Starting phenix.real_space_refine on Sun Apr 14 07:13:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvi_17967/04_2024/8pvi_17967.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvi_17967/04_2024/8pvi_17967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvi_17967/04_2024/8pvi_17967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvi_17967/04_2024/8pvi_17967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvi_17967/04_2024/8pvi_17967.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvi_17967/04_2024/8pvi_17967.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 150 5.16 5 C 19374 2.51 5 N 5442 2.21 5 O 5730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C GLU 610": "OE1" <-> "OE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D GLU 341": "OE1" <-> "OE2" Residue "D GLU 610": "OE1" <-> "OE2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E GLU 256": "OE1" <-> "OE2" Residue "E GLU 341": "OE1" <-> "OE2" Residue "E GLU 610": "OE1" <-> "OE2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F GLU 256": "OE1" <-> "OE2" Residue "F GLU 341": "OE1" <-> "OE2" Residue "F GLU 610": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 30696 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5116 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Conformer: "B" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} bond proxies already assigned to first conformer: 5202 Chain: "B" Number of atoms: 5116 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Conformer: "B" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} bond proxies already assigned to first conformer: 5202 Chain: "C" Number of atoms: 5116 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Conformer: "B" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} bond proxies already assigned to first conformer: 5202 Chain: "D" Number of atoms: 5116 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Conformer: "B" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} bond proxies already assigned to first conformer: 5202 Chain: "E" Number of atoms: 5116 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Conformer: "B" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} bond proxies already assigned to first conformer: 5202 Chain: "F" Number of atoms: 5116 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Conformer: "B" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} bond proxies already assigned to first conformer: 5202 Time building chain proxies: 30.41, per 1000 atoms: 0.99 Number of scatterers: 30696 At special positions: 0 Unit cell: (166.327, 177.912, 105.092, 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 150 16.00 O 5730 8.00 N 5442 7.00 C 19374 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: 12.24 Conformation dependent library (CDL) restraints added in 12.3 seconds 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7416 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 54 sheets defined 42.6% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.526A pdb=" N LYS A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 removed outlier: 3.626A pdb=" N MET A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 Processing helix chain 'A' and resid 78 through 88 removed outlier: 4.029A pdb=" N PHE A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 118 Processing helix chain 'A' and resid 161 through 174 removed outlier: 4.095A pdb=" N LYS A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 186 through 201 removed outlier: 3.878A pdb=" N THR A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 192 " --> pdb=" O GLN A 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 201 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.725A pdb=" N LEU A 222 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 242 removed outlier: 3.505A pdb=" N VAL A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 273 through 289 removed outlier: 4.010A pdb=" N ALA A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 293 Processing helix chain 'A' and resid 307 through 321 removed outlier: 3.532A pdb=" N VAL A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 356 Processing helix chain 'A' and resid 388 through 393 removed outlier: 3.678A pdb=" N VAL A 391 " --> pdb=" O THR A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 418 removed outlier: 3.920A pdb=" N LEU A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.955A pdb=" N LYS A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 486 through 492 removed outlier: 4.134A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 525 through 529 Processing helix chain 'A' and resid 548 through 560 Processing helix chain 'A' and resid 563 through 568 Processing helix chain 'A' and resid 568 through 574 removed outlier: 3.696A pdb=" N GLU A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 596 Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.526A pdb=" N LYS B 51 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 59 removed outlier: 3.626A pdb=" N MET B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 78 Processing helix chain 'B' and resid 78 through 88 removed outlier: 4.030A pdb=" N PHE B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 118 Processing helix chain 'B' and resid 161 through 174 removed outlier: 4.094A pdb=" N LYS B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 186 through 201 removed outlier: 3.879A pdb=" N THR B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY B 201 " --> pdb=" O ILE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.726A pdb=" N LEU B 222 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 242 removed outlier: 3.505A pdb=" N VAL B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 273 through 289 removed outlier: 4.010A pdb=" N ALA B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 293 Processing helix chain 'B' and resid 307 through 321 removed outlier: 3.532A pdb=" N VAL B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 356 Processing helix chain 'B' and resid 388 through 393 removed outlier: 3.678A pdb=" N VAL B 391 " --> pdb=" O THR B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 418 removed outlier: 3.920A pdb=" N LEU B 413 " --> pdb=" O GLN B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.954A pdb=" N LYS B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 486 through 492 removed outlier: 4.134A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS B 492 " --> pdb=" O ARG B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 511 Processing helix chain 'B' and resid 525 through 529 Processing helix chain 'B' and resid 548 through 560 Processing helix chain 'B' and resid 563 through 568 Processing helix chain 'B' and resid 568 through 574 removed outlier: 3.695A pdb=" N GLU B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 596 Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.526A pdb=" N LYS C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 59 removed outlier: 3.625A pdb=" N MET C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 78 Processing helix chain 'C' and resid 78 through 88 removed outlier: 4.030A pdb=" N PHE C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 118 Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.094A pdb=" N LYS C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Proline residue: C 170 - end of helix Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 186 through 201 removed outlier: 3.878A pdb=" N THR C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.725A pdb=" N LEU C 222 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.505A pdb=" N VAL C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 273 through 289 removed outlier: 4.010A pdb=" N ALA C 277 " --> pdb=" O GLN C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 293 Processing helix chain 'C' and resid 307 through 321 removed outlier: 3.532A pdb=" N VAL C 316 " --> pdb=" O SER C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 356 Processing helix chain 'C' and resid 388 through 393 removed outlier: 3.678A pdb=" N VAL C 391 " --> pdb=" O THR C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 418 removed outlier: 3.920A pdb=" N LEU C 413 " --> pdb=" O GLN C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 443 Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.955A pdb=" N LYS C 458 " --> pdb=" O GLU C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 486 through 492 removed outlier: 4.134A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS C 492 " --> pdb=" O ARG C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 511 Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 548 through 560 Processing helix chain 'C' and resid 563 through 568 Processing helix chain 'C' and resid 568 through 574 removed outlier: 3.696A pdb=" N GLU C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 596 Processing helix chain 'D' and resid 40 through 51 removed outlier: 3.526A pdb=" N LYS D 51 " --> pdb=" O PHE D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 59 removed outlier: 3.626A pdb=" N MET D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 78 Processing helix chain 'D' and resid 78 through 88 removed outlier: 4.029A pdb=" N PHE D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 118 Processing helix chain 'D' and resid 161 through 174 removed outlier: 4.095A pdb=" N LYS D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Proline residue: D 170 - end of helix Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 186 through 201 removed outlier: 3.878A pdb=" N THR D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 192 " --> pdb=" O GLN D 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D 201 " --> pdb=" O ILE D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 222 removed outlier: 3.725A pdb=" N LEU D 222 " --> pdb=" O LEU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 242 removed outlier: 3.505A pdb=" N VAL D 242 " --> pdb=" O GLN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 273 through 289 removed outlier: 4.010A pdb=" N ALA D 277 " --> pdb=" O GLN D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 293 Processing helix chain 'D' and resid 307 through 321 removed outlier: 3.532A pdb=" N VAL D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 356 Processing helix chain 'D' and resid 388 through 393 removed outlier: 3.678A pdb=" N VAL D 391 " --> pdb=" O THR D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 418 removed outlier: 3.920A pdb=" N LEU D 413 " --> pdb=" O GLN D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 443 Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.955A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 486 through 492 removed outlier: 4.134A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS D 492 " --> pdb=" O ARG D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 511 Processing helix chain 'D' and resid 525 through 529 Processing helix chain 'D' and resid 548 through 560 Processing helix chain 'D' and resid 563 through 568 Processing helix chain 'D' and resid 568 through 574 removed outlier: 3.696A pdb=" N GLU D 574 " --> pdb=" O ILE D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 596 Processing helix chain 'E' and resid 40 through 51 removed outlier: 3.526A pdb=" N LYS E 51 " --> pdb=" O PHE E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 59 removed outlier: 3.625A pdb=" N MET E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 78 Processing helix chain 'E' and resid 78 through 88 removed outlier: 4.030A pdb=" N PHE E 82 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 118 Processing helix chain 'E' and resid 161 through 174 removed outlier: 4.094A pdb=" N LYS E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Proline residue: E 170 - end of helix Processing helix chain 'E' and resid 183 through 185 No H-bonds generated for 'chain 'E' and resid 183 through 185' Processing helix chain 'E' and resid 186 through 201 removed outlier: 3.878A pdb=" N THR E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA E 192 " --> pdb=" O GLN E 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY E 201 " --> pdb=" O ILE E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 222 removed outlier: 3.725A pdb=" N LEU E 222 " --> pdb=" O LEU E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 242 removed outlier: 3.505A pdb=" N VAL E 242 " --> pdb=" O GLN E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 273 through 289 removed outlier: 4.010A pdb=" N ALA E 277 " --> pdb=" O GLN E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 293 Processing helix chain 'E' and resid 307 through 321 removed outlier: 3.532A pdb=" N VAL E 316 " --> pdb=" O SER E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 356 Processing helix chain 'E' and resid 388 through 393 removed outlier: 3.678A pdb=" N VAL E 391 " --> pdb=" O THR E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 418 removed outlier: 3.920A pdb=" N LEU E 413 " --> pdb=" O GLN E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 443 Processing helix chain 'E' and resid 453 through 458 removed outlier: 3.955A pdb=" N LYS E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 486 through 492 removed outlier: 4.134A pdb=" N VAL E 490 " --> pdb=" O GLY E 486 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS E 492 " --> pdb=" O ARG E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 511 Processing helix chain 'E' and resid 525 through 529 Processing helix chain 'E' and resid 548 through 560 Processing helix chain 'E' and resid 563 through 568 Processing helix chain 'E' and resid 568 through 574 removed outlier: 3.696A pdb=" N GLU E 574 " --> pdb=" O ILE E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 596 Processing helix chain 'F' and resid 40 through 51 removed outlier: 3.526A pdb=" N LYS F 51 " --> pdb=" O PHE F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 59 removed outlier: 3.626A pdb=" N MET F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 78 Processing helix chain 'F' and resid 78 through 88 removed outlier: 4.030A pdb=" N PHE F 82 " --> pdb=" O GLU F 78 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 118 Processing helix chain 'F' and resid 161 through 174 removed outlier: 4.094A pdb=" N LYS F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) Proline residue: F 170 - end of helix Processing helix chain 'F' and resid 183 through 185 No H-bonds generated for 'chain 'F' and resid 183 through 185' Processing helix chain 'F' and resid 186 through 201 removed outlier: 3.879A pdb=" N THR F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA F 192 " --> pdb=" O GLN F 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY F 201 " --> pdb=" O ILE F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 222 removed outlier: 3.726A pdb=" N LEU F 222 " --> pdb=" O LEU F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 242 removed outlier: 3.505A pdb=" N VAL F 242 " --> pdb=" O GLN F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 249 Processing helix chain 'F' and resid 273 through 289 removed outlier: 4.010A pdb=" N ALA F 277 " --> pdb=" O GLN F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 293 Processing helix chain 'F' and resid 307 through 321 removed outlier: 3.532A pdb=" N VAL F 316 " --> pdb=" O SER F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 356 Processing helix chain 'F' and resid 388 through 393 removed outlier: 3.678A pdb=" N VAL F 391 " --> pdb=" O THR F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 418 removed outlier: 3.920A pdb=" N LEU F 413 " --> pdb=" O GLN F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 443 Processing helix chain 'F' and resid 453 through 458 removed outlier: 3.954A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 486 through 492 removed outlier: 4.134A pdb=" N VAL F 490 " --> pdb=" O GLY F 486 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS F 492 " --> pdb=" O ARG F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 511 Processing helix chain 'F' and resid 525 through 529 Processing helix chain 'F' and resid 548 through 560 Processing helix chain 'F' and resid 563 through 568 Processing helix chain 'F' and resid 568 through 574 removed outlier: 3.695A pdb=" N GLU F 574 " --> pdb=" O ILE F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 596 Processing sheet with id= 1, first strand: chain 'A' and resid 6 through 8 Processing sheet with id= 2, first strand: chain 'A' and resid 20 through 23 Processing sheet with id= 3, first strand: chain 'A' and resid 124 through 125 Processing sheet with id= 4, first strand: chain 'A' and resid 124 through 125 Processing sheet with id= 5, first strand: chain 'A' and resid 208 through 210 removed outlier: 6.149A pdb=" N ALA A 151 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS A 181 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N HIS A 153 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 228 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLU A 256 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE A 230 " --> pdb=" O GLU A 256 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.254A pdb=" N LEU A 379 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ARG A 299 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN A 261 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE A 301 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS A 263 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL A 303 " --> pdb=" O CYS A 263 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A 265 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS A 262 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 423 " --> pdb=" O HIS A 446 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 472 through 473 Processing sheet with id= 8, first strand: chain 'A' and resid 520 through 521 removed outlier: 5.883A pdb=" N GLU A 520 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU A 541 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP A 538 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL A 626 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE A 656 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU A 628 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLU A 654 " --> pdb=" O LEU A 628 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS A 630 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA A 652 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY A 647 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU A 671 " --> pdb=" O GLY A 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A 649 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU A 669 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP A 651 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER A 667 " --> pdb=" O TRP A 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 653 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU A 665 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 655 " --> pdb=" O VAL A 663 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER A 667 " --> pdb=" O GLY A 608 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY A 608 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU A 669 " --> pdb=" O ASN A 606 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN A 606 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 671 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 545 through 546 removed outlier: 5.564A pdb=" N VAL A 626 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE A 656 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU A 628 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLU A 654 " --> pdb=" O LEU A 628 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS A 630 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA A 652 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY A 647 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU A 671 " --> pdb=" O GLY A 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A 649 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU A 669 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP A 651 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER A 667 " --> pdb=" O TRP A 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 653 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU A 665 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 655 " --> pdb=" O VAL A 663 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 665 " --> pdb=" O ARG A 613 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 613 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 6 through 8 Processing sheet with id= 11, first strand: chain 'B' and resid 20 through 23 Processing sheet with id= 12, first strand: chain 'B' and resid 124 through 125 Processing sheet with id= 13, first strand: chain 'B' and resid 124 through 125 Processing sheet with id= 14, first strand: chain 'B' and resid 208 through 210 removed outlier: 6.149A pdb=" N ALA B 151 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS B 181 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N HIS B 153 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 228 " --> pdb=" O THR B 254 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLU B 256 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE B 230 " --> pdb=" O GLU B 256 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.254A pdb=" N LEU B 379 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ARG B 299 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN B 261 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE B 301 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS B 263 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL B 303 " --> pdb=" O CYS B 263 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 265 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS B 262 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU B 423 " --> pdb=" O HIS B 446 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'B' and resid 472 through 473 Processing sheet with id= 17, first strand: chain 'B' and resid 520 through 521 removed outlier: 5.883A pdb=" N GLU B 520 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU B 541 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP B 538 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL B 626 " --> pdb=" O PHE B 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE B 656 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU B 628 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU B 654 " --> pdb=" O LEU B 628 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS B 630 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ALA B 652 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY B 647 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU B 671 " --> pdb=" O GLY B 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 649 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU B 669 " --> pdb=" O VAL B 649 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP B 651 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER B 667 " --> pdb=" O TRP B 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 653 " --> pdb=" O LEU B 665 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU B 665 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 655 " --> pdb=" O VAL B 663 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER B 667 " --> pdb=" O GLY B 608 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY B 608 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU B 669 " --> pdb=" O ASN B 606 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN B 606 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU B 671 " --> pdb=" O ILE B 604 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 545 through 546 removed outlier: 5.563A pdb=" N VAL B 626 " --> pdb=" O PHE B 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE B 656 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU B 628 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU B 654 " --> pdb=" O LEU B 628 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS B 630 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ALA B 652 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY B 647 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU B 671 " --> pdb=" O GLY B 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 649 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU B 669 " --> pdb=" O VAL B 649 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP B 651 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER B 667 " --> pdb=" O TRP B 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 653 " --> pdb=" O LEU B 665 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU B 665 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 655 " --> pdb=" O VAL B 663 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 665 " --> pdb=" O ARG B 613 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 613 " --> pdb=" O LEU B 665 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'C' and resid 6 through 8 Processing sheet with id= 20, first strand: chain 'C' and resid 20 through 23 Processing sheet with id= 21, first strand: chain 'C' and resid 124 through 125 Processing sheet with id= 22, first strand: chain 'C' and resid 124 through 125 Processing sheet with id= 23, first strand: chain 'C' and resid 208 through 210 removed outlier: 6.149A pdb=" N ALA C 151 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS C 181 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N HIS C 153 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL C 228 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLU C 256 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE C 230 " --> pdb=" O GLU C 256 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.254A pdb=" N LEU C 379 " --> pdb=" O ARG C 361 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ARG C 299 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN C 261 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE C 301 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS C 263 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL C 303 " --> pdb=" O CYS C 263 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU C 265 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS C 262 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU C 423 " --> pdb=" O HIS C 446 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 472 through 473 Processing sheet with id= 26, first strand: chain 'C' and resid 520 through 521 removed outlier: 5.883A pdb=" N GLU C 520 " --> pdb=" O SER C 539 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU C 541 " --> pdb=" O GLU C 520 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP C 538 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL C 626 " --> pdb=" O PHE C 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE C 656 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 628 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU C 654 " --> pdb=" O LEU C 628 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS C 630 " --> pdb=" O ALA C 652 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA C 652 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY C 647 " --> pdb=" O LEU C 671 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU C 671 " --> pdb=" O GLY C 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL C 649 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU C 669 " --> pdb=" O VAL C 649 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TRP C 651 " --> pdb=" O SER C 667 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER C 667 " --> pdb=" O TRP C 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 653 " --> pdb=" O LEU C 665 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU C 665 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 655 " --> pdb=" O VAL C 663 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER C 667 " --> pdb=" O GLY C 608 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY C 608 " --> pdb=" O SER C 667 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU C 669 " --> pdb=" O ASN C 606 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN C 606 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU C 671 " --> pdb=" O ILE C 604 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 545 through 546 removed outlier: 5.563A pdb=" N VAL C 626 " --> pdb=" O PHE C 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE C 656 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 628 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU C 654 " --> pdb=" O LEU C 628 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS C 630 " --> pdb=" O ALA C 652 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA C 652 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY C 647 " --> pdb=" O LEU C 671 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU C 671 " --> pdb=" O GLY C 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL C 649 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU C 669 " --> pdb=" O VAL C 649 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TRP C 651 " --> pdb=" O SER C 667 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER C 667 " --> pdb=" O TRP C 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 653 " --> pdb=" O LEU C 665 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU C 665 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 655 " --> pdb=" O VAL C 663 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 665 " --> pdb=" O ARG C 613 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 613 " --> pdb=" O LEU C 665 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'D' and resid 6 through 8 Processing sheet with id= 29, first strand: chain 'D' and resid 20 through 23 Processing sheet with id= 30, first strand: chain 'D' and resid 124 through 125 Processing sheet with id= 31, first strand: chain 'D' and resid 124 through 125 Processing sheet with id= 32, first strand: chain 'D' and resid 208 through 210 removed outlier: 6.149A pdb=" N ALA D 151 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS D 181 " --> pdb=" O ALA D 151 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N HIS D 153 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL D 228 " --> pdb=" O THR D 254 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLU D 256 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE D 230 " --> pdb=" O GLU D 256 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 359 through 362 removed outlier: 6.254A pdb=" N LEU D 379 " --> pdb=" O ARG D 361 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ARG D 299 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN D 261 " --> pdb=" O ARG D 299 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE D 301 " --> pdb=" O ASN D 261 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS D 263 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL D 303 " --> pdb=" O CYS D 263 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU D 265 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS D 262 " --> pdb=" O ALA D 424 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU D 423 " --> pdb=" O HIS D 446 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 472 through 473 Processing sheet with id= 35, first strand: chain 'D' and resid 520 through 521 removed outlier: 5.883A pdb=" N GLU D 520 " --> pdb=" O SER D 539 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU D 541 " --> pdb=" O GLU D 520 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP D 538 " --> pdb=" O CYS D 630 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL D 626 " --> pdb=" O PHE D 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE D 656 " --> pdb=" O VAL D 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU D 628 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLU D 654 " --> pdb=" O LEU D 628 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS D 630 " --> pdb=" O ALA D 652 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA D 652 " --> pdb=" O CYS D 630 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY D 647 " --> pdb=" O LEU D 671 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU D 671 " --> pdb=" O GLY D 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL D 649 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU D 669 " --> pdb=" O VAL D 649 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP D 651 " --> pdb=" O SER D 667 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER D 667 " --> pdb=" O TRP D 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL D 653 " --> pdb=" O LEU D 665 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU D 665 " --> pdb=" O VAL D 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL D 655 " --> pdb=" O VAL D 663 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER D 667 " --> pdb=" O GLY D 608 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY D 608 " --> pdb=" O SER D 667 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU D 669 " --> pdb=" O ASN D 606 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN D 606 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU D 671 " --> pdb=" O ILE D 604 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'D' and resid 545 through 546 removed outlier: 5.564A pdb=" N VAL D 626 " --> pdb=" O PHE D 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE D 656 " --> pdb=" O VAL D 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU D 628 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLU D 654 " --> pdb=" O LEU D 628 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS D 630 " --> pdb=" O ALA D 652 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA D 652 " --> pdb=" O CYS D 630 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY D 647 " --> pdb=" O LEU D 671 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU D 671 " --> pdb=" O GLY D 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL D 649 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU D 669 " --> pdb=" O VAL D 649 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP D 651 " --> pdb=" O SER D 667 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER D 667 " --> pdb=" O TRP D 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL D 653 " --> pdb=" O LEU D 665 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU D 665 " --> pdb=" O VAL D 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL D 655 " --> pdb=" O VAL D 663 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 665 " --> pdb=" O ARG D 613 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG D 613 " --> pdb=" O LEU D 665 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'E' and resid 6 through 8 Processing sheet with id= 38, first strand: chain 'E' and resid 20 through 23 Processing sheet with id= 39, first strand: chain 'E' and resid 124 through 125 Processing sheet with id= 40, first strand: chain 'E' and resid 124 through 125 Processing sheet with id= 41, first strand: chain 'E' and resid 208 through 210 removed outlier: 6.149A pdb=" N ALA E 151 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS E 181 " --> pdb=" O ALA E 151 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N HIS E 153 " --> pdb=" O LYS E 181 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL E 228 " --> pdb=" O THR E 254 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLU E 256 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE E 230 " --> pdb=" O GLU E 256 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'E' and resid 359 through 362 removed outlier: 6.254A pdb=" N LEU E 379 " --> pdb=" O ARG E 361 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ARG E 299 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN E 261 " --> pdb=" O ARG E 299 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE E 301 " --> pdb=" O ASN E 261 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS E 263 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL E 303 " --> pdb=" O CYS E 263 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU E 265 " --> pdb=" O VAL E 303 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS E 262 " --> pdb=" O ALA E 424 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU E 423 " --> pdb=" O HIS E 446 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'E' and resid 472 through 473 Processing sheet with id= 44, first strand: chain 'E' and resid 520 through 521 removed outlier: 5.883A pdb=" N GLU E 520 " --> pdb=" O SER E 539 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU E 541 " --> pdb=" O GLU E 520 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP E 538 " --> pdb=" O CYS E 630 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL E 626 " --> pdb=" O PHE E 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE E 656 " --> pdb=" O VAL E 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU E 628 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU E 654 " --> pdb=" O LEU E 628 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS E 630 " --> pdb=" O ALA E 652 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA E 652 " --> pdb=" O CYS E 630 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY E 647 " --> pdb=" O LEU E 671 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU E 671 " --> pdb=" O GLY E 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL E 649 " --> pdb=" O LEU E 669 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU E 669 " --> pdb=" O VAL E 649 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TRP E 651 " --> pdb=" O SER E 667 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER E 667 " --> pdb=" O TRP E 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL E 653 " --> pdb=" O LEU E 665 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU E 665 " --> pdb=" O VAL E 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL E 655 " --> pdb=" O VAL E 663 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER E 667 " --> pdb=" O GLY E 608 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY E 608 " --> pdb=" O SER E 667 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU E 669 " --> pdb=" O ASN E 606 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN E 606 " --> pdb=" O LEU E 669 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU E 671 " --> pdb=" O ILE E 604 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'E' and resid 545 through 546 removed outlier: 5.563A pdb=" N VAL E 626 " --> pdb=" O PHE E 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE E 656 " --> pdb=" O VAL E 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU E 628 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU E 654 " --> pdb=" O LEU E 628 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS E 630 " --> pdb=" O ALA E 652 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA E 652 " --> pdb=" O CYS E 630 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY E 647 " --> pdb=" O LEU E 671 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU E 671 " --> pdb=" O GLY E 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL E 649 " --> pdb=" O LEU E 669 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU E 669 " --> pdb=" O VAL E 649 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TRP E 651 " --> pdb=" O SER E 667 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER E 667 " --> pdb=" O TRP E 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL E 653 " --> pdb=" O LEU E 665 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU E 665 " --> pdb=" O VAL E 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL E 655 " --> pdb=" O VAL E 663 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU E 665 " --> pdb=" O ARG E 613 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG E 613 " --> pdb=" O LEU E 665 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'F' and resid 6 through 8 Processing sheet with id= 47, first strand: chain 'F' and resid 20 through 23 Processing sheet with id= 48, first strand: chain 'F' and resid 124 through 125 Processing sheet with id= 49, first strand: chain 'F' and resid 124 through 125 Processing sheet with id= 50, first strand: chain 'F' and resid 208 through 210 removed outlier: 6.149A pdb=" N ALA F 151 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS F 181 " --> pdb=" O ALA F 151 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N HIS F 153 " --> pdb=" O LYS F 181 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL F 228 " --> pdb=" O THR F 254 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLU F 256 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE F 230 " --> pdb=" O GLU F 256 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'F' and resid 359 through 362 removed outlier: 6.254A pdb=" N LEU F 379 " --> pdb=" O ARG F 361 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ARG F 299 " --> pdb=" O VAL F 400 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN F 261 " --> pdb=" O ARG F 299 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE F 301 " --> pdb=" O ASN F 261 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS F 263 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL F 303 " --> pdb=" O CYS F 263 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU F 265 " --> pdb=" O VAL F 303 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS F 262 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU F 423 " --> pdb=" O HIS F 446 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'F' and resid 472 through 473 Processing sheet with id= 53, first strand: chain 'F' and resid 520 through 521 removed outlier: 5.883A pdb=" N GLU F 520 " --> pdb=" O SER F 539 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU F 541 " --> pdb=" O GLU F 520 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP F 538 " --> pdb=" O CYS F 630 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL F 626 " --> pdb=" O PHE F 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE F 656 " --> pdb=" O VAL F 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU F 628 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU F 654 " --> pdb=" O LEU F 628 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS F 630 " --> pdb=" O ALA F 652 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ALA F 652 " --> pdb=" O CYS F 630 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY F 647 " --> pdb=" O LEU F 671 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU F 671 " --> pdb=" O GLY F 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL F 649 " --> pdb=" O LEU F 669 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU F 669 " --> pdb=" O VAL F 649 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP F 651 " --> pdb=" O SER F 667 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER F 667 " --> pdb=" O TRP F 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL F 653 " --> pdb=" O LEU F 665 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU F 665 " --> pdb=" O VAL F 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL F 655 " --> pdb=" O VAL F 663 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER F 667 " --> pdb=" O GLY F 608 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY F 608 " --> pdb=" O SER F 667 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU F 669 " --> pdb=" O ASN F 606 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN F 606 " --> pdb=" O LEU F 669 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU F 671 " --> pdb=" O ILE F 604 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'F' and resid 545 through 546 removed outlier: 5.563A pdb=" N VAL F 626 " --> pdb=" O PHE F 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE F 656 " --> pdb=" O VAL F 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU F 628 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU F 654 " --> pdb=" O LEU F 628 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS F 630 " --> pdb=" O ALA F 652 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ALA F 652 " --> pdb=" O CYS F 630 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY F 647 " --> pdb=" O LEU F 671 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU F 671 " --> pdb=" O GLY F 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL F 649 " --> pdb=" O LEU F 669 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU F 669 " --> pdb=" O VAL F 649 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP F 651 " --> pdb=" O SER F 667 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER F 667 " --> pdb=" O TRP F 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL F 653 " --> pdb=" O LEU F 665 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU F 665 " --> pdb=" O VAL F 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL F 655 " --> pdb=" O VAL F 663 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU F 665 " --> pdb=" O ARG F 613 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG F 613 " --> pdb=" O LEU F 665 " (cutoff:3.500A) 1386 hydrogen bonds defined for protein. 3834 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: 12.74 Time building geometry restraints manager: 13.20 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: 7640 1.34 - 1.47: 9578 1.47 - 1.59: 13862 1.59 - 1.72: 0 1.72 - 1.85: 240 Bond restraints: 31320 Sorted by residual: bond pdb=" C SER F 465 " pdb=" N PRO F 466 " ideal model delta sigma weight residual 1.335 1.373 -0.038 8.70e-03 1.32e+04 1.86e+01 bond pdb=" C SER B 465 " pdb=" N PRO B 466 " ideal model delta sigma weight residual 1.335 1.373 -0.038 8.70e-03 1.32e+04 1.86e+01 bond pdb=" C SER D 465 " pdb=" N PRO D 466 " ideal model delta sigma weight residual 1.335 1.372 -0.037 8.70e-03 1.32e+04 1.85e+01 bond pdb=" C SER A 465 " pdb=" N PRO A 466 " ideal model delta sigma weight residual 1.335 1.372 -0.037 8.70e-03 1.32e+04 1.85e+01 bond pdb=" C SER E 465 " pdb=" N PRO E 466 " ideal model delta sigma weight residual 1.335 1.372 -0.037 8.70e-03 1.32e+04 1.83e+01 ... (remaining 31315 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.22: 1006 106.22 - 113.41: 15074 113.41 - 120.59: 15308 120.59 - 127.77: 10776 127.77 - 134.96: 352 Bond angle restraints: 42516 Sorted by residual: angle pdb=" CB GLU D 348 " pdb=" CG GLU D 348 " pdb=" CD GLU D 348 " ideal model delta sigma weight residual 112.60 121.48 -8.88 1.70e+00 3.46e-01 2.73e+01 angle pdb=" CB GLU A 348 " pdb=" CG GLU A 348 " pdb=" CD GLU A 348 " ideal model delta sigma weight residual 112.60 121.48 -8.88 1.70e+00 3.46e-01 2.73e+01 angle pdb=" CB GLU F 348 " pdb=" CG GLU F 348 " pdb=" CD GLU F 348 " ideal model delta sigma weight residual 112.60 121.46 -8.86 1.70e+00 3.46e-01 2.72e+01 angle pdb=" CB GLU B 348 " pdb=" CG GLU B 348 " pdb=" CD GLU B 348 " ideal model delta sigma weight residual 112.60 121.46 -8.86 1.70e+00 3.46e-01 2.72e+01 angle pdb=" CB GLU E 348 " pdb=" CG GLU E 348 " pdb=" CD GLU E 348 " ideal model delta sigma weight residual 112.60 121.45 -8.85 1.70e+00 3.46e-01 2.71e+01 ... (remaining 42511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 16796 16.59 - 33.19: 1472 33.19 - 49.78: 362 49.78 - 66.37: 126 66.37 - 82.97: 84 Dihedral angle restraints: 18840 sinusoidal: 7296 harmonic: 11544 Sorted by residual: dihedral pdb=" CA THR A 542 " pdb=" C THR A 542 " pdb=" N PRO A 543 " pdb=" CA PRO A 543 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA THR D 542 " pdb=" C THR D 542 " pdb=" N PRO D 543 " pdb=" CA PRO D 543 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA THR E 542 " pdb=" C THR E 542 " pdb=" N PRO E 543 " pdb=" CA PRO E 543 " ideal model delta harmonic sigma weight residual 180.00 159.79 20.21 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 18837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2326 0.047 - 0.093: 1369 0.093 - 0.140: 749 0.140 - 0.187: 314 0.187 - 0.233: 84 Chirality restraints: 4842 Sorted by residual: chirality pdb=" CB ILE C 280 " pdb=" CA ILE C 280 " pdb=" CG1 ILE C 280 " pdb=" CG2 ILE C 280 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB ILE E 280 " pdb=" CA ILE E 280 " pdb=" CG1 ILE E 280 " pdb=" CG2 ILE E 280 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB ILE B 280 " pdb=" CA ILE B 280 " pdb=" CG1 ILE B 280 " pdb=" CG2 ILE B 280 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 4839 not shown) Planarity restraints: 5580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 470 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C LEU E 470 " -0.041 2.00e-02 2.50e+03 pdb=" O LEU E 470 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL E 471 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 470 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C LEU C 470 " 0.041 2.00e-02 2.50e+03 pdb=" O LEU C 470 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL C 471 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 470 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C LEU A 470 " -0.041 2.00e-02 2.50e+03 pdb=" O LEU A 470 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A 471 " 0.014 2.00e-02 2.50e+03 ... (remaining 5577 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 8669 2.85 - 3.36: 28419 3.36 - 3.87: 53342 3.87 - 4.39: 62060 4.39 - 4.90: 105164 Nonbonded interactions: 257654 Sorted by model distance: nonbonded pdb=" O ASN F 158 " pdb=" NZ LYS F 290 " model vdw 2.334 2.520 nonbonded pdb=" O ASN B 158 " pdb=" NZ LYS B 290 " model vdw 2.334 2.520 nonbonded pdb=" O ASN D 158 " pdb=" NZ LYS D 290 " model vdw 2.335 2.520 nonbonded pdb=" O ASN A 158 " pdb=" NZ LYS A 290 " model vdw 2.335 2.520 nonbonded pdb=" O ASN E 158 " pdb=" NZ LYS E 290 " model vdw 2.335 2.520 ... (remaining 257649 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' and (resid 2 through 514 or resid 516 through 679)) selection = (chain 'B' and (resid 2 through 514 or resid 516 through 679)) selection = (chain 'C' and (resid 2 through 514 or resid 516 through 679)) selection = (chain 'D' and (resid 2 through 514 or resid 516 through 679)) selection = (chain 'E' and (resid 2 through 514 or resid 516 through 679)) selection = (chain 'F' and (resid 2 through 514 or resid 516 through 679)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.450 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: 0.030 Extract box with map and model: 8.610 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 106.120 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.010 0.043 31320 Z= 0.660 Angle : 1.623 8.876 42516 Z= 1.084 Chirality : 0.078 0.233 4842 Planarity : 0.007 0.047 5580 Dihedral : 15.333 82.966 11424 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.48 % Favored : 98.37 % Rotamer: Outliers : 1.13 % Allowed : 8.87 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.12), residues: 4062 helix: 0.26 (0.13), residues: 1416 sheet: 0.96 (0.20), residues: 756 loop : -0.36 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.005 TRP B 172 HIS 0.012 0.003 HIS A 562 PHE 0.032 0.007 PHE B 586 TYR 0.027 0.008 TYR E 110 ARG 0.021 0.004 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 782 time to evaluate : 3.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 HIS cc_start: 0.6455 (t-90) cc_final: 0.5787 (t-170) REVERT: A 93 ARG cc_start: 0.7104 (mmm160) cc_final: 0.6667 (tpt-90) REVERT: A 158 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7731 (m-40) REVERT: A 196 SER cc_start: 0.8620 (m) cc_final: 0.8224 (t) REVERT: A 251 ILE cc_start: 0.9006 (mt) cc_final: 0.8790 (mm) REVERT: A 255 MET cc_start: 0.6195 (ttp) cc_final: 0.5988 (ptt) REVERT: A 273 GLN cc_start: 0.7635 (mt0) cc_final: 0.7374 (mt0) REVERT: A 410 ARG cc_start: 0.7651 (ttm-80) cc_final: 0.7160 (mpt180) REVERT: A 411 HIS cc_start: 0.7193 (t-90) cc_final: 0.6834 (t-90) REVERT: A 434 ILE cc_start: 0.6956 (mm) cc_final: 0.6610 (mt) REVERT: A 441 ASP cc_start: 0.8327 (m-30) cc_final: 0.7555 (m-30) REVERT: A 528 ARG cc_start: 0.7422 (mtt-85) cc_final: 0.7052 (mmm160) REVERT: A 610 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7145 (tp30) REVERT: A 622 ASP cc_start: 0.7244 (m-30) cc_final: 0.6964 (m-30) REVERT: B 74 HIS cc_start: 0.6530 (t-90) cc_final: 0.5356 (t70) REVERT: B 93 ARG cc_start: 0.7059 (mmm160) cc_final: 0.6330 (tpp80) REVERT: B 158 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7445 (m-40) REVERT: B 251 ILE cc_start: 0.8999 (mt) cc_final: 0.8792 (mm) REVERT: B 273 GLN cc_start: 0.7826 (mt0) cc_final: 0.7545 (mt0) REVERT: B 293 GLN cc_start: 0.6160 (mt0) cc_final: 0.5513 (mm-40) REVERT: B 410 ARG cc_start: 0.7740 (ttm-80) cc_final: 0.7269 (mpt180) REVERT: B 411 HIS cc_start: 0.7315 (t-90) cc_final: 0.6951 (t-90) REVERT: B 434 ILE cc_start: 0.6930 (mm) cc_final: 0.6565 (mt) REVERT: B 441 ASP cc_start: 0.8363 (m-30) cc_final: 0.7603 (m-30) REVERT: B 528 ARG cc_start: 0.7271 (mtt-85) cc_final: 0.6979 (mmm160) REVERT: B 568 ASP cc_start: 0.7790 (t0) cc_final: 0.7567 (t0) REVERT: B 607 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.7990 (p90) REVERT: B 610 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7218 (tp30) REVERT: C 29 GLU cc_start: 0.7237 (pt0) cc_final: 0.6999 (tt0) REVERT: C 60 THR cc_start: 0.8036 (p) cc_final: 0.7746 (t) REVERT: C 74 HIS cc_start: 0.6429 (t-90) cc_final: 0.5211 (t70) REVERT: C 158 ASN cc_start: 0.7949 (OUTLIER) cc_final: 0.7649 (m-40) REVERT: C 176 MET cc_start: 0.8899 (mtp) cc_final: 0.8690 (ttm) REVERT: C 236 THR cc_start: 0.6571 (m) cc_final: 0.6364 (p) REVERT: C 255 MET cc_start: 0.6292 (ttp) cc_final: 0.5937 (ttp) REVERT: C 273 GLN cc_start: 0.7768 (mt0) cc_final: 0.7515 (mt0) REVERT: C 293 GLN cc_start: 0.6226 (mt0) cc_final: 0.5499 (mm-40) REVERT: C 410 ARG cc_start: 0.7691 (ttm-80) cc_final: 0.7245 (mpt180) REVERT: C 411 HIS cc_start: 0.7418 (t-90) cc_final: 0.6907 (t-90) REVERT: C 434 ILE cc_start: 0.6730 (mm) cc_final: 0.6315 (mt) REVERT: C 441 ASP cc_start: 0.8302 (m-30) cc_final: 0.7470 (m-30) REVERT: C 528 ARG cc_start: 0.7300 (mtt-85) cc_final: 0.7009 (mmm160) REVERT: C 567 MET cc_start: 0.8102 (mmm) cc_final: 0.7818 (mmt) REVERT: C 568 ASP cc_start: 0.7734 (t0) cc_final: 0.7511 (t0) REVERT: C 607 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.8330 (p90) REVERT: C 610 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7391 (tp30) REVERT: C 622 ASP cc_start: 0.7299 (m-30) cc_final: 0.6956 (m-30) REVERT: D 74 HIS cc_start: 0.6452 (t-90) cc_final: 0.5785 (t-170) REVERT: D 93 ARG cc_start: 0.7102 (mmm160) cc_final: 0.6667 (tpt-90) REVERT: D 158 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7735 (m-40) REVERT: D 196 SER cc_start: 0.8620 (m) cc_final: 0.8220 (t) REVERT: D 251 ILE cc_start: 0.9007 (mt) cc_final: 0.8793 (mm) REVERT: D 255 MET cc_start: 0.6204 (ttp) cc_final: 0.5987 (ptt) REVERT: D 273 GLN cc_start: 0.7633 (mt0) cc_final: 0.7372 (mt0) REVERT: D 410 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.7161 (mpt180) REVERT: D 411 HIS cc_start: 0.7195 (t-90) cc_final: 0.6838 (t-90) REVERT: D 434 ILE cc_start: 0.6955 (mm) cc_final: 0.6615 (mt) REVERT: D 441 ASP cc_start: 0.8326 (m-30) cc_final: 0.7547 (m-30) REVERT: D 528 ARG cc_start: 0.7426 (mtt-85) cc_final: 0.7051 (mmm160) REVERT: D 610 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7145 (tp30) REVERT: D 622 ASP cc_start: 0.7243 (m-30) cc_final: 0.6964 (m-30) REVERT: E 29 GLU cc_start: 0.7208 (pt0) cc_final: 0.6967 (tt0) REVERT: E 60 THR cc_start: 0.8038 (p) cc_final: 0.7746 (t) REVERT: E 74 HIS cc_start: 0.6424 (t-90) cc_final: 0.5207 (t70) REVERT: E 158 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7647 (m-40) REVERT: E 176 MET cc_start: 0.8898 (mtp) cc_final: 0.8690 (ttm) REVERT: E 236 THR cc_start: 0.6572 (m) cc_final: 0.6362 (p) REVERT: E 255 MET cc_start: 0.6283 (ttp) cc_final: 0.5932 (ttp) REVERT: E 273 GLN cc_start: 0.7768 (mt0) cc_final: 0.7516 (mt0) REVERT: E 293 GLN cc_start: 0.6228 (mt0) cc_final: 0.5501 (mm-40) REVERT: E 410 ARG cc_start: 0.7695 (ttm-80) cc_final: 0.7248 (mpt180) REVERT: E 411 HIS cc_start: 0.7416 (t-90) cc_final: 0.6908 (t-90) REVERT: E 434 ILE cc_start: 0.6729 (mm) cc_final: 0.6312 (mt) REVERT: E 441 ASP cc_start: 0.8303 (m-30) cc_final: 0.7471 (m-30) REVERT: E 528 ARG cc_start: 0.7297 (mtt-85) cc_final: 0.7005 (mmm160) REVERT: E 567 MET cc_start: 0.8098 (mmm) cc_final: 0.7813 (mmt) REVERT: E 568 ASP cc_start: 0.7734 (t0) cc_final: 0.7510 (t0) REVERT: E 607 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.8328 (p90) REVERT: E 610 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7393 (tp30) REVERT: E 622 ASP cc_start: 0.7300 (m-30) cc_final: 0.6957 (m-30) REVERT: F 74 HIS cc_start: 0.6531 (t-90) cc_final: 0.5355 (t70) REVERT: F 93 ARG cc_start: 0.7055 (mmm160) cc_final: 0.6326 (tpp80) REVERT: F 158 ASN cc_start: 0.7906 (OUTLIER) cc_final: 0.7445 (m-40) REVERT: F 251 ILE cc_start: 0.9000 (mt) cc_final: 0.8794 (mm) REVERT: F 273 GLN cc_start: 0.7831 (mt0) cc_final: 0.7548 (mt0) REVERT: F 293 GLN cc_start: 0.6152 (mt0) cc_final: 0.5512 (mm-40) REVERT: F 410 ARG cc_start: 0.7699 (ttm-80) cc_final: 0.7225 (mpt180) REVERT: F 411 HIS cc_start: 0.7310 (t-90) cc_final: 0.6946 (t-90) REVERT: F 434 ILE cc_start: 0.6925 (mm) cc_final: 0.6563 (mt) REVERT: F 441 ASP cc_start: 0.8363 (m-30) cc_final: 0.7603 (m-30) REVERT: F 528 ARG cc_start: 0.7271 (mtt-85) cc_final: 0.6981 (mmm160) REVERT: F 568 ASP cc_start: 0.7784 (t0) cc_final: 0.7562 (t0) REVERT: F 607 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7988 (p90) REVERT: F 610 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7217 (tp30) outliers start: 36 outliers final: 6 residues processed: 794 average time/residue: 0.3942 time to fit residues: 478.1122 Evaluate side-chains 407 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 391 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 607 TYR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 158 ASN Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 158 ASN Chi-restraints excluded: chain E residue 607 TYR Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain F residue 607 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 339 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 205 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 315 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 234 optimal weight: 4.9990 chunk 365 optimal weight: 0.2980 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN A 409 GLN A 566 HIS A 676 HIS B 409 GLN B 450 GLN B 566 HIS B 676 HIS C 409 GLN C 566 HIS ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 GLN D 409 GLN D 566 HIS D 676 HIS E 409 GLN E 566 HIS F 409 GLN F 450 GLN F 566 HIS F 676 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 31320 Z= 0.341 Angle : 0.690 12.974 42516 Z= 0.355 Chirality : 0.045 0.164 4842 Planarity : 0.005 0.046 5580 Dihedral : 5.106 41.388 4382 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.58 % Allowed : 12.20 % Favored : 84.21 % 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: 0.62 (0.13), residues: 4062 helix: 1.08 (0.13), residues: 1452 sheet: 1.12 (0.19), residues: 780 loop : -0.38 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 651 HIS 0.006 0.002 HIS D 676 PHE 0.026 0.002 PHE C 595 TYR 0.024 0.002 TYR E 607 ARG 0.010 0.001 ARG E 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 381 time to evaluate : 3.747 Fit side-chains REVERT: A 60 THR cc_start: 0.7832 (p) cc_final: 0.7586 (t) REVERT: A 93 ARG cc_start: 0.7036 (mmm160) cc_final: 0.6659 (tpt-90) REVERT: A 410 ARG cc_start: 0.7787 (ttm-80) cc_final: 0.7535 (mmm160) REVERT: A 441 ASP cc_start: 0.8235 (m-30) cc_final: 0.7679 (m-30) REVERT: A 610 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7233 (tp30) REVERT: B 93 ARG cc_start: 0.7094 (mmm160) cc_final: 0.6671 (tpt-90) REVERT: B 158 ASN cc_start: 0.7729 (OUTLIER) cc_final: 0.7420 (m-40) REVERT: B 164 MET cc_start: 0.7508 (ttp) cc_final: 0.7170 (ttt) REVERT: B 273 GLN cc_start: 0.7718 (mt0) cc_final: 0.7437 (mt0) REVERT: B 293 GLN cc_start: 0.6276 (mt0) cc_final: 0.5898 (mt0) REVERT: B 410 ARG cc_start: 0.7736 (ttm-80) cc_final: 0.7503 (mmm160) REVERT: B 411 HIS cc_start: 0.7166 (t-90) cc_final: 0.6260 (t-90) REVERT: B 441 ASP cc_start: 0.8242 (m-30) cc_final: 0.7701 (m-30) REVERT: B 568 ASP cc_start: 0.7583 (t0) cc_final: 0.7273 (t0) REVERT: B 607 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8160 (p90) REVERT: C 60 THR cc_start: 0.7961 (p) cc_final: 0.7603 (t) REVERT: C 93 ARG cc_start: 0.7166 (mmm160) cc_final: 0.6600 (tpt170) REVERT: C 158 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7593 (m-40) REVERT: C 164 MET cc_start: 0.7583 (ttp) cc_final: 0.7241 (ttt) REVERT: C 273 GLN cc_start: 0.7637 (mt0) cc_final: 0.7318 (mt0) REVERT: C 293 GLN cc_start: 0.6349 (mt0) cc_final: 0.6020 (mt0) REVERT: C 410 ARG cc_start: 0.7715 (ttm-80) cc_final: 0.7407 (mmm160) REVERT: C 411 HIS cc_start: 0.7216 (t-90) cc_final: 0.6331 (t-90) REVERT: C 434 ILE cc_start: 0.6584 (mm) cc_final: 0.6377 (mt) REVERT: C 441 ASP cc_start: 0.8189 (m-30) cc_final: 0.7620 (m-30) REVERT: C 567 MET cc_start: 0.8116 (mmm) cc_final: 0.7816 (mmt) REVERT: C 607 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.8406 (p90) REVERT: D 60 THR cc_start: 0.7832 (p) cc_final: 0.7586 (t) REVERT: D 93 ARG cc_start: 0.7035 (mmm160) cc_final: 0.6656 (tpt-90) REVERT: D 410 ARG cc_start: 0.7787 (ttm-80) cc_final: 0.7534 (mmm160) REVERT: D 441 ASP cc_start: 0.8239 (m-30) cc_final: 0.7686 (m-30) REVERT: D 610 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7230 (tp30) REVERT: E 60 THR cc_start: 0.7963 (p) cc_final: 0.7604 (t) REVERT: E 93 ARG cc_start: 0.7168 (mmm160) cc_final: 0.6604 (tpt170) REVERT: E 116 ARG cc_start: 0.8412 (mtm110) cc_final: 0.7692 (ptm160) REVERT: E 158 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7590 (m-40) REVERT: E 164 MET cc_start: 0.7584 (ttp) cc_final: 0.7241 (ttt) REVERT: E 273 GLN cc_start: 0.7637 (mt0) cc_final: 0.7319 (mt0) REVERT: E 293 GLN cc_start: 0.6353 (mt0) cc_final: 0.6024 (mt0) REVERT: E 410 ARG cc_start: 0.7715 (ttm-80) cc_final: 0.7408 (mmm160) REVERT: E 411 HIS cc_start: 0.7208 (t-90) cc_final: 0.6326 (t-90) REVERT: E 434 ILE cc_start: 0.6583 (mm) cc_final: 0.6376 (mt) REVERT: E 441 ASP cc_start: 0.8192 (m-30) cc_final: 0.7622 (m-30) REVERT: E 567 MET cc_start: 0.8113 (mmm) cc_final: 0.7814 (mmt) REVERT: E 607 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.8406 (p90) REVERT: F 93 ARG cc_start: 0.7091 (mmm160) cc_final: 0.6670 (tpt-90) REVERT: F 158 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7421 (m-40) REVERT: F 164 MET cc_start: 0.7506 (ttp) cc_final: 0.7168 (ttt) REVERT: F 273 GLN cc_start: 0.7717 (mt0) cc_final: 0.7435 (mt0) REVERT: F 293 GLN cc_start: 0.6271 (mt0) cc_final: 0.5896 (mt0) REVERT: F 410 ARG cc_start: 0.7709 (ttm-80) cc_final: 0.7436 (mmm160) REVERT: F 411 HIS cc_start: 0.7164 (t-90) cc_final: 0.6266 (t-90) REVERT: F 441 ASP cc_start: 0.8245 (m-30) cc_final: 0.7703 (m-30) REVERT: F 568 ASP cc_start: 0.7579 (t0) cc_final: 0.7273 (t0) REVERT: F 607 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8157 (p90) outliers start: 114 outliers final: 56 residues processed: 467 average time/residue: 0.4380 time to fit residues: 329.6089 Evaluate side-chains 367 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 303 time to evaluate : 3.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 607 TYR Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 158 ASN Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 261 ASN Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 522 ASP Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 607 TYR Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 261 ASN Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 607 TYR Chi-restraints excluded: chain F residue 615 ILE Chi-restraints excluded: chain F residue 663 VAL Chi-restraints excluded: chain F residue 670 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 202 optimal weight: 0.0770 chunk 113 optimal weight: 5.9990 chunk 303 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 365 optimal weight: 3.9990 chunk 395 optimal weight: 4.9990 chunk 325 optimal weight: 5.9990 chunk 362 optimal weight: 0.1980 chunk 124 optimal weight: 9.9990 chunk 293 optimal weight: 7.9990 overall best weight: 3.0544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 HIS B 384 GLN C 384 GLN E 384 GLN F 74 HIS F 384 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2865 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: