+03 2.54e+01 bond pdb=" CD GLN C 286 " pdb=" OE1 GLN C 286 " ideal model delta sigma weight residual 1.231 1.326 -0.095 1.90e-02 2.77e+03 2.52e+01 bond pdb=" CD GLN G 286 " pdb=" OE1 GLN G 286 " ideal model delta sigma weight residual 1.231 1.326 -0.095 1.90e-02 2.77e+03 2.52e+01 ... (remaining 66705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 86838 1.27 - 2.55: 2527 2.55 - 3.82: 457 3.82 - 5.10: 138 5.10 - 6.37: 74 Bond angle restraints: 90034 Sorted by residual: angle pdb=" O ILE A 228 " pdb=" C ILE A 228 " pdb=" N GLN A 229 " ideal model delta sigma weight residual 121.80 115.43 6.37 1.13e+00 7.83e-01 3.18e+01 angle pdb=" CA ILE A 228 " pdb=" C ILE A 228 " pdb=" N GLN A 229 " ideal model delta sigma weight residual 117.69 123.85 -6.16 1.27e+00 6.20e-01 2.36e+01 angle pdb=" O ILE G 228 " pdb=" C ILE G 228 " pdb=" N GLN G 229 " ideal model delta sigma weight residual 121.80 116.64 5.16 1.13e+00 7.83e-01 2.08e+01 angle pdb=" O ILE I 228 " pdb=" C ILE I 228 " pdb=" N GLN I 229 " ideal model delta sigma weight residual 121.80 116.68 5.12 1.13e+00 7.83e-01 2.05e+01 angle pdb=" C PHE T 13 " pdb=" CA PHE T 13 " pdb=" CB PHE T 13 " ideal model delta sigma weight residual 117.23 111.17 6.06 1.36e+00 5.41e-01 1.98e+01 ... (remaining 90029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 38469 16.73 - 33.45: 2132 33.45 - 50.18: 659 50.18 - 66.91: 194 66.91 - 83.63: 112 Dihedral angle restraints: 41566 sinusoidal: 16814 harmonic: 24752 Sorted by residual: dihedral pdb=" CA GLY Y 7 " pdb=" C GLY Y 7 " pdb=" N ALA Y 8 " pdb=" CA ALA Y 8 " ideal model delta harmonic sigma weight residual -180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA GLY L 7 " pdb=" C GLY L 7 " pdb=" N ALA L 8 " pdb=" CA ALA L 8 " ideal model delta harmonic sigma weight residual 180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA GLY I 7 " pdb=" C GLY I 7 " pdb=" N ALA I 8 " pdb=" CA ALA I 8 " ideal model delta harmonic sigma weight residual -180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 41563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 9146 0.056 - 0.112: 1345 0.112 - 0.167: 317 0.167 - 0.223: 0 0.223 - 0.279: 42 Chirality restraints: 10850 Sorted by residual: chirality pdb=" C2' ATP L 601 " pdb=" C1' ATP L 601 " pdb=" C3' ATP L 601 " pdb=" O2' ATP L 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C2' ATP H 601 " pdb=" C1' ATP H 601 " pdb=" C3' ATP H 601 " pdb=" O2' ATP H 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C2' ATP N 601 " pdb=" C1' ATP N 601 " pdb=" C3' ATP N 601 " pdb=" O2' ATP N 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 10847 not shown) Planarity restraints: 11522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 199 " -0.064 5.00e-02 4.00e+02 9.52e-02 1.45e+01 pdb=" N PRO D 200 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO D 200 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 200 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 199 " 0.064 5.00e-02 4.00e+02 9.52e-02 1.45e+01 pdb=" N PRO H 200 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO H 200 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO H 200 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 199 " -0.064 5.00e-02 4.00e+02 9.52e-02 1.45e+01 pdb=" N PRO F 200 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO F 200 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO F 200 " -0.052 5.00e-02 4.00e+02 ... (remaining 11519 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.72: 1720 2.72 - 3.32: 74946 3.32 - 3.93: 124684 3.93 - 4.53: 168566 4.53 - 5.14: 263185 Nonbonded interactions: 633101 Sorted by model distance: nonbonded pdb=" O2G ATP N 601 " pdb="MG MG N 602 " model vdw 2.109 2.170 nonbonded pdb=" O2G ATP B 601 " pdb="MG MG B 602 " model vdw 2.110 2.170 nonbonded pdb=" O2G ATP Y 601 " pdb="MG MG Y 602 " model vdw 2.110 2.170 nonbonded pdb=" O2G ATP D 601 " pdb="MG MG D 602 " model vdw 2.110 2.170 nonbonded pdb=" O2G ATP I 601 " pdb="MG MG I 602 " model vdw 2.110 2.170 ... (remaining 633096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'Y' } 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: 6.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 1.980 Check model and map are aligned: 0.370 Set scattering table: 0.470 Process input model: 123.300 Find NCS groups from input model: 2.910 Set up NCS constraints: 0.560 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:10.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 : 0.003 0.097 66710 Z= 0.213 Angle : 0.573 6.369 90034 Z= 0.344 Chirality : 0.045 0.279 10850 Planarity : 0.005 0.095 11522 Dihedral : 13.363 83.635 25690 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.20 % Allowed : 0.20 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.66 (0.09), residues: 8722 helix: 2.55 (0.08), residues: 3850 sheet: 0.80 (0.15), residues: 1106 loop : -0.33 (0.09), residues: 3766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP Y 42 HIS 0.001 0.000 HIS I 314 PHE 0.006 0.001 PHE Z 89 TYR 0.011 0.001 TYR B 197 ARG 0.002 0.000 ARG I 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1176 time to evaluate : 5.781 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: A 212 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6688 (mm-30) REVERT: A 312 GLN cc_start: 0.7586 (mm-40) cc_final: 0.7282 (mm-40) REVERT: G 164 MET cc_start: 0.8562 (mtt) cc_final: 0.8361 (mtt) REVERT: G 212 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6552 (mm-30) REVERT: G 217 TYR cc_start: 0.8463 (m-80) cc_final: 0.8151 (m-80) REVERT: G 312 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7307 (mm-40) REVERT: F 312 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7372 (mm-40) REVERT: E 212 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6613 (mm-30) REVERT: E 340 GLN cc_start: 0.7822 (mm110) cc_final: 0.7601 (mm110) REVERT: D 212 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6610 (mm-30) REVERT: D 270 GLN cc_start: 0.8052 (mt0) cc_final: 0.7838 (mt0) REVERT: D 312 GLN cc_start: 0.7591 (mm-40) cc_final: 0.7342 (mm-40) REVERT: D 340 GLN cc_start: 0.7612 (mm110) cc_final: 0.7237 (mm110) REVERT: D 469 MET cc_start: 0.8622 (mtm) cc_final: 0.8421 (mtp) REVERT: C 212 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6711 (mm-30) REVERT: C 312 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7255 (mm-40) REVERT: B 212 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6550 (mm-30) REVERT: B 323 ILE cc_start: 0.8607 (mt) cc_final: 0.8323 (mt) REVERT: B 469 MET cc_start: 0.8600 (mtm) cc_final: 0.8235 (mtp) REVERT: J 212 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6689 (mm-30) REVERT: J 312 GLN cc_start: 0.7584 (mm-40) cc_final: 0.7280 (mm-40) REVERT: I 212 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6576 (mm-30) REVERT: I 217 TYR cc_start: 0.8463 (m-80) cc_final: 0.8161 (m-80) REVERT: I 312 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7317 (mm-40) REVERT: H 312 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7389 (mm-40) REVERT: N 212 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6609 (mm-30) REVERT: N 340 GLN cc_start: 0.7818 (mm110) cc_final: 0.7485 (mm110) REVERT: Y 212 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6607 (mm-30) REVERT: Y 312 GLN cc_start: 0.7602 (mm-40) cc_final: 0.7363 (mm-40) REVERT: Y 340 GLN cc_start: 0.7615 (mm110) cc_final: 0.7255 (mm110) REVERT: Y 469 MET cc_start: 0.8608 (mtm) cc_final: 0.8394 (mtp) REVERT: L 212 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6618 (mm-30) REVERT: L 312 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7253 (mm-40) REVERT: K 212 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6511 (mm-30) REVERT: K 469 MET cc_start: 0.8578 (mtm) cc_final: 0.8232 (mtp) REVERT: T 19 GLU cc_start: 0.7688 (tt0) cc_final: 0.7434 (tt0) REVERT: S 87 ASP cc_start: 0.7625 (m-30) cc_final: 0.7346 (m-30) REVERT: V 19 GLU cc_start: 0.7671 (tt0) cc_final: 0.7422 (tt0) REVERT: 2 87 ASP cc_start: 0.7624 (m-30) cc_final: 0.7347 (m-30) outliers start: 14 outliers final: 2 residues processed: 1190 average time/residue: 1.4737 time to fit residues: 2261.5536 Evaluate side-chains 898 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 896 time to evaluate : 5.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain Y residue 345 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 732 optimal weight: 10.0000 chunk 657 optimal weight: 0.7980 chunk 365 optimal weight: 2.9990 chunk 224 optimal weight: 0.0170 chunk 443 optimal weight: 8.9990 chunk 351 optimal weight: 5.9990 chunk 680 optimal weight: 0.0060 chunk 263 optimal weight: 2.9990 chunk 413 optimal weight: 1.9990 chunk 506 optimal weight: 0.9990 chunk 788 optimal weight: 7.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN G 239 ASN F 239 ASN F 346 GLN E 239 ASN D 239 ASN D 346 GLN C 239 ASN C 346 GLN B 239 ASN J 239 ASN I 239 ASN H 239 ASN H 346 GLN N 239 ASN Y 239 ASN Y 346 GLN L 239 ASN L 346 GLN K 239 ASN S 43 GLN 2 43 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 66710 Z= 0.143 Angle : 0.478 7.812 90034 Z= 0.262 Chirality : 0.042 0.140 10850 Planarity : 0.004 0.050 11522 Dihedral : 7.145 59.287 9664 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.78 % Allowed : 7.83 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.66 (0.09), residues: 8722 helix: 2.49 (0.08), residues: 3962 sheet: 1.04 (0.15), residues: 1106 loop : -0.45 (0.09), residues: 3654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 42 HIS 0.001 0.000 HIS L 314 PHE 0.009 0.001 PHE N 213 TYR 0.011 0.001 TYR A 197 ARG 0.002 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 932 time to evaluate : 5.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6739 (mm-30) REVERT: A 312 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7191 (mm-40) REVERT: G 212 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6563 (mm-30) REVERT: G 217 TYR cc_start: 0.8408 (m-80) cc_final: 0.8124 (m-80) REVERT: G 312 GLN cc_start: 0.7694 (mm-40) cc_final: 0.7345 (mm-40) REVERT: G 343 LYS cc_start: 0.8216 (mttm) cc_final: 0.7988 (mttp) REVERT: F 264 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7842 (tpt-90) REVERT: F 312 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7387 (mm-40) REVERT: F 362 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6727 (tt0) REVERT: E 212 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6714 (mm-30) REVERT: E 340 GLN cc_start: 0.7889 (mm110) cc_final: 0.7543 (mm110) REVERT: D 212 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6516 (mm-30) REVERT: D 312 GLN cc_start: 0.7599 (mm-40) cc_final: 0.7263 (mm-40) REVERT: D 340 GLN cc_start: 0.7638 (mm110) cc_final: 0.7362 (mm110) REVERT: D 343 LYS cc_start: 0.7990 (mtpp) cc_final: 0.7605 (mptt) REVERT: D 469 MET cc_start: 0.8562 (mtm) cc_final: 0.8356 (mtp) REVERT: C 212 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6673 (mm-30) REVERT: C 312 GLN cc_start: 0.7494 (mm-40) cc_final: 0.7192 (mm-40) REVERT: B 212 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6583 (mm-30) REVERT: B 312 GLN cc_start: 0.8094 (mm110) cc_final: 0.7765 (mm-40) REVERT: B 330 MET cc_start: 0.7150 (mtm) cc_final: 0.6888 (mmm) REVERT: J 212 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6739 (mm-30) REVERT: J 312 GLN cc_start: 0.7571 (mm-40) cc_final: 0.7190 (mm-40) REVERT: J 321 GLU cc_start: 0.7472 (tp30) cc_final: 0.7268 (tp30) REVERT: I 212 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6592 (mm-30) REVERT: I 217 TYR cc_start: 0.8401 (m-80) cc_final: 0.8122 (m-80) REVERT: I 312 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7332 (mm-40) REVERT: I 343 LYS cc_start: 0.8199 (mttm) cc_final: 0.7973 (mttp) REVERT: H 212 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6705 (mm-30) REVERT: H 264 ARG cc_start: 0.8106 (tpt90) cc_final: 0.7904 (tmt-80) REVERT: H 312 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7367 (mm-40) REVERT: H 362 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6737 (tt0) REVERT: N 212 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6702 (mm-30) REVERT: N 340 GLN cc_start: 0.7903 (mm110) cc_final: 0.7559 (mm110) REVERT: Y 212 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6561 (mm-30) REVERT: Y 312 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7265 (mm-40) REVERT: Y 340 GLN cc_start: 0.7642 (mm110) cc_final: 0.7362 (mm110) REVERT: Y 343 LYS cc_start: 0.7981 (mtpp) cc_final: 0.7626 (mptt) REVERT: Y 469 MET cc_start: 0.8564 (mtm) cc_final: 0.8362 (mtp) REVERT: L 212 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6670 (mm-30) REVERT: L 312 GLN cc_start: 0.7497 (mm-40) cc_final: 0.7183 (mm-40) REVERT: K 212 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6507 (mm-30) REVERT: K 312 GLN cc_start: 0.8080 (mm110) cc_final: 0.7744 (mm110) REVERT: K 330 MET cc_start: 0.7137 (mtm) cc_final: 0.6896 (mmm) REVERT: U 80 LYS cc_start: 0.8656 (tppt) cc_final: 0.8423 (tptm) REVERT: T 8 LYS cc_start: 0.8065 (mtmm) cc_final: 0.7853 (mtpt) REVERT: R 80 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8471 (tptt) REVERT: W 80 LYS cc_start: 0.8672 (tppt) cc_final: 0.8420 (tptm) REVERT: V 8 LYS cc_start: 0.8080 (mtmm) cc_final: 0.7847 (mtpt) REVERT: 1 80 LYS cc_start: 0.8669 (tptt) cc_final: 0.8467 (tptt) outliers start: 126 outliers final: 29 residues processed: 1025 average time/residue: 1.3889 time to fit residues: 1864.6128 Evaluate side-chains 911 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 878 time to evaluate : 6.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 266 LYS Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 266 LYS Chi-restraints excluded: chain F residue 350 GLU Chi-restraints excluded: chain F residue 362 GLU Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 350 GLU Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain H residue 266 LYS Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 362 GLU Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain N residue 266 LYS Chi-restraints excluded: chain N residue 350 GLU Chi-restraints excluded: chain Y residue 345 ILE Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 350 GLU Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain K residue 350 GLU Chi-restraints excluded: chain R residue 80 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 438 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 656 optimal weight: 1.9990 chunk 536 optimal weight: 0.0980 chunk 217 optimal weight: 0.9990 chunk 789 optimal weight: 7.9990 chunk 853 optimal weight: 5.9990 chunk 703 optimal weight: 10.0000 chunk 783 optimal weight: 7.9990 chunk 269 optimal weight: 3.9990 chunk 633 optimal weight: 3.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 285 ASN G 239 ASN F 239 ASN E 239 ASN E 285 ASN D 239 ASN C 239 ASN B 239 ASN J 239 ASN J 285 ASN I 239 ASN H 239 ASN N 239 ASN N 285 ASN Y 239 ASN L 239 ASN K 239 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 66710 Z= 0.252 Angle : 0.543 8.292 90034 Z= 0.297 Chirality : 0.045 0.143 10850 Planarity : 0.004 0.042 11522 Dihedral : 8.282 69.844 9664 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.94 % Allowed : 9.71 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.08), residues: 8722 helix: 2.13 (0.08), residues: 3976 sheet: 1.11 (0.15), residues: 1106 loop : -0.48 (0.09), residues: 3640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 42 HIS 0.002 0.001 HIS H 241 PHE 0.010 0.001 PHE M 89 TYR 0.007 0.001 TYR D 197 ARG 0.005 0.001 ARG E 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 910 time to evaluate : 5.953 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: A 212 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6916 (mm-30) REVERT: A 312 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7244 (mm-40) REVERT: A 362 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6307 (tt0) REVERT: G 212 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6630 (mm-30) REVERT: G 217 TYR cc_start: 0.8414 (m-80) cc_final: 0.8134 (m-80) REVERT: G 264 ARG cc_start: 0.7997 (tpt90) cc_final: 0.7676 (tpt-90) REVERT: G 312 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7368 (mm-40) REVERT: G 321 GLU cc_start: 0.7452 (tp30) cc_final: 0.7047 (tm-30) REVERT: G 326 LYS cc_start: 0.8171 (tmtm) cc_final: 0.7958 (tmtt) REVERT: G 362 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6435 (tt0) REVERT: F 220 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8468 (mt) REVERT: F 264 ARG cc_start: 0.8076 (tpt170) cc_final: 0.7827 (tpt-90) REVERT: F 312 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7389 (mm-40) REVERT: F 362 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6690 (tt0) REVERT: E 212 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6752 (mm-30) REVERT: E 275 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8068 (mmmm) REVERT: E 338 LYS cc_start: 0.7558 (mptm) cc_final: 0.7165 (mptt) REVERT: D 212 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6637 (mm-30) REVERT: D 312 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7303 (mm-40) REVERT: D 321 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: D 323 ILE cc_start: 0.8706 (mt) cc_final: 0.7861 (mt) REVERT: D 362 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6239 (tt0) REVERT: D 469 MET cc_start: 0.8640 (mtm) cc_final: 0.8426 (mtp) REVERT: C 212 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6832 (mt-10) REVERT: C 275 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7749 (mtmt) REVERT: C 312 GLN cc_start: 0.7533 (mm-40) cc_final: 0.7168 (mm-40) REVERT: C 321 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7266 (tp30) REVERT: C 362 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6322 (tt0) REVERT: B 212 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6675 (mm-30) REVERT: B 312 GLN cc_start: 0.8083 (mm110) cc_final: 0.7713 (mm110) REVERT: B 338 LYS cc_start: 0.7602 (mmtt) cc_final: 0.7333 (mmtp) REVERT: B 342 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7186 (mm-30) REVERT: B 362 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6193 (tt0) REVERT: J 212 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6918 (mm-30) REVERT: J 312 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7245 (mm-40) REVERT: J 362 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6302 (tt0) REVERT: I 212 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6634 (mm-30) REVERT: I 217 TYR cc_start: 0.8403 (m-80) cc_final: 0.8132 (m-80) REVERT: I 264 ARG cc_start: 0.7988 (tpt90) cc_final: 0.7657 (tpt-90) REVERT: I 312 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7394 (mm-40) REVERT: I 321 GLU cc_start: 0.7420 (tp30) cc_final: 0.7104 (tm-30) REVERT: I 340 GLN cc_start: 0.7603 (mm110) cc_final: 0.7330 (mm110) REVERT: I 362 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6429 (tt0) REVERT: H 220 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8475 (mt) REVERT: H 264 ARG cc_start: 0.8100 (tpt90) cc_final: 0.7770 (tpt-90) REVERT: H 312 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7399 (mm-40) REVERT: H 362 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6813 (tt0) REVERT: N 212 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6733 (mm-30) REVERT: N 338 LYS cc_start: 0.7493 (mptm) cc_final: 0.7145 (mptt) REVERT: Y 212 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6658 (mm-30) REVERT: Y 312 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7332 (mm-40) REVERT: Y 321 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7228 (tp30) REVERT: Y 362 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6236 (tt0) REVERT: Y 469 MET cc_start: 0.8634 (mtm) cc_final: 0.8404 (mtp) REVERT: L 212 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6814 (mt-10) REVERT: L 275 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7726 (mtmt) REVERT: L 312 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7190 (mm-40) REVERT: L 321 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7263 (tp30) REVERT: L 362 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6283 (tt0) REVERT: K 131 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7913 (mtmt) REVERT: K 212 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6657 (mm-30) REVERT: K 312 GLN cc_start: 0.8103 (mm110) cc_final: 0.7678 (mm-40) REVERT: K 338 LYS cc_start: 0.7592 (mmtt) cc_final: 0.7334 (mmtp) REVERT: K 342 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7214 (mm-30) REVERT: K 362 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6289 (tt0) REVERT: U 70 LYS cc_start: 0.8278 (mtpt) cc_final: 0.8070 (mmmt) REVERT: Q 92 ARG cc_start: 0.8343 (mtt-85) cc_final: 0.8107 (mmt180) REVERT: W 70 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7995 (mmmt) REVERT: V 80 LYS cc_start: 0.8735 (tptm) cc_final: 0.8348 (tptm) REVERT: 2 80 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8314 (tttm) REVERT: Z 92 ARG cc_start: 0.8343 (mtt-85) cc_final: 0.8109 (mmt180) REVERT: M 80 LYS cc_start: 0.8612 (tppt) cc_final: 0.7960 (tmtm) outliers start: 138 outliers final: 40 residues processed: 1007 average time/residue: 1.4557 time to fit residues: 1898.4611 Evaluate side-chains 948 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 884 time to evaluate : 5.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 266 LYS Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 362 GLU Chi-restraints excluded: chain F residue 191 MET Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 350 GLU Chi-restraints excluded: chain F residue 362 GLU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 350 GLU Chi-restraints excluded: chain J residue 362 GLU Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain I residue 362 GLU Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 362 GLU Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain N residue 274 VAL Chi-restraints excluded: chain N residue 350 GLU Chi-restraints excluded: chain Y residue 220 LEU Chi-restraints excluded: chain Y residue 321 GLU Chi-restraints excluded: chain Y residue 345 ILE Chi-restraints excluded: chain Y residue 362 GLU Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 275 LYS Chi-restraints excluded: chain L residue 321 GLU Chi-restraints excluded: chain L residue 350 GLU Chi-restraints excluded: chain L residue 362 GLU Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain K residue 350 GLU Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 522 GLU Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain W residue 70 LYS Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 2 residue 80 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 780 optimal weight: 9.9990 chunk 593 optimal weight: 6.9990 chunk 409 optimal weight: 0.0980 chunk 87 optimal weight: 0.0470 chunk 376 optimal weight: 0.9980 chunk 530 optimal weight: 0.1980 chunk 792 optimal weight: 1.9990 chunk 839 optimal weight: 0.3980 chunk 414 optimal weight: 0.7980 chunk 751 optimal weight: 30.0000 chunk 226 optimal weight: 9.9990 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN G 239 ASN G 282 ASN G 286 GLN F 214 GLN F 239 ASN E 239 ASN E 346 GLN D 239 ASN C 239 ASN B 239 ASN J 239 ASN I 239 ASN I 282 ASN I 286 GLN H 239 ASN N 239 ASN N 346 GLN Y 239 ASN L 239 ASN K 239 ASN T 43 GLN V 43 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 66710 Z= 0.111 Angle : 0.440 7.646 90034 Z= 0.238 Chirality : 0.041 0.144 10850 Planarity : 0.003 0.039 11522 Dihedral : 6.479 56.104 9664 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.76 % Allowed : 10.69 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.71 (0.09), residues: 8722 helix: 2.49 (0.08), residues: 3976 sheet: 1.24 (0.15), residues: 1190 loop : -0.51 (0.09), residues: 3556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 42 HIS 0.001 0.000 HIS I 314 PHE 0.008 0.001 PHE X 91 TYR 0.011 0.001 TYR C 201 ARG 0.003 0.000 ARG K 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 941 time to evaluate : 5.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7366 (mtp) REVERT: A 212 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6793 (mm-30) REVERT: A 312 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7240 (mm-40) REVERT: A 362 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6359 (tt0) REVERT: G 212 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6596 (mm-30) REVERT: G 217 TYR cc_start: 0.8349 (m-80) cc_final: 0.8081 (m-80) REVERT: G 264 ARG cc_start: 0.8005 (tpt90) cc_final: 0.7596 (tpt-90) REVERT: G 286 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7455 (mt0) REVERT: G 312 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7338 (mm-40) REVERT: F 212 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6696 (mm-30) REVERT: F 223 LYS cc_start: 0.8096 (mtpp) cc_final: 0.7761 (ttmm) REVERT: F 264 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7677 (tpt-90) REVERT: F 312 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7434 (mm-40) REVERT: E 212 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6739 (mm-30) REVERT: D 223 LYS cc_start: 0.8006 (mtpp) cc_final: 0.7693 (ttmm) REVERT: D 264 ARG cc_start: 0.7845 (tpt170) cc_final: 0.7611 (tpt-90) REVERT: D 312 GLN cc_start: 0.7726 (mm-40) cc_final: 0.7330 (mm-40) REVERT: D 321 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7216 (tp30) REVERT: D 340 GLN cc_start: 0.7542 (mm110) cc_final: 0.7194 (mm110) REVERT: D 469 MET cc_start: 0.8553 (mtm) cc_final: 0.8338 (mtp) REVERT: C 212 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6787 (mt-10) REVERT: C 264 ARG cc_start: 0.8047 (tpt90) cc_final: 0.7561 (ttt90) REVERT: C 312 GLN cc_start: 0.7528 (mm-40) cc_final: 0.7175 (mm-40) REVERT: C 321 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7226 (tp30) REVERT: B 312 GLN cc_start: 0.8079 (mm110) cc_final: 0.7698 (mm-40) REVERT: B 342 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7201 (mm-30) REVERT: J 212 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6805 (mm-30) REVERT: J 312 GLN cc_start: 0.7618 (mm-40) cc_final: 0.7243 (mm-40) REVERT: J 362 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6356 (tt0) REVERT: I 212 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6607 (mm-30) REVERT: I 217 TYR cc_start: 0.8312 (m-80) cc_final: 0.8046 (m-80) REVERT: I 262 LEU cc_start: 0.8381 (tt) cc_final: 0.8054 (tm) REVERT: I 264 ARG cc_start: 0.7999 (tpt90) cc_final: 0.7554 (tpt-90) REVERT: I 286 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7540 (mt0) REVERT: I 312 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7351 (mm-40) REVERT: I 340 GLN cc_start: 0.7576 (mm110) cc_final: 0.7363 (mm110) REVERT: H 212 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6661 (mm-30) REVERT: H 264 ARG cc_start: 0.8032 (tpt90) cc_final: 0.7598 (tpt-90) REVERT: H 312 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7459 (mm-40) REVERT: N 212 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6722 (mm-30) REVERT: N 338 LYS cc_start: 0.7408 (mptm) cc_final: 0.7074 (mptt) REVERT: Y 223 LYS cc_start: 0.8003 (mtpp) cc_final: 0.7677 (ttmm) REVERT: Y 264 ARG cc_start: 0.7807 (tpt170) cc_final: 0.7579 (tpt-90) REVERT: Y 312 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7340 (mm-40) REVERT: Y 321 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7209 (tp30) REVERT: Y 340 GLN cc_start: 0.7546 (mm110) cc_final: 0.7200 (mm110) REVERT: Y 469 MET cc_start: 0.8551 (mtm) cc_final: 0.8332 (mtp) REVERT: L 212 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6781 (mt-10) REVERT: L 264 ARG cc_start: 0.8044 (tpt90) cc_final: 0.7559 (ttt90) REVERT: L 312 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7184 (mm-40) REVERT: K 131 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7643 (mtmt) REVERT: K 312 GLN cc_start: 0.8092 (mm110) cc_final: 0.7694 (mm-40) REVERT: T 8 LYS cc_start: 0.8026 (mtmm) cc_final: 0.7822 (mtpt) REVERT: Q 80 LYS cc_start: 0.8587 (tptt) cc_final: 0.8004 (tptt) REVERT: Q 92 ARG cc_start: 0.8302 (mtt-85) cc_final: 0.7950 (mmt180) REVERT: V 8 LYS cc_start: 0.8032 (mtmm) cc_final: 0.7825 (mtpt) REVERT: 2 80 LYS cc_start: 0.8460 (tttm) cc_final: 0.8102 (tptt) REVERT: Z 92 ARG cc_start: 0.8284 (mtt-85) cc_final: 0.7938 (mmt180) outliers start: 125 outliers final: 32 residues processed: 1015 average time/residue: 1.3897 time to fit residues: 1844.8361 Evaluate side-chains 928 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 886 time to evaluate : 5.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 350 GLU Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 350 GLU Chi-restraints excluded: chain J residue 362 GLU Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain H residue 266 LYS Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain N residue 350 GLU Chi-restraints excluded: chain Y residue 321 GLU Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 350 GLU Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 451 MET Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain K residue 350 GLU Chi-restraints excluded: chain U residue 19 GLU Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain 2 residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 698 optimal weight: 9.9990 chunk 476 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 624 optimal weight: 2.9990 chunk 346 optimal weight: 2.9990 chunk 715 optimal weight: 2.9990 chunk 579 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 428 optimal weight: 1.9990 chunk 753 optimal weight: 0.9990 chunk 211 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 282 ASN G 239 ASN G 286 GLN F 214 GLN F 239 ASN E 239 ASN E 282 ASN D 239 ASN C 239 ASN B 239 ASN B 346 GLN J 239 ASN J 282 ASN I 214 GLN I 239 ASN I 286 GLN H 214 GLN H 239 ASN N 239 ASN N 282 ASN Y 239 ASN L 239 ASN K 239 ASN K 346 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 66710 Z= 0.269 Angle : 0.550 9.063 90034 Z= 0.298 Chirality : 0.045 0.154 10850 Planarity : 0.004 0.043 11522 Dihedral : 8.362 71.459 9660 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.56 % Allowed : 12.03 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.08), residues: 8722 helix: 2.12 (0.08), residues: 3976 sheet: 1.22 (0.16), residues: 1106 loop : -0.56 (0.09), residues: 3640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 42 HIS 0.002 0.001 HIS H 241 PHE 0.012 0.001 PHE M 89 TYR 0.011 0.001 TYR C 201 ARG 0.006 0.001 ARG K 420 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 911 time to evaluate : 5.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7332 (mtp) REVERT: A 212 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6908 (mm-30) REVERT: A 312 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7287 (mm-40) REVERT: A 362 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6320 (tt0) REVERT: G 212 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6593 (mm-30) REVERT: G 217 TYR cc_start: 0.8395 (m-80) cc_final: 0.8106 (m-80) REVERT: G 264 ARG cc_start: 0.8023 (tpt90) cc_final: 0.7665 (tpt-90) REVERT: G 312 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7428 (mm-40) REVERT: G 362 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6359 (tt0) REVERT: F 212 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6897 (mm-30) REVERT: F 223 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7859 (ttmm) REVERT: F 264 ARG cc_start: 0.7997 (tpt90) cc_final: 0.7709 (tpt-90) REVERT: F 312 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7430 (mm-40) REVERT: F 362 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6722 (tt0) REVERT: E 212 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6817 (mm-30) REVERT: E 338 LYS cc_start: 0.7439 (mptm) cc_final: 0.7173 (mptt) REVERT: E 340 GLN cc_start: 0.7957 (mm110) cc_final: 0.7724 (mm110) REVERT: D 223 LYS cc_start: 0.7984 (mtpp) cc_final: 0.7718 (ttmm) REVERT: D 312 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7394 (mm-40) REVERT: D 469 MET cc_start: 0.8650 (mtm) cc_final: 0.8425 (mtp) REVERT: C 212 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6826 (mt-10) REVERT: C 275 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7746 (mtmt) REVERT: C 312 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7198 (mm-40) REVERT: C 321 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7249 (tp30) REVERT: C 362 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6246 (tt0) REVERT: B 312 GLN cc_start: 0.8088 (mm110) cc_final: 0.7713 (mm110) REVERT: J 191 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7312 (mtp) REVERT: J 212 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6885 (mm-30) REVERT: J 312 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7291 (mm-40) REVERT: J 362 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6321 (tt0) REVERT: I 212 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6594 (mm-30) REVERT: I 217 TYR cc_start: 0.8379 (m-80) cc_final: 0.8118 (m-80) REVERT: I 264 ARG cc_start: 0.8034 (tpt90) cc_final: 0.7653 (tpt-90) REVERT: I 312 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7462 (mm-40) REVERT: I 340 GLN cc_start: 0.7616 (mm110) cc_final: 0.7380 (mm110) REVERT: I 362 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6348 (tt0) REVERT: H 212 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6808 (mm-30) REVERT: H 220 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8474 (mt) REVERT: H 264 ARG cc_start: 0.8033 (tpt90) cc_final: 0.7646 (tpt-90) REVERT: H 312 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7418 (mm-40) REVERT: H 343 LYS cc_start: 0.8382 (mptt) cc_final: 0.8129 (mttm) REVERT: N 212 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6816 (mm-30) REVERT: N 338 LYS cc_start: 0.7419 (mptm) cc_final: 0.7153 (mptt) REVERT: Y 312 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7399 (mm-40) REVERT: Y 469 MET cc_start: 0.8649 (mtm) cc_final: 0.8425 (mtp) REVERT: L 212 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6901 (mm-30) REVERT: L 275 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7763 (mtmt) REVERT: L 312 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7208 (mm-40) REVERT: L 362 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6370 (tt0) REVERT: K 312 GLN cc_start: 0.8132 (mm110) cc_final: 0.7709 (mm-40) REVERT: U 43 GLN cc_start: 0.8602 (mp-120) cc_final: 0.8385 (mp-120) REVERT: T 8 LYS cc_start: 0.8107 (mtmm) cc_final: 0.7861 (mtpt) REVERT: T 80 LYS cc_start: 0.8615 (tptm) cc_final: 0.8316 (tptt) REVERT: P 80 LYS cc_start: 0.8607 (tptt) cc_final: 0.7969 (tmtm) REVERT: W 43 GLN cc_start: 0.8594 (mp-120) cc_final: 0.8374 (mp-120) REVERT: W 70 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7385 (mmpt) REVERT: V 8 LYS cc_start: 0.8110 (mtmm) cc_final: 0.7859 (mtpt) REVERT: V 80 LYS cc_start: 0.8638 (tptm) cc_final: 0.8282 (tptt) REVERT: V 87 ASP cc_start: 0.7409 (m-30) cc_final: 0.6769 (m-30) REVERT: Z 70 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7576 (mmpt) outliers start: 111 outliers final: 38 residues processed: 988 average time/residue: 1.4448 time to fit residues: 1850.1189 Evaluate side-chains 948 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 895 time to evaluate : 5.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 362 GLU Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 350 GLU Chi-restraints excluded: chain F residue 362 GLU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain J residue 191 MET Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 350 GLU Chi-restraints excluded: chain J residue 362 GLU Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain I residue 362 GLU Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 350 GLU Chi-restraints excluded: chain Y residue 246 VAL Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 275 LYS Chi-restraints excluded: chain L residue 350 GLU Chi-restraints excluded: chain L residue 362 GLU Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain K residue 246 VAL Chi-restraints excluded: chain K residue 350 GLU Chi-restraints excluded: chain K residue 522 GLU Chi-restraints excluded: chain W residue 70 LYS Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain Z residue 70 LYS Chi-restraints excluded: chain M residue 80 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 282 optimal weight: 10.0000 chunk 755 optimal weight: 5.9990 chunk 165 optimal weight: 0.5980 chunk 492 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 839 optimal weight: 0.9990 chunk 697 optimal weight: 8.9990 chunk 388 optimal weight: 9.9990 chunk 69 optimal weight: 0.3980 chunk 277 optimal weight: 0.9990 chunk 440 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN G 239 ASN F 214 GLN F 239 ASN E 239 ASN D 239 ASN C 239 ASN B 239 ASN J 239 ASN I 214 GLN I 239 ASN H 214 GLN H 239 ASN N 239 ASN Y 239 ASN L 239 ASN K 239 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 66710 Z= 0.179 Angle : 0.499 9.006 90034 Z= 0.269 Chirality : 0.043 0.166 10850 Planarity : 0.004 0.042 11522 Dihedral : 7.555 65.680 9660 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.70 % Allowed : 12.93 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.46 (0.09), residues: 8722 helix: 2.24 (0.08), residues: 3976 sheet: 1.17 (0.16), residues: 1190 loop : -0.60 (0.09), residues: 3556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 42 HIS 0.001 0.001 HIS F 241 PHE 0.009 0.001 PHE D 213 TYR 0.012 0.001 TYR C 201 ARG 0.003 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 896 time to evaluate : 5.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7240 (mtp) REVERT: A 312 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7275 (mm-40) REVERT: A 323 ILE cc_start: 0.8597 (mt) cc_final: 0.8382 (mp) REVERT: A 362 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6537 (tt0) REVERT: A 392 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8436 (mtpt) REVERT: G 212 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6535 (mm-30) REVERT: G 217 TYR cc_start: 0.8369 (m-80) cc_final: 0.8083 (m-80) REVERT: G 264 ARG cc_start: 0.7967 (tpt90) cc_final: 0.7602 (tpt-90) REVERT: G 312 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7488 (mm-40) REVERT: G 362 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6376 (tt0) REVERT: F 195 ARG cc_start: 0.7507 (mmt-90) cc_final: 0.7262 (mmt180) REVERT: F 212 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6813 (mm-30) REVERT: F 220 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8469 (mt) REVERT: F 223 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7862 (ttmm) REVERT: F 264 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7692 (tpt-90) REVERT: F 312 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7409 (mm-40) REVERT: F 362 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6690 (tt0) REVERT: E 212 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6812 (mm-30) REVERT: E 362 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6201 (tt0) REVERT: D 223 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7719 (ttmm) REVERT: D 312 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7386 (mm-40) REVERT: D 469 MET cc_start: 0.8627 (mtm) cc_final: 0.8407 (mtp) REVERT: C 212 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6803 (mt-10) REVERT: C 275 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7690 (mtmt) REVERT: C 312 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7228 (mm-40) REVERT: C 321 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7213 (tp30) REVERT: C 362 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6306 (tt0) REVERT: C 522 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: B 312 GLN cc_start: 0.8083 (mm110) cc_final: 0.7706 (mm110) REVERT: B 321 GLU cc_start: 0.7243 (tp30) cc_final: 0.7006 (tp30) REVERT: J 191 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.7176 (mtp) REVERT: J 212 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6803 (mm-30) REVERT: J 312 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7287 (mm-40) REVERT: J 362 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6538 (tt0) REVERT: J 392 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8436 (mtpt) REVERT: I 212 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6582 (mm-30) REVERT: I 214 GLN cc_start: 0.7394 (mp-120) cc_final: 0.7100 (mp10) REVERT: I 217 TYR cc_start: 0.8341 (m-80) cc_final: 0.8086 (m-80) REVERT: I 264 ARG cc_start: 0.7989 (tpt90) cc_final: 0.7592 (tpt-90) REVERT: I 312 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7444 (mm-40) REVERT: I 321 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7123 (tp30) REVERT: I 340 GLN cc_start: 0.7623 (mm110) cc_final: 0.7379 (mm110) REVERT: I 362 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6365 (tt0) REVERT: H 195 ARG cc_start: 0.7492 (mmt-90) cc_final: 0.7240 (mmt180) REVERT: H 264 ARG cc_start: 0.8045 (tpt90) cc_final: 0.7640 (tpt-90) REVERT: H 312 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7387 (mm-40) REVERT: H 343 LYS cc_start: 0.8363 (mptt) cc_final: 0.8072 (mttm) REVERT: N 212 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6816 (mm-30) REVERT: N 338 LYS cc_start: 0.7354 (mptm) cc_final: 0.7132 (mmtp) REVERT: N 362 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6204 (tt0) REVERT: Y 312 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7390 (mm-40) REVERT: Y 469 MET cc_start: 0.8614 (mtm) cc_final: 0.8381 (mtp) REVERT: L 212 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6925 (mm-30) REVERT: L 275 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7730 (mtmt) REVERT: L 312 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7233 (mm-40) REVERT: L 362 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6363 (tt0) REVERT: K 312 GLN cc_start: 0.8122 (mm110) cc_final: 0.7722 (mm110) REVERT: U 43 GLN cc_start: 0.8571 (mp-120) cc_final: 0.8345 (mp-120) REVERT: T 80 LYS cc_start: 0.8660 (tptm) cc_final: 0.8455 (tptt) REVERT: T 93 ASP cc_start: 0.8249 (t0) cc_final: 0.7783 (t0) REVERT: V 80 LYS cc_start: 0.8656 (tptm) cc_final: 0.8291 (tptt) REVERT: V 87 ASP cc_start: 0.7440 (m-30) cc_final: 0.6800 (m-30) REVERT: V 93 ASP cc_start: 0.8256 (t0) cc_final: 0.7819 (t0) REVERT: 1 73 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8352 (mt) outliers start: 121 outliers final: 52 residues processed: 974 average time/residue: 1.3855 time to fit residues: 1767.4238 Evaluate side-chains 930 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 858 time to evaluate : 5.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 362 GLU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 350 GLU Chi-restraints excluded: chain F residue 362 GLU Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 333 LYS Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 362 GLU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 522 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain J residue 191 MET Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 350 GLU Chi-restraints excluded: chain J residue 362 GLU Chi-restraints excluded: chain J residue 392 LYS Chi-restraints excluded: chain J residue 469 MET Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain I residue 362 GLU Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 514 THR Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 274 VAL Chi-restraints excluded: chain N residue 350 GLU Chi-restraints excluded: chain N residue 362 GLU Chi-restraints excluded: chain Y residue 220 LEU Chi-restraints excluded: chain Y residue 246 VAL Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 275 LYS Chi-restraints excluded: chain L residue 350 GLU Chi-restraints excluded: chain L residue 362 GLU Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 350 GLU Chi-restraints excluded: chain K residue 522 GLU Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 1 residue 73 LEU Chi-restraints excluded: chain M residue 80 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 809 optimal weight: 0.6980 chunk 94 optimal weight: 0.0370 chunk 478 optimal weight: 2.9990 chunk 613 optimal weight: 5.9990 chunk 475 optimal weight: 0.7980 chunk 706 optimal weight: 0.0270 chunk 468 optimal weight: 0.7980 chunk 836 optimal weight: 6.9990 chunk 523 optimal weight: 2.9990 chunk 510 optimal weight: 0.0010 chunk 386 optimal weight: 9.9990 overall best weight: 0.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN G 214 GLN G 239 ASN F 40 GLN F 214 GLN F 239 ASN E 239 ASN D 40 GLN D 239 ASN C 239 ASN B 239 ASN B 282 ASN J 239 ASN I 239 ASN H 214 GLN H 239 ASN N 239 ASN Y 40 GLN Y 239 ASN Y 286 GLN L 40 GLN L 239 ASN K 40 GLN K 239 ASN K 282 ASN K 286 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 66710 Z= 0.110 Angle : 0.443 9.138 90034 Z= 0.237 Chirality : 0.041 0.155 10850 Planarity : 0.003 0.038 11522 Dihedral : 6.234 54.453 9660 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.42 % Allowed : 13.69 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.09), residues: 8722 helix: 2.46 (0.08), residues: 4004 sheet: 1.34 (0.16), residues: 1190 loop : -0.58 (0.09), residues: 3528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP J 42 HIS 0.001 0.001 HIS J 241 PHE 0.012 0.001 PHE D 213 TYR 0.011 0.001 TYR Z 88 ARG 0.002 0.000 ARG K 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1023 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 922 time to evaluate : 6.147 Fit side-chains revert: symmetry clash REVERT: A 312 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7260 (mm-40) REVERT: A 321 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7157 (tp30) REVERT: G 212 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6564 (mm-30) REVERT: G 217 TYR cc_start: 0.8283 (m-80) cc_final: 0.8029 (m-80) REVERT: G 264 ARG cc_start: 0.7960 (tpt90) cc_final: 0.7468 (ttt90) REVERT: G 312 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7443 (mm-40) REVERT: G 321 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7265 (tp30) REVERT: F 223 LYS cc_start: 0.8046 (mtpp) cc_final: 0.7845 (ttmm) REVERT: F 264 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7651 (tpt-90) REVERT: F 312 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7563 (mm110) REVERT: E 212 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6743 (mm-30) REVERT: E 330 MET cc_start: 0.7170 (mtm) cc_final: 0.6927 (mmm) REVERT: D 223 LYS cc_start: 0.7994 (mtpp) cc_final: 0.7706 (ttmm) REVERT: D 312 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7425 (mm-40) REVERT: D 323 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7888 (mm) REVERT: D 469 MET cc_start: 0.8562 (mtm) cc_final: 0.8338 (mtp) REVERT: C 212 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6766 (mt-10) REVERT: C 312 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7249 (mm-40) REVERT: B 312 GLN cc_start: 0.8075 (mm110) cc_final: 0.7705 (mm110) REVERT: B 342 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7301 (mm-30) REVERT: J 312 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7264 (mm-40) REVERT: I 212 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6690 (mm-30) REVERT: I 217 TYR cc_start: 0.8263 (m-80) cc_final: 0.7993 (m-80) REVERT: I 262 LEU cc_start: 0.8361 (tt) cc_final: 0.8086 (tm) REVERT: I 264 ARG cc_start: 0.7971 (tpt90) cc_final: 0.7481 (ttt90) REVERT: I 312 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7450 (mm-40) REVERT: I 340 GLN cc_start: 0.7617 (mm110) cc_final: 0.7360 (mm110) REVERT: H 264 ARG cc_start: 0.7927 (tpt90) cc_final: 0.7430 (tpt-90) REVERT: H 312 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7446 (mm-40) REVERT: H 343 LYS cc_start: 0.8330 (mptt) cc_final: 0.8035 (mttm) REVERT: N 212 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6767 (mm-30) REVERT: Y 312 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7423 (mm-40) REVERT: Y 469 MET cc_start: 0.8556 (mtm) cc_final: 0.8332 (mtp) REVERT: L 212 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6825 (mm-30) REVERT: L 312 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7233 (mm-40) REVERT: K 312 GLN cc_start: 0.8119 (mm110) cc_final: 0.7705 (mm-40) REVERT: T 8 LYS cc_start: 0.8100 (mtmm) cc_final: 0.7849 (mtpt) REVERT: T 80 LYS cc_start: 0.8649 (tptm) cc_final: 0.8305 (tptt) REVERT: T 87 ASP cc_start: 0.7359 (m-30) cc_final: 0.6723 (m-30) REVERT: T 93 ASP cc_start: 0.8203 (t0) cc_final: 0.7732 (t0) REVERT: R 73 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8338 (mt) REVERT: W 33 LEU cc_start: 0.7989 (mm) cc_final: 0.7732 (mm) REVERT: W 70 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7835 (mmmt) REVERT: V 8 LYS cc_start: 0.8092 (mtmm) cc_final: 0.7846 (mtpt) REVERT: V 80 LYS cc_start: 0.8674 (tptm) cc_final: 0.8319 (tptt) REVERT: V 87 ASP cc_start: 0.7411 (m-30) cc_final: 0.6785 (m-30) REVERT: V 93 ASP cc_start: 0.8255 (t0) cc_final: 0.7796 (t0) REVERT: 1 73 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8324 (mt) REVERT: 1 80 LYS cc_start: 0.8384 (tppt) cc_final: 0.8057 (tptt) REVERT: Z 80 LYS cc_start: 0.8731 (tptt) cc_final: 0.8001 (tptt) REVERT: M 32 MET cc_start: 0.7430 (mtm) cc_final: 0.7169 (ptp) outliers start: 101 outliers final: 47 residues processed: 983 average time/residue: 1.4855 time to fit residues: 1947.5501 Evaluate side-chains 921 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 869 time to evaluate : 5.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 350 GLU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 350 GLU Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 274 VAL Chi-restraints excluded: chain N residue 350 GLU Chi-restraints excluded: chain Y residue 246 VAL Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 451 MET Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain K residue 246 VAL Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 350 GLU Chi-restraints excluded: chain K residue 522 GLU Chi-restraints excluded: chain U residue 19 GLU Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain W residue 19 GLU Chi-restraints excluded: chain W residue 70 LYS Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 1 residue 45 THR Chi-restraints excluded: chain 1 residue 73 LEU Chi-restraints excluded: chain M residue 80 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 517 optimal weight: 1.9990 chunk 334 optimal weight: 10.0000 chunk 499 optimal weight: 0.2980 chunk 252 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 531 optimal weight: 0.0010 chunk 569 optimal weight: 3.9990 chunk 413 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 657 optimal weight: 7.9990 overall best weight: 1.0390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN G 239 ASN F 239 ASN F 282 ASN F 286 GLN E 239 ASN D 239 ASN C 239 ASN B 239 ASN B 286 GLN J 239 ASN I 214 GLN I 239 ASN H 239 ASN H 282 ASN H 286 GLN N 239 ASN Y 239 ASN L 239 ASN K 239 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 66710 Z= 0.153 Angle : 0.481 9.185 90034 Z= 0.256 Chirality : 0.042 0.170 10850 Planarity : 0.003 0.040 11522 Dihedral : 7.019 63.220 9660 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.14 % Allowed : 14.47 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.09), residues: 8722 helix: 2.42 (0.08), residues: 3990 sheet: 1.41 (0.16), residues: 1106 loop : -0.62 (0.09), residues: 3626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 42 HIS 0.001 0.001 HIS J 241 PHE 0.011 0.001 PHE J 213 TYR 0.012 0.001 TYR Z 88 ARG 0.008 0.000 ARG D 264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 883 time to evaluate : 5.813 Fit side-chains revert: symmetry clash REVERT: A 312 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7265 (mm-40) REVERT: A 321 GLU cc_start: 0.7249 (mt-10) cc_final: 0.7032 (tp30) REVERT: A 362 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6579 (tt0) REVERT: G 212 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6600 (mm-30) REVERT: G 217 TYR cc_start: 0.8312 (m-80) cc_final: 0.8046 (m-80) REVERT: G 264 ARG cc_start: 0.7980 (tpt90) cc_final: 0.7537 (tpt-90) REVERT: G 312 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7511 (mm-40) REVERT: G 321 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7337 (tp30) REVERT: F 223 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7853 (ttmm) REVERT: F 264 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7668 (tpt-90) REVERT: F 312 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7552 (mm110) REVERT: E 212 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6826 (mm-30) REVERT: E 469 MET cc_start: 0.8459 (mtp) cc_final: 0.8165 (mtt) REVERT: D 223 LYS cc_start: 0.7993 (mtpp) cc_final: 0.7708 (ttmm) REVERT: D 264 ARG cc_start: 0.7756 (tpt-90) cc_final: 0.7467 (ttt90) REVERT: D 312 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7419 (mm-40) REVERT: D 469 MET cc_start: 0.8602 (mtm) cc_final: 0.8376 (mtp) REVERT: C 212 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6902 (mm-30) REVERT: C 312 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7296 (mm-40) REVERT: B 312 GLN cc_start: 0.8084 (mm110) cc_final: 0.7683 (mm-40) REVERT: B 342 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7310 (mm-30) REVERT: B 362 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6768 (tt0) REVERT: J 312 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7277 (mm-40) REVERT: J 362 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6580 (tt0) REVERT: I 212 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6701 (mm-30) REVERT: I 217 TYR cc_start: 0.8290 (m-80) cc_final: 0.8051 (m-80) REVERT: I 262 LEU cc_start: 0.8439 (tt) cc_final: 0.8123 (tm) REVERT: I 264 ARG cc_start: 0.7981 (tpt90) cc_final: 0.7475 (ttt90) REVERT: I 312 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7465 (mm-40) REVERT: I 340 GLN cc_start: 0.7607 (mm110) cc_final: 0.7345 (mm110) REVERT: H 264 ARG cc_start: 0.7936 (tpt90) cc_final: 0.7450 (tpt-90) REVERT: H 312 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7556 (mm110) REVERT: H 343 LYS cc_start: 0.8299 (mptt) cc_final: 0.8014 (mttm) REVERT: N 212 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6781 (mm-30) REVERT: Y 223 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7828 (mttm) REVERT: Y 264 ARG cc_start: 0.7756 (tpt-90) cc_final: 0.7474 (ttt90) REVERT: Y 312 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7427 (mm-40) REVERT: Y 469 MET cc_start: 0.8593 (mtm) cc_final: 0.8367 (mtp) REVERT: L 212 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6844 (mm-30) REVERT: L 312 GLN cc_start: 0.7665 (mm-40) cc_final: 0.7292 (mm-40) REVERT: K 312 GLN cc_start: 0.8125 (mm110) cc_final: 0.7726 (mm110) REVERT: K 362 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6748 (tt0) REVERT: U 33 LEU cc_start: 0.8126 (mm) cc_final: 0.7856 (mm) REVERT: T 8 LYS cc_start: 0.8115 (mtmm) cc_final: 0.7889 (mtpt) REVERT: T 80 LYS cc_start: 0.8661 (tptm) cc_final: 0.8301 (tptt) REVERT: T 87 ASP cc_start: 0.7480 (m-30) cc_final: 0.6820 (m-30) REVERT: T 93 ASP cc_start: 0.8203 (t0) cc_final: 0.7730 (t0) REVERT: R 73 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8358 (mt) REVERT: R 87 ASP cc_start: 0.7403 (m-30) cc_final: 0.7112 (m-30) REVERT: W 8 LYS cc_start: 0.8196 (mtmp) cc_final: 0.7993 (mtmm) REVERT: W 33 LEU cc_start: 0.8077 (mm) cc_final: 0.7822 (mm) REVERT: W 70 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7387 (mmpt) REVERT: V 8 LYS cc_start: 0.8120 (mtmm) cc_final: 0.7881 (mtpt) REVERT: V 80 LYS cc_start: 0.8676 (tptm) cc_final: 0.8132 (tptt) REVERT: V 87 ASP cc_start: 0.7447 (m-30) cc_final: 0.6782 (m-30) REVERT: V 93 ASP cc_start: 0.8193 (t0) cc_final: 0.7726 (t0) REVERT: 1 73 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8345 (mt) REVERT: M 32 MET cc_start: 0.7453 (mtm) cc_final: 0.7146 (ptp) outliers start: 81 outliers final: 49 residues processed: 941 average time/residue: 1.3977 time to fit residues: 1731.2651 Evaluate side-chains 933 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 876 time to evaluate : 5.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 350 GLU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 333 LYS Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 350 GLU Chi-restraints excluded: chain J residue 362 GLU Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 274 VAL Chi-restraints excluded: chain N residue 350 GLU Chi-restraints excluded: chain Y residue 50 ASP Chi-restraints excluded: chain Y residue 220 LEU Chi-restraints excluded: chain Y residue 246 VAL Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 350 GLU Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain K residue 246 VAL Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 350 GLU Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain K residue 522 GLU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain W residue 70 LYS Chi-restraints excluded: chain 1 residue 73 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 80 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 761 optimal weight: 20.0000 chunk 801 optimal weight: 5.9990 chunk 731 optimal weight: 0.5980 chunk 779 optimal weight: 8.9990 chunk 469 optimal weight: 3.9990 chunk 339 optimal weight: 10.0000 chunk 612 optimal weight: 4.9990 chunk 239 optimal weight: 0.4980 chunk 704 optimal weight: 3.9990 chunk 737 optimal weight: 7.9990 chunk 776 optimal weight: 7.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN G 239 ASN F 239 ASN E 239 ASN D 239 ASN C 239 ASN B 239 ASN J 239 ASN I 214 GLN I 239 ASN H 239 ASN Y 239 ASN L 239 ASN K 239 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 66710 Z= 0.307 Angle : 0.584 9.545 90034 Z= 0.313 Chirality : 0.046 0.233 10850 Planarity : 0.004 0.042 11522 Dihedral : 8.505 72.752 9660 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.34 % Allowed : 14.62 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.09), residues: 8722 helix: 2.04 (0.08), residues: 3976 sheet: 1.26 (0.16), residues: 1106 loop : -0.66 (0.09), residues: 3640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 42 HIS 0.003 0.001 HIS L 241 PHE 0.013 0.001 PHE Q 89 TYR 0.013 0.001 TYR C 201 ARG 0.008 0.001 ARG N 420 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 908 time to evaluate : 5.960 Fit side-chains REVERT: A 312 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7276 (mm-40) REVERT: A 362 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6545 (tt0) REVERT: G 212 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6595 (mm-30) REVERT: G 217 TYR cc_start: 0.8393 (m-80) cc_final: 0.8153 (m-80) REVERT: G 264 ARG cc_start: 0.8033 (tpt90) cc_final: 0.7669 (tpt-90) REVERT: G 312 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7521 (mm-40) REVERT: F 264 ARG cc_start: 0.8008 (tpt90) cc_final: 0.7715 (tpt-90) REVERT: F 312 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7558 (mm110) REVERT: E 212 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6810 (mm-30) REVERT: E 362 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6201 (tt0) REVERT: D 223 LYS cc_start: 0.7975 (mtpp) cc_final: 0.7711 (ttmm) REVERT: D 312 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7388 (mm-40) REVERT: C 212 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6914 (mm-30) REVERT: C 312 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7281 (mm-40) REVERT: B 312 GLN cc_start: 0.8058 (mm110) cc_final: 0.7638 (mm-40) REVERT: B 362 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6764 (tt0) REVERT: J 312 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7284 (mm-40) REVERT: J 362 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6520 (tt0) REVERT: I 212 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6665 (mm-30) REVERT: I 214 GLN cc_start: 0.7371 (mp-120) cc_final: 0.7068 (mp10) REVERT: I 217 TYR cc_start: 0.8384 (m-80) cc_final: 0.8117 (m-80) REVERT: I 264 ARG cc_start: 0.8024 (tpt90) cc_final: 0.7654 (tpt-90) REVERT: I 312 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7498 (mm-40) REVERT: I 321 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7113 (tp30) REVERT: I 340 GLN cc_start: 0.7629 (mm110) cc_final: 0.7363 (mm110) REVERT: H 236 GLU cc_start: 0.7884 (tp30) cc_final: 0.7641 (tp30) REVERT: H 264 ARG cc_start: 0.8045 (tpt90) cc_final: 0.7640 (tpt-90) REVERT: H 312 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7622 (mm110) REVERT: N 212 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6817 (mm-30) REVERT: N 362 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6205 (tt0) REVERT: Y 312 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7425 (mm-40) REVERT: Y 469 MET cc_start: 0.8657 (mtm) cc_final: 0.8419 (mtp) REVERT: L 212 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6933 (mm-30) REVERT: L 275 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7780 (mtmt) REVERT: L 312 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7284 (mm-40) REVERT: K 312 GLN cc_start: 0.8138 (mm110) cc_final: 0.7688 (mm-40) REVERT: K 362 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6766 (tt0) REVERT: U 33 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7959 (mm) REVERT: U 43 GLN cc_start: 0.8563 (mp-120) cc_final: 0.8276 (mp-120) REVERT: T 80 LYS cc_start: 0.8719 (tptm) cc_final: 0.8342 (tptt) REVERT: T 87 ASP cc_start: 0.7548 (m-30) cc_final: 0.6845 (m-30) REVERT: T 93 ASP cc_start: 0.8248 (t0) cc_final: 0.7770 (t0) REVERT: S 80 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8149 (tttm) REVERT: W 8 LYS cc_start: 0.8239 (mtmp) cc_final: 0.8022 (mtmm) REVERT: W 33 LEU cc_start: 0.8151 (mm) cc_final: 0.7900 (mm) REVERT: W 43 GLN cc_start: 0.8568 (mp-120) cc_final: 0.8282 (mp-120) REVERT: W 45 THR cc_start: 0.8692 (m) cc_final: 0.7796 (m) REVERT: W 70 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7315 (mmpt) REVERT: V 80 LYS cc_start: 0.8700 (tptm) cc_final: 0.8155 (tptt) REVERT: V 87 ASP cc_start: 0.7485 (m-30) cc_final: 0.6809 (m-30) REVERT: V 93 ASP cc_start: 0.8247 (t0) cc_final: 0.7770 (t0) outliers start: 95 outliers final: 53 residues processed: 968 average time/residue: 1.4273 time to fit residues: 1808.2874 Evaluate side-chains 953 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 890 time to evaluate : 5.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 350 GLU Chi-restraints excluded: chain F residue 514 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 333 LYS Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 362 GLU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 350 GLU Chi-restraints excluded: chain J residue 362 GLU Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain I residue 514 THR Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 366 GLU Chi-restraints excluded: chain H residue 514 THR Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 274 VAL Chi-restraints excluded: chain N residue 333 LYS Chi-restraints excluded: chain N residue 350 GLU Chi-restraints excluded: chain N residue 362 GLU Chi-restraints excluded: chain Y residue 246 VAL Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain L residue 275 LYS Chi-restraints excluded: chain L residue 350 GLU Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain K residue 246 VAL Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 333 LYS Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 350 GLU Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain K residue 522 GLU Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain S residue 80 LYS Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain W residue 70 LYS Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain M residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 511 optimal weight: 0.0970 chunk 824 optimal weight: 3.9990 chunk 503 optimal weight: 4.9990 chunk 391 optimal weight: 0.6980 chunk 573 optimal weight: 1.9990 chunk 864 optimal weight: 0.6980 chunk 795 optimal weight: 8.9990 chunk 688 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 531 optimal weight: 0.9980 chunk 422 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN G 214 GLN G 239 ASN F 239 ASN E 239 ASN D 239 ASN C 239 ASN B 239 ASN J 239 ASN I 239 ASN H 239 ASN Y 239 ASN L 239 ASN K 239 ASN R 43 GLN 1 43 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 66710 Z= 0.133 Angle : 0.480 9.422 90034 Z= 0.254 Chirality : 0.042 0.204 10850 Planarity : 0.003 0.040 11522 Dihedral : 6.834 59.810 9660 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.83 % Allowed : 15.54 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.51 (0.09), residues: 8722 helix: 2.33 (0.08), residues: 3976 sheet: 1.33 (0.16), residues: 1106 loop : -0.64 (0.09), residues: 3640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP Y 42 HIS 0.001 0.000 HIS A 241 PHE 0.011 0.001 PHE H 213 TYR 0.013 0.001 TYR L 201 ARG 0.008 0.000 ARG Y 195 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17444 Ramachandran restraints generated. 8722 Oldfield, 0 Emsley, 8722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 885 time to evaluate : 6.088 Fit side-chains REVERT: A 312 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7303 (mm-40) REVERT: A 321 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7002 (tp30) REVERT: A 330 MET cc_start: 0.7161 (tpt) cc_final: 0.6934 (mmp) REVERT: A 362 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6557 (tt0) REVERT: G 212 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6654 (mm-30) REVERT: G 217 TYR cc_start: 0.8309 (m-80) cc_final: 0.8032 (m-80) REVERT: G 264 ARG cc_start: 0.7972 (tpt90) cc_final: 0.7565 (tpt-90) REVERT: G 312 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7411 (mm-40) REVERT: G 321 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7257 (tm-30) REVERT: F 236 GLU cc_start: 0.7865 (tp30) cc_final: 0.7647 (tp30) REVERT: F 264 ARG cc_start: 0.7999 (tpt90) cc_final: 0.7673 (tpt-90) REVERT: F 312 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7588 (mm110) REVERT: E 212 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6827 (mm-30) REVERT: E 321 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6896 (tp30) REVERT: D 223 LYS cc_start: 0.8012 (mtpp) cc_final: 0.7733 (ttmm) REVERT: D 264 ARG cc_start: 0.7745 (tpt-90) cc_final: 0.7475 (ttt90) REVERT: D 312 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7401 (mm-40) REVERT: D 469 MET cc_start: 0.8595 (mtm) cc_final: 0.8355 (mtp) REVERT: C 212 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6845 (mm-30) REVERT: C 312 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7288 (mm-40) REVERT: C 340 GLN cc_start: 0.7730 (mm110) cc_final: 0.7420 (mm-40) REVERT: B 312 GLN cc_start: 0.8086 (mm110) cc_final: 0.7665 (mm-40) REVERT: J 312 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7291 (mm-40) REVERT: J 330 MET cc_start: 0.7402 (tpt) cc_final: 0.7144 (mmp) REVERT: J 362 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6559 (tt0) REVERT: I 212 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6653 (mm-30) REVERT: I 217 TYR cc_start: 0.8295 (m-80) cc_final: 0.8045 (m-80) REVERT: I 262 LEU cc_start: 0.8398 (tt) cc_final: 0.8110 (tm) REVERT: I 264 ARG cc_start: 0.7966 (tpt90) cc_final: 0.7544 (tpt-90) REVERT: I 312 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7508 (mm-40) REVERT: I 340 GLN cc_start: 0.7621 (mm110) cc_final: 0.7339 (mm110) REVERT: H 236 GLU cc_start: 0.7923 (tp30) cc_final: 0.7689 (tp30) REVERT: H 264 ARG cc_start: 0.7965 (tpt90) cc_final: 0.7523 (tpt-90) REVERT: H 312 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7616 (mm110) REVERT: H 321 GLU cc_start: 0.6862 (tm-30) cc_final: 0.6588 (pp20) REVERT: N 212 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6782 (mm-30) REVERT: Y 264 ARG cc_start: 0.7751 (tpt-90) cc_final: 0.7469 (ttt90) REVERT: Y 312 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7425 (mm-40) REVERT: Y 469 MET cc_start: 0.8595 (mtm) cc_final: 0.8358 (mtp) REVERT: L 212 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6908 (mm-30) REVERT: L 275 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7802 (mtmt) REVERT: L 312 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7290 (mm-40) REVERT: K 312 GLN cc_start: 0.8127 (mm110) cc_final: 0.7691 (mm-40) REVERT: U 33 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7844 (mm) REVERT: T 8 LYS cc_start: 0.8236 (mtmm) cc_final: 0.7947 (mtpt) REVERT: T 80 LYS cc_start: 0.8646 (tptm) cc_final: 0.8290 (tptt) REVERT: T 87 ASP cc_start: 0.7496 (m-30) cc_final: 0.6817 (m-30) REVERT: T 93 ASP cc_start: 0.8210 (t0) cc_final: 0.7735 (t0) REVERT: S 32 MET cc_start: 0.7444 (mtm) cc_final: 0.7076 (ptp) REVERT: W 33 LEU cc_start: 0.8084 (mm) cc_final: 0.7847 (mm) REVERT: V 8 LYS cc_start: 0.8265 (mtmm) cc_final: 0.7962 (mtpt) REVERT: V 80 LYS cc_start: 0.8688 (tptm) cc_final: 0.8169 (tptt) REVERT: V 87 ASP cc_start: 0.7458 (m-30) cc_final: 0.6835 (m-30) REVERT: V 93 ASP cc_start: 0.8221 (t0) cc_final: 0.7758 (t0) REVERT: M 32 MET cc_start: 0.7557 (mtm) cc_final: 0.7202 (ptp) outliers start: 59 outliers final: 46 residues processed: 926 average time/residue: 1.3704 time to fit residues: 1665.3743 Evaluate side-chains 926 residues out of total 7098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 876 time to evaluate : 5.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 350 GLU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 333 LYS Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 350 GLU Chi-restraints excluded: chain J residue 362 GLU Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 274 VAL Chi-restraints excluded: chain N residue 333 LYS Chi-restraints excluded: chain N residue 350 GLU Chi-restraints excluded: chain Y residue 50 ASP Chi-restraints excluded: chain Y residue 246 VAL Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 275 LYS Chi-restraints excluded: chain L residue 350 GLU Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain K residue 246 VAL Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 350 GLU Chi-restraints excluded: chain K residue 522 GLU Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain M residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 546 optimal weight: 2.9990 chunk 733 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 634 optimal weight: 0.0370 chunk 101 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 689 optimal weight: 0.0070 chunk 288 optimal weight: 3.9990 chunk 708 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 127 optimal weight: 0.3980 overall best weight: 0.8278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN G 239 ASN F 239 ASN E 239 ASN D 239 ASN C 239 ASN C 282 ASN C 286 GLN B 239 ASN J 239 ASN J 241 HIS I 214 GLN I 239 ASN H 40 GLN H 239 ASN Y 239 ASN L 239 ASN L 282 ASN L 286 GLN K 239 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.180080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.141814 restraints weight = 68574.487| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.49 r_work: 0.3119 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 66710 Z= 0.142 Angle : 0.484 9.573 90034 Z= 0.256 Chirality : 0.042 0.199 10850 Planarity : 0.003 0.040 11522 Dihedral : 6.893 60.320 9660 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.93 % Allowed : 15.46 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.55 (0.09), residues: 8722 helix: 2.38 (0.08), residues: 3990 sheet: 1.36 (0.16), residues: 1106 loop : -0.66 (0.09), residues: 3626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP G 42 HIS 0.001 0.001 HIS A 241 PHE 0.009 0.001 PHE K 213 TYR 0.012 0.001 TYR C 201 ARG 0.007 0.000 ARG Y 195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24750.58 seconds wall clock time: 427 minutes 42.65 seconds (25662.65 seconds total)