Starting phenix.real_space_refine on Fri Feb 23 02:52:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqq_25390/02_2024/7sqq_25390.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqq_25390/02_2024/7sqq_25390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqq_25390/02_2024/7sqq_25390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqq_25390/02_2024/7sqq_25390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqq_25390/02_2024/7sqq_25390.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqq_25390/02_2024/7sqq_25390.pdb" } resolution = 4.2 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 336 5.16 5 C 64632 2.51 5 N 18768 2.21 5 O 19896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 103632 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "B" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "C" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "D" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "E" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "F" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "G" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "H" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "I" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "J" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "K" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "L" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "M" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "N" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "O" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "P" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "Q" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "R" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "S" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "T" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "V" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "W" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "X" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Chain: "Y" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4318 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 3 Time building chain proxies: 40.14, per 1000 atoms: 0.39 Number of scatterers: 103632 At special positions: 0 Unit cell: (220.375, 220.375, 220.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 336 16.00 O 19896 8.00 N 18768 7.00 C 64632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 28.96 Conformation dependent library (CDL) restraints added in 13.7 seconds 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 24480 Finding SS restraints... Secondary structure from input PDB file: 528 helices and 120 sheets defined 41.6% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.52 Creating SS restraints... Processing helix chain 'A' and resid 48 through 55 removed outlier: 3.881A pdb=" N SER A 52 " --> pdb=" O GLY A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 84 Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 162' Processing helix chain 'A' and resid 163 through 179 Processing helix chain 'A' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP A 201 " --> pdb=" O VAL A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 201' Processing helix chain 'A' and resid 202 through 226 Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.993A pdb=" N LYS A 236 " --> pdb=" O ALA A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 360 through 367 Proline residue: A 365 - end of helix Processing helix chain 'A' and resid 379 through 386 removed outlier: 4.032A pdb=" N MET A 385 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU A 434 " --> pdb=" O GLN A 430 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 458 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG A 465 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN A 472 " --> pdb=" O HIS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 522 " --> pdb=" O PHE A 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 523 " --> pdb=" O TYR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 544 Processing helix chain 'A' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN A 600 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 601 " --> pdb=" O ILE A 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 597 through 601' Processing helix chain 'B' and resid 49 through 55 Processing helix chain 'B' and resid 67 through 84 Processing helix chain 'B' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 162' Processing helix chain 'B' and resid 163 through 179 Processing helix chain 'B' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP B 201 " --> pdb=" O VAL B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 201' Processing helix chain 'B' and resid 202 through 226 Processing helix chain 'B' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS B 236 " --> pdb=" O ALA B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 351 removed outlier: 3.738A pdb=" N TYR B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 358 Processing helix chain 'B' and resid 360 through 367 Proline residue: B 365 - end of helix Processing helix chain 'B' and resid 379 through 386 removed outlier: 4.032A pdb=" N MET B 385 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 412 removed outlier: 3.610A pdb=" N GLY B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU B 434 " --> pdb=" O GLN B 430 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 458 Processing helix chain 'B' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG B 465 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN B 472 " --> pdb=" O HIS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 500 through 508 Processing helix chain 'B' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 522 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 523 " --> pdb=" O TYR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 544 Processing helix chain 'B' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN B 600 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 601 " --> pdb=" O ILE B 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 597 through 601' Processing helix chain 'C' and resid 49 through 55 Processing helix chain 'C' and resid 67 through 84 Processing helix chain 'C' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 157 through 162' Processing helix chain 'C' and resid 163 through 179 Processing helix chain 'C' and resid 198 through 201 removed outlier: 3.714A pdb=" N ASP C 201 " --> pdb=" O VAL C 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 201' Processing helix chain 'C' and resid 202 through 226 Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS C 236 " --> pdb=" O ALA C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP C 347 " --> pdb=" O PRO C 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 358 Processing helix chain 'C' and resid 360 through 367 Proline residue: C 365 - end of helix Processing helix chain 'C' and resid 379 through 386 removed outlier: 4.032A pdb=" N MET C 385 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY C 405 " --> pdb=" O ASP C 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN C 406 " --> pdb=" O ALA C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU C 434 " --> pdb=" O GLN C 430 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 440 " --> pdb=" O LEU C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 458 Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.667A pdb=" N ARG C 465 " --> pdb=" O GLY C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN C 472 " --> pdb=" O HIS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 499 No H-bonds generated for 'chain 'C' and resid 497 through 499' Processing helix chain 'C' and resid 500 through 508 Processing helix chain 'C' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE C 515 " --> pdb=" O ASN C 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN C 522 " --> pdb=" O PHE C 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 523 " --> pdb=" O TYR C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 544 Processing helix chain 'C' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE C 564 " --> pdb=" O ASN C 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN C 600 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN C 601 " --> pdb=" O ILE C 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 597 through 601' Processing helix chain 'D' and resid 49 through 55 Processing helix chain 'D' and resid 67 through 84 Processing helix chain 'D' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE D 162 " --> pdb=" O VAL D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 157 through 162' Processing helix chain 'D' and resid 163 through 179 Processing helix chain 'D' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP D 201 " --> pdb=" O VAL D 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 201' Processing helix chain 'D' and resid 202 through 226 Processing helix chain 'D' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS D 236 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR D 346 " --> pdb=" O THR D 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP D 347 " --> pdb=" O PRO D 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 358 Processing helix chain 'D' and resid 360 through 367 Proline residue: D 365 - end of helix Processing helix chain 'D' and resid 378 through 386 removed outlier: 4.020A pdb=" N ALA D 381 " --> pdb=" O ASP D 378 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET D 385 " --> pdb=" O LEU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY D 405 " --> pdb=" O ASP D 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU D 434 " --> pdb=" O GLN D 430 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 458 Processing helix chain 'D' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG D 465 " --> pdb=" O GLY D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 472 removed outlier: 3.847A pdb=" N GLN D 472 " --> pdb=" O HIS D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 499 No H-bonds generated for 'chain 'D' and resid 497 through 499' Processing helix chain 'D' and resid 500 through 508 Processing helix chain 'D' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE D 515 " --> pdb=" O ASN D 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN D 522 " --> pdb=" O PHE D 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU D 523 " --> pdb=" O TYR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 544 Processing helix chain 'D' and resid 560 through 574 removed outlier: 3.562A pdb=" N ILE D 564 " --> pdb=" O ASN D 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN D 600 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN D 601 " --> pdb=" O ILE D 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 597 through 601' Processing helix chain 'E' and resid 49 through 55 Processing helix chain 'E' and resid 67 through 84 Processing helix chain 'E' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL E 161 " --> pdb=" O ASP E 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE E 162 " --> pdb=" O VAL E 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 157 through 162' Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP E 201 " --> pdb=" O VAL E 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 201' Processing helix chain 'E' and resid 202 through 226 Processing helix chain 'E' and resid 231 through 236 removed outlier: 3.993A pdb=" N LYS E 236 " --> pdb=" O ALA E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR E 346 " --> pdb=" O THR E 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP E 347 " --> pdb=" O PRO E 343 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE E 348 " --> pdb=" O GLU E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 358 Processing helix chain 'E' and resid 360 through 367 Proline residue: E 365 - end of helix Processing helix chain 'E' and resid 379 through 386 removed outlier: 4.032A pdb=" N MET E 385 " --> pdb=" O LEU E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY E 405 " --> pdb=" O ASP E 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU E 434 " --> pdb=" O GLN E 430 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY E 440 " --> pdb=" O LEU E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 458 Processing helix chain 'E' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG E 465 " --> pdb=" O GLY E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN E 472 " --> pdb=" O HIS E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 499 No H-bonds generated for 'chain 'E' and resid 497 through 499' Processing helix chain 'E' and resid 500 through 508 Processing helix chain 'E' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE E 515 " --> pdb=" O ASN E 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN E 522 " --> pdb=" O PHE E 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU E 523 " --> pdb=" O TYR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 544 Processing helix chain 'E' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE E 564 " --> pdb=" O ASN E 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU E 565 " --> pdb=" O ALA E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN E 600 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN E 601 " --> pdb=" O ILE E 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 597 through 601' Processing helix chain 'F' and resid 49 through 55 Processing helix chain 'F' and resid 67 through 84 Processing helix chain 'F' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 157 through 162' Processing helix chain 'F' and resid 163 through 179 Processing helix chain 'F' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP F 201 " --> pdb=" O VAL F 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 198 through 201' Processing helix chain 'F' and resid 202 through 226 Processing helix chain 'F' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS F 236 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR F 346 " --> pdb=" O THR F 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP F 347 " --> pdb=" O PRO F 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE F 348 " --> pdb=" O GLU F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 358 Processing helix chain 'F' and resid 360 through 367 Proline residue: F 365 - end of helix Processing helix chain 'F' and resid 379 through 386 removed outlier: 4.032A pdb=" N MET F 385 " --> pdb=" O LEU F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY F 405 " --> pdb=" O ASP F 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU F 434 " --> pdb=" O GLN F 430 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY F 440 " --> pdb=" O LEU F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 458 Processing helix chain 'F' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG F 465 " --> pdb=" O GLY F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN F 472 " --> pdb=" O HIS F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 497 through 499 No H-bonds generated for 'chain 'F' and resid 497 through 499' Processing helix chain 'F' and resid 500 through 508 Processing helix chain 'F' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE F 515 " --> pdb=" O ASN F 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN F 522 " --> pdb=" O PHE F 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU F 523 " --> pdb=" O TYR F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 528 through 544 Processing helix chain 'F' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE F 564 " --> pdb=" O ASN F 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU F 565 " --> pdb=" O ALA F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN F 600 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN F 601 " --> pdb=" O ILE F 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 597 through 601' Processing helix chain 'G' and resid 49 through 55 Processing helix chain 'G' and resid 67 through 84 Processing helix chain 'G' and resid 157 through 162 removed outlier: 3.812A pdb=" N VAL G 161 " --> pdb=" O ASP G 157 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE G 162 " --> pdb=" O VAL G 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 157 through 162' Processing helix chain 'G' and resid 163 through 179 Processing helix chain 'G' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP G 201 " --> pdb=" O VAL G 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 198 through 201' Processing helix chain 'G' and resid 202 through 226 Processing helix chain 'G' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS G 236 " --> pdb=" O ALA G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR G 346 " --> pdb=" O THR G 342 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TRP G 347 " --> pdb=" O PRO G 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE G 348 " --> pdb=" O GLU G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 358 Processing helix chain 'G' and resid 360 through 367 Proline residue: G 365 - end of helix Processing helix chain 'G' and resid 378 through 386 removed outlier: 4.020A pdb=" N ALA G 381 " --> pdb=" O ASP G 378 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET G 385 " --> pdb=" O LEU G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY G 405 " --> pdb=" O ASP G 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN G 406 " --> pdb=" O ALA G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU G 434 " --> pdb=" O GLN G 430 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY G 440 " --> pdb=" O LEU G 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 444 through 458 Processing helix chain 'G' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG G 465 " --> pdb=" O GLY G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN G 472 " --> pdb=" O HIS G 469 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 499 No H-bonds generated for 'chain 'G' and resid 497 through 499' Processing helix chain 'G' and resid 500 through 508 Processing helix chain 'G' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE G 515 " --> pdb=" O ASN G 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN G 522 " --> pdb=" O PHE G 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU G 523 " --> pdb=" O TYR G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 528 through 544 Processing helix chain 'G' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE G 564 " --> pdb=" O ASN G 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU G 565 " --> pdb=" O ALA G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN G 600 " --> pdb=" O VAL G 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN G 601 " --> pdb=" O ILE G 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 597 through 601' Processing helix chain 'H' and resid 49 through 55 Processing helix chain 'H' and resid 67 through 84 Processing helix chain 'H' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL H 161 " --> pdb=" O ASP H 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 157 through 162' Processing helix chain 'H' and resid 163 through 179 Processing helix chain 'H' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP H 201 " --> pdb=" O VAL H 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 198 through 201' Processing helix chain 'H' and resid 202 through 226 Processing helix chain 'H' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS H 236 " --> pdb=" O ALA H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR H 346 " --> pdb=" O THR H 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP H 347 " --> pdb=" O PRO H 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE H 348 " --> pdb=" O GLU H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 352 through 358 Processing helix chain 'H' and resid 360 through 367 Proline residue: H 365 - end of helix Processing helix chain 'H' and resid 379 through 386 removed outlier: 4.032A pdb=" N MET H 385 " --> pdb=" O LEU H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY H 405 " --> pdb=" O ASP H 401 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN H 406 " --> pdb=" O ALA H 402 " (cutoff:3.500A) Processing helix chain 'H' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU H 434 " --> pdb=" O GLN H 430 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY H 440 " --> pdb=" O LEU H 436 " (cutoff:3.500A) Processing helix chain 'H' and resid 444 through 458 Processing helix chain 'H' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG H 465 " --> pdb=" O GLY H 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN H 472 " --> pdb=" O HIS H 469 " (cutoff:3.500A) Processing helix chain 'H' and resid 497 through 499 No H-bonds generated for 'chain 'H' and resid 497 through 499' Processing helix chain 'H' and resid 500 through 508 Processing helix chain 'H' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE H 515 " --> pdb=" O ASN H 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN H 522 " --> pdb=" O PHE H 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU H 523 " --> pdb=" O TYR H 519 " (cutoff:3.500A) Processing helix chain 'H' and resid 528 through 544 Processing helix chain 'H' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE H 564 " --> pdb=" O ASN H 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU H 565 " --> pdb=" O ALA H 561 " (cutoff:3.500A) Processing helix chain 'H' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN H 600 " --> pdb=" O VAL H 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN H 601 " --> pdb=" O ILE H 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 597 through 601' Processing helix chain 'I' and resid 49 through 55 Processing helix chain 'I' and resid 67 through 84 Processing helix chain 'I' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL I 161 " --> pdb=" O ASP I 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE I 162 " --> pdb=" O VAL I 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 157 through 162' Processing helix chain 'I' and resid 163 through 179 Processing helix chain 'I' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP I 201 " --> pdb=" O VAL I 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 198 through 201' Processing helix chain 'I' and resid 202 through 226 Processing helix chain 'I' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS I 236 " --> pdb=" O ALA I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR I 346 " --> pdb=" O THR I 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP I 347 " --> pdb=" O PRO I 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE I 348 " --> pdb=" O GLU I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 352 through 358 Processing helix chain 'I' and resid 360 through 367 Proline residue: I 365 - end of helix Processing helix chain 'I' and resid 379 through 386 removed outlier: 4.032A pdb=" N MET I 385 " --> pdb=" O LEU I 382 " (cutoff:3.500A) Processing helix chain 'I' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY I 405 " --> pdb=" O ASP I 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN I 406 " --> pdb=" O ALA I 402 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU I 434 " --> pdb=" O GLN I 430 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY I 440 " --> pdb=" O LEU I 436 " (cutoff:3.500A) Processing helix chain 'I' and resid 444 through 458 Processing helix chain 'I' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG I 465 " --> pdb=" O GLY I 462 " (cutoff:3.500A) Processing helix chain 'I' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN I 472 " --> pdb=" O HIS I 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 497 through 499 No H-bonds generated for 'chain 'I' and resid 497 through 499' Processing helix chain 'I' and resid 500 through 508 Processing helix chain 'I' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE I 515 " --> pdb=" O ASN I 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN I 522 " --> pdb=" O PHE I 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU I 523 " --> pdb=" O TYR I 519 " (cutoff:3.500A) Processing helix chain 'I' and resid 528 through 544 Processing helix chain 'I' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE I 564 " --> pdb=" O ASN I 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU I 565 " --> pdb=" O ALA I 561 " (cutoff:3.500A) Processing helix chain 'I' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN I 600 " --> pdb=" O VAL I 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN I 601 " --> pdb=" O ILE I 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 597 through 601' Processing helix chain 'J' and resid 49 through 55 Processing helix chain 'J' and resid 67 through 84 Processing helix chain 'J' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL J 161 " --> pdb=" O ASP J 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE J 162 " --> pdb=" O VAL J 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 157 through 162' Processing helix chain 'J' and resid 163 through 179 Processing helix chain 'J' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP J 201 " --> pdb=" O VAL J 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 198 through 201' Processing helix chain 'J' and resid 202 through 226 Processing helix chain 'J' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS J 236 " --> pdb=" O ALA J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR J 346 " --> pdb=" O THR J 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP J 347 " --> pdb=" O PRO J 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE J 348 " --> pdb=" O GLU J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 352 through 358 Processing helix chain 'J' and resid 360 through 367 Proline residue: J 365 - end of helix Processing helix chain 'J' and resid 379 through 386 removed outlier: 4.032A pdb=" N MET J 385 " --> pdb=" O LEU J 382 " (cutoff:3.500A) Processing helix chain 'J' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY J 405 " --> pdb=" O ASP J 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN J 406 " --> pdb=" O ALA J 402 " (cutoff:3.500A) Processing helix chain 'J' and resid 428 through 440 removed outlier: 3.811A pdb=" N LEU J 434 " --> pdb=" O GLN J 430 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY J 440 " --> pdb=" O LEU J 436 " (cutoff:3.500A) Processing helix chain 'J' and resid 444 through 458 Processing helix chain 'J' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG J 465 " --> pdb=" O GLY J 462 " (cutoff:3.500A) Processing helix chain 'J' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN J 472 " --> pdb=" O HIS J 469 " (cutoff:3.500A) Processing helix chain 'J' and resid 497 through 499 No H-bonds generated for 'chain 'J' and resid 497 through 499' Processing helix chain 'J' and resid 500 through 508 Processing helix chain 'J' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE J 515 " --> pdb=" O ASN J 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN J 522 " --> pdb=" O PHE J 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU J 523 " --> pdb=" O TYR J 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 528 through 544 Processing helix chain 'J' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE J 564 " --> pdb=" O ASN J 560 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU J 565 " --> pdb=" O ALA J 561 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN J 600 " --> pdb=" O VAL J 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN J 601 " --> pdb=" O ILE J 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 597 through 601' Processing helix chain 'K' and resid 49 through 55 Processing helix chain 'K' and resid 67 through 84 Processing helix chain 'K' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL K 161 " --> pdb=" O ASP K 157 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE K 162 " --> pdb=" O VAL K 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 157 through 162' Processing helix chain 'K' and resid 163 through 179 Processing helix chain 'K' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP K 201 " --> pdb=" O VAL K 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 198 through 201' Processing helix chain 'K' and resid 202 through 226 Processing helix chain 'K' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS K 236 " --> pdb=" O ALA K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR K 346 " --> pdb=" O THR K 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP K 347 " --> pdb=" O PRO K 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE K 348 " --> pdb=" O GLU K 344 " (cutoff:3.500A) Processing helix chain 'K' and resid 352 through 358 Processing helix chain 'K' and resid 360 through 367 Proline residue: K 365 - end of helix Processing helix chain 'K' and resid 378 through 386 removed outlier: 4.020A pdb=" N ALA K 381 " --> pdb=" O ASP K 378 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET K 385 " --> pdb=" O LEU K 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY K 405 " --> pdb=" O ASP K 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN K 406 " --> pdb=" O ALA K 402 " (cutoff:3.500A) Processing helix chain 'K' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU K 434 " --> pdb=" O GLN K 430 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY K 440 " --> pdb=" O LEU K 436 " (cutoff:3.500A) Processing helix chain 'K' and resid 444 through 458 Processing helix chain 'K' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG K 465 " --> pdb=" O GLY K 462 " (cutoff:3.500A) Processing helix chain 'K' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN K 472 " --> pdb=" O HIS K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 497 through 499 No H-bonds generated for 'chain 'K' and resid 497 through 499' Processing helix chain 'K' and resid 500 through 508 Processing helix chain 'K' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE K 515 " --> pdb=" O ASN K 511 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN K 522 " --> pdb=" O PHE K 518 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU K 523 " --> pdb=" O TYR K 519 " (cutoff:3.500A) Processing helix chain 'K' and resid 528 through 544 Processing helix chain 'K' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE K 564 " --> pdb=" O ASN K 560 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU K 565 " --> pdb=" O ALA K 561 " (cutoff:3.500A) Processing helix chain 'K' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN K 600 " --> pdb=" O VAL K 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN K 601 " --> pdb=" O ILE K 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 597 through 601' Processing helix chain 'L' and resid 49 through 55 Processing helix chain 'L' and resid 67 through 84 Processing helix chain 'L' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL L 161 " --> pdb=" O ASP L 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE L 162 " --> pdb=" O VAL L 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 157 through 162' Processing helix chain 'L' and resid 163 through 179 Processing helix chain 'L' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP L 201 " --> pdb=" O VAL L 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 198 through 201' Processing helix chain 'L' and resid 202 through 226 Processing helix chain 'L' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS L 236 " --> pdb=" O ALA L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR L 346 " --> pdb=" O THR L 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP L 347 " --> pdb=" O PRO L 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE L 348 " --> pdb=" O GLU L 344 " (cutoff:3.500A) Processing helix chain 'L' and resid 352 through 358 Processing helix chain 'L' and resid 360 through 367 Proline residue: L 365 - end of helix Processing helix chain 'L' and resid 379 through 386 removed outlier: 4.032A pdb=" N MET L 385 " --> pdb=" O LEU L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY L 405 " --> pdb=" O ASP L 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN L 406 " --> pdb=" O ALA L 402 " (cutoff:3.500A) Processing helix chain 'L' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU L 434 " --> pdb=" O GLN L 430 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY L 440 " --> pdb=" O LEU L 436 " (cutoff:3.500A) Processing helix chain 'L' and resid 444 through 458 Processing helix chain 'L' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG L 465 " --> pdb=" O GLY L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN L 472 " --> pdb=" O HIS L 469 " (cutoff:3.500A) Processing helix chain 'L' and resid 497 through 499 No H-bonds generated for 'chain 'L' and resid 497 through 499' Processing helix chain 'L' and resid 500 through 508 Processing helix chain 'L' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE L 515 " --> pdb=" O ASN L 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN L 522 " --> pdb=" O PHE L 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU L 523 " --> pdb=" O TYR L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 528 through 544 Processing helix chain 'L' and resid 560 through 574 removed outlier: 3.562A pdb=" N ILE L 564 " --> pdb=" O ASN L 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU L 565 " --> pdb=" O ALA L 561 " (cutoff:3.500A) Processing helix chain 'L' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN L 600 " --> pdb=" O VAL L 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN L 601 " --> pdb=" O ILE L 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 597 through 601' Processing helix chain 'M' and resid 49 through 55 Processing helix chain 'M' and resid 67 through 84 Processing helix chain 'M' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL M 161 " --> pdb=" O ASP M 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE M 162 " --> pdb=" O VAL M 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 157 through 162' Processing helix chain 'M' and resid 163 through 179 Processing helix chain 'M' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP M 201 " --> pdb=" O VAL M 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 198 through 201' Processing helix chain 'M' and resid 202 through 226 Processing helix chain 'M' and resid 231 through 236 removed outlier: 3.993A pdb=" N LYS M 236 " --> pdb=" O ALA M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR M 346 " --> pdb=" O THR M 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP M 347 " --> pdb=" O PRO M 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE M 348 " --> pdb=" O GLU M 344 " (cutoff:3.500A) Processing helix chain 'M' and resid 352 through 358 Processing helix chain 'M' and resid 360 through 367 Proline residue: M 365 - end of helix Processing helix chain 'M' and resid 379 through 386 removed outlier: 4.032A pdb=" N MET M 385 " --> pdb=" O LEU M 382 " (cutoff:3.500A) Processing helix chain 'M' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY M 405 " --> pdb=" O ASP M 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN M 406 " --> pdb=" O ALA M 402 " (cutoff:3.500A) Processing helix chain 'M' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU M 434 " --> pdb=" O GLN M 430 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY M 440 " --> pdb=" O LEU M 436 " (cutoff:3.500A) Processing helix chain 'M' and resid 444 through 458 Processing helix chain 'M' and resid 462 through 466 removed outlier: 3.667A pdb=" N ARG M 465 " --> pdb=" O GLY M 462 " (cutoff:3.500A) Processing helix chain 'M' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN M 472 " --> pdb=" O HIS M 469 " (cutoff:3.500A) Processing helix chain 'M' and resid 497 through 499 No H-bonds generated for 'chain 'M' and resid 497 through 499' Processing helix chain 'M' and resid 500 through 508 Processing helix chain 'M' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE M 515 " --> pdb=" O ASN M 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN M 522 " --> pdb=" O PHE M 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU M 523 " --> pdb=" O TYR M 519 " (cutoff:3.500A) Processing helix chain 'M' and resid 528 through 544 Processing helix chain 'M' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE M 564 " --> pdb=" O ASN M 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU M 565 " --> pdb=" O ALA M 561 " (cutoff:3.500A) Processing helix chain 'M' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN M 600 " --> pdb=" O VAL M 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN M 601 " --> pdb=" O ILE M 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 597 through 601' Processing helix chain 'N' and resid 49 through 55 Processing helix chain 'N' and resid 67 through 84 Processing helix chain 'N' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL N 161 " --> pdb=" O ASP N 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE N 162 " --> pdb=" O VAL N 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 157 through 162' Processing helix chain 'N' and resid 163 through 179 Processing helix chain 'N' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP N 201 " --> pdb=" O VAL N 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 198 through 201' Processing helix chain 'N' and resid 202 through 226 Processing helix chain 'N' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS N 236 " --> pdb=" O ALA N 233 " (cutoff:3.500A) Processing helix chain 'N' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR N 346 " --> pdb=" O THR N 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP N 347 " --> pdb=" O PRO N 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE N 348 " --> pdb=" O GLU N 344 " (cutoff:3.500A) Processing helix chain 'N' and resid 352 through 358 Processing helix chain 'N' and resid 360 through 367 Proline residue: N 365 - end of helix Processing helix chain 'N' and resid 379 through 386 removed outlier: 4.031A pdb=" N MET N 385 " --> pdb=" O LEU N 382 " (cutoff:3.500A) Processing helix chain 'N' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY N 405 " --> pdb=" O ASP N 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN N 406 " --> pdb=" O ALA N 402 " (cutoff:3.500A) Processing helix chain 'N' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU N 434 " --> pdb=" O GLN N 430 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY N 440 " --> pdb=" O LEU N 436 " (cutoff:3.500A) Processing helix chain 'N' and resid 444 through 458 Processing helix chain 'N' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG N 465 " --> pdb=" O GLY N 462 " (cutoff:3.500A) Processing helix chain 'N' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN N 472 " --> pdb=" O HIS N 469 " (cutoff:3.500A) Processing helix chain 'N' and resid 497 through 499 No H-bonds generated for 'chain 'N' and resid 497 through 499' Processing helix chain 'N' and resid 500 through 508 Processing helix chain 'N' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE N 515 " --> pdb=" O ASN N 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN N 522 " --> pdb=" O PHE N 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU N 523 " --> pdb=" O TYR N 519 " (cutoff:3.500A) Processing helix chain 'N' and resid 528 through 544 Processing helix chain 'N' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE N 564 " --> pdb=" O ASN N 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU N 565 " --> pdb=" O ALA N 561 " (cutoff:3.500A) Processing helix chain 'N' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN N 600 " --> pdb=" O VAL N 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN N 601 " --> pdb=" O ILE N 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 597 through 601' Processing helix chain 'O' and resid 49 through 55 Processing helix chain 'O' and resid 67 through 84 Processing helix chain 'O' and resid 157 through 162 removed outlier: 3.814A pdb=" N VAL O 161 " --> pdb=" O ASP O 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE O 162 " --> pdb=" O VAL O 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 157 through 162' Processing helix chain 'O' and resid 163 through 179 Processing helix chain 'O' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP O 201 " --> pdb=" O VAL O 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 198 through 201' Processing helix chain 'O' and resid 202 through 226 Processing helix chain 'O' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS O 236 " --> pdb=" O ALA O 233 " (cutoff:3.500A) Processing helix chain 'O' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR O 346 " --> pdb=" O THR O 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP O 347 " --> pdb=" O PRO O 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE O 348 " --> pdb=" O GLU O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 352 through 358 Processing helix chain 'O' and resid 360 through 367 Proline residue: O 365 - end of helix Processing helix chain 'O' and resid 379 through 386 removed outlier: 4.032A pdb=" N MET O 385 " --> pdb=" O LEU O 382 " (cutoff:3.500A) Processing helix chain 'O' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY O 405 " --> pdb=" O ASP O 401 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN O 406 " --> pdb=" O ALA O 402 " (cutoff:3.500A) Processing helix chain 'O' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU O 434 " --> pdb=" O GLN O 430 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY O 440 " --> pdb=" O LEU O 436 " (cutoff:3.500A) Processing helix chain 'O' and resid 444 through 458 Processing helix chain 'O' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG O 465 " --> pdb=" O GLY O 462 " (cutoff:3.500A) Processing helix chain 'O' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN O 472 " --> pdb=" O HIS O 469 " (cutoff:3.500A) Processing helix chain 'O' and resid 497 through 499 No H-bonds generated for 'chain 'O' and resid 497 through 499' Processing helix chain 'O' and resid 500 through 508 Processing helix chain 'O' and resid 511 through 524 removed outlier: 3.608A pdb=" N PHE O 515 " --> pdb=" O ASN O 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN O 522 " --> pdb=" O PHE O 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU O 523 " --> pdb=" O TYR O 519 " (cutoff:3.500A) Processing helix chain 'O' and resid 528 through 544 Processing helix chain 'O' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE O 564 " --> pdb=" O ASN O 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU O 565 " --> pdb=" O ALA O 561 " (cutoff:3.500A) Processing helix chain 'O' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN O 600 " --> pdb=" O VAL O 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN O 601 " --> pdb=" O ILE O 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 597 through 601' Processing helix chain 'P' and resid 49 through 55 Processing helix chain 'P' and resid 67 through 84 Processing helix chain 'P' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL P 161 " --> pdb=" O ASP P 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE P 162 " --> pdb=" O VAL P 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 157 through 162' Processing helix chain 'P' and resid 163 through 179 Processing helix chain 'P' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP P 201 " --> pdb=" O VAL P 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 198 through 201' Processing helix chain 'P' and resid 202 through 226 Processing helix chain 'P' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS P 236 " --> pdb=" O ALA P 233 " (cutoff:3.500A) Processing helix chain 'P' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR P 346 " --> pdb=" O THR P 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP P 347 " --> pdb=" O PRO P 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE P 348 " --> pdb=" O GLU P 344 " (cutoff:3.500A) Processing helix chain 'P' and resid 352 through 358 Processing helix chain 'P' and resid 360 through 367 Proline residue: P 365 - end of helix Processing helix chain 'P' and resid 379 through 386 removed outlier: 4.032A pdb=" N MET P 385 " --> pdb=" O LEU P 382 " (cutoff:3.500A) Processing helix chain 'P' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY P 405 " --> pdb=" O ASP P 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN P 406 " --> pdb=" O ALA P 402 " (cutoff:3.500A) Processing helix chain 'P' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU P 434 " --> pdb=" O GLN P 430 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY P 440 " --> pdb=" O LEU P 436 " (cutoff:3.500A) Processing helix chain 'P' and resid 444 through 458 Processing helix chain 'P' and resid 462 through 466 removed outlier: 3.667A pdb=" N ARG P 465 " --> pdb=" O GLY P 462 " (cutoff:3.500A) Processing helix chain 'P' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN P 472 " --> pdb=" O HIS P 469 " (cutoff:3.500A) Processing helix chain 'P' and resid 497 through 499 No H-bonds generated for 'chain 'P' and resid 497 through 499' Processing helix chain 'P' and resid 500 through 508 Processing helix chain 'P' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE P 515 " --> pdb=" O ASN P 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN P 522 " --> pdb=" O PHE P 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU P 523 " --> pdb=" O TYR P 519 " (cutoff:3.500A) Processing helix chain 'P' and resid 528 through 544 Processing helix chain 'P' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE P 564 " --> pdb=" O ASN P 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU P 565 " --> pdb=" O ALA P 561 " (cutoff:3.500A) Processing helix chain 'P' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN P 600 " --> pdb=" O VAL P 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN P 601 " --> pdb=" O ILE P 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 597 through 601' Processing helix chain 'Q' and resid 49 through 55 Processing helix chain 'Q' and resid 67 through 84 Processing helix chain 'Q' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL Q 161 " --> pdb=" O ASP Q 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE Q 162 " --> pdb=" O VAL Q 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 157 through 162' Processing helix chain 'Q' and resid 163 through 179 Processing helix chain 'Q' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP Q 201 " --> pdb=" O VAL Q 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 198 through 201' Processing helix chain 'Q' and resid 202 through 226 Processing helix chain 'Q' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS Q 236 " --> pdb=" O ALA Q 233 " (cutoff:3.500A) Processing helix chain 'Q' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR Q 346 " --> pdb=" O THR Q 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP Q 347 " --> pdb=" O PRO Q 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE Q 348 " --> pdb=" O GLU Q 344 " (cutoff:3.500A) Processing helix chain 'Q' and resid 352 through 358 Processing helix chain 'Q' and resid 360 through 367 Proline residue: Q 365 - end of helix Processing helix chain 'Q' and resid 379 through 386 removed outlier: 4.032A pdb=" N MET Q 385 " --> pdb=" O LEU Q 382 " (cutoff:3.500A) Processing helix chain 'Q' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY Q 405 " --> pdb=" O ASP Q 401 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN Q 406 " --> pdb=" O ALA Q 402 " (cutoff:3.500A) Processing helix chain 'Q' and resid 428 through 440 removed outlier: 3.811A pdb=" N LEU Q 434 " --> pdb=" O GLN Q 430 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY Q 440 " --> pdb=" O LEU Q 436 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 458 Processing helix chain 'Q' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG Q 465 " --> pdb=" O GLY Q 462 " (cutoff:3.500A) Processing helix chain 'Q' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN Q 472 " --> pdb=" O HIS Q 469 " (cutoff:3.500A) Processing helix chain 'Q' and resid 497 through 499 No H-bonds generated for 'chain 'Q' and resid 497 through 499' Processing helix chain 'Q' and resid 500 through 508 Processing helix chain 'Q' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE Q 515 " --> pdb=" O ASN Q 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN Q 522 " --> pdb=" O PHE Q 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU Q 523 " --> pdb=" O TYR Q 519 " (cutoff:3.500A) Processing helix chain 'Q' and resid 528 through 544 Processing helix chain 'Q' and resid 560 through 574 removed outlier: 3.562A pdb=" N ILE Q 564 " --> pdb=" O ASN Q 560 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU Q 565 " --> pdb=" O ALA Q 561 " (cutoff:3.500A) Processing helix chain 'Q' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN Q 600 " --> pdb=" O VAL Q 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN Q 601 " --> pdb=" O ILE Q 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 597 through 601' Processing helix chain 'R' and resid 49 through 55 Processing helix chain 'R' and resid 67 through 84 Processing helix chain 'R' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL R 161 " --> pdb=" O ASP R 157 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE R 162 " --> pdb=" O VAL R 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 157 through 162' Processing helix chain 'R' and resid 163 through 179 Processing helix chain 'R' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP R 201 " --> pdb=" O VAL R 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 198 through 201' Processing helix chain 'R' and resid 202 through 226 Processing helix chain 'R' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS R 236 " --> pdb=" O ALA R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR R 346 " --> pdb=" O THR R 342 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TRP R 347 " --> pdb=" O PRO R 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE R 348 " --> pdb=" O GLU R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 352 through 358 Processing helix chain 'R' and resid 360 through 367 Proline residue: R 365 - end of helix Processing helix chain 'R' and resid 379 through 386 removed outlier: 4.032A pdb=" N MET R 385 " --> pdb=" O LEU R 382 " (cutoff:3.500A) Processing helix chain 'R' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY R 405 " --> pdb=" O ASP R 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN R 406 " --> pdb=" O ALA R 402 " (cutoff:3.500A) Processing helix chain 'R' and resid 428 through 440 removed outlier: 3.811A pdb=" N LEU R 434 " --> pdb=" O GLN R 430 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY R 440 " --> pdb=" O LEU R 436 " (cutoff:3.500A) Processing helix chain 'R' and resid 444 through 458 Processing helix chain 'R' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG R 465 " --> pdb=" O GLY R 462 " (cutoff:3.500A) Processing helix chain 'R' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN R 472 " --> pdb=" O HIS R 469 " (cutoff:3.500A) Processing helix chain 'R' and resid 497 through 499 No H-bonds generated for 'chain 'R' and resid 497 through 499' Processing helix chain 'R' and resid 500 through 508 Processing helix chain 'R' and resid 511 through 524 removed outlier: 3.608A pdb=" N PHE R 515 " --> pdb=" O ASN R 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN R 522 " --> pdb=" O PHE R 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU R 523 " --> pdb=" O TYR R 519 " (cutoff:3.500A) Processing helix chain 'R' and resid 528 through 544 Processing helix chain 'R' and resid 560 through 574 removed outlier: 3.562A pdb=" N ILE R 564 " --> pdb=" O ASN R 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU R 565 " --> pdb=" O ALA R 561 " (cutoff:3.500A) Processing helix chain 'R' and resid 597 through 601 removed outlier: 3.502A pdb=" N ASN R 600 " --> pdb=" O VAL R 597 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN R 601 " --> pdb=" O ILE R 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 597 through 601' Processing helix chain 'S' and resid 49 through 55 Processing helix chain 'S' and resid 67 through 84 Processing helix chain 'S' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL S 161 " --> pdb=" O ASP S 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE S 162 " --> pdb=" O VAL S 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 157 through 162' Processing helix chain 'S' and resid 163 through 179 Processing helix chain 'S' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP S 201 " --> pdb=" O VAL S 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 198 through 201' Processing helix chain 'S' and resid 202 through 226 Processing helix chain 'S' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS S 236 " --> pdb=" O ALA S 233 " (cutoff:3.500A) Processing helix chain 'S' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR S 346 " --> pdb=" O THR S 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP S 347 " --> pdb=" O PRO S 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE S 348 " --> pdb=" O GLU S 344 " (cutoff:3.500A) Processing helix chain 'S' and resid 352 through 358 Processing helix chain 'S' and resid 360 through 367 Proline residue: S 365 - end of helix Processing helix chain 'S' and resid 379 through 386 removed outlier: 4.032A pdb=" N MET S 385 " --> pdb=" O LEU S 382 " (cutoff:3.500A) Processing helix chain 'S' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY S 405 " --> pdb=" O ASP S 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN S 406 " --> pdb=" O ALA S 402 " (cutoff:3.500A) Processing helix chain 'S' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU S 434 " --> pdb=" O GLN S 430 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY S 440 " --> pdb=" O LEU S 436 " (cutoff:3.500A) Processing helix chain 'S' and resid 444 through 458 Processing helix chain 'S' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG S 465 " --> pdb=" O GLY S 462 " (cutoff:3.500A) Processing helix chain 'S' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN S 472 " --> pdb=" O HIS S 469 " (cutoff:3.500A) Processing helix chain 'S' and resid 497 through 499 No H-bonds generated for 'chain 'S' and resid 497 through 499' Processing helix chain 'S' and resid 500 through 508 Processing helix chain 'S' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE S 515 " --> pdb=" O ASN S 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN S 522 " --> pdb=" O PHE S 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU S 523 " --> pdb=" O TYR S 519 " (cutoff:3.500A) Processing helix chain 'S' and resid 528 through 544 Processing helix chain 'S' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE S 564 " --> pdb=" O ASN S 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU S 565 " --> pdb=" O ALA S 561 " (cutoff:3.500A) Processing helix chain 'S' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN S 600 " --> pdb=" O VAL S 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN S 601 " --> pdb=" O ILE S 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 597 through 601' Processing helix chain 'T' and resid 49 through 55 Processing helix chain 'T' and resid 67 through 84 Processing helix chain 'T' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL T 161 " --> pdb=" O ASP T 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE T 162 " --> pdb=" O VAL T 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 157 through 162' Processing helix chain 'T' and resid 163 through 179 Processing helix chain 'T' and resid 198 through 201 removed outlier: 3.714A pdb=" N ASP T 201 " --> pdb=" O VAL T 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 198 through 201' Processing helix chain 'T' and resid 202 through 226 Processing helix chain 'T' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS T 236 " --> pdb=" O ALA T 233 " (cutoff:3.500A) Processing helix chain 'T' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR T 346 " --> pdb=" O THR T 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP T 347 " --> pdb=" O PRO T 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE T 348 " --> pdb=" O GLU T 344 " (cutoff:3.500A) Processing helix chain 'T' and resid 352 through 358 Processing helix chain 'T' and resid 360 through 367 Proline residue: T 365 - end of helix Processing helix chain 'T' and resid 379 through 386 removed outlier: 4.032A pdb=" N MET T 385 " --> pdb=" O LEU T 382 " (cutoff:3.500A) Processing helix chain 'T' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY T 405 " --> pdb=" O ASP T 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN T 406 " --> pdb=" O ALA T 402 " (cutoff:3.500A) Processing helix chain 'T' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU T 434 " --> pdb=" O GLN T 430 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY T 440 " --> pdb=" O LEU T 436 " (cutoff:3.500A) Processing helix chain 'T' and resid 444 through 458 Processing helix chain 'T' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG T 465 " --> pdb=" O GLY T 462 " (cutoff:3.500A) Processing helix chain 'T' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN T 472 " --> pdb=" O HIS T 469 " (cutoff:3.500A) Processing helix chain 'T' and resid 497 through 499 No H-bonds generated for 'chain 'T' and resid 497 through 499' Processing helix chain 'T' and resid 500 through 508 Processing helix chain 'T' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE T 515 " --> pdb=" O ASN T 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN T 522 " --> pdb=" O PHE T 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU T 523 " --> pdb=" O TYR T 519 " (cutoff:3.500A) Processing helix chain 'T' and resid 528 through 544 Processing helix chain 'T' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE T 564 " --> pdb=" O ASN T 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU T 565 " --> pdb=" O ALA T 561 " (cutoff:3.500A) Processing helix chain 'T' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN T 600 " --> pdb=" O VAL T 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN T 601 " --> pdb=" O ILE T 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 597 through 601' Processing helix chain 'V' and resid 49 through 55 Processing helix chain 'V' and resid 67 through 84 Processing helix chain 'V' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL V 161 " --> pdb=" O ASP V 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE V 162 " --> pdb=" O VAL V 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 157 through 162' Processing helix chain 'V' and resid 163 through 179 Processing helix chain 'V' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP V 201 " --> pdb=" O VAL V 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 198 through 201' Processing helix chain 'V' and resid 202 through 226 Processing helix chain 'V' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS V 236 " --> pdb=" O ALA V 233 " (cutoff:3.500A) Processing helix chain 'V' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR V 346 " --> pdb=" O THR V 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP V 347 " --> pdb=" O PRO V 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE V 348 " --> pdb=" O GLU V 344 " (cutoff:3.500A) Processing helix chain 'V' and resid 352 through 358 Processing helix chain 'V' and resid 360 through 367 Proline residue: V 365 - end of helix Processing helix chain 'V' and resid 378 through 386 removed outlier: 4.020A pdb=" N ALA V 381 " --> pdb=" O ASP V 378 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET V 385 " --> pdb=" O LEU V 382 " (cutoff:3.500A) Processing helix chain 'V' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY V 405 " --> pdb=" O ASP V 401 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN V 406 " --> pdb=" O ALA V 402 " (cutoff:3.500A) Processing helix chain 'V' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU V 434 " --> pdb=" O GLN V 430 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY V 440 " --> pdb=" O LEU V 436 " (cutoff:3.500A) Processing helix chain 'V' and resid 444 through 458 Processing helix chain 'V' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG V 465 " --> pdb=" O GLY V 462 " (cutoff:3.500A) Processing helix chain 'V' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN V 472 " --> pdb=" O HIS V 469 " (cutoff:3.500A) Processing helix chain 'V' and resid 497 through 499 No H-bonds generated for 'chain 'V' and resid 497 through 499' Processing helix chain 'V' and resid 500 through 508 Processing helix chain 'V' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE V 515 " --> pdb=" O ASN V 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN V 522 " --> pdb=" O PHE V 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU V 523 " --> pdb=" O TYR V 519 " (cutoff:3.500A) Processing helix chain 'V' and resid 528 through 544 Processing helix chain 'V' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE V 564 " --> pdb=" O ASN V 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU V 565 " --> pdb=" O ALA V 561 " (cutoff:3.500A) Processing helix chain 'V' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN V 600 " --> pdb=" O VAL V 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN V 601 " --> pdb=" O ILE V 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 597 through 601' Processing helix chain 'W' and resid 49 through 55 Processing helix chain 'W' and resid 67 through 84 Processing helix chain 'W' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL W 161 " --> pdb=" O ASP W 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE W 162 " --> pdb=" O VAL W 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 157 through 162' Processing helix chain 'W' and resid 163 through 179 Processing helix chain 'W' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP W 201 " --> pdb=" O VAL W 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 198 through 201' Processing helix chain 'W' and resid 202 through 226 Processing helix chain 'W' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS W 236 " --> pdb=" O ALA W 233 " (cutoff:3.500A) Processing helix chain 'W' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR W 346 " --> pdb=" O THR W 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP W 347 " --> pdb=" O PRO W 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE W 348 " --> pdb=" O GLU W 344 " (cutoff:3.500A) Processing helix chain 'W' and resid 352 through 358 Processing helix chain 'W' and resid 360 through 367 Proline residue: W 365 - end of helix Processing helix chain 'W' and resid 378 through 386 removed outlier: 4.020A pdb=" N ALA W 381 " --> pdb=" O ASP W 378 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET W 385 " --> pdb=" O LEU W 382 " (cutoff:3.500A) Processing helix chain 'W' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY W 405 " --> pdb=" O ASP W 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN W 406 " --> pdb=" O ALA W 402 " (cutoff:3.500A) Processing helix chain 'W' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU W 434 " --> pdb=" O GLN W 430 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY W 440 " --> pdb=" O LEU W 436 " (cutoff:3.500A) Processing helix chain 'W' and resid 444 through 458 Processing helix chain 'W' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG W 465 " --> pdb=" O GLY W 462 " (cutoff:3.500A) Processing helix chain 'W' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN W 472 " --> pdb=" O HIS W 469 " (cutoff:3.500A) Processing helix chain 'W' and resid 497 through 499 No H-bonds generated for 'chain 'W' and resid 497 through 499' Processing helix chain 'W' and resid 500 through 508 Processing helix chain 'W' and resid 511 through 524 removed outlier: 3.608A pdb=" N PHE W 515 " --> pdb=" O ASN W 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN W 522 " --> pdb=" O PHE W 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU W 523 " --> pdb=" O TYR W 519 " (cutoff:3.500A) Processing helix chain 'W' and resid 528 through 544 Processing helix chain 'W' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE W 564 " --> pdb=" O ASN W 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU W 565 " --> pdb=" O ALA W 561 " (cutoff:3.500A) Processing helix chain 'W' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN W 600 " --> pdb=" O VAL W 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN W 601 " --> pdb=" O ILE W 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 597 through 601' Processing helix chain 'X' and resid 49 through 55 Processing helix chain 'X' and resid 67 through 84 Processing helix chain 'X' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL X 161 " --> pdb=" O ASP X 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE X 162 " --> pdb=" O VAL X 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 157 through 162' Processing helix chain 'X' and resid 163 through 179 Processing helix chain 'X' and resid 198 through 201 removed outlier: 3.714A pdb=" N ASP X 201 " --> pdb=" O VAL X 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 198 through 201' Processing helix chain 'X' and resid 202 through 226 Processing helix chain 'X' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS X 236 " --> pdb=" O ALA X 233 " (cutoff:3.500A) Processing helix chain 'X' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR X 346 " --> pdb=" O THR X 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP X 347 " --> pdb=" O PRO X 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE X 348 " --> pdb=" O GLU X 344 " (cutoff:3.500A) Processing helix chain 'X' and resid 352 through 358 Processing helix chain 'X' and resid 360 through 367 Proline residue: X 365 - end of helix Processing helix chain 'X' and resid 379 through 386 removed outlier: 4.032A pdb=" N MET X 385 " --> pdb=" O LEU X 382 " (cutoff:3.500A) Processing helix chain 'X' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY X 405 " --> pdb=" O ASP X 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN X 406 " --> pdb=" O ALA X 402 " (cutoff:3.500A) Processing helix chain 'X' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU X 434 " --> pdb=" O GLN X 430 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY X 440 " --> pdb=" O LEU X 436 " (cutoff:3.500A) Processing helix chain 'X' and resid 444 through 458 Processing helix chain 'X' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG X 465 " --> pdb=" O GLY X 462 " (cutoff:3.500A) Processing helix chain 'X' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN X 472 " --> pdb=" O HIS X 469 " (cutoff:3.500A) Processing helix chain 'X' and resid 497 through 499 No H-bonds generated for 'chain 'X' and resid 497 through 499' Processing helix chain 'X' and resid 500 through 508 Processing helix chain 'X' and resid 511 through 524 removed outlier: 3.608A pdb=" N PHE X 515 " --> pdb=" O ASN X 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN X 522 " --> pdb=" O PHE X 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU X 523 " --> pdb=" O TYR X 519 " (cutoff:3.500A) Processing helix chain 'X' and resid 528 through 544 Processing helix chain 'X' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE X 564 " --> pdb=" O ASN X 560 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU X 565 " --> pdb=" O ALA X 561 " (cutoff:3.500A) Processing helix chain 'X' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN X 600 " --> pdb=" O VAL X 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN X 601 " --> pdb=" O ILE X 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 597 through 601' Processing helix chain 'Y' and resid 49 through 55 Processing helix chain 'Y' and resid 67 through 84 Processing helix chain 'Y' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL Y 161 " --> pdb=" O ASP Y 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE Y 162 " --> pdb=" O VAL Y 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 157 through 162' Processing helix chain 'Y' and resid 163 through 179 Processing helix chain 'Y' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP Y 201 " --> pdb=" O VAL Y 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 198 through 201' Processing helix chain 'Y' and resid 202 through 226 Processing helix chain 'Y' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS Y 236 " --> pdb=" O ALA Y 233 " (cutoff:3.500A) Processing helix chain 'Y' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR Y 346 " --> pdb=" O THR Y 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP Y 347 " --> pdb=" O PRO Y 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE Y 348 " --> pdb=" O GLU Y 344 " (cutoff:3.500A) Processing helix chain 'Y' and resid 352 through 358 Processing helix chain 'Y' and resid 360 through 367 Proline residue: Y 365 - end of helix Processing helix chain 'Y' and resid 378 through 386 removed outlier: 4.019A pdb=" N ALA Y 381 " --> pdb=" O ASP Y 378 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET Y 385 " --> pdb=" O LEU Y 382 " (cutoff:3.500A) Processing helix chain 'Y' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY Y 405 " --> pdb=" O ASP Y 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN Y 406 " --> pdb=" O ALA Y 402 " (cutoff:3.500A) Processing helix chain 'Y' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU Y 434 " --> pdb=" O GLN Y 430 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY Y 440 " --> pdb=" O LEU Y 436 " (cutoff:3.500A) Processing helix chain 'Y' and resid 444 through 458 Processing helix chain 'Y' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG Y 465 " --> pdb=" O GLY Y 462 " (cutoff:3.500A) Processing helix chain 'Y' and resid 468 through 472 removed outlier: 3.848A pdb=" N GLN Y 472 " --> pdb=" O HIS Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 497 through 499 No H-bonds generated for 'chain 'Y' and resid 497 through 499' Processing helix chain 'Y' and resid 500 through 508 Processing helix chain 'Y' and resid 511 through 524 removed outlier: 3.608A pdb=" N PHE Y 515 " --> pdb=" O ASN Y 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN Y 522 " --> pdb=" O PHE Y 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU Y 523 " --> pdb=" O TYR Y 519 " (cutoff:3.500A) Processing helix chain 'Y' and resid 528 through 544 Processing helix chain 'Y' and resid 560 through 574 removed outlier: 3.562A pdb=" N ILE Y 564 " --> pdb=" O ASN Y 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU Y 565 " --> pdb=" O ALA Y 561 " (cutoff:3.500A) Processing helix chain 'Y' and resid 597 through 601 removed outlier: 3.503A pdb=" N ASN Y 600 " --> pdb=" O VAL Y 597 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN Y 601 " --> pdb=" O ILE Y 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 597 through 601' Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 96 Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 145 removed outlier: 3.511A pdb=" N ILE A 143 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 493 through 495 removed outlier: 5.999A pdb=" N GLU A 476 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TYR A 559 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR A 478 " --> pdb=" O CYS A 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS A 557 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN A 480 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU A 555 " --> pdb=" O GLN A 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 482 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS A 553 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 484 " --> pdb=" O THR A 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 559 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE A 418 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP A 331 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA A 294 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL A 332 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN A 292 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A 291 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 270 " --> pdb=" O ASN A 291 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU A 243 " --> pdb=" O THR A 579 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 254 through 255 Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 96 Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 96 Processing sheet with id=AA8, first strand: chain 'B' and resid 140 through 145 removed outlier: 3.512A pdb=" N ILE B 143 " --> pdb=" O ASP B 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 493 through 495 removed outlier: 6.000A pdb=" N GLU B 476 " --> pdb=" O TYR B 559 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TYR B 559 " --> pdb=" O GLU B 476 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR B 478 " --> pdb=" O CYS B 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS B 557 " --> pdb=" O THR B 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN B 480 " --> pdb=" O GLU B 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU B 555 " --> pdb=" O GLN B 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 482 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS B 553 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU B 484 " --> pdb=" O THR B 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR B 559 " --> pdb=" O PHE B 418 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE B 418 " --> pdb=" O TYR B 559 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP B 331 " --> pdb=" O ASP B 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA B 294 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL B 332 " --> pdb=" O GLN B 292 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLN B 292 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN B 291 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 270 " --> pdb=" O ASN B 291 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU B 243 " --> pdb=" O THR B 579 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 254 through 255 Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 96 Processing sheet with id=AB3, first strand: chain 'C' and resid 92 through 96 Processing sheet with id=AB4, first strand: chain 'C' and resid 140 through 145 removed outlier: 3.512A pdb=" N ILE C 143 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 493 through 495 removed outlier: 6.000A pdb=" N GLU C 476 " --> pdb=" O TYR C 559 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR C 559 " --> pdb=" O GLU C 476 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR C 478 " --> pdb=" O CYS C 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS C 557 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN C 480 " --> pdb=" O GLU C 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU C 555 " --> pdb=" O GLN C 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE C 482 " --> pdb=" O LYS C 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS C 553 " --> pdb=" O ILE C 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 484 " --> pdb=" O THR C 551 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 559 " --> pdb=" O PHE C 418 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE C 418 " --> pdb=" O TYR C 559 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP C 331 " --> pdb=" O ASP C 421 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA C 294 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL C 332 " --> pdb=" O GLN C 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN C 292 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN C 291 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 270 " --> pdb=" O ASN C 291 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU C 243 " --> pdb=" O THR C 579 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 254 through 255 Processing sheet with id=AB7, first strand: chain 'D' and resid 92 through 96 Processing sheet with id=AB8, first strand: chain 'D' and resid 92 through 96 Processing sheet with id=AB9, first strand: chain 'D' and resid 140 through 145 removed outlier: 3.511A pdb=" N ILE D 143 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 493 through 495 removed outlier: 5.999A pdb=" N GLU D 476 " --> pdb=" O TYR D 559 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR D 559 " --> pdb=" O GLU D 476 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR D 478 " --> pdb=" O CYS D 557 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N CYS D 557 " --> pdb=" O THR D 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN D 480 " --> pdb=" O GLU D 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU D 555 " --> pdb=" O GLN D 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE D 482 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS D 553 " --> pdb=" O ILE D 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU D 484 " --> pdb=" O THR D 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR D 559 " --> pdb=" O PHE D 418 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE D 418 " --> pdb=" O TYR D 559 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP D 331 " --> pdb=" O ASP D 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA D 294 " --> pdb=" O THR D 330 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL D 332 " --> pdb=" O GLN D 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN D 292 " --> pdb=" O VAL D 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN D 291 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR D 270 " --> pdb=" O ASN D 291 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU D 243 " --> pdb=" O THR D 579 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 254 through 255 Processing sheet with id=AC3, first strand: chain 'E' and resid 92 through 96 Processing sheet with id=AC4, first strand: chain 'E' and resid 92 through 96 Processing sheet with id=AC5, first strand: chain 'E' and resid 140 through 145 removed outlier: 3.512A pdb=" N ILE E 143 " --> pdb=" O ASP E 150 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 493 through 495 removed outlier: 5.999A pdb=" N GLU E 476 " --> pdb=" O TYR E 559 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR E 559 " --> pdb=" O GLU E 476 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR E 478 " --> pdb=" O CYS E 557 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N CYS E 557 " --> pdb=" O THR E 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN E 480 " --> pdb=" O GLU E 555 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU E 555 " --> pdb=" O GLN E 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE E 482 " --> pdb=" O LYS E 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS E 553 " --> pdb=" O ILE E 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU E 484 " --> pdb=" O THR E 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR E 559 " --> pdb=" O PHE E 418 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE E 418 " --> pdb=" O TYR E 559 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP E 331 " --> pdb=" O ASP E 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA E 294 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL E 332 " --> pdb=" O GLN E 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN E 292 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN E 291 " --> pdb=" O THR E 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR E 270 " --> pdb=" O ASN E 291 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU E 243 " --> pdb=" O THR E 579 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 254 through 255 Processing sheet with id=AC8, first strand: chain 'F' and resid 92 through 96 Processing sheet with id=AC9, first strand: chain 'F' and resid 92 through 96 Processing sheet with id=AD1, first strand: chain 'F' and resid 140 through 145 removed outlier: 3.512A pdb=" N ILE F 143 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 493 through 495 removed outlier: 6.000A pdb=" N GLU F 476 " --> pdb=" O TYR F 559 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TYR F 559 " --> pdb=" O GLU F 476 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR F 478 " --> pdb=" O CYS F 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS F 557 " --> pdb=" O THR F 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN F 480 " --> pdb=" O GLU F 555 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU F 555 " --> pdb=" O GLN F 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE F 482 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS F 553 " --> pdb=" O ILE F 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU F 484 " --> pdb=" O THR F 551 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR F 559 " --> pdb=" O PHE F 418 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE F 418 " --> pdb=" O TYR F 559 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP F 331 " --> pdb=" O ASP F 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA F 294 " --> pdb=" O THR F 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL F 332 " --> pdb=" O GLN F 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN F 292 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN F 291 " --> pdb=" O THR F 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR F 270 " --> pdb=" O ASN F 291 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU F 243 " --> pdb=" O THR F 579 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 254 through 255 Processing sheet with id=AD4, first strand: chain 'G' and resid 92 through 96 Processing sheet with id=AD5, first strand: chain 'G' and resid 92 through 96 Processing sheet with id=AD6, first strand: chain 'G' and resid 140 through 145 removed outlier: 3.512A pdb=" N ILE G 143 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 493 through 495 removed outlier: 6.000A pdb=" N GLU G 476 " --> pdb=" O TYR G 559 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR G 559 " --> pdb=" O GLU G 476 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR G 478 " --> pdb=" O CYS G 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS G 557 " --> pdb=" O THR G 478 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLN G 480 " --> pdb=" O GLU G 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU G 555 " --> pdb=" O GLN G 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE G 482 " --> pdb=" O LYS G 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS G 553 " --> pdb=" O ILE G 482 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU G 484 " --> pdb=" O THR G 551 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR G 559 " --> pdb=" O PHE G 418 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE G 418 " --> pdb=" O TYR G 559 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP G 331 " --> pdb=" O ASP G 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA G 294 " --> pdb=" O THR G 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL G 332 " --> pdb=" O GLN G 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN G 292 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN G 291 " --> pdb=" O THR G 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR G 270 " --> pdb=" O ASN G 291 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU G 243 " --> pdb=" O THR G 579 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 254 through 255 Processing sheet with id=AD9, first strand: chain 'H' and resid 92 through 96 Processing sheet with id=AE1, first strand: chain 'H' and resid 92 through 96 Processing sheet with id=AE2, first strand: chain 'H' and resid 140 through 145 removed outlier: 3.511A pdb=" N ILE H 143 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 493 through 495 removed outlier: 5.999A pdb=" N GLU H 476 " --> pdb=" O TYR H 559 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR H 559 " --> pdb=" O GLU H 476 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR H 478 " --> pdb=" O CYS H 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS H 557 " --> pdb=" O THR H 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN H 480 " --> pdb=" O GLU H 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU H 555 " --> pdb=" O GLN H 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE H 482 " --> pdb=" O LYS H 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS H 553 " --> pdb=" O ILE H 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU H 484 " --> pdb=" O THR H 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR H 559 " --> pdb=" O PHE H 418 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE H 418 " --> pdb=" O TYR H 559 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP H 331 " --> pdb=" O ASP H 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA H 294 " --> pdb=" O THR H 330 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL H 332 " --> pdb=" O GLN H 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN H 292 " --> pdb=" O VAL H 332 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN H 291 " --> pdb=" O THR H 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR H 270 " --> pdb=" O ASN H 291 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU H 243 " --> pdb=" O THR H 579 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 254 through 255 Processing sheet with id=AE5, first strand: chain 'I' and resid 92 through 96 Processing sheet with id=AE6, first strand: chain 'I' and resid 92 through 96 Processing sheet with id=AE7, first strand: chain 'I' and resid 140 through 145 removed outlier: 3.512A pdb=" N ILE I 143 " --> pdb=" O ASP I 150 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 493 through 495 removed outlier: 5.999A pdb=" N GLU I 476 " --> pdb=" O TYR I 559 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR I 559 " --> pdb=" O GLU I 476 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR I 478 " --> pdb=" O CYS I 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS I 557 " --> pdb=" O THR I 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN I 480 " --> pdb=" O GLU I 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU I 555 " --> pdb=" O GLN I 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE I 482 " --> pdb=" O LYS I 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS I 553 " --> pdb=" O ILE I 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU I 484 " --> pdb=" O THR I 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR I 559 " --> pdb=" O PHE I 418 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE I 418 " --> pdb=" O TYR I 559 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP I 331 " --> pdb=" O ASP I 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA I 294 " --> pdb=" O THR I 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL I 332 " --> pdb=" O GLN I 292 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLN I 292 " --> pdb=" O VAL I 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN I 291 " --> pdb=" O THR I 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR I 270 " --> pdb=" O ASN I 291 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU I 243 " --> pdb=" O THR I 579 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 254 through 255 Processing sheet with id=AF1, first strand: chain 'J' and resid 92 through 96 Processing sheet with id=AF2, first strand: chain 'J' and resid 92 through 96 Processing sheet with id=AF3, first strand: chain 'J' and resid 140 through 145 removed outlier: 3.513A pdb=" N ILE J 143 " --> pdb=" O ASP J 150 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 493 through 495 removed outlier: 5.999A pdb=" N GLU J 476 " --> pdb=" O TYR J 559 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TYR J 559 " --> pdb=" O GLU J 476 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR J 478 " --> pdb=" O CYS J 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS J 557 " --> pdb=" O THR J 478 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLN J 480 " --> pdb=" O GLU J 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU J 555 " --> pdb=" O GLN J 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE J 482 " --> pdb=" O LYS J 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS J 553 " --> pdb=" O ILE J 482 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU J 484 " --> pdb=" O THR J 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR J 559 " --> pdb=" O PHE J 418 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE J 418 " --> pdb=" O TYR J 559 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP J 331 " --> pdb=" O ASP J 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA J 294 " --> pdb=" O THR J 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL J 332 " --> pdb=" O GLN J 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN J 292 " --> pdb=" O VAL J 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN J 291 " --> pdb=" O THR J 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR J 270 " --> pdb=" O ASN J 291 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU J 243 " --> pdb=" O THR J 579 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 254 through 255 Processing sheet with id=AF6, first strand: chain 'K' and resid 92 through 96 Processing sheet with id=AF7, first strand: chain 'K' and resid 92 through 96 Processing sheet with id=AF8, first strand: chain 'K' and resid 140 through 145 removed outlier: 3.512A pdb=" N ILE K 143 " --> pdb=" O ASP K 150 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 493 through 495 removed outlier: 5.998A pdb=" N GLU K 476 " --> pdb=" O TYR K 559 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TYR K 559 " --> pdb=" O GLU K 476 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR K 478 " --> pdb=" O CYS K 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS K 557 " --> pdb=" O THR K 478 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLN K 480 " --> pdb=" O GLU K 555 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU K 555 " --> pdb=" O GLN K 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE K 482 " --> pdb=" O LYS K 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS K 553 " --> pdb=" O ILE K 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU K 484 " --> pdb=" O THR K 551 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR K 559 " --> pdb=" O PHE K 418 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE K 418 " --> pdb=" O TYR K 559 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP K 331 " --> pdb=" O ASP K 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA K 294 " --> pdb=" O THR K 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL K 332 " --> pdb=" O GLN K 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN K 292 " --> pdb=" O VAL K 332 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN K 291 " --> pdb=" O THR K 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR K 270 " --> pdb=" O ASN K 291 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU K 243 " --> pdb=" O THR K 579 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 254 through 255 Processing sheet with id=AG2, first strand: chain 'L' and resid 92 through 96 Processing sheet with id=AG3, first strand: chain 'L' and resid 92 through 96 Processing sheet with id=AG4, first strand: chain 'L' and resid 140 through 145 removed outlier: 3.513A pdb=" N ILE L 143 " --> pdb=" O ASP L 150 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 493 through 495 removed outlier: 5.998A pdb=" N GLU L 476 " --> pdb=" O TYR L 559 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TYR L 559 " --> pdb=" O GLU L 476 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR L 478 " --> pdb=" O CYS L 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS L 557 " --> pdb=" O THR L 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN L 480 " --> pdb=" O GLU L 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU L 555 " --> pdb=" O GLN L 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE L 482 " --> pdb=" O LYS L 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS L 553 " --> pdb=" O ILE L 482 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU L 484 " --> pdb=" O THR L 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR L 559 " --> pdb=" O PHE L 418 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE L 418 " --> pdb=" O TYR L 559 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP L 331 " --> pdb=" O ASP L 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA L 294 " --> pdb=" O THR L 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL L 332 " --> pdb=" O GLN L 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN L 292 " --> pdb=" O VAL L 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN L 291 " --> pdb=" O THR L 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR L 270 " --> pdb=" O ASN L 291 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU L 243 " --> pdb=" O THR L 579 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 254 through 255 Processing sheet with id=AG7, first strand: chain 'M' and resid 92 through 96 Processing sheet with id=AG8, first strand: chain 'M' and resid 92 through 96 Processing sheet with id=AG9, first strand: chain 'M' and resid 140 through 145 removed outlier: 3.511A pdb=" N ILE M 143 " --> pdb=" O ASP M 150 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'M' and resid 493 through 495 removed outlier: 6.000A pdb=" N GLU M 476 " --> pdb=" O TYR M 559 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR M 559 " --> pdb=" O GLU M 476 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR M 478 " --> pdb=" O CYS M 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS M 557 " --> pdb=" O THR M 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN M 480 " --> pdb=" O GLU M 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU M 555 " --> pdb=" O GLN M 480 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE M 482 " --> pdb=" O LYS M 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS M 553 " --> pdb=" O ILE M 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU M 484 " --> pdb=" O THR M 551 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR M 559 " --> pdb=" O PHE M 418 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE M 418 " --> pdb=" O TYR M 559 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP M 331 " --> pdb=" O ASP M 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA M 294 " --> pdb=" O THR M 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL M 332 " --> pdb=" O GLN M 292 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLN M 292 " --> pdb=" O VAL M 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN M 291 " --> pdb=" O THR M 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR M 270 " --> pdb=" O ASN M 291 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU M 243 " --> pdb=" O THR M 579 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'M' and resid 254 through 255 Processing sheet with id=AH3, first strand: chain 'N' and resid 92 through 96 Processing sheet with id=AH4, first strand: chain 'N' and resid 92 through 96 Processing sheet with id=AH5, first strand: chain 'N' and resid 140 through 145 removed outlier: 3.512A pdb=" N ILE N 143 " --> pdb=" O ASP N 150 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'N' and resid 493 through 495 removed outlier: 6.000A pdb=" N GLU N 476 " --> pdb=" O TYR N 559 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR N 559 " --> pdb=" O GLU N 476 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR N 478 " --> pdb=" O CYS N 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS N 557 " --> pdb=" O THR N 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN N 480 " --> pdb=" O GLU N 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU N 555 " --> pdb=" O GLN N 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE N 482 " --> pdb=" O LYS N 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS N 553 " --> pdb=" O ILE N 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU N 484 " --> pdb=" O THR N 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR N 559 " --> pdb=" O PHE N 418 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE N 418 " --> pdb=" O TYR N 559 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP N 331 " --> pdb=" O ASP N 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA N 294 " --> pdb=" O THR N 330 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL N 332 " --> pdb=" O GLN N 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN N 292 " --> pdb=" O VAL N 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN N 291 " --> pdb=" O THR N 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR N 270 " --> pdb=" O ASN N 291 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU N 243 " --> pdb=" O THR N 579 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'N' and resid 254 through 255 Processing sheet with id=AH8, first strand: chain 'O' and resid 92 through 96 Processing sheet with id=AH9, first strand: chain 'O' and resid 92 through 96 Processing sheet with id=AI1, first strand: chain 'O' and resid 140 through 145 removed outlier: 3.511A pdb=" N ILE O 143 " --> pdb=" O ASP O 150 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'O' and resid 493 through 495 removed outlier: 6.000A pdb=" N GLU O 476 " --> pdb=" O TYR O 559 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR O 559 " --> pdb=" O GLU O 476 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR O 478 " --> pdb=" O CYS O 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS O 557 " --> pdb=" O THR O 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN O 480 " --> pdb=" O GLU O 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU O 555 " --> pdb=" O GLN O 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE O 482 " --> pdb=" O LYS O 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS O 553 " --> pdb=" O ILE O 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU O 484 " --> pdb=" O THR O 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR O 559 " --> pdb=" O PHE O 418 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE O 418 " --> pdb=" O TYR O 559 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP O 331 " --> pdb=" O ASP O 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA O 294 " --> pdb=" O THR O 330 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL O 332 " --> pdb=" O GLN O 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN O 292 " --> pdb=" O VAL O 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN O 291 " --> pdb=" O THR O 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR O 270 " --> pdb=" O ASN O 291 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU O 243 " --> pdb=" O THR O 579 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'O' and resid 254 through 255 Processing sheet with id=AI4, first strand: chain 'P' and resid 92 through 96 Processing sheet with id=AI5, first strand: chain 'P' and resid 92 through 96 Processing sheet with id=AI6, first strand: chain 'P' and resid 140 through 145 removed outlier: 3.512A pdb=" N ILE P 143 " --> pdb=" O ASP P 150 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'P' and resid 493 through 495 removed outlier: 5.999A pdb=" N GLU P 476 " --> pdb=" O TYR P 559 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR P 559 " --> pdb=" O GLU P 476 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR P 478 " --> pdb=" O CYS P 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS P 557 " --> pdb=" O THR P 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN P 480 " --> pdb=" O GLU P 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU P 555 " --> pdb=" O GLN P 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE P 482 " --> pdb=" O LYS P 553 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LYS P 553 " --> pdb=" O ILE P 482 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU P 484 " --> pdb=" O THR P 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR P 559 " --> pdb=" O PHE P 418 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE P 418 " --> pdb=" O TYR P 559 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP P 331 " --> pdb=" O ASP P 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA P 294 " --> pdb=" O THR P 330 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL P 332 " --> pdb=" O GLN P 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN P 292 " --> pdb=" O VAL P 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN P 291 " --> pdb=" O THR P 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR P 270 " --> pdb=" O ASN P 291 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU P 243 " --> pdb=" O THR P 579 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'P' and resid 254 through 255 Processing sheet with id=AI9, first strand: chain 'Q' and resid 92 through 96 Processing sheet with id=AJ1, first strand: chain 'Q' and resid 92 through 96 Processing sheet with id=AJ2, first strand: chain 'Q' and resid 140 through 145 removed outlier: 3.512A pdb=" N ILE Q 143 " --> pdb=" O ASP Q 150 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'Q' and resid 493 through 495 removed outlier: 5.999A pdb=" N GLU Q 476 " --> pdb=" O TYR Q 559 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR Q 559 " --> pdb=" O GLU Q 476 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR Q 478 " --> pdb=" O CYS Q 557 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N CYS Q 557 " --> pdb=" O THR Q 478 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLN Q 480 " --> pdb=" O GLU Q 555 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU Q 555 " --> pdb=" O GLN Q 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE Q 482 " --> pdb=" O LYS Q 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS Q 553 " --> pdb=" O ILE Q 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU Q 484 " --> pdb=" O THR Q 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR Q 559 " --> pdb=" O PHE Q 418 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE Q 418 " --> pdb=" O TYR Q 559 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP Q 331 " --> pdb=" O ASP Q 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA Q 294 " --> pdb=" O THR Q 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL Q 332 " --> pdb=" O GLN Q 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN Q 292 " --> pdb=" O VAL Q 332 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN Q 291 " --> pdb=" O THR Q 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR Q 270 " --> pdb=" O ASN Q 291 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU Q 243 " --> pdb=" O THR Q 579 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'Q' and resid 254 through 255 Processing sheet with id=AJ5, first strand: chain 'R' and resid 92 through 96 Processing sheet with id=AJ6, first strand: chain 'R' and resid 92 through 96 Processing sheet with id=AJ7, first strand: chain 'R' and resid 140 through 145 removed outlier: 3.512A pdb=" N ILE R 143 " --> pdb=" O ASP R 150 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'R' and resid 493 through 495 removed outlier: 5.999A pdb=" N GLU R 476 " --> pdb=" O TYR R 559 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR R 559 " --> pdb=" O GLU R 476 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR R 478 " --> pdb=" O CYS R 557 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N CYS R 557 " --> pdb=" O THR R 478 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLN R 480 " --> pdb=" O GLU R 555 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU R 555 " --> pdb=" O GLN R 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE R 482 " --> pdb=" O LYS R 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS R 553 " --> pdb=" O ILE R 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU R 484 " --> pdb=" O THR R 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR R 559 " --> pdb=" O PHE R 418 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE R 418 " --> pdb=" O TYR R 559 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP R 331 " --> pdb=" O ASP R 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA R 294 " --> pdb=" O THR R 330 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL R 332 " --> pdb=" O GLN R 292 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLN R 292 " --> pdb=" O VAL R 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN R 291 " --> pdb=" O THR R 270 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR R 270 " --> pdb=" O ASN R 291 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU R 243 " --> pdb=" O THR R 579 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'R' and resid 254 through 255 Processing sheet with id=AK1, first strand: chain 'S' and resid 92 through 96 Processing sheet with id=AK2, first strand: chain 'S' and resid 92 through 96 Processing sheet with id=AK3, first strand: chain 'S' and resid 140 through 145 removed outlier: 3.512A pdb=" N ILE S 143 " --> pdb=" O ASP S 150 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'S' and resid 493 through 495 removed outlier: 5.999A pdb=" N GLU S 476 " --> pdb=" O TYR S 559 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR S 559 " --> pdb=" O GLU S 476 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR S 478 " --> pdb=" O CYS S 557 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N CYS S 557 " --> pdb=" O THR S 478 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLN S 480 " --> pdb=" O GLU S 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU S 555 " --> pdb=" O GLN S 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE S 482 " --> pdb=" O LYS S 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS S 553 " --> pdb=" O ILE S 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU S 484 " --> pdb=" O THR S 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR S 559 " --> pdb=" O PHE S 418 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE S 418 " --> pdb=" O TYR S 559 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP S 331 " --> pdb=" O ASP S 421 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA S 294 " --> pdb=" O THR S 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL S 332 " --> pdb=" O GLN S 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN S 292 " --> pdb=" O VAL S 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN S 291 " --> pdb=" O THR S 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR S 270 " --> pdb=" O ASN S 291 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU S 243 " --> pdb=" O THR S 579 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'S' and resid 254 through 255 Processing sheet with id=AK6, first strand: chain 'T' and resid 92 through 96 Processing sheet with id=AK7, first strand: chain 'T' and resid 92 through 96 Processing sheet with id=AK8, first strand: chain 'T' and resid 140 through 145 removed outlier: 3.512A pdb=" N ILE T 143 " --> pdb=" O ASP T 150 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'T' and resid 493 through 495 removed outlier: 6.000A pdb=" N GLU T 476 " --> pdb=" O TYR T 559 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TYR T 559 " --> pdb=" O GLU T 476 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR T 478 " --> pdb=" O CYS T 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS T 557 " --> pdb=" O THR T 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN T 480 " --> pdb=" O GLU T 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU T 555 " --> pdb=" O GLN T 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE T 482 " --> pdb=" O LYS T 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS T 553 " --> pdb=" O ILE T 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU T 484 " --> pdb=" O THR T 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR T 559 " --> pdb=" O PHE T 418 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE T 418 " --> pdb=" O TYR T 559 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP T 331 " --> pdb=" O ASP T 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA T 294 " --> pdb=" O THR T 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL T 332 " --> pdb=" O GLN T 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN T 292 " --> pdb=" O VAL T 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN T 291 " --> pdb=" O THR T 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR T 270 " --> pdb=" O ASN T 291 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU T 243 " --> pdb=" O THR T 579 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'T' and resid 254 through 255 Processing sheet with id=AL2, first strand: chain 'V' and resid 92 through 96 Processing sheet with id=AL3, first strand: chain 'V' and resid 92 through 96 Processing sheet with id=AL4, first strand: chain 'V' and resid 140 through 145 removed outlier: 3.512A pdb=" N ILE V 143 " --> pdb=" O ASP V 150 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'V' and resid 493 through 495 removed outlier: 6.000A pdb=" N GLU V 476 " --> pdb=" O TYR V 559 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR V 559 " --> pdb=" O GLU V 476 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR V 478 " --> pdb=" O CYS V 557 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N CYS V 557 " --> pdb=" O THR V 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN V 480 " --> pdb=" O GLU V 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU V 555 " --> pdb=" O GLN V 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE V 482 " --> pdb=" O LYS V 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS V 553 " --> pdb=" O ILE V 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU V 484 " --> pdb=" O THR V 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR V 559 " --> pdb=" O PHE V 418 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE V 418 " --> pdb=" O TYR V 559 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP V 331 " --> pdb=" O ASP V 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA V 294 " --> pdb=" O THR V 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL V 332 " --> pdb=" O GLN V 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN V 292 " --> pdb=" O VAL V 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN V 291 " --> pdb=" O THR V 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR V 270 " --> pdb=" O ASN V 291 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU V 243 " --> pdb=" O THR V 579 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'V' and resid 254 through 255 Processing sheet with id=AL7, first strand: chain 'W' and resid 92 through 96 Processing sheet with id=AL8, first strand: chain 'W' and resid 92 through 96 Processing sheet with id=AL9, first strand: chain 'W' and resid 140 through 145 removed outlier: 3.512A pdb=" N ILE W 143 " --> pdb=" O ASP W 150 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'W' and resid 493 through 495 removed outlier: 5.999A pdb=" N GLU W 476 " --> pdb=" O TYR W 559 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR W 559 " --> pdb=" O GLU W 476 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR W 478 " --> pdb=" O CYS W 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS W 557 " --> pdb=" O THR W 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN W 480 " --> pdb=" O GLU W 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU W 555 " --> pdb=" O GLN W 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE W 482 " --> pdb=" O LYS W 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS W 553 " --> pdb=" O ILE W 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU W 484 " --> pdb=" O THR W 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR W 559 " --> pdb=" O PHE W 418 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE W 418 " --> pdb=" O TYR W 559 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP W 331 " --> pdb=" O ASP W 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA W 294 " --> pdb=" O THR W 330 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL W 332 " --> pdb=" O GLN W 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN W 292 " --> pdb=" O VAL W 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN W 291 " --> pdb=" O THR W 270 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR W 270 " --> pdb=" O ASN W 291 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU W 243 " --> pdb=" O THR W 579 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'W' and resid 254 through 255 Processing sheet with id=AM3, first strand: chain 'X' and resid 92 through 96 Processing sheet with id=AM4, first strand: chain 'X' and resid 92 through 96 Processing sheet with id=AM5, first strand: chain 'X' and resid 140 through 145 removed outlier: 3.512A pdb=" N ILE X 143 " --> pdb=" O ASP X 150 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'X' and resid 493 through 495 removed outlier: 5.999A pdb=" N GLU X 476 " --> pdb=" O TYR X 559 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR X 559 " --> pdb=" O GLU X 476 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR X 478 " --> pdb=" O CYS X 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS X 557 " --> pdb=" O THR X 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN X 480 " --> pdb=" O GLU X 555 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU X 555 " --> pdb=" O GLN X 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE X 482 " --> pdb=" O LYS X 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS X 553 " --> pdb=" O ILE X 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU X 484 " --> pdb=" O THR X 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR X 559 " --> pdb=" O PHE X 418 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE X 418 " --> pdb=" O TYR X 559 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP X 331 " --> pdb=" O ASP X 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA X 294 " --> pdb=" O THR X 330 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL X 332 " --> pdb=" O GLN X 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN X 292 " --> pdb=" O VAL X 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN X 291 " --> pdb=" O THR X 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR X 270 " --> pdb=" O ASN X 291 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU X 243 " --> pdb=" O THR X 579 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'X' and resid 254 through 255 Processing sheet with id=AM8, first strand: chain 'Y' and resid 92 through 96 Processing sheet with id=AM9, first strand: chain 'Y' and resid 92 through 96 Processing sheet with id=AN1, first strand: chain 'Y' and resid 140 through 145 removed outlier: 3.512A pdb=" N ILE Y 143 " --> pdb=" O ASP Y 150 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'Y' and resid 493 through 495 removed outlier: 5.998A pdb=" N GLU Y 476 " --> pdb=" O TYR Y 559 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR Y 559 " --> pdb=" O GLU Y 476 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR Y 478 " --> pdb=" O CYS Y 557 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N CYS Y 557 " --> pdb=" O THR Y 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN Y 480 " --> pdb=" O GLU Y 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU Y 555 " --> pdb=" O GLN Y 480 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE Y 482 " --> pdb=" O LYS Y 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS Y 553 " --> pdb=" O ILE Y 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU Y 484 " --> pdb=" O THR Y 551 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR Y 559 " --> pdb=" O PHE Y 418 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE Y 418 " --> pdb=" O TYR Y 559 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP Y 331 " --> pdb=" O ASP Y 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA Y 294 " --> pdb=" O THR Y 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL Y 332 " --> pdb=" O GLN Y 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN Y 292 " --> pdb=" O VAL Y 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN Y 291 " --> pdb=" O THR Y 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR Y 270 " --> pdb=" O ASN Y 291 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU Y 243 " --> pdb=" O THR Y 579 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'Y' and resid 254 through 255 4584 hydrogen bonds defined for protein. 11808 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: 53.77 Time building geometry restraints manager: 31.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 35992 1.34 - 1.46: 13213 1.46 - 1.57: 55699 1.57 - 1.69: 0 1.69 - 1.81: 624 Bond restraints: 105528 Sorted by residual: bond pdb=" CG LEU A 527 " pdb=" CD2 LEU A 527 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.96e+00 bond pdb=" CG LEU D 527 " pdb=" CD2 LEU D 527 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.92e+00 bond pdb=" CG LEU I 527 " pdb=" CD2 LEU I 527 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.92e+00 bond pdb=" CG LEU Y 527 " pdb=" CD2 LEU Y 527 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.91e+00 bond pdb=" CG LEU B 527 " pdb=" CD2 LEU B 527 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.91e+00 ... (remaining 105523 not shown) Histogram of bond angle deviations from ideal: 96.21 - 103.77: 1416 103.77 - 111.33: 42690 111.33 - 118.90: 40951 118.90 - 126.46: 56639 126.46 - 134.02: 1368 Bond angle restraints: 143064 Sorted by residual: angle pdb=" CA GLN N 278 " pdb=" C GLN N 278 " pdb=" N GLN N 279 " ideal model delta sigma weight residual 114.90 119.79 -4.89 1.37e+00 5.33e-01 1.28e+01 angle pdb=" CA GLN T 278 " pdb=" C GLN T 278 " pdb=" N GLN T 279 " ideal model delta sigma weight residual 114.90 119.79 -4.89 1.37e+00 5.33e-01 1.27e+01 angle pdb=" CA GLN F 278 " pdb=" C GLN F 278 " pdb=" N GLN F 279 " ideal model delta sigma weight residual 114.90 119.78 -4.88 1.37e+00 5.33e-01 1.27e+01 angle pdb=" CA GLN I 278 " pdb=" C GLN I 278 " pdb=" N GLN I 279 " ideal model delta sigma weight residual 114.90 119.78 -4.88 1.37e+00 5.33e-01 1.27e+01 angle pdb=" CA GLN L 278 " pdb=" C GLN L 278 " pdb=" N GLN L 279 " ideal model delta sigma weight residual 114.90 119.78 -4.88 1.37e+00 5.33e-01 1.27e+01 ... (remaining 143059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 57701 17.91 - 35.82: 4939 35.82 - 53.73: 456 53.73 - 71.65: 144 71.65 - 89.56: 168 Dihedral angle restraints: 63408 sinusoidal: 25440 harmonic: 37968 Sorted by residual: dihedral pdb=" CA ARG T 76 " pdb=" CB ARG T 76 " pdb=" CG ARG T 76 " pdb=" CD ARG T 76 " ideal model delta sinusoidal sigma weight residual -60.00 -111.87 51.87 3 1.50e+01 4.44e-03 9.06e+00 dihedral pdb=" CA ARG X 76 " pdb=" CB ARG X 76 " pdb=" CG ARG X 76 " pdb=" CD ARG X 76 " ideal model delta sinusoidal sigma weight residual -60.00 -111.87 51.87 3 1.50e+01 4.44e-03 9.06e+00 dihedral pdb=" CA ARG R 76 " pdb=" CB ARG R 76 " pdb=" CG ARG R 76 " pdb=" CD ARG R 76 " ideal model delta sinusoidal sigma weight residual -60.00 -111.86 51.86 3 1.50e+01 4.44e-03 9.06e+00 ... (remaining 63405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 9895 0.032 - 0.064: 3864 0.064 - 0.096: 1004 0.096 - 0.128: 833 0.128 - 0.161: 148 Chirality restraints: 15744 Sorted by residual: chirality pdb=" CA MET G 602 " pdb=" N MET G 602 " pdb=" C MET G 602 " pdb=" CB MET G 602 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CA MET F 602 " pdb=" N MET F 602 " pdb=" C MET F 602 " pdb=" CB MET F 602 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA MET A 602 " pdb=" N MET A 602 " pdb=" C MET A 602 " pdb=" CB MET A 602 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 15741 not shown) Planarity restraints: 19272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA H 321 " 0.064 5.00e-02 4.00e+02 9.60e-02 1.48e+01 pdb=" N PRO H 322 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO H 322 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 322 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA J 321 " 0.064 5.00e-02 4.00e+02 9.60e-02 1.48e+01 pdb=" N PRO J 322 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO J 322 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO J 322 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA Q 321 " 0.064 5.00e-02 4.00e+02 9.60e-02 1.48e+01 pdb=" N PRO Q 322 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO Q 322 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO Q 322 " 0.053 5.00e-02 4.00e+02 ... (remaining 19269 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.89: 144 1.89 - 2.64: 1536 2.64 - 3.39: 134164 3.39 - 4.15: 221542 4.15 - 4.90: 408298 Nonbonded interactions: 765684 Sorted by model distance: nonbonded pdb=" CB ASN C 526 " pdb=" SD MET J 147 " model vdw 1.134 3.800 nonbonded pdb=" CB ASN K 526 " pdb=" SD MET P 147 " model vdw 1.134 3.800 nonbonded pdb=" CB ASN B 526 " pdb=" SD MET D 147 " model vdw 1.134 3.800 nonbonded pdb=" CB ASN X 526 " pdb=" SD MET Y 147 " model vdw 1.134 3.800 nonbonded pdb=" CB ASN A 526 " pdb=" SD MET F 147 " model vdw 1.134 3.800 ... (remaining 765679 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' 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' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 15.190 Check model and map are aligned: 1.100 Set scattering table: 0.680 Process input model: 216.820 Find NCS groups from input model: 5.710 Set up NCS constraints: 0.810 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 246.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 105528 Z= 0.183 Angle : 0.634 7.811 143064 Z= 0.351 Chirality : 0.044 0.161 15744 Planarity : 0.005 0.096 19272 Dihedral : 13.761 89.556 38928 Min Nonbonded Distance : 1.134 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 1.04 (0.08), residues: 13104 helix: 2.12 (0.08), residues: 4464 sheet: 0.47 (0.10), residues: 3144 loop : -0.31 (0.09), residues: 5496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 516 HIS 0.001 0.000 HIS Y 255 PHE 0.016 0.001 PHE Q 466 TYR 0.010 0.001 TYR J 539 ARG 0.007 0.000 ARG Y 541 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 9.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 MET cc_start: 0.9616 (mtp) cc_final: 0.9307 (mpp) REVERT: A 345 MET cc_start: 0.8990 (mtm) cc_final: 0.8557 (ptp) REVERT: A 425 MET cc_start: 0.9219 (tpp) cc_final: 0.8701 (tpp) REVERT: A 602 MET cc_start: 0.7877 (mmt) cc_final: 0.7448 (tpp) REVERT: B 295 MET cc_start: 0.9618 (mtp) cc_final: 0.9311 (mpp) REVERT: B 345 MET cc_start: 0.9035 (mtm) cc_final: 0.8611 (ptp) REVERT: B 425 MET cc_start: 0.9219 (tpp) cc_final: 0.8698 (tpp) REVERT: B 602 MET cc_start: 0.7870 (mmt) cc_final: 0.7440 (tpp) REVERT: C 295 MET cc_start: 0.9618 (mtp) cc_final: 0.9312 (mpp) REVERT: C 345 MET cc_start: 0.9035 (mtm) cc_final: 0.8623 (ptp) REVERT: C 425 MET cc_start: 0.9219 (tpp) cc_final: 0.8695 (tpp) REVERT: C 602 MET cc_start: 0.7873 (mmt) cc_final: 0.7443 (tpp) REVERT: D 295 MET cc_start: 0.9619 (mtp) cc_final: 0.9307 (mpp) REVERT: D 345 MET cc_start: 0.9040 (mtm) cc_final: 0.8615 (ptp) REVERT: D 425 MET cc_start: 0.9221 (tpp) cc_final: 0.8699 (tpp) REVERT: D 602 MET cc_start: 0.7859 (mmt) cc_final: 0.7430 (tpp) REVERT: E 295 MET cc_start: 0.9616 (mtp) cc_final: 0.9310 (mpp) REVERT: E 345 MET cc_start: 0.9034 (mtm) cc_final: 0.8607 (ptp) REVERT: E 425 MET cc_start: 0.9219 (tpp) cc_final: 0.8696 (tpp) REVERT: E 602 MET cc_start: 0.7873 (mmt) cc_final: 0.7442 (tpp) REVERT: F 295 MET cc_start: 0.9622 (mtp) cc_final: 0.9311 (mpp) REVERT: F 345 MET cc_start: 0.9037 (mtm) cc_final: 0.8613 (ptp) REVERT: F 425 MET cc_start: 0.9222 (tpp) cc_final: 0.8698 (tpp) REVERT: F 602 MET cc_start: 0.7859 (mmt) cc_final: 0.7430 (tpp) REVERT: G 295 MET cc_start: 0.9617 (mtp) cc_final: 0.9301 (mpp) REVERT: G 345 MET cc_start: 0.8981 (mtm) cc_final: 0.8542 (ptp) REVERT: G 425 MET cc_start: 0.9221 (tpp) cc_final: 0.8704 (tpp) REVERT: G 602 MET cc_start: 0.7867 (mmt) cc_final: 0.7437 (tpp) REVERT: H 295 MET cc_start: 0.9615 (mtp) cc_final: 0.9307 (mpp) REVERT: H 345 MET cc_start: 0.9033 (mtm) cc_final: 0.8622 (ptp) REVERT: H 425 MET cc_start: 0.9216 (tpp) cc_final: 0.8695 (tpp) REVERT: H 602 MET cc_start: 0.7875 (mmt) cc_final: 0.7446 (tpp) REVERT: I 295 MET cc_start: 0.9621 (mtp) cc_final: 0.9309 (mpp) REVERT: I 345 MET cc_start: 0.8984 (mtm) cc_final: 0.8543 (ptp) REVERT: I 425 MET cc_start: 0.9224 (tpp) cc_final: 0.8702 (tpp) REVERT: I 602 MET cc_start: 0.7853 (mmt) cc_final: 0.7422 (tpp) REVERT: J 295 MET cc_start: 0.9621 (mtp) cc_final: 0.9308 (mpp) REVERT: J 345 MET cc_start: 0.8986 (mtm) cc_final: 0.8541 (ptp) REVERT: J 425 MET cc_start: 0.9223 (tpp) cc_final: 0.8704 (tpp) REVERT: J 602 MET cc_start: 0.7855 (mmt) cc_final: 0.7424 (tpp) REVERT: K 295 MET cc_start: 0.9620 (mtp) cc_final: 0.9314 (mpp) REVERT: K 345 MET cc_start: 0.9033 (mtm) cc_final: 0.8607 (ptp) REVERT: K 425 MET cc_start: 0.9220 (tpp) cc_final: 0.8696 (tpp) REVERT: K 602 MET cc_start: 0.7862 (mmt) cc_final: 0.7433 (tpp) REVERT: L 295 MET cc_start: 0.9619 (mtp) cc_final: 0.9309 (mpp) REVERT: L 345 MET cc_start: 0.9038 (mtm) cc_final: 0.8610 (ptp) REVERT: L 425 MET cc_start: 0.9219 (tpp) cc_final: 0.8697 (tpp) REVERT: L 602 MET cc_start: 0.7861 (mmt) cc_final: 0.7431 (tpp) REVERT: M 295 MET cc_start: 0.9617 (mtp) cc_final: 0.9306 (mpp) REVERT: M 345 MET cc_start: 0.8984 (mtm) cc_final: 0.8559 (ptp) REVERT: M 425 MET cc_start: 0.9220 (tpp) cc_final: 0.8702 (tpp) REVERT: M 602 MET cc_start: 0.7896 (mmt) cc_final: 0.7467 (tpp) REVERT: N 295 MET cc_start: 0.9612 (mtp) cc_final: 0.9302 (mpp) REVERT: N 345 MET cc_start: 0.9028 (mtm) cc_final: 0.8620 (ptp) REVERT: N 425 MET cc_start: 0.9216 (tpp) cc_final: 0.8696 (tpp) REVERT: N 602 MET cc_start: 0.7905 (mmt) cc_final: 0.7476 (tpp) REVERT: O 295 MET cc_start: 0.9614 (mtp) cc_final: 0.9304 (mpp) REVERT: O 345 MET cc_start: 0.8985 (mtm) cc_final: 0.8554 (ptp) REVERT: O 425 MET cc_start: 0.9217 (tpp) cc_final: 0.8699 (tpp) REVERT: O 602 MET cc_start: 0.7897 (mmt) cc_final: 0.7469 (tpp) REVERT: P 295 MET cc_start: 0.9616 (mtp) cc_final: 0.9305 (mpp) REVERT: P 345 MET cc_start: 0.8982 (mtm) cc_final: 0.8557 (ptp) REVERT: P 425 MET cc_start: 0.9219 (tpp) cc_final: 0.8699 (tpp) REVERT: P 602 MET cc_start: 0.7896 (mmt) cc_final: 0.7466 (tpp) REVERT: Q 295 MET cc_start: 0.9614 (mtp) cc_final: 0.9305 (mpp) REVERT: Q 345 MET cc_start: 0.9035 (mtm) cc_final: 0.8624 (ptp) REVERT: Q 425 MET cc_start: 0.9216 (tpp) cc_final: 0.8695 (tpp) REVERT: Q 602 MET cc_start: 0.7874 (mmt) cc_final: 0.7444 (tpp) REVERT: R 295 MET cc_start: 0.9617 (mtp) cc_final: 0.9301 (mpp) REVERT: R 345 MET cc_start: 0.8984 (mtm) cc_final: 0.8545 (ptp) REVERT: R 425 MET cc_start: 0.9220 (tpp) cc_final: 0.8701 (tpp) REVERT: R 602 MET cc_start: 0.7858 (mmt) cc_final: 0.7426 (tpp) REVERT: S 295 MET cc_start: 0.9619 (mtp) cc_final: 0.9305 (mpp) REVERT: S 345 MET cc_start: 0.8985 (mtm) cc_final: 0.8543 (ptp) REVERT: S 425 MET cc_start: 0.9223 (tpp) cc_final: 0.8705 (tpp) REVERT: S 602 MET cc_start: 0.7857 (mmt) cc_final: 0.7426 (tpp) REVERT: T 295 MET cc_start: 0.9618 (mtp) cc_final: 0.9305 (mpp) REVERT: T 345 MET cc_start: 0.9029 (mtm) cc_final: 0.8607 (ptp) REVERT: T 425 MET cc_start: 0.9222 (tpp) cc_final: 0.8701 (tpp) REVERT: T 602 MET cc_start: 0.7860 (mmt) cc_final: 0.7428 (tpp) REVERT: V 295 MET cc_start: 0.9617 (mtp) cc_final: 0.9307 (mpp) REVERT: V 345 MET cc_start: 0.8986 (mtm) cc_final: 0.8557 (ptp) REVERT: V 425 MET cc_start: 0.9221 (tpp) cc_final: 0.8701 (tpp) REVERT: V 602 MET cc_start: 0.7864 (mmt) cc_final: 0.7431 (tpp) REVERT: W 295 MET cc_start: 0.9612 (mtp) cc_final: 0.9301 (mpp) REVERT: W 345 MET cc_start: 0.8981 (mtm) cc_final: 0.8552 (ptp) REVERT: W 425 MET cc_start: 0.9217 (tpp) cc_final: 0.8700 (tpp) REVERT: W 602 MET cc_start: 0.7904 (mmt) cc_final: 0.7474 (tpp) REVERT: X 295 MET cc_start: 0.9618 (mtp) cc_final: 0.9301 (mpp) REVERT: X 345 MET cc_start: 0.8991 (mtm) cc_final: 0.8562 (ptp) REVERT: X 425 MET cc_start: 0.9220 (tpp) cc_final: 0.8703 (tpp) REVERT: X 602 MET cc_start: 0.7859 (mmt) cc_final: 0.7429 (tpp) REVERT: Y 295 MET cc_start: 0.9616 (mtp) cc_final: 0.9308 (mpp) REVERT: Y 345 MET cc_start: 0.9037 (mtm) cc_final: 0.8623 (ptp) REVERT: Y 425 MET cc_start: 0.9216 (tpp) cc_final: 0.8693 (tpp) REVERT: Y 602 MET cc_start: 0.7868 (mmt) cc_final: 0.7440 (tpp) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.9222 time to fit residues: 726.0297 Evaluate side-chains 312 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 9.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 1114 optimal weight: 30.0000 chunk 1000 optimal weight: 10.0000 chunk 555 optimal weight: 7.9990 chunk 341 optimal weight: 8.9990 chunk 674 optimal weight: 20.0000 chunk 534 optimal weight: 30.0000 chunk 1034 optimal weight: 40.0000 chunk 400 optimal weight: 5.9990 chunk 629 optimal weight: 9.9990 chunk 770 optimal weight: 8.9990 chunk 1198 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 ASN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 ASN ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 ASN ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN ** F 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 ASN ** G 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 ASN ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 ASN ** I 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 176 ASN ** J 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 ASN ** K 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 176 ASN ** L 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 176 ASN ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 176 ASN ** N 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 176 ASN ** O 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 176 ASN ** P 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 176 ASN ** Q 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 176 ASN ** R 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 176 ASN ** S 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 176 ASN ** T 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 176 ASN ** V 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 176 ASN ** W 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 ASN ** X 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 176 ASN ** Y 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 105528 Z= 0.246 Angle : 0.588 10.390 143064 Z= 0.304 Chirality : 0.041 0.162 15744 Planarity : 0.005 0.051 19272 Dihedral : 3.728 21.043 14328 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.22 % Allowed : 3.24 % Favored : 96.54 % 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: 1.03 (0.08), residues: 13104 helix: 2.36 (0.08), residues: 4488 sheet: 0.30 (0.10), residues: 3048 loop : -0.47 (0.08), residues: 5568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 487 HIS 0.008 0.002 HIS X 610 PHE 0.011 0.001 PHE G 354 TYR 0.009 0.001 TYR J 166 ARG 0.003 0.000 ARG L 301 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 288 time to evaluate : 9.248 Fit side-chains REVERT: A 345 MET cc_start: 0.9276 (mtm) cc_final: 0.8684 (mtm) REVERT: A 425 MET cc_start: 0.9410 (tpp) cc_final: 0.9053 (tpp) REVERT: A 602 MET cc_start: 0.8238 (mmt) cc_final: 0.7730 (tpp) REVERT: B 345 MET cc_start: 0.9296 (mtm) cc_final: 0.8717 (mtm) REVERT: B 425 MET cc_start: 0.9419 (tpp) cc_final: 0.9069 (tpp) REVERT: B 602 MET cc_start: 0.8236 (mmt) cc_final: 0.7728 (tpp) REVERT: C 345 MET cc_start: 0.9295 (mtm) cc_final: 0.8716 (mtm) REVERT: C 425 MET cc_start: 0.9412 (tpp) cc_final: 0.9049 (tpp) REVERT: C 602 MET cc_start: 0.8235 (mmt) cc_final: 0.7727 (tpp) REVERT: D 345 MET cc_start: 0.9279 (mtm) cc_final: 0.8670 (mtm) REVERT: D 425 MET cc_start: 0.9423 (tpp) cc_final: 0.9075 (tpp) REVERT: D 602 MET cc_start: 0.8233 (mmt) cc_final: 0.7725 (tpp) REVERT: E 345 MET cc_start: 0.9294 (mtm) cc_final: 0.8716 (mtm) REVERT: E 425 MET cc_start: 0.9411 (tpp) cc_final: 0.9048 (tpp) REVERT: E 602 MET cc_start: 0.8235 (mmt) cc_final: 0.7728 (tpp) REVERT: F 345 MET cc_start: 0.9278 (mtm) cc_final: 0.8671 (mtm) REVERT: F 425 MET cc_start: 0.9422 (tpp) cc_final: 0.9062 (tpp) REVERT: F 602 MET cc_start: 0.8229 (mmt) cc_final: 0.7721 (tpp) REVERT: G 345 MET cc_start: 0.9254 (mtm) cc_final: 0.8633 (mtm) REVERT: G 425 MET cc_start: 0.9422 (tpp) cc_final: 0.9079 (tpp) REVERT: G 602 MET cc_start: 0.8232 (mmt) cc_final: 0.7725 (tpp) REVERT: H 345 MET cc_start: 0.9275 (mtm) cc_final: 0.8681 (mtm) REVERT: H 425 MET cc_start: 0.9413 (tpp) cc_final: 0.9052 (tpp) REVERT: H 602 MET cc_start: 0.8238 (mmt) cc_final: 0.7730 (tpp) REVERT: I 345 MET cc_start: 0.9260 (mtm) cc_final: 0.8639 (mtm) REVERT: I 425 MET cc_start: 0.9422 (tpp) cc_final: 0.9064 (tpp) REVERT: I 602 MET cc_start: 0.8226 (mmt) cc_final: 0.7718 (tpp) REVERT: J 345 MET cc_start: 0.9263 (mtm) cc_final: 0.8642 (mtm) REVERT: J 425 MET cc_start: 0.9423 (tpp) cc_final: 0.9077 (tpp) REVERT: J 602 MET cc_start: 0.8229 (mmt) cc_final: 0.7719 (tpp) REVERT: K 345 MET cc_start: 0.9297 (mtm) cc_final: 0.8720 (mtm) REVERT: K 425 MET cc_start: 0.9413 (tpp) cc_final: 0.9049 (tpp) REVERT: K 602 MET cc_start: 0.8231 (mmt) cc_final: 0.7722 (tpp) REVERT: L 345 MET cc_start: 0.9298 (mtm) cc_final: 0.8719 (mtm) REVERT: L 425 MET cc_start: 0.9421 (tpp) cc_final: 0.9066 (tpp) REVERT: L 602 MET cc_start: 0.8232 (mmt) cc_final: 0.7723 (tpp) REVERT: M 345 MET cc_start: 0.9271 (mtm) cc_final: 0.8680 (mtm) REVERT: M 425 MET cc_start: 0.9422 (tpp) cc_final: 0.9077 (tpp) REVERT: M 602 MET cc_start: 0.8237 (mmt) cc_final: 0.7729 (tpp) REVERT: N 345 MET cc_start: 0.9270 (mtm) cc_final: 0.8676 (mtm) REVERT: N 425 MET cc_start: 0.9411 (tpp) cc_final: 0.9052 (tpp) REVERT: N 602 MET cc_start: 0.8240 (mmt) cc_final: 0.7732 (tpp) REVERT: O 345 MET cc_start: 0.9274 (mtm) cc_final: 0.8680 (mtm) REVERT: O 425 MET cc_start: 0.9410 (tpp) cc_final: 0.9053 (tpp) REVERT: O 602 MET cc_start: 0.8238 (mmt) cc_final: 0.7730 (tpp) REVERT: P 345 MET cc_start: 0.9271 (mtm) cc_final: 0.8681 (mtm) REVERT: P 425 MET cc_start: 0.9420 (tpp) cc_final: 0.9073 (tpp) REVERT: P 602 MET cc_start: 0.8235 (mmt) cc_final: 0.7727 (tpp) REVERT: Q 345 MET cc_start: 0.9273 (mtm) cc_final: 0.8678 (mtm) REVERT: Q 425 MET cc_start: 0.9410 (tpp) cc_final: 0.9049 (tpp) REVERT: Q 602 MET cc_start: 0.8238 (mmt) cc_final: 0.7730 (tpp) REVERT: R 345 MET cc_start: 0.9256 (mtm) cc_final: 0.8633 (mtm) REVERT: R 425 MET cc_start: 0.9424 (tpp) cc_final: 0.9078 (tpp) REVERT: R 602 MET cc_start: 0.8240 (mmt) cc_final: 0.7742 (tpp) REVERT: S 345 MET cc_start: 0.9259 (mtm) cc_final: 0.8636 (mtm) REVERT: S 425 MET cc_start: 0.9422 (tpp) cc_final: 0.9075 (tpp) REVERT: S 602 MET cc_start: 0.8235 (mmt) cc_final: 0.7739 (tpp) REVERT: T 345 MET cc_start: 0.9274 (mtm) cc_final: 0.8682 (mtm) REVERT: T 425 MET cc_start: 0.9421 (tpp) cc_final: 0.9070 (tpp) REVERT: T 602 MET cc_start: 0.8229 (mmt) cc_final: 0.7722 (tpp) REVERT: V 345 MET cc_start: 0.9273 (mtm) cc_final: 0.8681 (mtm) REVERT: V 425 MET cc_start: 0.9421 (tpp) cc_final: 0.9072 (tpp) REVERT: V 602 MET cc_start: 0.8232 (mmt) cc_final: 0.7723 (tpp) REVERT: W 345 MET cc_start: 0.9274 (mtm) cc_final: 0.8680 (mtm) REVERT: W 425 MET cc_start: 0.9410 (tpp) cc_final: 0.9056 (tpp) REVERT: W 602 MET cc_start: 0.8239 (mmt) cc_final: 0.7731 (tpp) REVERT: X 345 MET cc_start: 0.9256 (mtm) cc_final: 0.8633 (mtm) REVERT: X 425 MET cc_start: 0.9421 (tpp) cc_final: 0.9077 (tpp) REVERT: X 602 MET cc_start: 0.8239 (mmt) cc_final: 0.7742 (tpp) REVERT: Y 345 MET cc_start: 0.9294 (mtm) cc_final: 0.8713 (mtm) REVERT: Y 425 MET cc_start: 0.9413 (tpp) cc_final: 0.9051 (tpp) REVERT: Y 602 MET cc_start: 0.8238 (mmt) cc_final: 0.7730 (tpp) outliers start: 24 outliers final: 0 residues processed: 312 average time/residue: 0.8463 time to fit residues: 482.1540 Evaluate side-chains 288 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 9.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 666 optimal weight: 9.9990 chunk 372 optimal weight: 20.0000 chunk 997 optimal weight: 5.9990 chunk 816 optimal weight: 4.9990 chunk 330 optimal weight: 40.0000 chunk 1200 optimal weight: 7.9990 chunk 1297 optimal weight: 30.0000 chunk 1069 optimal weight: 0.7980 chunk 1190 optimal weight: 3.9990 chunk 409 optimal weight: 20.0000 chunk 963 optimal weight: 4.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 105528 Z= 0.143 Angle : 0.471 7.340 143064 Z= 0.240 Chirality : 0.040 0.138 15744 Planarity : 0.003 0.040 19272 Dihedral : 3.187 12.091 14328 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: 1.04 (0.08), residues: 13104 helix: 2.40 (0.08), residues: 4536 sheet: 0.16 (0.10), residues: 3024 loop : -0.42 (0.08), residues: 5544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 323 HIS 0.002 0.001 HIS R 610 PHE 0.009 0.001 PHE H 488 TYR 0.004 0.001 TYR N 570 ARG 0.002 0.000 ARG Y 541 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 9.137 Fit side-chains REVERT: A 147 MET cc_start: 0.8463 (tmm) cc_final: 0.7931 (mtt) REVERT: A 295 MET cc_start: 0.9569 (mtm) cc_final: 0.9169 (mpp) REVERT: A 345 MET cc_start: 0.9372 (mtm) cc_final: 0.8833 (ptp) REVERT: A 602 MET cc_start: 0.8215 (mmt) cc_final: 0.7683 (tpp) REVERT: B 147 MET cc_start: 0.8466 (tmm) cc_final: 0.7934 (mtt) REVERT: B 295 MET cc_start: 0.9571 (mtm) cc_final: 0.9172 (mpp) REVERT: B 345 MET cc_start: 0.9374 (mtm) cc_final: 0.8832 (ptp) REVERT: B 602 MET cc_start: 0.8243 (mmt) cc_final: 0.7710 (tpp) REVERT: C 147 MET cc_start: 0.8463 (tmm) cc_final: 0.7931 (mtt) REVERT: C 295 MET cc_start: 0.9571 (mtm) cc_final: 0.9175 (mpp) REVERT: C 345 MET cc_start: 0.9388 (mtm) cc_final: 0.8851 (ptp) REVERT: C 602 MET cc_start: 0.8244 (mmt) cc_final: 0.7711 (tpp) REVERT: D 147 MET cc_start: 0.8464 (tmm) cc_final: 0.7932 (mtt) REVERT: D 295 MET cc_start: 0.9570 (mtm) cc_final: 0.9174 (mpp) REVERT: D 345 MET cc_start: 0.9373 (mtm) cc_final: 0.8832 (ptp) REVERT: D 602 MET cc_start: 0.8244 (mmt) cc_final: 0.7709 (tpp) REVERT: E 147 MET cc_start: 0.8457 (tmm) cc_final: 0.7924 (mtt) REVERT: E 295 MET cc_start: 0.9571 (mtm) cc_final: 0.9175 (mpp) REVERT: E 345 MET cc_start: 0.9387 (mtm) cc_final: 0.8848 (ptp) REVERT: E 602 MET cc_start: 0.8244 (mmt) cc_final: 0.7711 (tpp) REVERT: F 147 MET cc_start: 0.8463 (tmm) cc_final: 0.7934 (mtt) REVERT: F 295 MET cc_start: 0.9572 (mtm) cc_final: 0.9176 (mpp) REVERT: F 345 MET cc_start: 0.9373 (mtm) cc_final: 0.8830 (ptp) REVERT: F 602 MET cc_start: 0.8239 (mmt) cc_final: 0.7706 (tpp) REVERT: G 147 MET cc_start: 0.8466 (tmm) cc_final: 0.7937 (mtt) REVERT: G 295 MET cc_start: 0.9567 (mtm) cc_final: 0.9169 (mpp) REVERT: G 345 MET cc_start: 0.9355 (mtm) cc_final: 0.8788 (ptp) REVERT: G 602 MET cc_start: 0.8209 (mmt) cc_final: 0.7679 (tpp) REVERT: H 147 MET cc_start: 0.8463 (tmm) cc_final: 0.7930 (mtt) REVERT: H 295 MET cc_start: 0.9568 (mtm) cc_final: 0.9169 (mpp) REVERT: H 345 MET cc_start: 0.9393 (mtm) cc_final: 0.8853 (ptp) REVERT: H 602 MET cc_start: 0.8215 (mmt) cc_final: 0.7685 (tpp) REVERT: I 147 MET cc_start: 0.8518 (tmm) cc_final: 0.8005 (mtt) REVERT: I 295 MET cc_start: 0.9571 (mtm) cc_final: 0.9175 (mpp) REVERT: I 345 MET cc_start: 0.9361 (mtm) cc_final: 0.8793 (ptp) REVERT: I 602 MET cc_start: 0.8203 (mmt) cc_final: 0.7671 (tpp) REVERT: J 147 MET cc_start: 0.8485 (tmm) cc_final: 0.7959 (mtt) REVERT: J 295 MET cc_start: 0.9571 (mtm) cc_final: 0.9175 (mpp) REVERT: J 345 MET cc_start: 0.9364 (mtm) cc_final: 0.8795 (ptp) REVERT: J 602 MET cc_start: 0.8207 (mmt) cc_final: 0.7676 (tpp) REVERT: K 147 MET cc_start: 0.8463 (tmm) cc_final: 0.7933 (mtt) REVERT: K 295 MET cc_start: 0.9572 (mtm) cc_final: 0.9175 (mpp) REVERT: K 345 MET cc_start: 0.9392 (mtm) cc_final: 0.8853 (ptp) REVERT: K 602 MET cc_start: 0.8209 (mmt) cc_final: 0.7678 (tpp) REVERT: L 147 MET cc_start: 0.8461 (tmm) cc_final: 0.7932 (mtt) REVERT: L 295 MET cc_start: 0.9572 (mtm) cc_final: 0.9175 (mpp) REVERT: L 345 MET cc_start: 0.9375 (mtm) cc_final: 0.8832 (ptp) REVERT: L 602 MET cc_start: 0.8240 (mmt) cc_final: 0.7706 (tpp) REVERT: M 147 MET cc_start: 0.8465 (tmm) cc_final: 0.7933 (mtt) REVERT: M 295 MET cc_start: 0.9568 (mtm) cc_final: 0.9169 (mpp) REVERT: M 345 MET cc_start: 0.9369 (mtm) cc_final: 0.8830 (ptp) REVERT: M 602 MET cc_start: 0.8214 (mmt) cc_final: 0.7682 (tpp) REVERT: N 147 MET cc_start: 0.8464 (tmm) cc_final: 0.7931 (mtt) REVERT: N 295 MET cc_start: 0.9565 (mtm) cc_final: 0.9166 (mpp) REVERT: N 345 MET cc_start: 0.9384 (mtm) cc_final: 0.8847 (ptp) REVERT: N 602 MET cc_start: 0.8217 (mmt) cc_final: 0.7686 (tpp) REVERT: O 147 MET cc_start: 0.8462 (tmm) cc_final: 0.7931 (mtt) REVERT: O 295 MET cc_start: 0.9567 (mtm) cc_final: 0.9170 (mpp) REVERT: O 345 MET cc_start: 0.9385 (mtm) cc_final: 0.8849 (ptp) REVERT: O 602 MET cc_start: 0.8214 (mmt) cc_final: 0.7683 (tpp) REVERT: P 147 MET cc_start: 0.8465 (tmm) cc_final: 0.7934 (mtt) REVERT: P 295 MET cc_start: 0.9566 (mtm) cc_final: 0.9166 (mpp) REVERT: P 345 MET cc_start: 0.9372 (mtm) cc_final: 0.8835 (ptp) REVERT: P 602 MET cc_start: 0.8212 (mmt) cc_final: 0.7681 (tpp) REVERT: Q 147 MET cc_start: 0.8463 (tmm) cc_final: 0.7931 (mtt) REVERT: Q 295 MET cc_start: 0.9567 (mtm) cc_final: 0.9170 (mpp) REVERT: Q 345 MET cc_start: 0.9388 (mtm) cc_final: 0.8848 (ptp) REVERT: Q 602 MET cc_start: 0.8215 (mmt) cc_final: 0.7683 (tpp) REVERT: R 147 MET cc_start: 0.8483 (tmm) cc_final: 0.7955 (mtt) REVERT: R 295 MET cc_start: 0.9567 (mtm) cc_final: 0.9170 (mpp) REVERT: R 345 MET cc_start: 0.9372 (mtm) cc_final: 0.8833 (ptp) REVERT: R 602 MET cc_start: 0.8212 (mmt) cc_final: 0.7680 (tpp) REVERT: S 147 MET cc_start: 0.8512 (tmm) cc_final: 0.7999 (mtt) REVERT: S 295 MET cc_start: 0.9570 (mtm) cc_final: 0.9172 (mpp) REVERT: S 345 MET cc_start: 0.9359 (mtm) cc_final: 0.8791 (ptp) REVERT: S 602 MET cc_start: 0.8207 (mmt) cc_final: 0.7675 (tpp) REVERT: T 147 MET cc_start: 0.8496 (tmm) cc_final: 0.7981 (mtt) REVERT: T 295 MET cc_start: 0.9570 (mtm) cc_final: 0.9171 (mpp) REVERT: T 345 MET cc_start: 0.9371 (mtm) cc_final: 0.8831 (ptp) REVERT: T 602 MET cc_start: 0.8206 (mmt) cc_final: 0.7677 (tpp) REVERT: V 147 MET cc_start: 0.8463 (tmm) cc_final: 0.7933 (mtt) REVERT: V 295 MET cc_start: 0.9569 (mtm) cc_final: 0.9174 (mpp) REVERT: V 345 MET cc_start: 0.9370 (mtm) cc_final: 0.8829 (ptp) REVERT: V 602 MET cc_start: 0.8210 (mmt) cc_final: 0.7678 (tpp) REVERT: W 147 MET cc_start: 0.8460 (tmm) cc_final: 0.7926 (mtt) REVERT: W 295 MET cc_start: 0.9565 (mtm) cc_final: 0.9163 (mpp) REVERT: W 345 MET cc_start: 0.9385 (mtm) cc_final: 0.8849 (ptp) REVERT: W 602 MET cc_start: 0.8228 (mmt) cc_final: 0.7698 (tpp) REVERT: X 147 MET cc_start: 0.8468 (tmm) cc_final: 0.7938 (mtt) REVERT: X 295 MET cc_start: 0.9568 (mtm) cc_final: 0.9168 (mpp) REVERT: X 345 MET cc_start: 0.9374 (mtm) cc_final: 0.8835 (ptp) REVERT: X 602 MET cc_start: 0.8209 (mmt) cc_final: 0.7678 (tpp) REVERT: Y 147 MET cc_start: 0.8460 (tmm) cc_final: 0.7928 (mtt) REVERT: Y 295 MET cc_start: 0.9569 (mtm) cc_final: 0.9174 (mpp) REVERT: Y 345 MET cc_start: 0.9386 (mtm) cc_final: 0.8847 (ptp) REVERT: Y 602 MET cc_start: 0.8247 (mmt) cc_final: 0.7713 (tpp) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.8388 time to fit residues: 440.4225 Evaluate side-chains 288 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 8.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 1186 optimal weight: 0.0370 chunk 902 optimal weight: 9.9990 chunk 623 optimal weight: 40.0000 chunk 132 optimal weight: 30.0000 chunk 573 optimal weight: 0.5980 chunk 806 optimal weight: 0.9990 chunk 1205 optimal weight: 20.0000 chunk 1275 optimal weight: 30.0000 chunk 629 optimal weight: 20.0000 chunk 1142 optimal weight: 6.9990 chunk 343 optimal weight: 20.0000 overall best weight: 3.7264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 105528 Z= 0.139 Angle : 0.454 7.498 143064 Z= 0.232 Chirality : 0.039 0.139 15744 Planarity : 0.003 0.036 19272 Dihedral : 3.215 13.538 14328 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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: 1.12 (0.08), residues: 13104 helix: 2.39 (0.08), residues: 4560 sheet: 0.30 (0.10), residues: 3024 loop : -0.38 (0.08), residues: 5520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 323 HIS 0.004 0.001 HIS V 610 PHE 0.007 0.001 PHE X 488 TYR 0.003 0.001 TYR P 173 ARG 0.002 0.000 ARG T 541 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 9.860 Fit side-chains REVERT: A 295 MET cc_start: 0.9529 (mtm) cc_final: 0.9155 (mpp) REVERT: A 345 MET cc_start: 0.9492 (mtm) cc_final: 0.8904 (ptp) REVERT: A 602 MET cc_start: 0.8398 (mmt) cc_final: 0.7957 (tpp) REVERT: B 295 MET cc_start: 0.9529 (mtm) cc_final: 0.9154 (mpp) REVERT: B 345 MET cc_start: 0.9495 (mtm) cc_final: 0.8908 (ptp) REVERT: B 602 MET cc_start: 0.8395 (mmt) cc_final: 0.7954 (tpp) REVERT: C 295 MET cc_start: 0.9530 (mtm) cc_final: 0.9160 (mpp) REVERT: C 345 MET cc_start: 0.9494 (mtm) cc_final: 0.8908 (ptp) REVERT: C 602 MET cc_start: 0.8395 (mmt) cc_final: 0.7953 (tpp) REVERT: D 295 MET cc_start: 0.9528 (mtm) cc_final: 0.9155 (mpp) REVERT: D 345 MET cc_start: 0.9493 (mtm) cc_final: 0.8904 (ptp) REVERT: D 602 MET cc_start: 0.8418 (mmt) cc_final: 0.7995 (tpp) REVERT: E 295 MET cc_start: 0.9530 (mtm) cc_final: 0.9160 (mpp) REVERT: E 345 MET cc_start: 0.9494 (mtm) cc_final: 0.8907 (ptp) REVERT: E 602 MET cc_start: 0.8396 (mmt) cc_final: 0.7955 (tpp) REVERT: F 295 MET cc_start: 0.9532 (mtm) cc_final: 0.9159 (mpp) REVERT: F 345 MET cc_start: 0.9492 (mtm) cc_final: 0.8905 (ptp) REVERT: F 602 MET cc_start: 0.8390 (mmt) cc_final: 0.7950 (tpp) REVERT: G 295 MET cc_start: 0.9526 (mtm) cc_final: 0.9153 (mpp) REVERT: G 345 MET cc_start: 0.9490 (mtm) cc_final: 0.8905 (ptp) REVERT: G 602 MET cc_start: 0.8397 (mmt) cc_final: 0.7960 (tpp) REVERT: H 295 MET cc_start: 0.9528 (mtm) cc_final: 0.9153 (mpp) REVERT: H 345 MET cc_start: 0.9498 (mtm) cc_final: 0.8912 (ptp) REVERT: H 602 MET cc_start: 0.8397 (mmt) cc_final: 0.7956 (tpp) REVERT: I 295 MET cc_start: 0.9530 (mtm) cc_final: 0.9158 (mpp) REVERT: I 345 MET cc_start: 0.9493 (mtm) cc_final: 0.8907 (ptp) REVERT: I 602 MET cc_start: 0.8392 (mmt) cc_final: 0.7956 (tpp) REVERT: J 295 MET cc_start: 0.9530 (mtm) cc_final: 0.9157 (mpp) REVERT: J 345 MET cc_start: 0.9495 (mtm) cc_final: 0.8909 (ptp) REVERT: J 602 MET cc_start: 0.8395 (mmt) cc_final: 0.7959 (tpp) REVERT: K 295 MET cc_start: 0.9530 (mtm) cc_final: 0.9157 (mpp) REVERT: K 345 MET cc_start: 0.9496 (mtm) cc_final: 0.8911 (ptp) REVERT: K 602 MET cc_start: 0.8393 (mmt) cc_final: 0.7952 (tpp) REVERT: L 295 MET cc_start: 0.9532 (mtm) cc_final: 0.9160 (mpp) REVERT: L 345 MET cc_start: 0.9495 (mtm) cc_final: 0.8907 (ptp) REVERT: L 602 MET cc_start: 0.8397 (mmt) cc_final: 0.7960 (tpp) REVERT: M 295 MET cc_start: 0.9525 (mtm) cc_final: 0.9151 (mpp) REVERT: M 345 MET cc_start: 0.9489 (mtm) cc_final: 0.8902 (ptp) REVERT: M 602 MET cc_start: 0.8399 (mmt) cc_final: 0.7963 (tpp) REVERT: N 295 MET cc_start: 0.9525 (mtm) cc_final: 0.9152 (mpp) REVERT: N 345 MET cc_start: 0.9489 (mtm) cc_final: 0.8903 (ptp) REVERT: N 602 MET cc_start: 0.8401 (mmt) cc_final: 0.7965 (tpp) REVERT: O 295 MET cc_start: 0.9526 (mtm) cc_final: 0.9154 (mpp) REVERT: O 345 MET cc_start: 0.9492 (mtm) cc_final: 0.8906 (ptp) REVERT: O 602 MET cc_start: 0.8401 (mmt) cc_final: 0.7964 (tpp) REVERT: P 295 MET cc_start: 0.9525 (mtm) cc_final: 0.9148 (mpp) REVERT: P 345 MET cc_start: 0.9493 (mtm) cc_final: 0.8910 (ptp) REVERT: P 602 MET cc_start: 0.8398 (mmt) cc_final: 0.7962 (tpp) REVERT: Q 295 MET cc_start: 0.9529 (mtm) cc_final: 0.9155 (mpp) REVERT: Q 345 MET cc_start: 0.9493 (mtm) cc_final: 0.8907 (ptp) REVERT: Q 602 MET cc_start: 0.8401 (mmt) cc_final: 0.7964 (tpp) REVERT: R 295 MET cc_start: 0.9526 (mtm) cc_final: 0.9152 (mpp) REVERT: R 345 MET cc_start: 0.9491 (mtm) cc_final: 0.8904 (ptp) REVERT: R 602 MET cc_start: 0.8398 (mmt) cc_final: 0.7962 (tpp) REVERT: S 295 MET cc_start: 0.9529 (mtm) cc_final: 0.9157 (mpp) REVERT: S 345 MET cc_start: 0.9492 (mtm) cc_final: 0.8907 (ptp) REVERT: S 602 MET cc_start: 0.8394 (mmt) cc_final: 0.7958 (tpp) REVERT: T 295 MET cc_start: 0.9528 (mtm) cc_final: 0.9155 (mpp) REVERT: T 345 MET cc_start: 0.9492 (mtm) cc_final: 0.8907 (ptp) REVERT: T 602 MET cc_start: 0.8395 (mmt) cc_final: 0.7959 (tpp) REVERT: V 295 MET cc_start: 0.9526 (mtm) cc_final: 0.9155 (mpp) REVERT: V 345 MET cc_start: 0.9489 (mtm) cc_final: 0.8901 (ptp) REVERT: V 602 MET cc_start: 0.8397 (mmt) cc_final: 0.7961 (tpp) REVERT: W 295 MET cc_start: 0.9524 (mtm) cc_final: 0.9148 (mpp) REVERT: W 345 MET cc_start: 0.9490 (mtm) cc_final: 0.8904 (ptp) REVERT: W 602 MET cc_start: 0.8410 (mmt) cc_final: 0.7973 (tpp) REVERT: X 295 MET cc_start: 0.9529 (mtm) cc_final: 0.9152 (mpp) REVERT: X 345 MET cc_start: 0.9493 (mtm) cc_final: 0.8907 (ptp) REVERT: X 602 MET cc_start: 0.8396 (mmt) cc_final: 0.7960 (tpp) REVERT: Y 295 MET cc_start: 0.9527 (mtm) cc_final: 0.9157 (mpp) REVERT: Y 345 MET cc_start: 0.9494 (mtm) cc_final: 0.8906 (ptp) REVERT: Y 602 MET cc_start: 0.8396 (mmt) cc_final: 0.7956 (tpp) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.8466 time to fit residues: 448.6727 Evaluate side-chains 288 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 8.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 1062 optimal weight: 7.9990 chunk 724 optimal weight: 30.0000 chunk 18 optimal weight: 40.0000 chunk 950 optimal weight: 20.0000 chunk 526 optimal weight: 40.0000 chunk 1088 optimal weight: 20.0000 chunk 881 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 651 optimal weight: 20.0000 chunk 1145 optimal weight: 30.0000 chunk 321 optimal weight: 1.9990 overall best weight: 11.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 GLN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 GLN ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 GLN ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 GLN ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 GLN ** G 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 411 GLN ** H 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 411 GLN ** I 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 411 GLN ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 411 GLN ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 411 GLN ** L 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 411 GLN ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 411 GLN ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 411 GLN ** O 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 411 GLN ** P 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 411 GLN ** Q 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 411 GLN ** R 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 411 GLN ** S 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 411 GLN ** T 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 411 GLN ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 411 GLN ** W 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 411 GLN ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 411 GLN ** Y 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 411 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 105528 Z= 0.288 Angle : 0.645 12.465 143064 Z= 0.332 Chirality : 0.041 0.145 15744 Planarity : 0.004 0.033 19272 Dihedral : 4.115 19.053 14328 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % 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: 0.71 (0.07), residues: 13104 helix: 1.62 (0.08), residues: 4584 sheet: 0.55 (0.10), residues: 3072 loop : -0.52 (0.08), residues: 5448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 323 HIS 0.005 0.002 HIS S 255 PHE 0.014 0.002 PHE A 488 TYR 0.013 0.002 TYR L 166 ARG 0.005 0.001 ARG X 496 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 9.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 MET cc_start: 0.9522 (mtm) cc_final: 0.9263 (pmm) REVERT: A 345 MET cc_start: 0.9578 (mtm) cc_final: 0.9020 (ptp) REVERT: A 602 MET cc_start: 0.8608 (mmt) cc_final: 0.8317 (tpp) REVERT: B 295 MET cc_start: 0.9581 (mtm) cc_final: 0.9363 (pmm) REVERT: B 345 MET cc_start: 0.9574 (mtm) cc_final: 0.9008 (ptp) REVERT: B 602 MET cc_start: 0.8605 (mmt) cc_final: 0.8313 (tpp) REVERT: C 295 MET cc_start: 0.9521 (mtm) cc_final: 0.9264 (pmm) REVERT: C 345 MET cc_start: 0.9579 (mtm) cc_final: 0.9018 (ptp) REVERT: C 602 MET cc_start: 0.8607 (mmt) cc_final: 0.8315 (tpp) REVERT: D 295 MET cc_start: 0.9582 (mtm) cc_final: 0.9363 (pmm) REVERT: D 345 MET cc_start: 0.9570 (mtm) cc_final: 0.9008 (ptp) REVERT: D 602 MET cc_start: 0.8605 (mmt) cc_final: 0.8315 (tpp) REVERT: E 295 MET cc_start: 0.9582 (mtm) cc_final: 0.9361 (pmm) REVERT: E 345 MET cc_start: 0.9574 (mtm) cc_final: 0.9010 (ptp) REVERT: E 602 MET cc_start: 0.8605 (mmt) cc_final: 0.8315 (tpp) REVERT: F 295 MET cc_start: 0.9581 (mtm) cc_final: 0.9363 (pmm) REVERT: F 345 MET cc_start: 0.9571 (mtm) cc_final: 0.9008 (ptp) REVERT: F 602 MET cc_start: 0.8606 (mmt) cc_final: 0.8315 (tpp) REVERT: G 295 MET cc_start: 0.9524 (mtm) cc_final: 0.9267 (pmm) REVERT: G 345 MET cc_start: 0.9576 (mtm) cc_final: 0.9018 (ptp) REVERT: G 602 MET cc_start: 0.8607 (mmt) cc_final: 0.8303 (tpp) REVERT: H 295 MET cc_start: 0.9521 (mtm) cc_final: 0.9263 (pmm) REVERT: H 345 MET cc_start: 0.9579 (mtm) cc_final: 0.9016 (ptp) REVERT: H 602 MET cc_start: 0.8607 (mmt) cc_final: 0.8316 (tpp) REVERT: I 295 MET cc_start: 0.9582 (mtm) cc_final: 0.9365 (pmm) REVERT: I 345 MET cc_start: 0.9571 (mtm) cc_final: 0.9008 (ptp) REVERT: I 602 MET cc_start: 0.8605 (mmt) cc_final: 0.8314 (tpp) REVERT: J 295 MET cc_start: 0.9582 (mtm) cc_final: 0.9364 (pmm) REVERT: J 345 MET cc_start: 0.9572 (mtm) cc_final: 0.9011 (ptp) REVERT: J 602 MET cc_start: 0.8606 (mmt) cc_final: 0.8315 (tpp) REVERT: K 295 MET cc_start: 0.9581 (mtm) cc_final: 0.9362 (pmm) REVERT: K 345 MET cc_start: 0.9573 (mtm) cc_final: 0.9010 (ptp) REVERT: K 602 MET cc_start: 0.8604 (mmt) cc_final: 0.8315 (tpp) REVERT: L 295 MET cc_start: 0.9582 (mtm) cc_final: 0.9364 (pmm) REVERT: L 345 MET cc_start: 0.9573 (mtm) cc_final: 0.9010 (ptp) REVERT: L 602 MET cc_start: 0.8607 (mmt) cc_final: 0.8316 (tpp) REVERT: M 295 MET cc_start: 0.9523 (mtm) cc_final: 0.9267 (pmm) REVERT: M 345 MET cc_start: 0.9577 (mtm) cc_final: 0.9019 (ptp) REVERT: M 602 MET cc_start: 0.8610 (mmt) cc_final: 0.8304 (tpp) REVERT: N 295 MET cc_start: 0.9522 (mtm) cc_final: 0.9266 (pmm) REVERT: N 345 MET cc_start: 0.9577 (mtm) cc_final: 0.9017 (ptp) REVERT: N 602 MET cc_start: 0.8608 (mmt) cc_final: 0.8316 (tpp) REVERT: O 295 MET cc_start: 0.9521 (mtm) cc_final: 0.9263 (pmm) REVERT: O 345 MET cc_start: 0.9580 (mtm) cc_final: 0.9023 (ptp) REVERT: O 602 MET cc_start: 0.8609 (mmt) cc_final: 0.8304 (tpp) REVERT: P 295 MET cc_start: 0.9521 (mtm) cc_final: 0.9265 (pmm) REVERT: P 345 MET cc_start: 0.9580 (mtm) cc_final: 0.9022 (ptp) REVERT: P 602 MET cc_start: 0.8608 (mmt) cc_final: 0.8316 (tpp) REVERT: Q 295 MET cc_start: 0.9522 (mtm) cc_final: 0.9265 (pmm) REVERT: Q 345 MET cc_start: 0.9579 (mtm) cc_final: 0.9019 (ptp) REVERT: Q 602 MET cc_start: 0.8607 (mmt) cc_final: 0.8315 (tpp) REVERT: R 295 MET cc_start: 0.9522 (mtm) cc_final: 0.9262 (pmm) REVERT: R 345 MET cc_start: 0.9579 (mtm) cc_final: 0.9022 (ptp) REVERT: R 602 MET cc_start: 0.8609 (mmt) cc_final: 0.8304 (tpp) REVERT: S 295 MET cc_start: 0.9581 (mtm) cc_final: 0.9362 (pmm) REVERT: S 345 MET cc_start: 0.9571 (mtm) cc_final: 0.9010 (ptp) REVERT: S 602 MET cc_start: 0.8606 (mmt) cc_final: 0.8315 (tpp) REVERT: T 295 MET cc_start: 0.9581 (mtm) cc_final: 0.9362 (pmm) REVERT: T 345 MET cc_start: 0.9571 (mtm) cc_final: 0.9006 (ptp) REVERT: T 602 MET cc_start: 0.8606 (mmt) cc_final: 0.8315 (tpp) REVERT: V 295 MET cc_start: 0.9524 (mtm) cc_final: 0.9268 (pmm) REVERT: V 345 MET cc_start: 0.9577 (mtm) cc_final: 0.9019 (ptp) REVERT: V 602 MET cc_start: 0.8608 (mmt) cc_final: 0.8304 (tpp) REVERT: W 295 MET cc_start: 0.9523 (mtm) cc_final: 0.9265 (pmm) REVERT: W 345 MET cc_start: 0.9578 (mtm) cc_final: 0.9021 (ptp) REVERT: W 602 MET cc_start: 0.8608 (mmt) cc_final: 0.8316 (tpp) REVERT: X 295 MET cc_start: 0.9521 (mtm) cc_final: 0.9263 (pmm) REVERT: X 345 MET cc_start: 0.9578 (mtm) cc_final: 0.9020 (ptp) REVERT: X 602 MET cc_start: 0.8606 (mmt) cc_final: 0.8303 (tpp) REVERT: Y 295 MET cc_start: 0.9521 (mtm) cc_final: 0.9264 (pmm) REVERT: Y 345 MET cc_start: 0.9578 (mtm) cc_final: 0.9019 (ptp) REVERT: Y 602 MET cc_start: 0.8608 (mmt) cc_final: 0.8316 (tpp) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.8473 time to fit residues: 483.7667 Evaluate side-chains 312 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 9.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 429 optimal weight: 30.0000 chunk 1149 optimal weight: 9.9990 chunk 252 optimal weight: 50.0000 chunk 749 optimal weight: 8.9990 chunk 314 optimal weight: 20.0000 chunk 1277 optimal weight: 9.9990 chunk 1060 optimal weight: 9.9990 chunk 591 optimal weight: 30.0000 chunk 106 optimal weight: 9.9990 chunk 422 optimal weight: 30.0000 chunk 670 optimal weight: 30.0000 overall best weight: 9.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 105528 Z= 0.252 Angle : 0.576 10.188 143064 Z= 0.296 Chirality : 0.040 0.140 15744 Planarity : 0.004 0.029 19272 Dihedral : 4.079 15.954 14328 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: 0.60 (0.07), residues: 13104 helix: 1.55 (0.08), residues: 4560 sheet: 0.58 (0.10), residues: 2928 loop : -0.62 (0.08), residues: 5616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP Q 323 HIS 0.005 0.002 HIS A 528 PHE 0.014 0.002 PHE L 488 TYR 0.008 0.001 TYR I 166 ARG 0.003 0.000 ARG L 541 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 9.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 MET cc_start: 0.9623 (mtm) cc_final: 0.9052 (ptp) REVERT: A 425 MET cc_start: 0.9151 (tpp) cc_final: 0.8852 (tpp) REVERT: A 602 MET cc_start: 0.8783 (mmt) cc_final: 0.8400 (tpp) REVERT: B 295 MET cc_start: 0.9446 (mpp) cc_final: 0.8744 (mpp) REVERT: B 345 MET cc_start: 0.9626 (mtm) cc_final: 0.9049 (ptp) REVERT: B 425 MET cc_start: 0.9143 (tpp) cc_final: 0.8882 (tpp) REVERT: B 602 MET cc_start: 0.8786 (mmt) cc_final: 0.8404 (tpp) REVERT: C 345 MET cc_start: 0.9625 (mtm) cc_final: 0.9050 (ptp) REVERT: C 425 MET cc_start: 0.9149 (tpp) cc_final: 0.8850 (tpp) REVERT: C 602 MET cc_start: 0.8785 (mmt) cc_final: 0.8404 (tpp) REVERT: D 295 MET cc_start: 0.9446 (mpp) cc_final: 0.8744 (mpp) REVERT: D 345 MET cc_start: 0.9624 (mtm) cc_final: 0.9050 (ptp) REVERT: D 425 MET cc_start: 0.9140 (tpp) cc_final: 0.8777 (tpp) REVERT: D 602 MET cc_start: 0.8782 (mmt) cc_final: 0.8405 (tpp) REVERT: E 295 MET cc_start: 0.9450 (mpp) cc_final: 0.8744 (mpp) REVERT: E 345 MET cc_start: 0.9625 (mtm) cc_final: 0.9050 (ptp) REVERT: E 425 MET cc_start: 0.9145 (tpp) cc_final: 0.8849 (tpp) REVERT: E 602 MET cc_start: 0.8785 (mmt) cc_final: 0.8404 (tpp) REVERT: F 295 MET cc_start: 0.9446 (mpp) cc_final: 0.8742 (mpp) REVERT: F 345 MET cc_start: 0.9625 (mtm) cc_final: 0.9050 (ptp) REVERT: F 425 MET cc_start: 0.9141 (tpp) cc_final: 0.8848 (tpp) REVERT: F 602 MET cc_start: 0.8785 (mmt) cc_final: 0.8403 (tpp) REVERT: G 345 MET cc_start: 0.9622 (mtm) cc_final: 0.9050 (ptp) REVERT: G 425 MET cc_start: 0.9130 (tpp) cc_final: 0.8774 (tpp) REVERT: G 602 MET cc_start: 0.8793 (mmt) cc_final: 0.8413 (tpp) REVERT: H 345 MET cc_start: 0.9627 (mtm) cc_final: 0.9054 (ptp) REVERT: H 425 MET cc_start: 0.9150 (tpp) cc_final: 0.8851 (tpp) REVERT: H 602 MET cc_start: 0.8786 (mmt) cc_final: 0.8405 (tpp) REVERT: I 295 MET cc_start: 0.9447 (mpp) cc_final: 0.8744 (mpp) REVERT: I 345 MET cc_start: 0.9624 (mtm) cc_final: 0.9049 (ptp) REVERT: I 425 MET cc_start: 0.9145 (tpp) cc_final: 0.8886 (tpp) REVERT: I 602 MET cc_start: 0.8792 (mmt) cc_final: 0.8415 (tpp) REVERT: J 295 MET cc_start: 0.9444 (mpp) cc_final: 0.8742 (mpp) REVERT: J 345 MET cc_start: 0.9624 (mtm) cc_final: 0.9050 (ptp) REVERT: J 425 MET cc_start: 0.9146 (tpp) cc_final: 0.8852 (tpp) REVERT: J 602 MET cc_start: 0.8794 (mmt) cc_final: 0.8415 (tpp) REVERT: K 295 MET cc_start: 0.9445 (mpp) cc_final: 0.8743 (mpp) REVERT: K 345 MET cc_start: 0.9625 (mtm) cc_final: 0.9050 (ptp) REVERT: K 425 MET cc_start: 0.9143 (tpp) cc_final: 0.8848 (tpp) REVERT: K 602 MET cc_start: 0.8781 (mmt) cc_final: 0.8404 (tpp) REVERT: L 295 MET cc_start: 0.9448 (mpp) cc_final: 0.8743 (mpp) REVERT: L 345 MET cc_start: 0.9626 (mtm) cc_final: 0.9049 (ptp) REVERT: L 425 MET cc_start: 0.9144 (tpp) cc_final: 0.8849 (tpp) REVERT: L 602 MET cc_start: 0.8785 (mmt) cc_final: 0.8403 (tpp) REVERT: M 345 MET cc_start: 0.9623 (mtm) cc_final: 0.9052 (ptp) REVERT: M 425 MET cc_start: 0.9149 (tpp) cc_final: 0.8851 (tpp) REVERT: M 602 MET cc_start: 0.8794 (mmt) cc_final: 0.8413 (tpp) REVERT: N 345 MET cc_start: 0.9622 (mtm) cc_final: 0.9048 (ptp) REVERT: N 425 MET cc_start: 0.9133 (tpp) cc_final: 0.8776 (tpp) REVERT: N 602 MET cc_start: 0.8794 (mmt) cc_final: 0.8414 (tpp) REVERT: O 345 MET cc_start: 0.9625 (mtm) cc_final: 0.9053 (ptp) REVERT: O 425 MET cc_start: 0.9151 (tpp) cc_final: 0.8886 (tpp) REVERT: O 602 MET cc_start: 0.8796 (mmt) cc_final: 0.8413 (tpp) REVERT: P 345 MET cc_start: 0.9625 (mtm) cc_final: 0.9054 (ptp) REVERT: P 425 MET cc_start: 0.9135 (tpp) cc_final: 0.8815 (tpp) REVERT: P 602 MET cc_start: 0.8793 (mmt) cc_final: 0.8413 (tpp) REVERT: Q 345 MET cc_start: 0.9625 (mtm) cc_final: 0.9051 (ptp) REVERT: Q 425 MET cc_start: 0.9148 (tpp) cc_final: 0.8848 (tpp) REVERT: Q 602 MET cc_start: 0.8794 (mmt) cc_final: 0.8417 (tpp) REVERT: R 345 MET cc_start: 0.9624 (mtm) cc_final: 0.9053 (ptp) REVERT: R 425 MET cc_start: 0.9137 (tpp) cc_final: 0.8782 (tpp) REVERT: R 602 MET cc_start: 0.8794 (mmt) cc_final: 0.8413 (tpp) REVERT: S 295 MET cc_start: 0.9446 (mpp) cc_final: 0.8744 (mpp) REVERT: S 345 MET cc_start: 0.9624 (mtm) cc_final: 0.9051 (ptp) REVERT: S 425 MET cc_start: 0.9147 (tpp) cc_final: 0.8852 (tpp) REVERT: S 602 MET cc_start: 0.8793 (mmt) cc_final: 0.8412 (tpp) REVERT: T 295 MET cc_start: 0.9448 (mpp) cc_final: 0.8746 (mpp) REVERT: T 345 MET cc_start: 0.9624 (mtm) cc_final: 0.9048 (ptp) REVERT: T 425 MET cc_start: 0.9145 (tpp) cc_final: 0.8851 (tpp) REVERT: T 602 MET cc_start: 0.8792 (mmt) cc_final: 0.8415 (tpp) REVERT: V 345 MET cc_start: 0.9623 (mtm) cc_final: 0.9052 (ptp) REVERT: V 425 MET cc_start: 0.9133 (tpp) cc_final: 0.8776 (tpp) REVERT: V 602 MET cc_start: 0.8793 (mmt) cc_final: 0.8413 (tpp) REVERT: W 345 MET cc_start: 0.9623 (mtm) cc_final: 0.9053 (ptp) REVERT: W 425 MET cc_start: 0.9154 (tpp) cc_final: 0.8889 (tpp) REVERT: W 602 MET cc_start: 0.8794 (mmt) cc_final: 0.8414 (tpp) REVERT: X 345 MET cc_start: 0.9623 (mtm) cc_final: 0.9052 (ptp) REVERT: X 425 MET cc_start: 0.9133 (tpp) cc_final: 0.8777 (tpp) REVERT: X 602 MET cc_start: 0.8793 (mmt) cc_final: 0.8413 (tpp) REVERT: Y 345 MET cc_start: 0.9625 (mtm) cc_final: 0.9052 (ptp) REVERT: Y 425 MET cc_start: 0.9152 (tpp) cc_final: 0.8887 (tpp) REVERT: Y 602 MET cc_start: 0.8784 (mmt) cc_final: 0.8401 (tpp) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.8460 time to fit residues: 481.3875 Evaluate side-chains 312 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 8.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 1231 optimal weight: 20.0000 chunk 143 optimal weight: 0.0040 chunk 727 optimal weight: 8.9990 chunk 932 optimal weight: 40.0000 chunk 722 optimal weight: 7.9990 chunk 1075 optimal weight: 0.7980 chunk 713 optimal weight: 6.9990 chunk 1272 optimal weight: 0.7980 chunk 796 optimal weight: 7.9990 chunk 775 optimal weight: 7.9990 chunk 587 optimal weight: 30.0000 overall best weight: 3.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN B 339 GLN C 339 GLN D 339 GLN E 339 GLN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 GLN G 339 GLN H 339 GLN I 339 GLN ** J 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 339 GLN ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 339 GLN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 339 GLN ** N 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 339 GLN O 339 GLN P 339 GLN Q 339 GLN R 339 GLN S 339 GLN ** T 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 339 GLN V 339 GLN ** W 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 339 GLN Y 339 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 105528 Z= 0.134 Angle : 0.468 5.561 143064 Z= 0.240 Chirality : 0.040 0.137 15744 Planarity : 0.003 0.028 19272 Dihedral : 3.586 13.906 14328 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: 0.85 (0.08), residues: 13104 helix: 2.07 (0.08), residues: 4560 sheet: 0.42 (0.10), residues: 3072 loop : -0.63 (0.08), residues: 5472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP P 516 HIS 0.002 0.001 HIS F 255 PHE 0.008 0.001 PHE Q 283 TYR 0.003 0.001 TYR P 173 ARG 0.002 0.000 ARG O 541 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 9.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 MET cc_start: 0.9608 (mtm) cc_final: 0.8981 (ptp) REVERT: A 425 MET cc_start: 0.9256 (tpp) cc_final: 0.8800 (tpp) REVERT: A 602 MET cc_start: 0.8723 (mmt) cc_final: 0.8334 (tpp) REVERT: B 345 MET cc_start: 0.9609 (mtm) cc_final: 0.9000 (ptp) REVERT: B 425 MET cc_start: 0.9253 (tpp) cc_final: 0.8796 (tpp) REVERT: B 602 MET cc_start: 0.8722 (mmt) cc_final: 0.8333 (tpp) REVERT: C 345 MET cc_start: 0.9609 (mtm) cc_final: 0.8984 (ptp) REVERT: C 425 MET cc_start: 0.9256 (tpp) cc_final: 0.8799 (tpp) REVERT: C 602 MET cc_start: 0.8722 (mmt) cc_final: 0.8332 (tpp) REVERT: D 345 MET cc_start: 0.9608 (mtm) cc_final: 0.8998 (ptp) REVERT: D 425 MET cc_start: 0.9251 (tpp) cc_final: 0.8770 (tpp) REVERT: D 602 MET cc_start: 0.8707 (mmt) cc_final: 0.8312 (tpp) REVERT: E 345 MET cc_start: 0.9610 (mtm) cc_final: 0.9000 (ptp) REVERT: E 425 MET cc_start: 0.9240 (tpp) cc_final: 0.8785 (tpp) REVERT: E 602 MET cc_start: 0.8719 (mmt) cc_final: 0.8331 (tpp) REVERT: F 345 MET cc_start: 0.9608 (mtm) cc_final: 0.8999 (ptp) REVERT: F 425 MET cc_start: 0.9248 (tpp) cc_final: 0.8795 (tpp) REVERT: F 602 MET cc_start: 0.8712 (mmt) cc_final: 0.8316 (tpp) REVERT: G 345 MET cc_start: 0.9608 (mtm) cc_final: 0.8983 (ptp) REVERT: G 425 MET cc_start: 0.9248 (tpp) cc_final: 0.8734 (tpp) REVERT: G 602 MET cc_start: 0.8721 (mmt) cc_final: 0.8332 (tpp) REVERT: H 345 MET cc_start: 0.9611 (mtm) cc_final: 0.8983 (ptp) REVERT: H 425 MET cc_start: 0.9240 (tpp) cc_final: 0.8785 (tpp) REVERT: H 602 MET cc_start: 0.8722 (mmt) cc_final: 0.8333 (tpp) REVERT: I 345 MET cc_start: 0.9606 (mtm) cc_final: 0.8996 (ptp) REVERT: I 425 MET cc_start: 0.9257 (tpp) cc_final: 0.8801 (tpp) REVERT: I 602 MET cc_start: 0.8716 (mmt) cc_final: 0.8331 (tpp) REVERT: J 345 MET cc_start: 0.9608 (mtm) cc_final: 0.8997 (ptp) REVERT: J 425 MET cc_start: 0.9257 (tpp) cc_final: 0.8802 (tpp) REVERT: J 602 MET cc_start: 0.8720 (mmt) cc_final: 0.8331 (tpp) REVERT: K 345 MET cc_start: 0.9610 (mtm) cc_final: 0.8999 (ptp) REVERT: K 425 MET cc_start: 0.9237 (tpp) cc_final: 0.8782 (tpp) REVERT: K 602 MET cc_start: 0.8711 (mmt) cc_final: 0.8317 (tpp) REVERT: L 345 MET cc_start: 0.9609 (mtm) cc_final: 0.8999 (ptp) REVERT: L 425 MET cc_start: 0.9254 (tpp) cc_final: 0.8798 (tpp) REVERT: L 602 MET cc_start: 0.8713 (mmt) cc_final: 0.8319 (tpp) REVERT: M 345 MET cc_start: 0.9608 (mtm) cc_final: 0.8982 (ptp) REVERT: M 425 MET cc_start: 0.9241 (tpp) cc_final: 0.8786 (tpp) REVERT: M 602 MET cc_start: 0.8724 (mmt) cc_final: 0.8333 (tpp) REVERT: N 345 MET cc_start: 0.9609 (mtm) cc_final: 0.8984 (ptp) REVERT: N 425 MET cc_start: 0.9233 (tpp) cc_final: 0.8750 (tpp) REVERT: N 602 MET cc_start: 0.8720 (mmt) cc_final: 0.8332 (tpp) REVERT: O 345 MET cc_start: 0.9611 (mtm) cc_final: 0.8985 (ptp) REVERT: O 425 MET cc_start: 0.9241 (tpp) cc_final: 0.8816 (tpp) REVERT: O 602 MET cc_start: 0.8726 (mmt) cc_final: 0.8335 (tpp) REVERT: P 345 MET cc_start: 0.9611 (mtm) cc_final: 0.8988 (ptp) REVERT: P 425 MET cc_start: 0.9236 (tpp) cc_final: 0.8754 (tpp) REVERT: P 602 MET cc_start: 0.8721 (mmt) cc_final: 0.8333 (tpp) REVERT: Q 345 MET cc_start: 0.9611 (mtm) cc_final: 0.8984 (ptp) REVERT: Q 425 MET cc_start: 0.9238 (tpp) cc_final: 0.8782 (tpp) REVERT: Q 602 MET cc_start: 0.8725 (mmt) cc_final: 0.8335 (tpp) REVERT: R 345 MET cc_start: 0.9608 (mtm) cc_final: 0.8983 (ptp) REVERT: R 425 MET cc_start: 0.9255 (tpp) cc_final: 0.8773 (tpp) REVERT: R 602 MET cc_start: 0.8723 (mmt) cc_final: 0.8335 (tpp) REVERT: S 345 MET cc_start: 0.9608 (mtm) cc_final: 0.8997 (ptp) REVERT: S 425 MET cc_start: 0.9259 (tpp) cc_final: 0.8803 (tpp) REVERT: S 602 MET cc_start: 0.8718 (mmt) cc_final: 0.8331 (tpp) REVERT: T 345 MET cc_start: 0.9609 (mtm) cc_final: 0.9000 (ptp) REVERT: T 425 MET cc_start: 0.9257 (tpp) cc_final: 0.8800 (tpp) REVERT: T 602 MET cc_start: 0.8718 (mmt) cc_final: 0.8332 (tpp) REVERT: V 345 MET cc_start: 0.9607 (mtm) cc_final: 0.8981 (ptp) REVERT: V 425 MET cc_start: 0.9233 (tpp) cc_final: 0.8751 (tpp) REVERT: V 602 MET cc_start: 0.8724 (mmt) cc_final: 0.8333 (tpp) REVERT: W 345 MET cc_start: 0.9609 (mtm) cc_final: 0.8982 (ptp) REVERT: W 425 MET cc_start: 0.9244 (tpp) cc_final: 0.8819 (tpp) REVERT: W 602 MET cc_start: 0.8724 (mmt) cc_final: 0.8334 (tpp) REVERT: X 345 MET cc_start: 0.9610 (mtm) cc_final: 0.8984 (ptp) REVERT: X 425 MET cc_start: 0.9251 (tpp) cc_final: 0.8768 (tpp) REVERT: X 602 MET cc_start: 0.8723 (mmt) cc_final: 0.8335 (tpp) REVERT: Y 345 MET cc_start: 0.9610 (mtm) cc_final: 0.8985 (ptp) REVERT: Y 425 MET cc_start: 0.9259 (tpp) cc_final: 0.8834 (tpp) REVERT: Y 602 MET cc_start: 0.8723 (mmt) cc_final: 0.8333 (tpp) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.8423 time to fit residues: 480.3307 Evaluate side-chains 312 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 9.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 787 optimal weight: 9.9990 chunk 508 optimal weight: 8.9990 chunk 759 optimal weight: 20.0000 chunk 383 optimal weight: 8.9990 chunk 249 optimal weight: 20.0000 chunk 246 optimal weight: 20.0000 chunk 808 optimal weight: 40.0000 chunk 866 optimal weight: 3.9990 chunk 629 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 1000 optimal weight: 30.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 ASN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 501 ASN ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 501 ASN ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 501 ASN ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 501 ASN ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 501 ASN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 501 ASN ** N 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 501 ASN ** T 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 501 ASN ** V 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 501 ASN ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 105528 Z= 0.204 Angle : 0.525 9.193 143064 Z= 0.271 Chirality : 0.040 0.140 15744 Planarity : 0.004 0.029 19272 Dihedral : 3.751 14.393 14328 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.08), residues: 13104 helix: 2.17 (0.08), residues: 4392 sheet: 0.36 (0.10), residues: 3072 loop : -0.58 (0.08), residues: 5640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 516 HIS 0.004 0.001 HIS N 528 PHE 0.012 0.001 PHE X 488 TYR 0.005 0.001 TYR L 166 ARG 0.003 0.000 ARG M 591 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 11.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 MET cc_start: 0.9447 (mpp) cc_final: 0.8681 (mpp) REVERT: A 345 MET cc_start: 0.9608 (mtm) cc_final: 0.9018 (ptp) REVERT: A 425 MET cc_start: 0.9317 (tpp) cc_final: 0.9028 (tpp) REVERT: A 602 MET cc_start: 0.8779 (mmt) cc_final: 0.8418 (tpp) REVERT: B 295 MET cc_start: 0.9423 (mpp) cc_final: 0.8655 (mpp) REVERT: B 345 MET cc_start: 0.9610 (mtm) cc_final: 0.9013 (ptp) REVERT: B 425 MET cc_start: 0.9311 (tpp) cc_final: 0.9021 (tpp) REVERT: B 602 MET cc_start: 0.8780 (mmt) cc_final: 0.8420 (tpp) REVERT: C 295 MET cc_start: 0.9446 (mpp) cc_final: 0.8680 (mpp) REVERT: C 345 MET cc_start: 0.9608 (mtm) cc_final: 0.9015 (ptp) REVERT: C 425 MET cc_start: 0.9315 (tpp) cc_final: 0.9026 (tpp) REVERT: C 602 MET cc_start: 0.8779 (mmt) cc_final: 0.8418 (tpp) REVERT: D 295 MET cc_start: 0.9428 (mpp) cc_final: 0.8655 (mpp) REVERT: D 345 MET cc_start: 0.9610 (mtm) cc_final: 0.9017 (ptp) REVERT: D 425 MET cc_start: 0.9312 (tpp) cc_final: 0.9053 (tpp) REVERT: D 602 MET cc_start: 0.8736 (mmt) cc_final: 0.8361 (tpp) REVERT: E 295 MET cc_start: 0.9425 (mpp) cc_final: 0.8657 (mpp) REVERT: E 345 MET cc_start: 0.9611 (mtm) cc_final: 0.9017 (ptp) REVERT: E 425 MET cc_start: 0.9303 (tpp) cc_final: 0.9016 (tpp) REVERT: E 602 MET cc_start: 0.8776 (mmt) cc_final: 0.8416 (tpp) REVERT: F 295 MET cc_start: 0.9430 (mpp) cc_final: 0.8654 (mpp) REVERT: F 345 MET cc_start: 0.9609 (mtm) cc_final: 0.9015 (ptp) REVERT: F 425 MET cc_start: 0.9307 (tpp) cc_final: 0.9022 (tpp) REVERT: F 602 MET cc_start: 0.8736 (mmt) cc_final: 0.8361 (tpp) REVERT: G 295 MET cc_start: 0.9452 (mpp) cc_final: 0.8681 (mpp) REVERT: G 345 MET cc_start: 0.9606 (mtm) cc_final: 0.9003 (ptp) REVERT: G 425 MET cc_start: 0.9310 (tpp) cc_final: 0.9021 (tpp) REVERT: G 602 MET cc_start: 0.8779 (mmt) cc_final: 0.8420 (tpp) REVERT: H 295 MET cc_start: 0.9449 (mpp) cc_final: 0.8682 (mpp) REVERT: H 345 MET cc_start: 0.9610 (mtm) cc_final: 0.9018 (ptp) REVERT: H 425 MET cc_start: 0.9303 (tpp) cc_final: 0.9017 (tpp) REVERT: H 602 MET cc_start: 0.8779 (mmt) cc_final: 0.8419 (tpp) REVERT: I 295 MET cc_start: 0.9422 (mpp) cc_final: 0.8656 (mpp) REVERT: I 345 MET cc_start: 0.9609 (mtm) cc_final: 0.9014 (ptp) REVERT: I 425 MET cc_start: 0.9314 (tpp) cc_final: 0.9026 (tpp) REVERT: I 602 MET cc_start: 0.8736 (mmt) cc_final: 0.8360 (tpp) REVERT: J 295 MET cc_start: 0.9429 (mpp) cc_final: 0.8654 (mpp) REVERT: J 345 MET cc_start: 0.9611 (mtm) cc_final: 0.9018 (ptp) REVERT: J 425 MET cc_start: 0.9316 (tpp) cc_final: 0.9029 (tpp) REVERT: J 602 MET cc_start: 0.8738 (mmt) cc_final: 0.8360 (tpp) REVERT: K 295 MET cc_start: 0.9428 (mpp) cc_final: 0.8654 (mpp) REVERT: K 345 MET cc_start: 0.9611 (mtm) cc_final: 0.9017 (ptp) REVERT: K 425 MET cc_start: 0.9299 (tpp) cc_final: 0.9011 (tpp) REVERT: K 602 MET cc_start: 0.8736 (mmt) cc_final: 0.8361 (tpp) REVERT: L 295 MET cc_start: 0.9421 (mpp) cc_final: 0.8654 (mpp) REVERT: L 345 MET cc_start: 0.9611 (mtm) cc_final: 0.9016 (ptp) REVERT: L 425 MET cc_start: 0.9315 (tpp) cc_final: 0.9027 (tpp) REVERT: L 602 MET cc_start: 0.8737 (mmt) cc_final: 0.8360 (tpp) REVERT: M 295 MET cc_start: 0.9447 (mpp) cc_final: 0.8680 (mpp) REVERT: M 345 MET cc_start: 0.9607 (mtm) cc_final: 0.9016 (ptp) REVERT: M 425 MET cc_start: 0.9302 (tpp) cc_final: 0.9015 (tpp) REVERT: M 602 MET cc_start: 0.8782 (mmt) cc_final: 0.8420 (tpp) REVERT: N 295 MET cc_start: 0.9450 (mpp) cc_final: 0.8682 (mpp) REVERT: N 345 MET cc_start: 0.9609 (mtm) cc_final: 0.9016 (ptp) REVERT: N 425 MET cc_start: 0.9299 (tpp) cc_final: 0.9040 (tpp) REVERT: N 602 MET cc_start: 0.8779 (mmt) cc_final: 0.8419 (tpp) REVERT: O 295 MET cc_start: 0.9447 (mpp) cc_final: 0.8681 (mpp) REVERT: O 345 MET cc_start: 0.9612 (mtm) cc_final: 0.9020 (ptp) REVERT: O 425 MET cc_start: 0.9304 (tpp) cc_final: 0.9046 (tpp) REVERT: O 602 MET cc_start: 0.8781 (mmt) cc_final: 0.8420 (tpp) REVERT: P 295 MET cc_start: 0.9445 (mpp) cc_final: 0.8680 (mpp) REVERT: P 345 MET cc_start: 0.9607 (mtm) cc_final: 0.9003 (ptp) REVERT: P 425 MET cc_start: 0.9299 (tpp) cc_final: 0.9042 (tpp) REVERT: P 602 MET cc_start: 0.8741 (mmt) cc_final: 0.8362 (tpp) REVERT: Q 295 MET cc_start: 0.9449 (mpp) cc_final: 0.8682 (mpp) REVERT: Q 345 MET cc_start: 0.9611 (mtm) cc_final: 0.9015 (ptp) REVERT: Q 425 MET cc_start: 0.9301 (tpp) cc_final: 0.9014 (tpp) REVERT: Q 602 MET cc_start: 0.8782 (mmt) cc_final: 0.8421 (tpp) REVERT: R 295 MET cc_start: 0.9449 (mpp) cc_final: 0.8684 (mpp) REVERT: R 345 MET cc_start: 0.9607 (mtm) cc_final: 0.9005 (ptp) REVERT: R 425 MET cc_start: 0.9317 (tpp) cc_final: 0.9058 (tpp) REVERT: R 602 MET cc_start: 0.8740 (mmt) cc_final: 0.8362 (tpp) REVERT: S 295 MET cc_start: 0.9428 (mpp) cc_final: 0.8655 (mpp) REVERT: S 345 MET cc_start: 0.9611 (mtm) cc_final: 0.9020 (ptp) REVERT: S 425 MET cc_start: 0.9317 (tpp) cc_final: 0.9029 (tpp) REVERT: S 602 MET cc_start: 0.8736 (mmt) cc_final: 0.8359 (tpp) REVERT: T 295 MET cc_start: 0.9423 (mpp) cc_final: 0.8654 (mpp) REVERT: T 345 MET cc_start: 0.9609 (mtm) cc_final: 0.9015 (ptp) REVERT: T 425 MET cc_start: 0.9315 (tpp) cc_final: 0.9028 (tpp) REVERT: T 602 MET cc_start: 0.8737 (mmt) cc_final: 0.8361 (tpp) REVERT: V 295 MET cc_start: 0.9443 (mpp) cc_final: 0.8682 (mpp) REVERT: V 345 MET cc_start: 0.9607 (mtm) cc_final: 0.9016 (ptp) REVERT: V 425 MET cc_start: 0.9298 (tpp) cc_final: 0.9039 (tpp) REVERT: V 602 MET cc_start: 0.8740 (mmt) cc_final: 0.8363 (tpp) REVERT: W 295 MET cc_start: 0.9448 (mpp) cc_final: 0.8683 (mpp) REVERT: W 345 MET cc_start: 0.9609 (mtm) cc_final: 0.9016 (ptp) REVERT: W 425 MET cc_start: 0.9306 (tpp) cc_final: 0.9048 (tpp) REVERT: W 602 MET cc_start: 0.8780 (mmt) cc_final: 0.8419 (tpp) REVERT: X 295 MET cc_start: 0.9450 (mpp) cc_final: 0.8682 (mpp) REVERT: X 345 MET cc_start: 0.9606 (mtm) cc_final: 0.9001 (ptp) REVERT: X 425 MET cc_start: 0.9311 (tpp) cc_final: 0.9023 (tpp) REVERT: X 602 MET cc_start: 0.8740 (mmt) cc_final: 0.8363 (tpp) REVERT: Y 295 MET cc_start: 0.9450 (mpp) cc_final: 0.8682 (mpp) REVERT: Y 345 MET cc_start: 0.9610 (mtm) cc_final: 0.9019 (ptp) REVERT: Y 425 MET cc_start: 0.9317 (tpp) cc_final: 0.9058 (tpp) REVERT: Y 602 MET cc_start: 0.8780 (mmt) cc_final: 0.8419 (tpp) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.8326 time to fit residues: 475.4271 Evaluate side-chains 312 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 9.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 1157 optimal weight: 9.9990 chunk 1218 optimal weight: 4.9990 chunk 1112 optimal weight: 8.9990 chunk 1185 optimal weight: 2.9990 chunk 713 optimal weight: 30.0000 chunk 516 optimal weight: 7.9990 chunk 930 optimal weight: 9.9990 chunk 363 optimal weight: 4.9990 chunk 1071 optimal weight: 20.0000 chunk 1121 optimal weight: 0.8980 chunk 1181 optimal weight: 30.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 105528 Z= 0.146 Angle : 0.465 5.768 143064 Z= 0.239 Chirality : 0.040 0.135 15744 Planarity : 0.003 0.029 19272 Dihedral : 3.513 13.518 14328 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 1.04 (0.08), residues: 13104 helix: 2.40 (0.08), residues: 4392 sheet: 0.38 (0.10), residues: 3072 loop : -0.49 (0.08), residues: 5640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Y 516 HIS 0.003 0.001 HIS M 528 PHE 0.009 0.001 PHE H 488 TYR 0.003 0.001 TYR P 173 ARG 0.002 0.000 ARG S 541 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 9.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.8761 (tmm) cc_final: 0.8526 (mtt) REVERT: A 345 MET cc_start: 0.9612 (mtm) cc_final: 0.8969 (ptp) REVERT: A 425 MET cc_start: 0.9254 (tpp) cc_final: 0.8795 (tpp) REVERT: A 602 MET cc_start: 0.8784 (mmt) cc_final: 0.8405 (tpp) REVERT: B 147 MET cc_start: 0.8759 (tmm) cc_final: 0.8526 (mtt) REVERT: B 345 MET cc_start: 0.9612 (mtm) cc_final: 0.8967 (ptp) REVERT: B 425 MET cc_start: 0.9261 (tpp) cc_final: 0.8801 (tpp) REVERT: B 602 MET cc_start: 0.8783 (mmt) cc_final: 0.8405 (tpp) REVERT: C 147 MET cc_start: 0.8757 (tmm) cc_final: 0.8534 (mtt) REVERT: C 345 MET cc_start: 0.9613 (mtm) cc_final: 0.8969 (ptp) REVERT: C 425 MET cc_start: 0.9252 (tpp) cc_final: 0.8794 (tpp) REVERT: C 602 MET cc_start: 0.8783 (mmt) cc_final: 0.8404 (tpp) REVERT: D 147 MET cc_start: 0.8758 (tmm) cc_final: 0.8523 (mtt) REVERT: D 345 MET cc_start: 0.9612 (mtm) cc_final: 0.8969 (ptp) REVERT: D 425 MET cc_start: 0.9249 (tpp) cc_final: 0.8847 (tpp) REVERT: D 602 MET cc_start: 0.8779 (mmt) cc_final: 0.8416 (tpp) REVERT: E 147 MET cc_start: 0.8758 (tmm) cc_final: 0.8536 (mtt) REVERT: E 345 MET cc_start: 0.9612 (mtm) cc_final: 0.8967 (ptp) REVERT: E 425 MET cc_start: 0.9251 (tpp) cc_final: 0.8793 (tpp) REVERT: E 602 MET cc_start: 0.8782 (mmt) cc_final: 0.8403 (tpp) REVERT: F 147 MET cc_start: 0.8759 (tmm) cc_final: 0.8528 (mtt) REVERT: F 345 MET cc_start: 0.9613 (mtm) cc_final: 0.8968 (ptp) REVERT: F 425 MET cc_start: 0.9259 (tpp) cc_final: 0.8766 (tpp) REVERT: F 602 MET cc_start: 0.8782 (mmt) cc_final: 0.8415 (tpp) REVERT: G 147 MET cc_start: 0.8758 (tmm) cc_final: 0.8526 (mtt) REVERT: G 345 MET cc_start: 0.9613 (mtm) cc_final: 0.8971 (ptp) REVERT: G 425 MET cc_start: 0.9249 (tpp) cc_final: 0.8844 (tpp) REVERT: G 602 MET cc_start: 0.8785 (mmt) cc_final: 0.8406 (tpp) REVERT: H 147 MET cc_start: 0.8760 (tmm) cc_final: 0.8526 (mtt) REVERT: H 345 MET cc_start: 0.9614 (mtm) cc_final: 0.8968 (ptp) REVERT: H 425 MET cc_start: 0.9254 (tpp) cc_final: 0.8796 (tpp) REVERT: H 602 MET cc_start: 0.8783 (mmt) cc_final: 0.8405 (tpp) REVERT: I 147 MET cc_start: 0.8757 (tmm) cc_final: 0.8536 (mtt) REVERT: I 345 MET cc_start: 0.9612 (mtm) cc_final: 0.8965 (ptp) REVERT: I 425 MET cc_start: 0.9249 (tpp) cc_final: 0.8792 (tpp) REVERT: I 602 MET cc_start: 0.8782 (mmt) cc_final: 0.8404 (tpp) REVERT: J 147 MET cc_start: 0.8759 (tmm) cc_final: 0.8526 (mtt) REVERT: J 345 MET cc_start: 0.9614 (mtm) cc_final: 0.8966 (ptp) REVERT: J 425 MET cc_start: 0.9252 (tpp) cc_final: 0.8796 (tpp) REVERT: J 602 MET cc_start: 0.8784 (mmt) cc_final: 0.8406 (tpp) REVERT: K 147 MET cc_start: 0.8760 (tmm) cc_final: 0.8529 (mtt) REVERT: K 345 MET cc_start: 0.9614 (mtm) cc_final: 0.8969 (ptp) REVERT: K 425 MET cc_start: 0.9249 (tpp) cc_final: 0.8792 (tpp) REVERT: K 602 MET cc_start: 0.8779 (mmt) cc_final: 0.8417 (tpp) REVERT: L 147 MET cc_start: 0.8761 (tmm) cc_final: 0.8530 (mtt) REVERT: L 345 MET cc_start: 0.9613 (mtm) cc_final: 0.8967 (ptp) REVERT: L 425 MET cc_start: 0.9252 (tpp) cc_final: 0.8793 (tpp) REVERT: L 602 MET cc_start: 0.8780 (mmt) cc_final: 0.8417 (tpp) REVERT: M 147 MET cc_start: 0.8763 (tmm) cc_final: 0.8529 (mtt) REVERT: M 345 MET cc_start: 0.9612 (mtm) cc_final: 0.8969 (ptp) REVERT: M 425 MET cc_start: 0.9253 (tpp) cc_final: 0.8795 (tpp) REVERT: M 602 MET cc_start: 0.8785 (mmt) cc_final: 0.8405 (tpp) REVERT: N 147 MET cc_start: 0.8761 (tmm) cc_final: 0.8530 (mtt) REVERT: N 345 MET cc_start: 0.9612 (mtm) cc_final: 0.8968 (ptp) REVERT: N 425 MET cc_start: 0.9250 (tpp) cc_final: 0.8845 (tpp) REVERT: N 602 MET cc_start: 0.8784 (mmt) cc_final: 0.8404 (tpp) REVERT: O 147 MET cc_start: 0.8759 (tmm) cc_final: 0.8525 (mtt) REVERT: O 345 MET cc_start: 0.9613 (mtm) cc_final: 0.8970 (ptp) REVERT: O 425 MET cc_start: 0.9255 (tpp) cc_final: 0.8797 (tpp) REVERT: O 602 MET cc_start: 0.8785 (mmt) cc_final: 0.8406 (tpp) REVERT: P 147 MET cc_start: 0.8760 (tmm) cc_final: 0.8526 (mtt) REVERT: P 345 MET cc_start: 0.9613 (mtm) cc_final: 0.8969 (ptp) REVERT: P 425 MET cc_start: 0.9252 (tpp) cc_final: 0.8849 (tpp) REVERT: P 602 MET cc_start: 0.8784 (mmt) cc_final: 0.8406 (tpp) REVERT: Q 147 MET cc_start: 0.8758 (tmm) cc_final: 0.8537 (mtt) REVERT: Q 345 MET cc_start: 0.9612 (mtm) cc_final: 0.8966 (ptp) REVERT: Q 425 MET cc_start: 0.9253 (tpp) cc_final: 0.8795 (tpp) REVERT: Q 602 MET cc_start: 0.8784 (mmt) cc_final: 0.8405 (tpp) REVERT: R 147 MET cc_start: 0.8758 (tmm) cc_final: 0.8524 (mtt) REVERT: R 345 MET cc_start: 0.9613 (mtm) cc_final: 0.8971 (ptp) REVERT: R 425 MET cc_start: 0.9257 (tpp) cc_final: 0.8854 (tpp) REVERT: R 602 MET cc_start: 0.8786 (mmt) cc_final: 0.8407 (tpp) REVERT: S 147 MET cc_start: 0.8758 (tmm) cc_final: 0.8536 (mtt) REVERT: S 345 MET cc_start: 0.9612 (mtm) cc_final: 0.8969 (ptp) REVERT: S 425 MET cc_start: 0.9252 (tpp) cc_final: 0.8794 (tpp) REVERT: S 602 MET cc_start: 0.8784 (mmt) cc_final: 0.8405 (tpp) REVERT: T 147 MET cc_start: 0.8761 (tmm) cc_final: 0.8532 (mtt) REVERT: T 345 MET cc_start: 0.9614 (mtm) cc_final: 0.8969 (ptp) REVERT: T 425 MET cc_start: 0.9251 (tpp) cc_final: 0.8793 (tpp) REVERT: T 602 MET cc_start: 0.8783 (mmt) cc_final: 0.8415 (tpp) REVERT: V 147 MET cc_start: 0.8754 (tmm) cc_final: 0.8533 (mtt) REVERT: V 345 MET cc_start: 0.9612 (mtm) cc_final: 0.8969 (ptp) REVERT: V 425 MET cc_start: 0.9250 (tpp) cc_final: 0.8846 (tpp) REVERT: V 602 MET cc_start: 0.8784 (mmt) cc_final: 0.8406 (tpp) REVERT: W 147 MET cc_start: 0.8761 (tmm) cc_final: 0.8525 (mtt) REVERT: W 345 MET cc_start: 0.9613 (mtm) cc_final: 0.8967 (ptp) REVERT: W 425 MET cc_start: 0.9257 (tpp) cc_final: 0.8799 (tpp) REVERT: W 602 MET cc_start: 0.8784 (mmt) cc_final: 0.8404 (tpp) REVERT: X 147 MET cc_start: 0.8760 (tmm) cc_final: 0.8527 (mtt) REVERT: X 345 MET cc_start: 0.9611 (mtm) cc_final: 0.8967 (ptp) REVERT: X 425 MET cc_start: 0.9248 (tpp) cc_final: 0.8844 (tpp) REVERT: X 602 MET cc_start: 0.8784 (mmt) cc_final: 0.8407 (tpp) REVERT: Y 147 MET cc_start: 0.8755 (tmm) cc_final: 0.8532 (mtt) REVERT: Y 345 MET cc_start: 0.9613 (mtm) cc_final: 0.8970 (ptp) REVERT: Y 425 MET cc_start: 0.9255 (tpp) cc_final: 0.8797 (tpp) REVERT: Y 602 MET cc_start: 0.8785 (mmt) cc_final: 0.8405 (tpp) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.9623 time to fit residues: 558.3939 Evaluate side-chains 304 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 9.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 778 optimal weight: 0.0470 chunk 1253 optimal weight: 0.0870 chunk 765 optimal weight: 7.9990 chunk 594 optimal weight: 7.9990 chunk 871 optimal weight: 0.0060 chunk 1315 optimal weight: 8.9990 chunk 1210 optimal weight: 30.0000 chunk 1047 optimal weight: 10.0000 chunk 108 optimal weight: 0.0170 chunk 808 optimal weight: 30.0000 chunk 642 optimal weight: 20.0000 overall best weight: 1.6312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 339 GLN ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 339 GLN ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 105528 Z= 0.109 Angle : 0.435 5.531 143064 Z= 0.221 Chirality : 0.040 0.138 15744 Planarity : 0.003 0.032 19272 Dihedral : 3.180 12.392 14328 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 1.09 (0.08), residues: 13104 helix: 2.48 (0.08), residues: 4560 sheet: 0.09 (0.10), residues: 2928 loop : -0.36 (0.08), residues: 5616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 516 HIS 0.001 0.000 HIS G 255 PHE 0.006 0.001 PHE Y 74 TYR 0.003 0.001 TYR L 559 ARG 0.002 0.000 ARG O 591 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26208 Ramachandran restraints generated. 13104 Oldfield, 0 Emsley, 13104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 9.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.8726 (tmm) cc_final: 0.8462 (mtt) REVERT: A 345 MET cc_start: 0.9628 (mtm) cc_final: 0.8981 (ptp) REVERT: A 425 MET cc_start: 0.9183 (tpp) cc_final: 0.8643 (tpp) REVERT: A 602 MET cc_start: 0.8738 (mmt) cc_final: 0.8357 (tpp) REVERT: B 147 MET cc_start: 0.8727 (tmm) cc_final: 0.8464 (mtt) REVERT: B 345 MET cc_start: 0.9631 (mtm) cc_final: 0.8984 (ptp) REVERT: B 425 MET cc_start: 0.9178 (tpp) cc_final: 0.8636 (tpp) REVERT: B 602 MET cc_start: 0.8738 (mmt) cc_final: 0.8357 (tpp) REVERT: C 147 MET cc_start: 0.8724 (tmm) cc_final: 0.8461 (mtt) REVERT: C 345 MET cc_start: 0.9631 (mtm) cc_final: 0.8984 (ptp) REVERT: C 425 MET cc_start: 0.9182 (tpp) cc_final: 0.8644 (tpp) REVERT: C 602 MET cc_start: 0.8739 (mmt) cc_final: 0.8357 (tpp) REVERT: D 147 MET cc_start: 0.8721 (tmm) cc_final: 0.8455 (mtt) REVERT: D 345 MET cc_start: 0.9630 (mtm) cc_final: 0.8985 (ptp) REVERT: D 425 MET cc_start: 0.9215 (tpp) cc_final: 0.8672 (tpp) REVERT: D 602 MET cc_start: 0.8721 (mmt) cc_final: 0.8326 (tpp) REVERT: E 147 MET cc_start: 0.8725 (tmm) cc_final: 0.8461 (mtt) REVERT: E 345 MET cc_start: 0.9631 (mtm) cc_final: 0.8983 (ptp) REVERT: E 425 MET cc_start: 0.9188 (tpp) cc_final: 0.8649 (tpp) REVERT: E 602 MET cc_start: 0.8741 (mmt) cc_final: 0.8362 (tpp) REVERT: F 147 MET cc_start: 0.8716 (tmm) cc_final: 0.8455 (mtt) REVERT: F 345 MET cc_start: 0.9631 (mtm) cc_final: 0.8984 (ptp) REVERT: F 425 MET cc_start: 0.9195 (tpp) cc_final: 0.8640 (tpp) REVERT: F 602 MET cc_start: 0.8744 (mmt) cc_final: 0.8368 (tpp) REVERT: G 147 MET cc_start: 0.8721 (tmm) cc_final: 0.8459 (mtt) REVERT: G 345 MET cc_start: 0.9630 (mtm) cc_final: 0.8986 (ptp) REVERT: G 425 MET cc_start: 0.9194 (tpp) cc_final: 0.8661 (tpp) REVERT: G 602 MET cc_start: 0.8743 (mmt) cc_final: 0.8364 (tpp) REVERT: H 147 MET cc_start: 0.8725 (tmm) cc_final: 0.8460 (mtt) REVERT: H 345 MET cc_start: 0.9629 (mtm) cc_final: 0.8980 (ptp) REVERT: H 425 MET cc_start: 0.9184 (tpp) cc_final: 0.8646 (tpp) REVERT: H 602 MET cc_start: 0.8738 (mmt) cc_final: 0.8357 (tpp) REVERT: I 147 MET cc_start: 0.8720 (tmm) cc_final: 0.8457 (mtt) REVERT: I 345 MET cc_start: 0.9632 (mtm) cc_final: 0.8986 (ptp) REVERT: I 425 MET cc_start: 0.9182 (tpp) cc_final: 0.8644 (tpp) REVERT: I 602 MET cc_start: 0.8743 (mmt) cc_final: 0.8365 (tpp) REVERT: J 147 MET cc_start: 0.8724 (tmm) cc_final: 0.8462 (mtt) REVERT: J 345 MET cc_start: 0.9631 (mtm) cc_final: 0.8978 (ptp) REVERT: J 425 MET cc_start: 0.9184 (tpp) cc_final: 0.8617 (tpp) REVERT: J 602 MET cc_start: 0.8744 (mmt) cc_final: 0.8365 (tpp) REVERT: K 147 MET cc_start: 0.8721 (tmm) cc_final: 0.8460 (mtt) REVERT: K 345 MET cc_start: 0.9631 (mtm) cc_final: 0.8984 (ptp) REVERT: K 425 MET cc_start: 0.9180 (tpp) cc_final: 0.8642 (tpp) REVERT: K 602 MET cc_start: 0.8722 (mmt) cc_final: 0.8327 (tpp) REVERT: L 147 MET cc_start: 0.8719 (tmm) cc_final: 0.8457 (mtt) REVERT: L 345 MET cc_start: 0.9631 (mtm) cc_final: 0.8987 (ptp) REVERT: L 425 MET cc_start: 0.9182 (tpp) cc_final: 0.8643 (tpp) REVERT: L 602 MET cc_start: 0.8744 (mmt) cc_final: 0.8369 (tpp) REVERT: M 147 MET cc_start: 0.8719 (tmm) cc_final: 0.8457 (mtt) REVERT: M 345 MET cc_start: 0.9629 (mtm) cc_final: 0.8984 (ptp) REVERT: M 425 MET cc_start: 0.9191 (tpp) cc_final: 0.8653 (tpp) REVERT: M 602 MET cc_start: 0.8749 (mmt) cc_final: 0.8371 (tpp) REVERT: N 147 MET cc_start: 0.8719 (tmm) cc_final: 0.8458 (mtt) REVERT: N 345 MET cc_start: 0.9630 (mtm) cc_final: 0.8986 (ptp) REVERT: N 425 MET cc_start: 0.9201 (tpp) cc_final: 0.8670 (tpp) REVERT: N 602 MET cc_start: 0.8735 (mmt) cc_final: 0.8353 (tpp) REVERT: O 147 MET cc_start: 0.8721 (tmm) cc_final: 0.8456 (mtt) REVERT: O 345 MET cc_start: 0.9631 (mtm) cc_final: 0.8985 (ptp) REVERT: O 425 MET cc_start: 0.9185 (tpp) cc_final: 0.8646 (tpp) REVERT: O 602 MET cc_start: 0.8740 (mmt) cc_final: 0.8358 (tpp) REVERT: P 147 MET cc_start: 0.8722 (tmm) cc_final: 0.8458 (mtt) REVERT: P 345 MET cc_start: 0.9630 (mtm) cc_final: 0.8983 (ptp) REVERT: P 425 MET cc_start: 0.9219 (tpp) cc_final: 0.8677 (tpp) REVERT: P 602 MET cc_start: 0.8746 (mmt) cc_final: 0.8365 (tpp) REVERT: Q 147 MET cc_start: 0.8727 (tmm) cc_final: 0.8464 (mtt) REVERT: Q 345 MET cc_start: 0.9633 (mtm) cc_final: 0.8988 (ptp) REVERT: Q 425 MET cc_start: 0.9182 (tpp) cc_final: 0.8642 (tpp) REVERT: Q 602 MET cc_start: 0.8741 (mmt) cc_final: 0.8362 (tpp) REVERT: R 147 MET cc_start: 0.8720 (tmm) cc_final: 0.8455 (mtt) REVERT: R 345 MET cc_start: 0.9630 (mtm) cc_final: 0.8985 (ptp) REVERT: R 425 MET cc_start: 0.9203 (tpp) cc_final: 0.8648 (tpp) REVERT: R 602 MET cc_start: 0.8739 (mmt) cc_final: 0.8358 (tpp) REVERT: S 147 MET cc_start: 0.8721 (tmm) cc_final: 0.8456 (mtt) REVERT: S 345 MET cc_start: 0.9631 (mtm) cc_final: 0.8984 (ptp) REVERT: S 425 MET cc_start: 0.9185 (tpp) cc_final: 0.8645 (tpp) REVERT: S 602 MET cc_start: 0.8744 (mmt) cc_final: 0.8364 (tpp) REVERT: T 147 MET cc_start: 0.8719 (tmm) cc_final: 0.8460 (mtt) REVERT: T 345 MET cc_start: 0.9632 (mtm) cc_final: 0.8984 (ptp) REVERT: T 425 MET cc_start: 0.9184 (tpp) cc_final: 0.8645 (tpp) REVERT: T 602 MET cc_start: 0.8749 (mmt) cc_final: 0.8377 (tpp) REVERT: V 147 MET cc_start: 0.8718 (tmm) cc_final: 0.8454 (mtt) REVERT: V 345 MET cc_start: 0.9627 (mtm) cc_final: 0.8980 (ptp) REVERT: V 425 MET cc_start: 0.9216 (tpp) cc_final: 0.8673 (tpp) REVERT: V 602 MET cc_start: 0.8741 (mmt) cc_final: 0.8359 (tpp) REVERT: W 147 MET cc_start: 0.8727 (tmm) cc_final: 0.8461 (mtt) REVERT: W 345 MET cc_start: 0.9628 (mtm) cc_final: 0.8976 (ptp) REVERT: W 425 MET cc_start: 0.9187 (tpp) cc_final: 0.8647 (tpp) REVERT: W 602 MET cc_start: 0.8748 (mmt) cc_final: 0.8371 (tpp) REVERT: X 147 MET cc_start: 0.8723 (tmm) cc_final: 0.8460 (mtt) REVERT: X 345 MET cc_start: 0.9632 (mtm) cc_final: 0.8987 (ptp) REVERT: X 425 MET cc_start: 0.9195 (tpp) cc_final: 0.8663 (tpp) REVERT: X 602 MET cc_start: 0.8740 (mmt) cc_final: 0.8358 (tpp) REVERT: Y 147 MET cc_start: 0.8723 (tmm) cc_final: 0.8458 (mtt) REVERT: Y 345 MET cc_start: 0.9632 (mtm) cc_final: 0.8987 (ptp) REVERT: Y 425 MET cc_start: 0.9186 (tpp) cc_final: 0.8647 (tpp) REVERT: Y 602 MET cc_start: 0.8738 (mmt) cc_final: 0.8356 (tpp) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.9543 time to fit residues: 553.0778 Evaluate side-chains 312 residues out of total 10992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 9.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 831 optimal weight: 50.0000 chunk 1115 optimal weight: 9.9990 chunk 320 optimal weight: 10.0000 chunk 965 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 291 optimal weight: 8.9990 chunk 1048 optimal weight: 5.9990 chunk 438 optimal weight: 20.0000 chunk 1077 optimal weight: 0.9990 chunk 132 optimal weight: 30.0000 chunk 193 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 501 ASN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 501 ASN ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 501 ASN ** O 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 501 ASN ** P 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 501 ASN ** Q 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 501 ASN ** R 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 501 ASN ** S 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 501 ASN ** Y 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.028694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.021717 restraints weight = 1607384.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.022117 restraints weight = 1251302.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.022355 restraints weight = 1056408.737| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 105528 Z= 0.163 Angle : 0.476 6.588 143064 Z= 0.244 Chirality : 0.040 0.134 15744 Planarity : 0.003 0.031 19272 Dihedral : 3.385 13.070 14328 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: 1.22 (0.08), residues: 13104 helix: 2.66 (0.08), residues: 4392 sheet: 0.40 (0.10), residues: 3072 loop : -0.43 (0.08), residues: 5640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 516 HIS 0.003 0.001 HIS F 469 PHE 0.010 0.001 PHE Y 488 TYR 0.005 0.001 TYR X 539 ARG 0.004 0.000 ARG J 541 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12455.23 seconds wall clock time: 226 minutes 41.80 seconds (13601.80 seconds total)