Starting phenix.real_space_refine on Sun Dec 29 06:18:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7l_29815/12_2024/8g7l_29815.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7l_29815/12_2024/8g7l_29815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g7l_29815/12_2024/8g7l_29815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7l_29815/12_2024/8g7l_29815.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7l_29815/12_2024/8g7l_29815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7l_29815/12_2024/8g7l_29815.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.188 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 196 5.16 5 C 34664 2.51 5 N 9464 2.21 5 O 11116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 238 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 55510 Number of models: 1 Model: "" Number of chains: 28 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: "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: "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: "M" 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: "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: "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} 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: "M" 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} Time building chain proxies: 22.75, per 1000 atoms: 0.41 Number of scatterers: 55510 At special positions: 0 Unit cell: (160.371, 156.663, 173.349, 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 196 16.00 P 42 15.00 Mg 14 11.99 O 11116 8.00 N 9464 7.00 C 34664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.05 Conformation dependent library (CDL) restraints added in 5.8 seconds 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13468 Finding SS restraints... Secondary structure from input PDB file: 305 helices and 84 sheets defined 59.4% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.13 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 removed outlier: 3.931A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 57 removed outlier: 3.612A pdb=" N SER A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 83 removed outlier: 3.703A pdb=" N ILE A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 103 Processing helix chain 'A' and resid 110 through 133 Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 153 through 168 removed outlier: 3.535A pdb=" N GLY A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.643A pdb=" N PHE A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 241 Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 279 through 295 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 337 through 355 removed outlier: 3.872A pdb=" N ASP A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR A 355 " --> pdb=" O GLN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 373 Processing helix chain 'A' and resid 384 through 408 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.705A pdb=" N SER A 427 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 428 " --> pdb=" O LEU A 425 " (cutoff:3.500A) 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: 3.837A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 27 removed outlier: 3.931A pdb=" N VAL G 27 " --> pdb=" O ASP G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 57 removed outlier: 3.612A pdb=" N SER G 57 " --> pdb=" O THR G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 83 removed outlier: 3.703A pdb=" N ILE G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY G 68 " --> pdb=" O TYR G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 103 Processing helix chain 'G' and resid 110 through 133 Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 153 through 168 removed outlier: 3.535A pdb=" N GLY G 157 " --> pdb=" O ASP G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 203 removed outlier: 3.668A pdb=" N PHE G 202 " --> pdb=" O SER G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 241 Proline residue: G 233 - end of helix Processing helix chain 'G' and resid 253 through 267 Processing helix chain 'G' and resid 280 through 295 Processing helix chain 'G' and resid 312 through 316 Processing helix chain 'G' and resid 337 through 355 removed outlier: 3.863A pdb=" N ASP G 353 " --> pdb=" O ILE G 349 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR G 355 " --> pdb=" O GLN G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 373 Processing helix chain 'G' and resid 384 through 408 Processing helix chain 'G' and resid 415 through 420 Processing helix chain 'G' and resid 421 through 428 removed outlier: 3.705A pdb=" N SER G 427 " --> pdb=" O ALA G 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU G 428 " --> pdb=" O LEU G 425 " (cutoff:3.500A) 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: 3.837A pdb=" N LEU G 512 " --> pdb=" O GLY G 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 27 removed outlier: 3.931A pdb=" N VAL F 27 " --> pdb=" O ASP F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 57 removed outlier: 3.612A pdb=" N SER F 57 " --> pdb=" O THR F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 83 removed outlier: 3.703A pdb=" N ILE F 67 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY F 68 " --> pdb=" O TYR F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 110 through 133 Processing helix chain 'F' and resid 138 through 150 Processing helix chain 'F' and resid 153 through 168 removed outlier: 3.535A pdb=" N GLY F 157 " --> pdb=" O ASP F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 203 removed outlier: 3.640A pdb=" N PHE F 202 " --> pdb=" O SER F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 241 Proline residue: F 233 - end of helix Processing helix chain 'F' and resid 253 through 267 Processing helix chain 'F' and resid 280 through 295 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 337 through 355 removed outlier: 3.872A pdb=" N ASP F 353 " --> pdb=" O ILE F 349 " (cutoff:3.500A) removed outlier: 3.909A 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 Processing helix chain 'F' and resid 415 through 420 Processing helix chain 'F' and resid 421 through 428 removed outlier: 3.705A pdb=" N SER F 427 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU F 428 " --> pdb=" O LEU F 425 " (cutoff:3.500A) 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: 3.837A pdb=" N LEU F 512 " --> pdb=" O GLY F 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 27 removed outlier: 3.931A pdb=" N VAL E 27 " --> pdb=" O ASP E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 57 removed outlier: 3.611A pdb=" N SER E 57 " --> pdb=" O THR E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 83 removed outlier: 3.702A pdb=" N ILE E 67 " --> pdb=" O LYS E 63 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY E 68 " --> pdb=" O TYR E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 103 Processing helix chain 'E' and resid 110 through 133 Processing helix chain 'E' and resid 138 through 150 Processing helix chain 'E' and resid 153 through 168 removed outlier: 3.535A pdb=" N GLY E 157 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.642A pdb=" N PHE E 202 " --> pdb=" O SER E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 241 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 Processing helix chain 'E' and resid 337 through 355 removed outlier: 3.863A pdb=" N ASP E 353 " --> pdb=" O ILE E 349 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR E 355 " --> pdb=" O GLN E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 373 Processing helix chain 'E' and resid 384 through 408 Processing helix chain 'E' and resid 415 through 420 Processing helix chain 'E' and resid 421 through 428 removed outlier: 3.705A pdb=" N SER E 427 " --> pdb=" O ALA E 424 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU E 428 " --> pdb=" O LEU E 425 " (cutoff:3.500A) 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: 3.837A pdb=" N LEU E 512 " --> pdb=" O GLY E 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 27 removed outlier: 3.930A pdb=" N VAL D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 57 removed outlier: 3.611A pdb=" N SER D 57 " --> pdb=" O THR D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 83 removed outlier: 3.703A pdb=" N ILE D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY D 68 " --> pdb=" O TYR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 103 Processing helix chain 'D' and resid 110 through 133 Processing helix chain 'D' and resid 138 through 150 Processing helix chain 'D' and resid 153 through 168 removed outlier: 3.535A pdb=" N GLY D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 203 removed outlier: 3.650A pdb=" N PHE D 202 " --> pdb=" O SER D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 253 through 267 Processing helix chain 'D' and resid 280 through 295 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 337 through 355 removed outlier: 3.853A pdb=" N ASP D 353 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR D 355 " --> pdb=" O GLN D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 373 Processing helix chain 'D' and resid 384 through 408 Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 421 through 428 removed outlier: 3.706A pdb=" N SER D 427 " --> pdb=" O ALA D 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 428 " --> pdb=" O LEU D 425 " (cutoff:3.500A) 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: 3.837A pdb=" N LEU D 512 " --> pdb=" O GLY D 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 27 removed outlier: 3.931A pdb=" N VAL C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 57 removed outlier: 3.612A pdb=" N SER C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 83 removed outlier: 3.703A pdb=" N ILE C 67 " --> pdb=" O LYS C 63 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY C 68 " --> pdb=" O TYR C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 103 Processing helix chain 'C' and resid 110 through 133 Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 153 through 168 removed outlier: 3.535A pdb=" N GLY C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.664A pdb=" N PHE C 202 " --> pdb=" O SER C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 241 Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 253 through 267 Processing helix chain 'C' and resid 280 through 295 Processing helix chain 'C' and resid 337 through 355 removed outlier: 3.880A pdb=" N ASP C 353 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR C 355 " --> pdb=" O GLN C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 373 Processing helix chain 'C' and resid 384 through 408 Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 421 through 428 removed outlier: 3.705A pdb=" N SER C 427 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 428 " --> pdb=" O LEU C 425 " (cutoff:3.500A) 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: 3.837A pdb=" N LEU C 512 " --> pdb=" O GLY C 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 27 removed outlier: 3.931A pdb=" N VAL B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 57 removed outlier: 3.612A pdb=" N SER B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 83 removed outlier: 3.703A pdb=" N ILE B 67 " --> pdb=" O LYS B 63 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY B 68 " --> pdb=" O TYR B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 103 Processing helix chain 'B' and resid 110 through 133 Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 153 through 168 removed outlier: 3.535A pdb=" N GLY B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.664A pdb=" N PHE B 202 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 241 Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 253 through 267 Processing helix chain 'B' and resid 280 through 295 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 337 through 355 removed outlier: 3.858A pdb=" N ASP B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 3.921A 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 Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 421 through 428 removed outlier: 3.705A pdb=" N SER B 427 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 428 " --> pdb=" O LEU B 425 " (cutoff:3.500A) 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: 3.837A pdb=" N LEU B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 27 removed outlier: 3.931A pdb=" N VAL K 27 " --> pdb=" O ASP K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 57 removed outlier: 3.612A pdb=" N SER K 57 " --> pdb=" O THR K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 83 removed outlier: 3.703A pdb=" N ILE K 67 " --> pdb=" O LYS K 63 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 103 Processing helix chain 'K' and resid 110 through 133 Processing helix chain 'K' and resid 138 through 150 Processing helix chain 'K' and resid 153 through 168 removed outlier: 3.535A pdb=" N GLY K 157 " --> pdb=" O ASP K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 203 removed outlier: 3.614A pdb=" N PHE K 202 " --> pdb=" O SER K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 241 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 Processing helix chain 'K' and resid 312 through 316 Processing helix chain 'K' and resid 337 through 355 removed outlier: 3.881A pdb=" N ASP K 353 " --> pdb=" O ILE K 349 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR K 355 " --> pdb=" O GLN K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 357 through 373 Processing helix chain 'K' and resid 384 through 408 Processing helix chain 'K' and resid 415 through 420 Processing helix chain 'K' and resid 421 through 428 removed outlier: 3.705A pdb=" N SER K 427 " --> pdb=" O ALA K 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU K 428 " --> pdb=" O LEU K 425 " (cutoff:3.500A) 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: 3.837A pdb=" N LEU K 512 " --> pdb=" O GLY K 508 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 27 removed outlier: 3.931A pdb=" N VAL J 27 " --> pdb=" O ASP J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 57 removed outlier: 3.612A pdb=" N SER J 57 " --> pdb=" O THR J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 83 removed outlier: 3.704A pdb=" N ILE J 67 " --> pdb=" O LYS J 63 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY J 68 " --> pdb=" O TYR J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 103 Processing helix chain 'J' and resid 110 through 133 Processing helix chain 'J' and resid 138 through 150 Processing helix chain 'J' and resid 153 through 168 removed outlier: 3.535A pdb=" N GLY J 157 " --> pdb=" O ASP J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 203 removed outlier: 3.629A pdb=" N PHE J 202 " --> pdb=" O SER J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 241 Proline residue: J 233 - end of helix Processing helix chain 'J' and resid 253 through 267 Processing helix chain 'J' and resid 280 through 295 Processing helix chain 'J' and resid 312 through 316 Processing helix chain 'J' and resid 337 through 355 removed outlier: 3.856A pdb=" N ASP J 353 " --> pdb=" O ILE J 349 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR J 355 " --> pdb=" O GLN J 351 " (cutoff:3.500A) Processing helix chain 'J' and resid 357 through 373 Processing helix chain 'J' and resid 384 through 408 Processing helix chain 'J' and resid 415 through 420 Processing helix chain 'J' and resid 421 through 428 removed outlier: 3.705A pdb=" N SER J 427 " --> pdb=" O ALA J 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU J 428 " --> pdb=" O LEU J 425 " (cutoff:3.500A) 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: 3.837A pdb=" N LEU J 512 " --> pdb=" O GLY J 508 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 27 removed outlier: 3.931A pdb=" N VAL I 27 " --> pdb=" O ASP I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 57 removed outlier: 3.612A pdb=" N SER I 57 " --> pdb=" O THR I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 83 removed outlier: 3.704A pdb=" N ILE I 67 " --> pdb=" O LYS I 63 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY I 68 " --> pdb=" O TYR I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 103 Processing helix chain 'I' and resid 110 through 133 Processing helix chain 'I' and resid 138 through 150 Processing helix chain 'I' and resid 153 through 168 removed outlier: 3.535A pdb=" N GLY I 157 " --> pdb=" O ASP I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 203 removed outlier: 3.658A pdb=" N PHE I 202 " --> pdb=" O SER I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 241 Proline residue: I 233 - end of helix Processing helix chain 'I' and resid 253 through 267 Processing helix chain 'I' and resid 280 through 295 Processing helix chain 'I' and resid 312 through 316 Processing helix chain 'I' and resid 337 through 355 removed outlier: 3.863A pdb=" N ASP I 353 " --> pdb=" O ILE I 349 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR I 355 " --> pdb=" O GLN I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 357 through 373 Processing helix chain 'I' and resid 384 through 408 Processing helix chain 'I' and resid 415 through 420 Processing helix chain 'I' and resid 421 through 428 removed outlier: 3.705A pdb=" N SER I 427 " --> pdb=" O ALA I 424 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU I 428 " --> pdb=" O LEU I 425 " (cutoff:3.500A) 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: 3.837A pdb=" N LEU I 512 " --> pdb=" O GLY I 508 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 27 removed outlier: 3.930A pdb=" N VAL H 27 " --> pdb=" O ASP H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 57 removed outlier: 3.612A pdb=" N SER H 57 " --> pdb=" O THR H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 83 removed outlier: 3.704A pdb=" N ILE H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY H 68 " --> pdb=" O TYR H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 103 Processing helix chain 'H' and resid 110 through 133 Processing helix chain 'H' and resid 138 through 150 Processing helix chain 'H' and resid 153 through 168 removed outlier: 3.535A pdb=" N GLY H 157 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 203 removed outlier: 3.625A pdb=" N PHE H 202 " --> pdb=" O SER H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 241 Proline residue: H 233 - end of helix Processing helix chain 'H' and resid 253 through 267 Processing helix chain 'H' and resid 280 through 295 Processing helix chain 'H' and resid 312 through 316 Processing helix chain 'H' and resid 337 through 355 removed outlier: 3.874A pdb=" N ASP H 353 " --> pdb=" O ILE H 349 " (cutoff:3.500A) removed outlier: 3.960A 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 Processing helix chain 'H' and resid 415 through 420 Processing helix chain 'H' and resid 421 through 428 removed outlier: 3.705A pdb=" N SER H 427 " --> pdb=" O ALA H 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU H 428 " --> pdb=" O LEU H 425 " (cutoff:3.500A) 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: 3.837A pdb=" N LEU H 512 " --> pdb=" O GLY H 508 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 27 removed outlier: 3.931A pdb=" N VAL N 27 " --> pdb=" O ASP N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 57 removed outlier: 3.612A pdb=" N SER N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 83 removed outlier: 3.703A pdb=" N ILE N 67 " --> pdb=" O LYS N 63 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY N 68 " --> pdb=" O TYR N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 103 Processing helix chain 'N' and resid 110 through 133 Processing helix chain 'N' and resid 138 through 150 Processing helix chain 'N' and resid 153 through 168 removed outlier: 3.534A pdb=" N GLY N 157 " --> pdb=" O ASP N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 203 removed outlier: 3.662A pdb=" N PHE N 202 " --> pdb=" O SER N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 241 Proline residue: N 233 - end of helix Processing helix chain 'N' and resid 253 through 267 Processing helix chain 'N' and resid 280 through 295 Processing helix chain 'N' and resid 337 through 355 removed outlier: 3.852A pdb=" N ASP N 353 " --> pdb=" O ILE N 349 " (cutoff:3.500A) removed outlier: 3.886A 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 Processing helix chain 'N' and resid 415 through 420 Processing helix chain 'N' and resid 421 through 428 removed outlier: 3.705A pdb=" N SER N 427 " --> pdb=" O ALA N 424 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU N 428 " --> pdb=" O LEU N 425 " (cutoff:3.500A) 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: 3.837A pdb=" N LEU N 512 " --> pdb=" O GLY N 508 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 27 removed outlier: 3.930A pdb=" N VAL M 27 " --> pdb=" O ASP M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 57 removed outlier: 3.612A pdb=" N SER M 57 " --> pdb=" O THR M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 83 removed outlier: 3.704A pdb=" N ILE M 67 " --> pdb=" O LYS M 63 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY M 68 " --> pdb=" O TYR M 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 103 Processing helix chain 'M' and resid 110 through 133 Processing helix chain 'M' and resid 138 through 150 Processing helix chain 'M' and resid 153 through 168 removed outlier: 3.534A pdb=" N GLY M 157 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 203 removed outlier: 3.663A pdb=" N PHE M 202 " --> pdb=" O SER M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 241 Proline residue: M 233 - end of helix Processing helix chain 'M' and resid 253 through 268 Processing helix chain 'M' and resid 280 through 295 Processing helix chain 'M' and resid 312 through 316 Processing helix chain 'M' and resid 337 through 355 removed outlier: 3.885A pdb=" N ASP M 353 " --> pdb=" O ILE M 349 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR M 355 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 357 through 373 Processing helix chain 'M' and resid 384 through 408 Processing helix chain 'M' and resid 415 through 420 Processing helix chain 'M' and resid 421 through 428 removed outlier: 3.705A pdb=" N SER M 427 " --> pdb=" O ALA M 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU M 428 " --> pdb=" O LEU M 425 " (cutoff:3.500A) Processing helix chain 'M' and resid 432 through 446 Processing helix chain 'M' and resid 447 through 457 Processing helix chain 'M' and resid 460 through 470 Processing helix chain 'M' and resid 487 through 491 Processing helix chain 'M' and resid 496 through 514 removed outlier: 3.837A pdb=" N LEU M 512 " --> pdb=" O GLY M 508 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 27 removed outlier: 3.931A pdb=" N VAL L 27 " --> pdb=" O ASP L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 57 removed outlier: 3.612A pdb=" N SER L 57 " --> pdb=" O THR L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 83 removed outlier: 3.703A pdb=" N ILE L 67 " --> pdb=" O LYS L 63 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY L 68 " --> pdb=" O TYR L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 103 Processing helix chain 'L' and resid 110 through 133 Processing helix chain 'L' and resid 138 through 150 Processing helix chain 'L' and resid 153 through 168 removed outlier: 3.535A pdb=" N GLY L 157 " --> pdb=" O ASP L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 199 through 203 removed outlier: 3.589A pdb=" N PHE L 202 " --> pdb=" O SER L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 241 Proline residue: L 233 - end of helix Processing helix chain 'L' and resid 253 through 267 Processing helix chain 'L' and resid 280 through 295 Processing helix chain 'L' and resid 312 through 316 Processing helix chain 'L' and resid 337 through 355 removed outlier: 3.864A pdb=" N ASP L 353 " --> pdb=" O ILE L 349 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR L 355 " --> pdb=" O GLN L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 357 through 373 Processing helix chain 'L' and resid 384 through 408 Processing helix chain 'L' and resid 415 through 420 Processing helix chain 'L' and resid 421 through 428 removed outlier: 3.705A pdb=" N SER L 427 " --> pdb=" O ALA L 424 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU L 428 " --> pdb=" O LEU L 425 " (cutoff:3.500A) 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: 3.838A pdb=" N LEU L 512 " --> pdb=" O GLY L 508 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 removed outlier: 4.802A pdb=" N ALA A 516 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE B 37 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 6.538A 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: 5.881A pdb=" N THR A 35 " --> pdb=" O ALA G 516 " (cutoff:3.500A) removed outlier: 3.558A 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: 6.700A pdb=" N VAL A 172 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU A 378 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR A 174 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL A 380 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 7.250A 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: 6.190A pdb=" N LYS A 318 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TYR A 217 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLY A 320 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL A 246 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TYR A 217 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE A 248 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A 219 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A 245 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL A 274 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 6.294A 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: 6.190A pdb=" N LYS A 318 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TYR A 217 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLY A 320 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N PHE A 299 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 7.014A 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: 5.886A pdb=" N THR G 35 " --> pdb=" O ALA F 516 " (cutoff:3.500A) removed outlier: 3.559A 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: 6.696A pdb=" N VAL G 172 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU G 378 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR G 174 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL G 380 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 7.230A 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: 6.175A pdb=" N LYS G 318 " --> pdb=" O TYR G 217 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TYR G 217 " --> pdb=" O LYS G 318 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY G 320 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL G 246 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TYR G 217 " --> pdb=" O VAL G 246 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE G 248 " --> pdb=" O TYR G 217 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU G 219 " --> pdb=" O ILE G 248 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU G 245 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL G 274 " --> pdb=" O LEU G 245 " (cutoff:3.500A) removed outlier: 6.278A 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: 6.175A pdb=" N LYS G 318 " --> pdb=" O TYR G 217 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TYR G 217 " --> pdb=" O LYS G 318 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY G 320 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N PHE G 299 " --> pdb=" O VAL G 218 " (cutoff:3.500A) removed outlier: 7.010A 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: 5.896A pdb=" N THR F 35 " --> pdb=" O ALA E 516 " (cutoff:3.500A) removed outlier: 3.561A 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: 6.718A pdb=" N VAL F 172 " --> pdb=" O ALA F 376 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU F 378 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR F 174 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL F 380 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 7.245A 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: 6.224A pdb=" N LYS F 318 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR F 217 " --> pdb=" O LYS F 318 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY F 320 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL F 246 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR F 217 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE F 248 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU F 219 " --> pdb=" O ILE F 248 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU F 245 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL F 274 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 6.245A 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: 6.224A pdb=" N LYS F 318 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR F 217 " --> pdb=" O LYS F 318 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY F 320 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N PHE F 299 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.046A 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: 5.886A pdb=" N THR E 35 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 3.562A 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: 6.598A pdb=" N VAL E 172 " --> pdb=" O ALA E 376 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU E 378 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR E 174 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL E 380 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 7.233A 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: 6.207A pdb=" N LYS E 318 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR E 217 " --> pdb=" O LYS E 318 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY E 320 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N VAL E 246 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR E 217 " --> pdb=" O VAL E 246 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE E 248 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU E 219 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU E 245 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL E 274 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 6.265A 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: 6.207A pdb=" N LYS E 318 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR E 217 " --> pdb=" O LYS E 318 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY E 320 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N PHE E 299 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.035A 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: 5.893A pdb=" N THR D 35 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 3.571A 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 removed outlier: 6.659A pdb=" N VAL D 172 " --> pdb=" O ALA D 376 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU D 378 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR D 174 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL D 380 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LYS D 176 " --> pdb=" O VAL D 380 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 191 through 192 removed outlier: 6.183A pdb=" N LYS D 318 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR D 217 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLY D 320 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL D 246 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR D 217 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE D 248 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU D 219 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU D 245 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N VAL D 274 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 6.305A 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: 6.183A pdb=" N LYS D 318 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR D 217 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLY D 320 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N PHE D 299 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.038A 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: 5.885A pdb=" N THR C 35 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 3.564A 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: 6.659A pdb=" N VAL C 172 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU C 378 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR C 174 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL C 380 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 7.227A 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: 6.183A pdb=" N LYS C 318 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR C 217 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY C 320 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N VAL C 246 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR C 217 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE C 248 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU C 219 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU C 245 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL C 274 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 6.271A 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: 6.183A pdb=" N LYS C 318 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR C 217 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY C 320 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N PHE C 299 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 7.029A 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: 6.657A pdb=" N VAL B 172 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU B 378 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR B 174 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL B 380 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 7.238A 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: 6.181A pdb=" N LYS B 318 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR B 217 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY B 320 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N VAL B 246 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR B 217 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE B 248 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 219 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 245 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL B 274 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 6.274A 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: 6.181A pdb=" N LYS B 318 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR B 217 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY B 320 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N PHE B 299 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 7.008A 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 'K' and resid 2 through 6 removed outlier: 4.813A pdb=" N ALA K 516 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE L 37 " --> pdb=" O ALA K 516 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL K 518 " --> pdb=" O ILE L 37 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 46 through 48 removed outlier: 5.887A pdb=" N THR K 35 " --> pdb=" O ALA J 516 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL J 518 " --> pdb=" O THR K 35 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 172 through 177 removed outlier: 6.661A pdb=" N VAL K 172 " --> pdb=" O ALA K 376 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU K 378 " --> pdb=" O VAL K 172 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR K 174 " --> pdb=" O LEU K 378 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL K 380 " --> pdb=" O THR K 174 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LYS K 176 " --> pdb=" O VAL K 380 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 191 through 192 removed outlier: 6.204A pdb=" N LYS K 318 " --> pdb=" O TYR K 217 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR K 217 " --> pdb=" O LYS K 318 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLY K 320 " --> pdb=" O ASP K 215 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL K 246 " --> pdb=" O ASP K 215 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR K 217 " --> pdb=" O VAL K 246 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE K 248 " --> pdb=" O TYR K 217 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU K 219 " --> pdb=" O ILE K 248 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU K 245 " --> pdb=" O VAL K 272 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL K 274 " --> pdb=" O LEU K 245 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE K 247 " --> pdb=" O VAL K 274 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 191 through 192 removed outlier: 6.204A pdb=" N LYS K 318 " --> pdb=" O TYR K 217 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR K 217 " --> pdb=" O LYS K 318 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLY K 320 " --> pdb=" O ASP K 215 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N PHE K 299 " --> pdb=" O VAL K 218 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU K 220 " --> pdb=" O PHE K 299 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 410 through 412 Processing sheet with id=AF4, first strand: chain 'K' and resid 475 through 478 Processing sheet with id=AF5, first strand: chain 'J' and resid 46 through 48 removed outlier: 5.890A pdb=" N THR J 35 " --> pdb=" O ALA I 516 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL I 518 " --> pdb=" O THR J 35 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 172 through 177 removed outlier: 6.569A pdb=" N VAL J 172 " --> pdb=" O ALA J 376 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU J 378 " --> pdb=" O VAL J 172 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR J 174 " --> pdb=" O LEU J 378 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL J 380 " --> pdb=" O THR J 174 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS J 176 " --> pdb=" O VAL J 380 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 191 through 192 removed outlier: 6.177A pdb=" N LYS J 318 " --> pdb=" O TYR J 217 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR J 217 " --> pdb=" O LYS J 318 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY J 320 " --> pdb=" O ASP J 215 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N VAL J 246 " --> pdb=" O ASP J 215 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR J 217 " --> pdb=" O VAL J 246 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ILE J 248 " --> pdb=" O TYR J 217 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU J 219 " --> pdb=" O ILE J 248 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU J 245 " --> pdb=" O VAL J 272 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL J 274 " --> pdb=" O LEU J 245 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE J 247 " --> pdb=" O VAL J 274 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 191 through 192 removed outlier: 6.177A pdb=" N LYS J 318 " --> pdb=" O TYR J 217 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR J 217 " --> pdb=" O LYS J 318 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY J 320 " --> pdb=" O ASP J 215 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N PHE J 299 " --> pdb=" O VAL J 218 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU J 220 " --> pdb=" O PHE J 299 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 410 through 412 Processing sheet with id=AG1, first strand: chain 'J' and resid 475 through 478 Processing sheet with id=AG2, first strand: chain 'I' and resid 46 through 48 removed outlier: 5.896A pdb=" N THR I 35 " --> pdb=" O ALA H 516 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL H 518 " --> pdb=" O THR I 35 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 172 through 177 removed outlier: 6.594A pdb=" N VAL I 172 " --> pdb=" O ALA I 376 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU I 378 " --> pdb=" O VAL I 172 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR I 174 " --> pdb=" O LEU I 378 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL I 380 " --> pdb=" O THR I 174 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LYS I 176 " --> pdb=" O VAL I 380 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 191 through 192 removed outlier: 6.178A pdb=" N LYS I 318 " --> pdb=" O TYR I 217 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR I 217 " --> pdb=" O LYS I 318 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY I 320 " --> pdb=" O ASP I 215 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL I 246 " --> pdb=" O ASP I 215 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR I 217 " --> pdb=" O VAL I 246 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ILE I 248 " --> pdb=" O TYR I 217 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU I 219 " --> pdb=" O ILE I 248 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU I 245 " --> pdb=" O VAL I 272 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL I 274 " --> pdb=" O LEU I 245 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE I 247 " --> pdb=" O VAL I 274 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 191 through 192 removed outlier: 6.178A pdb=" N LYS I 318 " --> pdb=" O TYR I 217 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR I 217 " --> pdb=" O LYS I 318 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY I 320 " --> pdb=" O ASP I 215 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N PHE I 299 " --> pdb=" O VAL I 218 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU I 220 " --> pdb=" O PHE I 299 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 410 through 412 Processing sheet with id=AG7, first strand: chain 'I' and resid 475 through 478 Processing sheet with id=AG8, first strand: chain 'H' and resid 46 through 48 removed outlier: 5.887A pdb=" N THR H 35 " --> pdb=" O ALA N 516 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL N 518 " --> pdb=" O THR H 35 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 172 through 177 removed outlier: 6.550A pdb=" N VAL H 172 " --> pdb=" O ALA H 376 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU H 378 " --> pdb=" O VAL H 172 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N THR H 174 " --> pdb=" O LEU H 378 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL H 380 " --> pdb=" O THR H 174 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LYS H 176 " --> pdb=" O VAL H 380 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 191 through 192 removed outlier: 6.168A pdb=" N LYS H 318 " --> pdb=" O TYR H 217 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR H 217 " --> pdb=" O LYS H 318 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY H 320 " --> pdb=" O ASP H 215 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL H 246 " --> pdb=" O ASP H 215 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TYR H 217 " --> pdb=" O VAL H 246 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE H 248 " --> pdb=" O TYR H 217 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU H 219 " --> pdb=" O ILE H 248 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU H 245 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL H 274 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE H 247 " --> pdb=" O VAL H 274 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 191 through 192 removed outlier: 6.168A pdb=" N LYS H 318 " --> pdb=" O TYR H 217 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR H 217 " --> pdb=" O LYS H 318 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY H 320 " --> pdb=" O ASP H 215 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N PHE H 299 " --> pdb=" O VAL H 218 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU H 220 " --> pdb=" O PHE H 299 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 410 through 412 Processing sheet with id=AH4, first strand: chain 'H' and resid 475 through 478 Processing sheet with id=AH5, first strand: chain 'N' and resid 46 through 48 removed outlier: 5.877A pdb=" N THR N 35 " --> pdb=" O ALA M 516 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL M 518 " --> pdb=" O THR N 35 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'N' and resid 172 through 177 removed outlier: 6.597A pdb=" N VAL N 172 " --> pdb=" O ALA N 376 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU N 378 " --> pdb=" O VAL N 172 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR N 174 " --> pdb=" O LEU N 378 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL N 380 " --> pdb=" O THR N 174 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LYS N 176 " --> pdb=" O VAL N 380 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'N' and resid 191 through 192 removed outlier: 6.173A pdb=" N LYS N 318 " --> pdb=" O TYR N 217 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR N 217 " --> pdb=" O LYS N 318 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY N 320 " --> pdb=" O ASP N 215 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL N 246 " --> pdb=" O ASP N 215 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR N 217 " --> pdb=" O VAL N 246 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE N 248 " --> pdb=" O TYR N 217 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU N 219 " --> pdb=" O ILE N 248 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU N 245 " --> pdb=" O VAL N 272 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL N 274 " --> pdb=" O LEU N 245 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE N 247 " --> pdb=" O VAL N 274 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'N' and resid 191 through 192 removed outlier: 6.173A pdb=" N LYS N 318 " --> pdb=" O TYR N 217 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR N 217 " --> pdb=" O LYS N 318 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY N 320 " --> pdb=" O ASP N 215 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N PHE N 299 " --> pdb=" O VAL N 218 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU N 220 " --> pdb=" O PHE N 299 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'N' and resid 410 through 412 Processing sheet with id=AI1, first strand: chain 'N' and resid 475 through 478 Processing sheet with id=AI2, first strand: chain 'M' and resid 46 through 48 removed outlier: 5.885A pdb=" N THR M 35 " --> pdb=" O ALA L 516 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL L 518 " --> pdb=" O THR M 35 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 172 through 177 removed outlier: 6.627A pdb=" N VAL M 172 " --> pdb=" O ALA M 376 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU M 378 " --> pdb=" O VAL M 172 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR M 174 " --> pdb=" O LEU M 378 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL M 380 " --> pdb=" O THR M 174 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LYS M 176 " --> pdb=" O VAL M 380 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 191 through 192 removed outlier: 6.159A pdb=" N LYS M 318 " --> pdb=" O TYR M 217 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR M 217 " --> pdb=" O LYS M 318 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY M 320 " --> pdb=" O ASP M 215 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N VAL M 246 " --> pdb=" O ASP M 215 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR M 217 " --> pdb=" O VAL M 246 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE M 248 " --> pdb=" O TYR M 217 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU M 219 " --> pdb=" O ILE M 248 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU M 245 " --> pdb=" O VAL M 272 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL M 274 " --> pdb=" O LEU M 245 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE M 247 " --> pdb=" O VAL M 274 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 191 through 192 removed outlier: 6.159A pdb=" N LYS M 318 " --> pdb=" O TYR M 217 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR M 217 " --> pdb=" O LYS M 318 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY M 320 " --> pdb=" O ASP M 215 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N PHE M 299 " --> pdb=" O VAL M 218 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU M 220 " --> pdb=" O PHE M 299 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 410 through 412 Processing sheet with id=AI7, first strand: chain 'M' and resid 475 through 478 Processing sheet with id=AI8, first strand: chain 'L' and resid 172 through 177 removed outlier: 6.694A pdb=" N VAL L 172 " --> pdb=" O ALA L 376 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LEU L 378 " --> pdb=" O VAL L 172 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR L 174 " --> pdb=" O LEU L 378 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL L 380 " --> pdb=" O THR L 174 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LYS L 176 " --> pdb=" O VAL L 380 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 191 through 192 removed outlier: 6.188A pdb=" N LYS L 318 " --> pdb=" O TYR L 217 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR L 217 " --> pdb=" O LYS L 318 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY L 320 " --> pdb=" O ASP L 215 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL L 246 " --> pdb=" O ASP L 215 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR L 217 " --> pdb=" O VAL L 246 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE L 248 " --> pdb=" O TYR L 217 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU L 219 " --> pdb=" O ILE L 248 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU L 245 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N VAL L 274 " --> pdb=" O LEU L 245 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE L 247 " --> pdb=" O VAL L 274 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 191 through 192 removed outlier: 6.188A pdb=" N LYS L 318 " --> pdb=" O TYR L 217 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR L 217 " --> pdb=" O LYS L 318 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY L 320 " --> pdb=" O ASP L 215 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N PHE L 299 " --> pdb=" O VAL L 218 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU L 220 " --> pdb=" O PHE L 299 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 410 through 412 Processing sheet with id=AJ3, first strand: chain 'L' and resid 475 through 478 3565 hydrogen bonds defined for protein. 10125 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: 26.02 Time building geometry restraints manager: 13.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 10411 1.31 - 1.44: 10760 1.44 - 1.57: 34367 1.57 - 1.70: 70 1.70 - 1.82: 350 Bond restraints: 55958 Sorted by residual: bond pdb=" CZ ARG A 283 " pdb=" NH2 ARG A 283 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.17e+00 bond pdb=" CZ ARG E 242 " pdb=" NH2 ARG E 242 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.68e+00 bond pdb=" CZ ARG H 283 " pdb=" NH2 ARG H 283 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.65e+00 bond pdb=" CZ ARG E 283 " pdb=" NH2 ARG E 283 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.65e+00 bond pdb=" CZ ARG C 283 " pdb=" NH2 ARG C 283 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.61e+00 ... (remaining 55953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 65136 1.60 - 3.20: 8425 3.20 - 4.81: 1807 4.81 - 6.41: 193 6.41 - 8.01: 25 Bond angle restraints: 75586 Sorted by residual: angle pdb=" CA ASP K 253 " pdb=" CB ASP K 253 " pdb=" CG ASP K 253 " ideal model delta sigma weight residual 112.60 119.78 -7.18 1.00e+00 1.00e+00 5.15e+01 angle pdb=" CA ASP L 253 " pdb=" CB ASP L 253 " pdb=" CG ASP L 253 " ideal model delta sigma weight residual 112.60 119.77 -7.17 1.00e+00 1.00e+00 5.15e+01 angle pdb=" CA ASP E 253 " pdb=" CB ASP E 253 " pdb=" CG ASP E 253 " ideal model delta sigma weight residual 112.60 119.72 -7.12 1.00e+00 1.00e+00 5.06e+01 angle pdb=" CA ASP J 253 " pdb=" CB ASP J 253 " pdb=" CG ASP J 253 " ideal model delta sigma weight residual 112.60 119.71 -7.11 1.00e+00 1.00e+00 5.06e+01 angle pdb=" CA ASP I 253 " pdb=" CB ASP I 253 " pdb=" CG ASP I 253 " ideal model delta sigma weight residual 112.60 119.70 -7.10 1.00e+00 1.00e+00 5.05e+01 ... (remaining 75581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 32348 17.87 - 35.75: 1846 35.75 - 53.62: 584 53.62 - 71.49: 232 71.49 - 89.37: 88 Dihedral angle restraints: 35098 sinusoidal: 14182 harmonic: 20916 Sorted by residual: dihedral pdb=" C PHE M 193 " pdb=" N PHE M 193 " pdb=" CA PHE M 193 " pdb=" CB PHE M 193 " ideal model delta harmonic sigma weight residual -122.60 -132.51 9.91 0 2.50e+00 1.60e-01 1.57e+01 dihedral pdb=" C PHE H 193 " pdb=" N PHE H 193 " pdb=" CA PHE H 193 " pdb=" CB PHE H 193 " ideal model delta harmonic sigma weight residual -122.60 -132.04 9.44 0 2.50e+00 1.60e-01 1.43e+01 dihedral pdb=" C PHE J 193 " pdb=" N PHE J 193 " pdb=" CA PHE J 193 " pdb=" CB PHE J 193 " ideal model delta harmonic sigma weight residual -122.60 -132.04 9.44 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 35095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 7069 0.066 - 0.131: 1677 0.131 - 0.197: 363 0.197 - 0.262: 81 0.262 - 0.328: 22 Chirality restraints: 9212 Sorted by residual: chirality pdb=" CA PHE M 193 " pdb=" N PHE M 193 " pdb=" C PHE M 193 " pdb=" CB PHE M 193 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA PHE D 193 " pdb=" N PHE D 193 " pdb=" C PHE D 193 " pdb=" CB PHE D 193 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CA PHE J 193 " pdb=" N PHE J 193 " pdb=" C PHE J 193 " pdb=" CB PHE J 193 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 9209 not shown) Planarity restraints: 9660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 359 " 0.074 2.00e-02 2.50e+03 4.28e-02 3.67e+01 pdb=" CG TYR G 359 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR G 359 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR G 359 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR G 359 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR G 359 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR G 359 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR G 359 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 359 " 0.075 2.00e-02 2.50e+03 4.28e-02 3.66e+01 pdb=" CG TYR N 359 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR N 359 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR N 359 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR N 359 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR N 359 " -0.027 2.00e-02 2.50e+03 pdb=" CZ TYR N 359 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR N 359 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 217 " 0.083 2.00e-02 2.50e+03 4.23e-02 3.58e+01 pdb=" CG TYR G 217 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR G 217 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR G 217 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR G 217 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR G 217 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR G 217 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR G 217 " 0.051 2.00e-02 2.50e+03 ... (remaining 9657 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 16346 2.86 - 3.43: 61064 3.43 - 4.00: 104287 4.00 - 4.57: 143552 4.57 - 5.14: 213720 Nonbonded interactions: 538969 Sorted by model distance: nonbonded pdb=" OG SER I 44 " pdb=" OD2 ASP H 74 " model vdw 2.287 3.040 nonbonded pdb=" OG SER D 44 " pdb=" OD2 ASP C 74 " model vdw 2.289 3.040 nonbonded pdb=" OG SER N 44 " pdb=" OD2 ASP M 74 " model vdw 2.293 3.040 nonbonded pdb=" OG SER C 44 " pdb=" OD2 ASP B 74 " model vdw 2.294 3.040 nonbonded pdb=" OD2 ASP A 74 " pdb=" OG SER B 44 " model vdw 2.298 3.040 ... (remaining 538964 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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 'M' selection = chain 'N' } 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: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.780 Check model and map are aligned: 0.330 Set scattering table: 0.410 Process input model: 103.280 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 55958 Z= 0.517 Angle : 1.142 8.009 75586 Z= 0.764 Chirality : 0.063 0.328 9212 Planarity : 0.007 0.097 9660 Dihedral : 14.599 89.368 21630 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.79 % Allowed : 5.33 % Favored : 93.88 % 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: 1.52 (0.09), residues: 7350 helix: 1.69 (0.08), residues: 4018 sheet: 0.67 (0.17), residues: 896 loop : 0.10 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP N 42 HIS 0.004 0.002 HIS E 241 PHE 0.062 0.012 PHE M 202 TYR 0.083 0.012 TYR G 217 ARG 0.009 0.001 ARG G 195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 405 time to evaluate : 4.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7425 (pt0) cc_final: 0.6935 (pp20) REVERT: A 330 MET cc_start: 0.5358 (mtm) cc_final: 0.4722 (mmm) REVERT: A 403 ARG cc_start: 0.7683 (mtm-85) cc_final: 0.7451 (mtt90) REVERT: G 164 MET cc_start: 0.8416 (mtt) cc_final: 0.8205 (mtt) REVERT: G 186 GLU cc_start: 0.7354 (pt0) cc_final: 0.6751 (pp20) REVERT: G 379 LYS cc_start: 0.8104 (mttp) cc_final: 0.7885 (mtmp) REVERT: G 403 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7276 (mtm110) REVERT: F 29 MET cc_start: 0.8667 (ttt) cc_final: 0.8449 (ttt) REVERT: F 186 GLU cc_start: 0.7372 (pt0) cc_final: 0.6609 (pp20) REVERT: E 469 MET cc_start: 0.8295 (mtp) cc_final: 0.8074 (mtp) REVERT: D 176 LYS cc_start: 0.7194 (mtpt) cc_final: 0.6955 (mtpt) REVERT: D 186 GLU cc_start: 0.7363 (pt0) cc_final: 0.6836 (pp20) REVERT: C 186 GLU cc_start: 0.7263 (pt0) cc_final: 0.6749 (pp20) REVERT: C 403 ARG cc_start: 0.7777 (mtm-85) cc_final: 0.7467 (mtm110) REVERT: B 186 GLU cc_start: 0.7353 (pt0) cc_final: 0.6725 (pp20) REVERT: B 385 ASP cc_start: 0.7670 (m-30) cc_final: 0.7426 (m-30) REVERT: B 469 MET cc_start: 0.8395 (mtp) cc_final: 0.8069 (mtp) REVERT: K 330 MET cc_start: 0.5107 (mtm) cc_final: 0.4520 (mmm) REVERT: K 403 ARG cc_start: 0.7684 (mtm-85) cc_final: 0.7448 (mtt90) REVERT: J 164 MET cc_start: 0.8429 (mtt) cc_final: 0.8218 (mtt) REVERT: J 186 GLU cc_start: 0.6947 (pt0) cc_final: 0.6560 (pp20) REVERT: I 186 GLU cc_start: 0.7567 (pt0) cc_final: 0.6644 (pp20) REVERT: I 403 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.7304 (mtt90) REVERT: H 469 MET cc_start: 0.8292 (mtp) cc_final: 0.8066 (mtp) REVERT: N 186 GLU cc_start: 0.6977 (pt0) cc_final: 0.6522 (pp20) REVERT: M 403 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7472 (mtm110) REVERT: L 186 GLU cc_start: 0.7346 (pt0) cc_final: 0.6800 (pp20) REVERT: L 385 ASP cc_start: 0.7649 (m-30) cc_final: 0.7409 (m-30) REVERT: L 469 MET cc_start: 0.8375 (mtp) cc_final: 0.8048 (mtp) outliers start: 47 outliers final: 16 residues processed: 437 average time/residue: 1.3732 time to fit residues: 758.4375 Evaluate side-chains 362 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 346 time to evaluate : 4.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain G residue 264 ARG Chi-restraints excluded: chain G residue 427 SER Chi-restraints excluded: chain F residue 427 SER Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain K residue 427 SER Chi-restraints excluded: chain J residue 427 SER Chi-restraints excluded: chain I residue 195 ARG Chi-restraints excluded: chain I residue 427 SER Chi-restraints excluded: chain H residue 427 SER Chi-restraints excluded: chain N residue 427 SER Chi-restraints excluded: chain L residue 427 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 2.9990 chunk 551 optimal weight: 0.0060 chunk 306 optimal weight: 8.9990 chunk 188 optimal weight: 7.9990 chunk 372 optimal weight: 7.9990 chunk 294 optimal weight: 20.0000 chunk 570 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 346 optimal weight: 20.0000 chunk 424 optimal weight: 6.9990 chunk 661 optimal weight: 6.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 55958 Z= 0.262 Angle : 0.580 7.107 75586 Z= 0.318 Chirality : 0.045 0.135 9212 Planarity : 0.004 0.039 9660 Dihedral : 10.551 87.200 8190 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.49 % Allowed : 6.94 % Favored : 92.57 % 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: 1.70 (0.09), residues: 7350 helix: 1.96 (0.08), residues: 4116 sheet: 0.69 (0.17), residues: 896 loop : -0.13 (0.11), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 42 HIS 0.002 0.001 HIS B 241 PHE 0.010 0.001 PHE G 484 TYR 0.014 0.002 TYR D 359 ARG 0.003 0.001 ARG M 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 356 time to evaluate : 4.750 Fit side-chains REVERT: A 186 GLU cc_start: 0.7411 (pt0) cc_final: 0.6784 (pp20) REVERT: A 330 MET cc_start: 0.5281 (mtm) cc_final: 0.4689 (mmm) REVERT: G 186 GLU cc_start: 0.7470 (pt0) cc_final: 0.7250 (pt0) REVERT: G 379 LYS cc_start: 0.8094 (mttp) cc_final: 0.7830 (mtmp) REVERT: G 403 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.7362 (mtm110) REVERT: F 186 GLU cc_start: 0.7477 (pt0) cc_final: 0.6481 (pp20) REVERT: F 403 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7364 (mtt90) REVERT: E 330 MET cc_start: 0.4963 (mtm) cc_final: 0.4408 (mmm) REVERT: E 469 MET cc_start: 0.8302 (mtp) cc_final: 0.8066 (mtp) REVERT: D 186 GLU cc_start: 0.7303 (pt0) cc_final: 0.6588 (pp20) REVERT: D 403 ARG cc_start: 0.7722 (mtm-85) cc_final: 0.7371 (mtt90) REVERT: C 186 GLU cc_start: 0.7252 (pt0) cc_final: 0.7010 (pt0) REVERT: C 403 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7569 (mtm110) REVERT: B 186 GLU cc_start: 0.7405 (pt0) cc_final: 0.6616 (pp20) REVERT: B 385 ASP cc_start: 0.7651 (m-30) cc_final: 0.7419 (m-30) REVERT: B 469 MET cc_start: 0.8344 (mtp) cc_final: 0.8078 (mtp) REVERT: K 379 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8216 (mtmp) REVERT: I 186 GLU cc_start: 0.7452 (pt0) cc_final: 0.7177 (pt0) REVERT: I 403 ARG cc_start: 0.7809 (mtm-85) cc_final: 0.7368 (mtt90) REVERT: H 469 MET cc_start: 0.8305 (mtp) cc_final: 0.8063 (mtp) REVERT: N 403 ARG cc_start: 0.7718 (mtm-85) cc_final: 0.7373 (mtt90) REVERT: M 403 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7568 (mtm110) REVERT: L 186 GLU cc_start: 0.7394 (pt0) cc_final: 0.6627 (pp20) REVERT: L 385 ASP cc_start: 0.7637 (m-30) cc_final: 0.7406 (m-30) REVERT: L 469 MET cc_start: 0.8346 (mtp) cc_final: 0.8082 (mtp) outliers start: 29 outliers final: 2 residues processed: 371 average time/residue: 1.4924 time to fit residues: 689.1999 Evaluate side-chains 324 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 321 time to evaluate : 4.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain K residue 379 LYS Chi-restraints excluded: chain N residue 120 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 550 optimal weight: 20.0000 chunk 450 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 662 optimal weight: 0.3980 chunk 715 optimal weight: 0.9980 chunk 589 optimal weight: 1.9990 chunk 656 optimal weight: 0.0570 chunk 225 optimal weight: 0.7980 chunk 531 optimal weight: 2.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 55958 Z= 0.131 Angle : 0.462 7.269 75586 Z= 0.255 Chirality : 0.041 0.131 9212 Planarity : 0.003 0.027 9660 Dihedral : 9.631 89.968 8162 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.82 % Allowed : 6.96 % Favored : 92.22 % 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: 2.05 (0.10), residues: 7350 helix: 2.27 (0.08), residues: 4172 sheet: 1.15 (0.18), residues: 854 loop : -0.22 (0.11), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP H 42 HIS 0.001 0.001 HIS M 241 PHE 0.006 0.001 PHE I 484 TYR 0.009 0.001 TYR D 359 ARG 0.003 0.000 ARG F 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 358 time to evaluate : 4.721 Fit side-chains REVERT: G 61 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8008 (tptt) REVERT: G 379 LYS cc_start: 0.8064 (mttp) cc_final: 0.7765 (mtmm) REVERT: F 176 LYS cc_start: 0.7393 (mtpt) cc_final: 0.6614 (mttt) REVERT: E 330 MET cc_start: 0.5051 (mtm) cc_final: 0.4444 (mmm) REVERT: E 403 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7443 (mtm110) REVERT: E 469 MET cc_start: 0.8251 (mtp) cc_final: 0.8019 (mtp) REVERT: D 403 ARG cc_start: 0.7613 (mtm-85) cc_final: 0.7297 (mtm110) REVERT: C 403 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.7396 (mtm110) REVERT: C 487 MET cc_start: 0.8667 (mmm) cc_final: 0.8449 (mmm) REVERT: B 385 ASP cc_start: 0.7373 (m-30) cc_final: 0.7171 (m-30) REVERT: B 469 MET cc_start: 0.8284 (mtp) cc_final: 0.8032 (mtp) REVERT: K 186 GLU cc_start: 0.7336 (pt0) cc_final: 0.6770 (pp20) REVERT: J 61 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.8011 (tptt) REVERT: I 176 LYS cc_start: 0.7357 (mtpt) cc_final: 0.6562 (mttt) REVERT: I 186 GLU cc_start: 0.7379 (pt0) cc_final: 0.7101 (pt0) REVERT: I 403 ARG cc_start: 0.7685 (mtm-85) cc_final: 0.7261 (mtm110) REVERT: H 469 MET cc_start: 0.8234 (mtp) cc_final: 0.7938 (mtp) REVERT: N 403 ARG cc_start: 0.7586 (mtm-85) cc_final: 0.7276 (mtm110) REVERT: M 403 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.7404 (mtm110) REVERT: L 186 GLU cc_start: 0.7461 (pt0) cc_final: 0.6636 (pp20) REVERT: L 469 MET cc_start: 0.8282 (mtp) cc_final: 0.8015 (mtp) outliers start: 49 outliers final: 6 residues processed: 391 average time/residue: 1.5047 time to fit residues: 731.5700 Evaluate side-chains 333 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 325 time to evaluate : 4.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 61 LYS Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 379 LYS Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain M residue 375 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 7.9990 chunk 497 optimal weight: 0.2980 chunk 343 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 316 optimal weight: 3.9990 chunk 444 optimal weight: 6.9990 chunk 664 optimal weight: 2.9990 chunk 703 optimal weight: 9.9990 chunk 347 optimal weight: 5.9990 chunk 629 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 470 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 55958 Z= 0.228 Angle : 0.531 6.334 75586 Z= 0.291 Chirality : 0.044 0.183 9212 Planarity : 0.003 0.034 9660 Dihedral : 9.824 89.510 8162 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.45 % Allowed : 7.23 % Favored : 92.32 % 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: 1.92 (0.09), residues: 7350 helix: 2.22 (0.08), residues: 4116 sheet: 1.16 (0.18), residues: 854 loop : -0.35 (0.11), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP H 42 HIS 0.002 0.001 HIS L 241 PHE 0.010 0.001 PHE J 484 TYR 0.012 0.002 TYR D 359 ARG 0.002 0.000 ARG F 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 347 time to evaluate : 4.828 Fit side-chains REVERT: G 379 LYS cc_start: 0.8000 (mttp) cc_final: 0.7741 (mtmt) REVERT: F 176 LYS cc_start: 0.7326 (mtpt) cc_final: 0.6532 (mttt) REVERT: F 403 ARG cc_start: 0.7777 (mtm-85) cc_final: 0.7341 (mtm110) REVERT: E 330 MET cc_start: 0.5011 (mtm) cc_final: 0.4400 (mmm) REVERT: E 403 ARG cc_start: 0.7909 (mtm-85) cc_final: 0.7558 (mtm110) REVERT: E 469 MET cc_start: 0.8313 (mtp) cc_final: 0.8033 (mtp) REVERT: D 403 ARG cc_start: 0.7669 (mtm-85) cc_final: 0.7307 (mtt90) REVERT: C 403 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7536 (mtm110) REVERT: B 385 ASP cc_start: 0.7587 (m-30) cc_final: 0.7348 (m-30) REVERT: B 469 MET cc_start: 0.8352 (mtp) cc_final: 0.8087 (mtp) REVERT: K 186 GLU cc_start: 0.7417 (pt0) cc_final: 0.6807 (pp20) REVERT: J 379 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8149 (mtmt) REVERT: I 176 LYS cc_start: 0.7293 (mtpt) cc_final: 0.6512 (mttt) REVERT: I 186 GLU cc_start: 0.7399 (pt0) cc_final: 0.7118 (pt0) REVERT: I 403 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.7345 (mtm110) REVERT: H 469 MET cc_start: 0.8309 (mtp) cc_final: 0.8029 (mtp) REVERT: N 403 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7366 (mtt90) REVERT: M 403 ARG cc_start: 0.7879 (mtm-85) cc_final: 0.7537 (mtm110) REVERT: L 186 GLU cc_start: 0.7394 (pt0) cc_final: 0.7189 (pt0) REVERT: L 469 MET cc_start: 0.8347 (mtp) cc_final: 0.8086 (mtp) outliers start: 27 outliers final: 3 residues processed: 359 average time/residue: 1.5239 time to fit residues: 679.4878 Evaluate side-chains 321 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 317 time to evaluate : 4.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain J residue 379 LYS Chi-restraints excluded: chain N residue 120 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 4.9990 chunk 399 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 523 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 chunk 600 optimal weight: 5.9990 chunk 486 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 359 optimal weight: 0.9990 chunk 631 optimal weight: 0.5980 chunk 177 optimal weight: 40.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 55958 Z= 0.228 Angle : 0.531 6.859 75586 Z= 0.291 Chirality : 0.044 0.156 9212 Planarity : 0.003 0.029 9660 Dihedral : 9.675 88.774 8162 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.54 % Allowed : 7.76 % Favored : 91.70 % 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: 1.77 (0.09), residues: 7350 helix: 2.09 (0.08), residues: 4116 sheet: 1.20 (0.18), residues: 854 loop : -0.47 (0.11), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 42 HIS 0.002 0.001 HIS L 241 PHE 0.010 0.001 PHE F 484 TYR 0.012 0.002 TYR D 359 ARG 0.004 0.000 ARG I 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 346 time to evaluate : 4.818 Fit side-chains REVERT: A 186 GLU cc_start: 0.7432 (pt0) cc_final: 0.7057 (pm20) REVERT: G 379 LYS cc_start: 0.8053 (mttp) cc_final: 0.7726 (mtmt) REVERT: F 403 ARG cc_start: 0.7800 (mtm-85) cc_final: 0.7339 (mtt90) REVERT: E 403 ARG cc_start: 0.7923 (mtm-85) cc_final: 0.7557 (mtm110) REVERT: E 469 MET cc_start: 0.8302 (mtp) cc_final: 0.8028 (mtp) REVERT: D 191 MET cc_start: 0.5226 (OUTLIER) cc_final: 0.5015 (ttp) REVERT: D 403 ARG cc_start: 0.7784 (mtm-85) cc_final: 0.7406 (mtt90) REVERT: C 181 LEU cc_start: 0.7638 (mt) cc_final: 0.7224 (tp) REVERT: C 403 ARG cc_start: 0.7874 (mtm-85) cc_final: 0.7516 (mtm110) REVERT: B 385 ASP cc_start: 0.7610 (m-30) cc_final: 0.7369 (m-30) REVERT: B 469 MET cc_start: 0.8346 (mtp) cc_final: 0.8088 (mtp) REVERT: K 186 GLU cc_start: 0.7440 (pt0) cc_final: 0.6978 (pp20) REVERT: I 186 GLU cc_start: 0.7420 (pt0) cc_final: 0.7152 (pt0) REVERT: I 403 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7343 (mtt90) REVERT: H 469 MET cc_start: 0.8311 (mtp) cc_final: 0.8038 (mtp) REVERT: N 186 GLU cc_start: 0.7429 (pt0) cc_final: 0.6957 (pp20) REVERT: N 379 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8271 (mtmp) REVERT: N 403 ARG cc_start: 0.7793 (mtm-85) cc_final: 0.7420 (mtt90) REVERT: M 181 LEU cc_start: 0.7635 (mt) cc_final: 0.7219 (tp) REVERT: M 186 GLU cc_start: 0.7535 (pt0) cc_final: 0.7277 (pt0) REVERT: M 403 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7514 (mtm110) REVERT: L 186 GLU cc_start: 0.7362 (pt0) cc_final: 0.7161 (pt0) REVERT: L 469 MET cc_start: 0.8348 (mtp) cc_final: 0.8082 (mtp) outliers start: 32 outliers final: 3 residues processed: 365 average time/residue: 1.5479 time to fit residues: 701.9546 Evaluate side-chains 328 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 323 time to evaluate : 4.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 379 LYS Chi-restraints excluded: chain M residue 379 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 3.9990 chunk 633 optimal weight: 0.6980 chunk 139 optimal weight: 6.9990 chunk 413 optimal weight: 0.6980 chunk 173 optimal weight: 5.9990 chunk 704 optimal weight: 10.0000 chunk 584 optimal weight: 2.9990 chunk 326 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 232 optimal weight: 8.9990 chunk 369 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 55958 Z= 0.213 Angle : 0.517 6.489 75586 Z= 0.284 Chirality : 0.043 0.139 9212 Planarity : 0.003 0.028 9660 Dihedral : 9.585 89.723 8162 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.57 % Allowed : 8.07 % Favored : 91.36 % 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: 1.76 (0.09), residues: 7350 helix: 2.09 (0.08), residues: 4116 sheet: 1.23 (0.18), residues: 854 loop : -0.51 (0.11), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 42 HIS 0.002 0.001 HIS F 314 PHE 0.009 0.001 PHE J 484 TYR 0.011 0.002 TYR K 197 ARG 0.004 0.000 ARG I 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 333 time to evaluate : 4.777 Fit side-chains REVERT: A 186 GLU cc_start: 0.7524 (pt0) cc_final: 0.6954 (pp20) REVERT: G 379 LYS cc_start: 0.8127 (mttp) cc_final: 0.7769 (mtmt) REVERT: F 186 GLU cc_start: 0.7297 (pt0) cc_final: 0.7030 (pt0) REVERT: F 403 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7392 (mtm110) REVERT: E 403 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7510 (mtm110) REVERT: E 469 MET cc_start: 0.8270 (mtp) cc_final: 0.8018 (mtp) REVERT: D 379 LYS cc_start: 0.8176 (mtmp) cc_final: 0.7796 (mmmt) REVERT: D 403 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7419 (mtm110) REVERT: C 181 LEU cc_start: 0.7677 (mt) cc_final: 0.7211 (tp) REVERT: C 186 GLU cc_start: 0.7572 (pt0) cc_final: 0.7301 (pt0) REVERT: C 403 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7517 (mtm110) REVERT: B 385 ASP cc_start: 0.7592 (m-30) cc_final: 0.7356 (m-30) REVERT: B 434 ASP cc_start: 0.7577 (m-30) cc_final: 0.7307 (m-30) REVERT: B 469 MET cc_start: 0.8360 (mtp) cc_final: 0.8110 (mtp) REVERT: K 186 GLU cc_start: 0.7457 (pt0) cc_final: 0.7005 (pp20) REVERT: J 186 GLU cc_start: 0.7209 (pt0) cc_final: 0.6988 (pt0) REVERT: I 186 GLU cc_start: 0.7323 (pt0) cc_final: 0.7049 (pt0) REVERT: I 403 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7393 (mtm110) REVERT: H 403 ARG cc_start: 0.7879 (mtm-85) cc_final: 0.7512 (mtm110) REVERT: H 469 MET cc_start: 0.8284 (mtp) cc_final: 0.8026 (mtp) REVERT: N 186 GLU cc_start: 0.7545 (pt0) cc_final: 0.7009 (pp20) REVERT: N 403 ARG cc_start: 0.7762 (mtm-85) cc_final: 0.7421 (mtm110) REVERT: M 181 LEU cc_start: 0.7671 (mt) cc_final: 0.7205 (tp) REVERT: M 186 GLU cc_start: 0.7543 (pt0) cc_final: 0.7286 (pt0) REVERT: M 403 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7498 (mtm110) REVERT: L 434 ASP cc_start: 0.7544 (m-30) cc_final: 0.7278 (m-30) REVERT: L 469 MET cc_start: 0.8351 (mtp) cc_final: 0.8100 (mtp) outliers start: 34 outliers final: 5 residues processed: 354 average time/residue: 1.4882 time to fit residues: 657.5039 Evaluate side-chains 323 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 318 time to evaluate : 4.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 292 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 401 optimal weight: 20.0000 chunk 514 optimal weight: 4.9990 chunk 398 optimal weight: 3.9990 chunk 592 optimal weight: 1.9990 chunk 393 optimal weight: 8.9990 chunk 701 optimal weight: 30.0000 chunk 439 optimal weight: 4.9990 chunk 427 optimal weight: 0.5980 chunk 323 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 239 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 55958 Z= 0.167 Angle : 0.486 6.196 75586 Z= 0.266 Chirality : 0.042 0.139 9212 Planarity : 0.003 0.029 9660 Dihedral : 9.224 87.234 8162 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.42 % Allowed : 8.42 % Favored : 91.16 % 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: 1.89 (0.10), residues: 7350 helix: 2.21 (0.08), residues: 4116 sheet: 1.27 (0.18), residues: 854 loop : -0.47 (0.11), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 42 HIS 0.001 0.001 HIS L 241 PHE 0.008 0.001 PHE G 484 TYR 0.010 0.001 TYR L 197 ARG 0.004 0.000 ARG I 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 340 time to evaluate : 4.854 Fit side-chains REVERT: A 186 GLU cc_start: 0.7553 (pt0) cc_final: 0.6988 (pp20) REVERT: G 379 LYS cc_start: 0.8045 (mttp) cc_final: 0.7735 (mtmt) REVERT: F 186 GLU cc_start: 0.7294 (pt0) cc_final: 0.7005 (pt0) REVERT: E 403 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.7471 (mtm110) REVERT: E 469 MET cc_start: 0.8246 (mtp) cc_final: 0.8000 (mtp) REVERT: D 403 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7354 (mtm110) REVERT: C 181 LEU cc_start: 0.7741 (mt) cc_final: 0.7201 (tp) REVERT: C 186 GLU cc_start: 0.7483 (pt0) cc_final: 0.7251 (pt0) REVERT: C 403 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7483 (mtm110) REVERT: B 385 ASP cc_start: 0.7510 (m-30) cc_final: 0.7268 (m-30) REVERT: B 434 ASP cc_start: 0.7431 (m-30) cc_final: 0.7142 (m-30) REVERT: B 469 MET cc_start: 0.8337 (mtp) cc_final: 0.8088 (mtp) REVERT: K 186 GLU cc_start: 0.7441 (pt0) cc_final: 0.7017 (pp20) REVERT: J 186 GLU cc_start: 0.7162 (pt0) cc_final: 0.6916 (pt0) REVERT: I 186 GLU cc_start: 0.7316 (pt0) cc_final: 0.7046 (pt0) REVERT: I 403 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7359 (mtm110) REVERT: H 403 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7473 (mtm110) REVERT: H 469 MET cc_start: 0.8251 (mtp) cc_final: 0.8003 (mtp) REVERT: N 186 GLU cc_start: 0.7583 (pt0) cc_final: 0.7122 (pp20) REVERT: N 403 ARG cc_start: 0.7723 (mtm-85) cc_final: 0.7388 (mtm110) REVERT: M 181 LEU cc_start: 0.7733 (mt) cc_final: 0.7190 (tp) REVERT: M 186 GLU cc_start: 0.7502 (pt0) cc_final: 0.7241 (pt0) REVERT: M 403 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.7484 (mtm110) REVERT: L 434 ASP cc_start: 0.7462 (m-30) cc_final: 0.7180 (m-30) REVERT: L 469 MET cc_start: 0.8334 (mtp) cc_final: 0.8087 (mtp) outliers start: 25 outliers final: 6 residues processed: 358 average time/residue: 1.4818 time to fit residues: 662.3165 Evaluate side-chains 329 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 323 time to evaluate : 4.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 292 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 0.8980 chunk 280 optimal weight: 9.9990 chunk 419 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 137 optimal weight: 40.0000 chunk 135 optimal weight: 4.9990 chunk 446 optimal weight: 9.9990 chunk 478 optimal weight: 0.3980 chunk 346 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 551 optimal weight: 4.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 55958 Z= 0.237 Angle : 0.535 6.877 75586 Z= 0.293 Chirality : 0.044 0.139 9212 Planarity : 0.004 0.034 9660 Dihedral : 9.623 89.095 8162 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.29 % Allowed : 8.62 % Favored : 91.10 % 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: 1.70 (0.10), residues: 7350 helix: 2.05 (0.08), residues: 4116 sheet: 1.22 (0.18), residues: 854 loop : -0.56 (0.11), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 42 HIS 0.002 0.001 HIS B 241 PHE 0.010 0.001 PHE G 484 TYR 0.012 0.002 TYR L 197 ARG 0.005 0.000 ARG I 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 342 time to evaluate : 4.829 Fit side-chains REVERT: A 186 GLU cc_start: 0.7619 (pt0) cc_final: 0.7042 (pp20) REVERT: G 379 LYS cc_start: 0.8077 (mttp) cc_final: 0.7826 (mtmp) REVERT: F 186 GLU cc_start: 0.7362 (pt0) cc_final: 0.7131 (pt0) REVERT: E 403 ARG cc_start: 0.7921 (mtm-85) cc_final: 0.7562 (mtm110) REVERT: E 469 MET cc_start: 0.8276 (mtp) cc_final: 0.8024 (mtp) REVERT: D 191 MET cc_start: 0.5286 (pmt) cc_final: 0.4918 (mtt) REVERT: D 403 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7490 (mtm110) REVERT: C 181 LEU cc_start: 0.7750 (mt) cc_final: 0.7173 (tp) REVERT: C 186 GLU cc_start: 0.7484 (pt0) cc_final: 0.7267 (pt0) REVERT: C 403 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7544 (mtm110) REVERT: B 385 ASP cc_start: 0.7628 (m-30) cc_final: 0.7382 (m-30) REVERT: B 469 MET cc_start: 0.8368 (mtp) cc_final: 0.8108 (mtp) REVERT: K 186 GLU cc_start: 0.7432 (pt0) cc_final: 0.7060 (pp20) REVERT: K 191 MET cc_start: 0.4824 (pmt) cc_final: 0.4597 (tmt) REVERT: J 186 GLU cc_start: 0.7255 (pt0) cc_final: 0.7047 (pt0) REVERT: I 186 GLU cc_start: 0.7329 (pt0) cc_final: 0.7054 (pt0) REVERT: I 403 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7399 (mtm110) REVERT: H 186 GLU cc_start: 0.7474 (pt0) cc_final: 0.7232 (pt0) REVERT: H 403 ARG cc_start: 0.7922 (mtm-85) cc_final: 0.7561 (mtm110) REVERT: H 469 MET cc_start: 0.8276 (mtp) cc_final: 0.8022 (mtp) REVERT: N 186 GLU cc_start: 0.7643 (pt0) cc_final: 0.7115 (pp20) REVERT: N 403 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7464 (mtt90) REVERT: M 181 LEU cc_start: 0.7745 (mt) cc_final: 0.7167 (tp) REVERT: M 186 GLU cc_start: 0.7546 (pt0) cc_final: 0.7257 (pt0) REVERT: M 403 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7546 (mtm110) REVERT: L 469 MET cc_start: 0.8368 (mtp) cc_final: 0.8107 (mtp) outliers start: 17 outliers final: 7 residues processed: 355 average time/residue: 1.5056 time to fit residues: 666.2545 Evaluate side-chains 334 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 327 time to evaluate : 4.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 292 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 5.9990 chunk 672 optimal weight: 6.9990 chunk 613 optimal weight: 4.9990 chunk 653 optimal weight: 10.0000 chunk 393 optimal weight: 8.9990 chunk 284 optimal weight: 7.9990 chunk 513 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 chunk 590 optimal weight: 6.9990 chunk 618 optimal weight: 3.9990 chunk 651 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 432 ASN ** I 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 55958 Z= 0.285 Angle : 0.569 7.640 75586 Z= 0.311 Chirality : 0.045 0.132 9212 Planarity : 0.004 0.041 9660 Dihedral : 9.826 89.459 8162 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.22 % Allowed : 8.79 % Favored : 91.00 % 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: 1.48 (0.09), residues: 7350 helix: 1.88 (0.08), residues: 4116 sheet: 1.15 (0.18), residues: 854 loop : -0.67 (0.11), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 42 HIS 0.002 0.001 HIS F 314 PHE 0.011 0.002 PHE G 484 TYR 0.014 0.002 TYR K 197 ARG 0.005 0.001 ARG I 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 346 time to evaluate : 4.754 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7631 (pt0) cc_final: 0.7052 (pp20) REVERT: A 191 MET cc_start: 0.4898 (pmt) cc_final: 0.4576 (tmt) REVERT: G 379 LYS cc_start: 0.8182 (mttp) cc_final: 0.7823 (mtmp) REVERT: F 186 GLU cc_start: 0.7391 (pt0) cc_final: 0.7165 (pt0) REVERT: F 403 ARG cc_start: 0.7856 (mtm-85) cc_final: 0.7390 (mtt90) REVERT: E 191 MET cc_start: 0.4759 (OUTLIER) cc_final: 0.4463 (tmt) REVERT: E 403 ARG cc_start: 0.7947 (mtm-85) cc_final: 0.7582 (mtm110) REVERT: E 469 MET cc_start: 0.8303 (mtp) cc_final: 0.8054 (mtp) REVERT: D 181 LEU cc_start: 0.7707 (mt) cc_final: 0.7309 (tp) REVERT: D 191 MET cc_start: 0.5321 (pmt) cc_final: 0.5000 (mtt) REVERT: D 403 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7456 (mtt90) REVERT: C 181 LEU cc_start: 0.7784 (mt) cc_final: 0.7201 (tp) REVERT: C 186 GLU cc_start: 0.7493 (pt0) cc_final: 0.7251 (pt0) REVERT: C 191 MET cc_start: 0.5211 (pmt) cc_final: 0.4715 (tmt) REVERT: C 403 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7552 (mtm110) REVERT: B 186 GLU cc_start: 0.7431 (pt0) cc_final: 0.7217 (pt0) REVERT: B 385 ASP cc_start: 0.7653 (m-30) cc_final: 0.7415 (m-30) REVERT: B 469 MET cc_start: 0.8367 (mtp) cc_final: 0.8105 (mtp) REVERT: K 186 GLU cc_start: 0.7390 (pt0) cc_final: 0.7037 (pp20) REVERT: K 191 MET cc_start: 0.4958 (pmt) cc_final: 0.4620 (tmt) REVERT: J 186 GLU cc_start: 0.7222 (pt0) cc_final: 0.7004 (pt0) REVERT: I 186 GLU cc_start: 0.7337 (pt0) cc_final: 0.7054 (pt0) REVERT: I 403 ARG cc_start: 0.7858 (mtm-85) cc_final: 0.7392 (mtt90) REVERT: H 186 GLU cc_start: 0.7467 (pt0) cc_final: 0.7209 (pt0) REVERT: H 403 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7565 (mtm110) REVERT: H 469 MET cc_start: 0.8297 (mtp) cc_final: 0.8046 (mtp) REVERT: N 186 GLU cc_start: 0.7685 (pt0) cc_final: 0.7057 (pp20) REVERT: N 191 MET cc_start: 0.5351 (pmt) cc_final: 0.4999 (mtt) REVERT: N 403 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7457 (mtt90) REVERT: M 181 LEU cc_start: 0.7780 (mt) cc_final: 0.7196 (tp) REVERT: M 186 GLU cc_start: 0.7543 (pt0) cc_final: 0.7245 (pt0) REVERT: M 403 ARG cc_start: 0.7903 (mtm-85) cc_final: 0.7549 (mtm110) REVERT: L 186 GLU cc_start: 0.7374 (pt0) cc_final: 0.7000 (pt0) REVERT: L 469 MET cc_start: 0.8368 (mtp) cc_final: 0.8103 (mtp) outliers start: 13 outliers final: 4 residues processed: 355 average time/residue: 1.4786 time to fit residues: 657.7349 Evaluate side-chains 347 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 342 time to evaluate : 4.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain M residue 119 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 0.8980 chunk 691 optimal weight: 5.9990 chunk 422 optimal weight: 3.9990 chunk 328 optimal weight: 4.9990 chunk 480 optimal weight: 1.9990 chunk 725 optimal weight: 0.1980 chunk 667 optimal weight: 0.8980 chunk 577 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 446 optimal weight: 6.9990 chunk 354 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 432 ASN J 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 55958 Z= 0.129 Angle : 0.463 8.033 75586 Z= 0.254 Chirality : 0.041 0.150 9212 Planarity : 0.003 0.028 9660 Dihedral : 8.803 87.448 8162 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.12 % Allowed : 8.97 % Favored : 90.91 % 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: 1.90 (0.10), residues: 7350 helix: 2.21 (0.08), residues: 4158 sheet: 1.27 (0.18), residues: 854 loop : -0.50 (0.12), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 42 HIS 0.001 0.001 HIS H 241 PHE 0.013 0.001 PHE L 193 TYR 0.010 0.001 TYR B 197 ARG 0.007 0.000 ARG I 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14700 Ramachandran restraints generated. 7350 Oldfield, 0 Emsley, 7350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 337 time to evaluate : 4.832 Fit side-chains REVERT: A 186 GLU cc_start: 0.7613 (pt0) cc_final: 0.7064 (pp20) REVERT: G 379 LYS cc_start: 0.8097 (mttp) cc_final: 0.7837 (mtmp) REVERT: F 176 LYS cc_start: 0.7289 (mtpt) cc_final: 0.6588 (mttt) REVERT: F 186 GLU cc_start: 0.7254 (pt0) cc_final: 0.6980 (pt0) REVERT: E 186 GLU cc_start: 0.7399 (pt0) cc_final: 0.7178 (pt0) REVERT: E 403 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7430 (mtm110) REVERT: E 469 MET cc_start: 0.8180 (mtp) cc_final: 0.7955 (mtp) REVERT: D 181 LEU cc_start: 0.7641 (mt) cc_final: 0.7291 (tp) REVERT: D 403 ARG cc_start: 0.7623 (mtm-85) cc_final: 0.7305 (mtm110) REVERT: C 181 LEU cc_start: 0.7706 (mt) cc_final: 0.7146 (tp) REVERT: C 186 GLU cc_start: 0.7373 (pt0) cc_final: 0.7147 (pt0) REVERT: C 403 ARG cc_start: 0.7746 (mtm-85) cc_final: 0.7418 (mtm110) REVERT: B 186 GLU cc_start: 0.7367 (pt0) cc_final: 0.7149 (pt0) REVERT: B 385 ASP cc_start: 0.7417 (m-30) cc_final: 0.7192 (m-30) REVERT: B 469 MET cc_start: 0.8285 (mtp) cc_final: 0.8032 (mtp) REVERT: K 181 LEU cc_start: 0.7671 (mt) cc_final: 0.7094 (tp) REVERT: J 186 GLU cc_start: 0.7120 (pt0) cc_final: 0.6909 (pt0) REVERT: I 186 GLU cc_start: 0.7321 (pt0) cc_final: 0.7059 (pt0) REVERT: I 403 ARG cc_start: 0.7719 (mtm-85) cc_final: 0.7342 (mtm110) REVERT: H 186 GLU cc_start: 0.7356 (pt0) cc_final: 0.7130 (pt0) REVERT: H 403 ARG cc_start: 0.7784 (mtm-85) cc_final: 0.7436 (mtm110) REVERT: H 469 MET cc_start: 0.8186 (mtp) cc_final: 0.7954 (mtp) REVERT: N 181 LEU cc_start: 0.7672 (mt) cc_final: 0.7257 (tp) REVERT: N 186 GLU cc_start: 0.7643 (pt0) cc_final: 0.7096 (pp20) REVERT: N 403 ARG cc_start: 0.7625 (mtm-85) cc_final: 0.7307 (mtm110) REVERT: M 181 LEU cc_start: 0.7705 (mt) cc_final: 0.7139 (tp) REVERT: M 186 GLU cc_start: 0.7454 (pt0) cc_final: 0.7169 (pt0) REVERT: M 403 ARG cc_start: 0.7748 (mtm-85) cc_final: 0.7418 (mtm110) REVERT: L 181 LEU cc_start: 0.7663 (mt) cc_final: 0.7226 (tp) REVERT: L 186 GLU cc_start: 0.7333 (pt0) cc_final: 0.6995 (pt0) REVERT: L 469 MET cc_start: 0.8284 (mtp) cc_final: 0.8030 (mtp) outliers start: 7 outliers final: 4 residues processed: 342 average time/residue: 1.5054 time to fit residues: 641.5168 Evaluate side-chains 329 residues out of total 5964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 325 time to evaluate : 4.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain N residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 1.9990 chunk 615 optimal weight: 0.9980 chunk 176 optimal weight: 0.7980 chunk 532 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 578 optimal weight: 1.9990 chunk 242 optimal weight: 9.9990 chunk 593 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.220376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.129215 restraints weight = 53243.728| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 6.24 r_work: 0.3165 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 55958 Z= 0.145 Angle : 0.469 6.897 75586 Z= 0.256 Chirality : 0.042 0.133 9212 Planarity : 0.003 0.028 9660 Dihedral : 8.740 88.217 8162 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.13 % Allowed : 9.05 % Favored : 90.81 % 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: 1.95 (0.10), residues: 7350 helix: 2.27 (0.08), residues: 4172 sheet: 1.28 (0.18), residues: 854 loop : -0.55 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP H 42 HIS 0.001 0.001 HIS B 241 PHE 0.016 0.001 PHE K 193 TYR 0.010 0.001 TYR I 197 ARG 0.002 0.000 ARG N 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12975.32 seconds wall clock time: 227 minutes 36.90 seconds (13656.90 seconds total)