Starting phenix.real_space_refine on Tue Aug 26 14:45:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5nv3_3699/08_2025/5nv3_3699.cif Found real_map, /net/cci-nas-00/data/ceres_data/5nv3_3699/08_2025/5nv3_3699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5nv3_3699/08_2025/5nv3_3699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5nv3_3699/08_2025/5nv3_3699.map" model { file = "/net/cci-nas-00/data/ceres_data/5nv3_3699/08_2025/5nv3_3699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5nv3_3699/08_2025/5nv3_3699.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.273 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 240 5.16 5 C 23960 2.51 5 N 6544 2.21 5 O 7048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37816 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "B" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "C" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "D" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "E" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "F" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "G" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "H" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 128 residue: pdb=" N GLY A 464 " occ=0.40 ... (2 atoms not shown) pdb=" O GLY A 464 " occ=0.40 residue: pdb=" N ASN A 465 " occ=0.40 ... (6 atoms not shown) pdb=" ND2 ASN A 465 " occ=0.40 residue: pdb=" N ILE A 466 " occ=0.40 ... (6 atoms not shown) pdb=" CD1 ILE A 466 " occ=0.40 residue: pdb=" N THR A 467 " occ=0.40 ... (5 atoms not shown) pdb=" CG2 THR A 467 " occ=0.40 residue: pdb=" N PHE A 468 " occ=0.40 ... (9 atoms not shown) pdb=" CZ PHE A 468 " occ=0.40 residue: pdb=" N ASN A 469 " occ=0.40 ... (6 atoms not shown) pdb=" ND2 ASN A 469 " occ=0.40 residue: pdb=" N TYR A 470 " occ=0.40 ... (10 atoms not shown) pdb=" OH TYR A 470 " occ=0.40 residue: pdb=" N THR A 471 " occ=0.40 ... (5 atoms not shown) pdb=" CG2 THR A 471 " occ=0.40 residue: pdb=" N SER A 472 " occ=0.40 ... (4 atoms not shown) pdb=" OG SER A 472 " occ=0.40 residue: pdb=" N THR A 473 " occ=0.40 ... (5 atoms not shown) pdb=" CG2 THR A 473 " occ=0.40 residue: pdb=" N ASP A 474 " occ=0.40 ... (6 atoms not shown) pdb=" OD2 ASP A 474 " occ=0.40 residue: pdb=" N THR A 475 " occ=0.40 ... (5 atoms not shown) pdb=" CG2 THR A 475 " occ=0.40 ... (remaining 116 not shown) Time building chain proxies: 7.93, per 1000 atoms: 0.21 Number of scatterers: 37816 At special positions: 0 Unit cell: (132.08, 132.08, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 240 16.00 P 16 15.00 Mg 8 11.99 O 7048 8.00 N 6544 7.00 C 23960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8656 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 34 sheets defined 41.6% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 51 through 63 removed outlier: 3.551A pdb=" N SER A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.564A pdb=" N ASP A 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 removed outlier: 3.808A pdb=" N TYR A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 114 through 123 removed outlier: 3.682A pdb=" N LEU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 148 removed outlier: 3.537A pdb=" N LYS A 148 " --> pdb=" O VAL A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 removed outlier: 3.659A pdb=" N GLY A 159 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 198 removed outlier: 3.608A pdb=" N GLY A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 235 removed outlier: 3.582A pdb=" N LEU A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 224 " --> pdb=" O PHE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 263 removed outlier: 3.502A pdb=" N ARG A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 removed outlier: 3.604A pdb=" N SER A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 removed outlier: 3.607A pdb=" N ILE A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 352 removed outlier: 3.549A pdb=" N TYR A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS A 350 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 387 through 395 removed outlier: 3.504A pdb=" N SER A 393 " --> pdb=" O HIS A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.027A pdb=" N ILE A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 435 Processing helix chain 'A' and resid 441 through 450 Processing helix chain 'A' and resid 453 through 463 removed outlier: 3.683A pdb=" N GLU A 457 " --> pdb=" O CYS A 453 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 30 Processing helix chain 'I' and resid 60 through 75 removed outlier: 4.173A pdb=" N VAL I 64 " --> pdb=" O ASP I 60 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET I 65 " --> pdb=" O PRO I 61 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU I 67 " --> pdb=" O GLY I 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 51 through 63 removed outlier: 3.546A pdb=" N SER B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.601A pdb=" N ASP B 74 " --> pdb=" O VAL B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.800A pdb=" N TYR B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 114 through 123 removed outlier: 3.699A pdb=" N LEU B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 148 removed outlier: 3.535A pdb=" N LYS B 148 " --> pdb=" O VAL B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.655A pdb=" N GLY B 159 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 198 removed outlier: 3.592A pdb=" N GLY B 188 " --> pdb=" O GLY B 184 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 198 " --> pdb=" O GLY B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 235 removed outlier: 3.599A pdb=" N LEU B 221 " --> pdb=" O ARG B 217 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET B 224 " --> pdb=" O PHE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 263 removed outlier: 3.503A pdb=" N ARG B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 removed outlier: 3.599A pdb=" N SER B 280 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 323 removed outlier: 3.621A pdb=" N ILE B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 352 removed outlier: 3.535A pdb=" N TYR B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 387 through 395 removed outlier: 3.503A pdb=" N SER B 393 " --> pdb=" O HIS B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.045A pdb=" N ILE B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 435 Processing helix chain 'B' and resid 441 through 450 Processing helix chain 'B' and resid 453 through 463 removed outlier: 3.700A pdb=" N GLU B 457 " --> pdb=" O CYS B 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 30 Processing helix chain 'J' and resid 60 through 75 removed outlier: 4.169A pdb=" N VAL J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET J 65 " --> pdb=" O PRO J 61 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 51 through 63 removed outlier: 3.541A pdb=" N SER C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.563A pdb=" N ASP C 74 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 83 removed outlier: 3.802A pdb=" N TYR C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 114 through 123 removed outlier: 3.698A pdb=" N LEU C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 148 removed outlier: 3.542A pdb=" N LYS C 148 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 165 removed outlier: 3.653A pdb=" N GLY C 159 " --> pdb=" O THR C 155 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG C 163 " --> pdb=" O GLY C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 198 removed outlier: 3.599A pdb=" N GLY C 188 " --> pdb=" O GLY C 184 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C 198 " --> pdb=" O GLY C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 235 removed outlier: 3.599A pdb=" N LEU C 221 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET C 224 " --> pdb=" O PHE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 263 Processing helix chain 'C' and resid 274 through 287 removed outlier: 3.603A pdb=" N SER C 280 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 323 removed outlier: 3.622A pdb=" N ILE C 315 " --> pdb=" O SER C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 352 removed outlier: 3.549A pdb=" N TYR C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 386 No H-bonds generated for 'chain 'C' and resid 384 through 386' Processing helix chain 'C' and resid 387 through 395 Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.035A pdb=" N ILE C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 435 Processing helix chain 'C' and resid 441 through 450 Processing helix chain 'C' and resid 453 through 463 removed outlier: 3.693A pdb=" N GLU C 457 " --> pdb=" O CYS C 453 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 30 Processing helix chain 'K' and resid 60 through 75 removed outlier: 4.174A pdb=" N VAL K 64 " --> pdb=" O ASP K 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET K 65 " --> pdb=" O PRO K 61 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU K 67 " --> pdb=" O GLY K 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 51 through 63 removed outlier: 3.540A pdb=" N SER D 63 " --> pdb=" O VAL D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 76 removed outlier: 3.607A pdb=" N ASP D 74 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 removed outlier: 3.795A pdb=" N TYR D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 114 through 123 removed outlier: 3.692A pdb=" N LEU D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 148 removed outlier: 3.541A pdb=" N LYS D 148 " --> pdb=" O VAL D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 165 removed outlier: 3.659A pdb=" N GLY D 159 " --> pdb=" O THR D 155 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 198 removed outlier: 3.596A pdb=" N GLY D 188 " --> pdb=" O GLY D 184 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 189 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY D 198 " --> pdb=" O GLY D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 235 removed outlier: 3.603A pdb=" N LEU D 221 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET D 224 " --> pdb=" O PHE D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 263 Processing helix chain 'D' and resid 274 through 287 removed outlier: 3.598A pdb=" N SER D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 281 " --> pdb=" O ALA D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 removed outlier: 3.609A pdb=" N ILE D 315 " --> pdb=" O SER D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 352 removed outlier: 3.546A pdb=" N TYR D 346 " --> pdb=" O THR D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 386 No H-bonds generated for 'chain 'D' and resid 384 through 386' Processing helix chain 'D' and resid 387 through 395 removed outlier: 3.513A pdb=" N SER D 393 " --> pdb=" O HIS D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 409 removed outlier: 4.030A pdb=" N ILE D 408 " --> pdb=" O GLY D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 435 Processing helix chain 'D' and resid 441 through 450 Processing helix chain 'D' and resid 453 through 463 removed outlier: 3.692A pdb=" N GLU D 457 " --> pdb=" O CYS D 453 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 30 Processing helix chain 'L' and resid 61 through 75 removed outlier: 3.646A pdb=" N MET L 65 " --> pdb=" O PRO L 61 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU L 67 " --> pdb=" O GLY L 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 51 through 63 removed outlier: 3.534A pdb=" N SER E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 76 removed outlier: 3.589A pdb=" N ASP E 74 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.801A pdb=" N TYR E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' Processing helix chain 'E' and resid 114 through 123 removed outlier: 3.696A pdb=" N LEU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 148 removed outlier: 3.541A pdb=" N LYS E 148 " --> pdb=" O VAL E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 165 removed outlier: 3.671A pdb=" N GLY E 159 " --> pdb=" O THR E 155 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG E 163 " --> pdb=" O GLY E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 198 removed outlier: 3.591A pdb=" N GLY E 188 " --> pdb=" O GLY E 184 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY E 198 " --> pdb=" O GLY E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 235 removed outlier: 3.618A pdb=" N LEU E 221 " --> pdb=" O ARG E 217 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET E 224 " --> pdb=" O PHE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 263 Processing helix chain 'E' and resid 274 through 287 removed outlier: 3.591A pdb=" N SER E 280 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E 281 " --> pdb=" O ALA E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 323 removed outlier: 3.626A pdb=" N ILE E 315 " --> pdb=" O SER E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 352 removed outlier: 3.533A pdb=" N TYR E 346 " --> pdb=" O THR E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 386 No H-bonds generated for 'chain 'E' and resid 384 through 386' Processing helix chain 'E' and resid 387 through 395 removed outlier: 3.506A pdb=" N SER E 393 " --> pdb=" O HIS E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 409 removed outlier: 4.026A pdb=" N ILE E 408 " --> pdb=" O GLY E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 435 removed outlier: 3.502A pdb=" N GLY E 435 " --> pdb=" O ALA E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 450 Processing helix chain 'E' and resid 453 through 463 removed outlier: 3.705A pdb=" N GLU E 457 " --> pdb=" O CYS E 453 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 30 Processing helix chain 'M' and resid 60 through 75 removed outlier: 4.170A pdb=" N VAL M 64 " --> pdb=" O ASP M 60 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET M 65 " --> pdb=" O PRO M 61 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU M 67 " --> pdb=" O GLY M 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 25 Processing helix chain 'F' and resid 51 through 63 removed outlier: 3.545A pdb=" N SER F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 76 removed outlier: 3.593A pdb=" N ASP F 74 " --> pdb=" O VAL F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.803A pdb=" N TYR F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 114 through 123 removed outlier: 3.691A pdb=" N LEU F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 148 removed outlier: 3.520A pdb=" N LYS F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 165 removed outlier: 3.657A pdb=" N GLY F 159 " --> pdb=" O THR F 155 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG F 163 " --> pdb=" O GLY F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 198 removed outlier: 3.596A pdb=" N GLY F 188 " --> pdb=" O GLY F 184 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG F 189 " --> pdb=" O LYS F 185 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY F 198 " --> pdb=" O GLY F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 235 removed outlier: 3.599A pdb=" N LEU F 221 " --> pdb=" O ARG F 217 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET F 224 " --> pdb=" O PHE F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 263 Processing helix chain 'F' and resid 274 through 287 removed outlier: 3.587A pdb=" N SER F 280 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE F 281 " --> pdb=" O ALA F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 323 removed outlier: 3.618A pdb=" N ILE F 315 " --> pdb=" O SER F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 352 removed outlier: 3.532A pdb=" N TYR F 346 " --> pdb=" O THR F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 386 No H-bonds generated for 'chain 'F' and resid 384 through 386' Processing helix chain 'F' and resid 387 through 395 removed outlier: 3.501A pdb=" N SER F 393 " --> pdb=" O HIS F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 409 removed outlier: 4.036A pdb=" N ILE F 408 " --> pdb=" O GLY F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 435 Processing helix chain 'F' and resid 441 through 450 Processing helix chain 'F' and resid 453 through 463 removed outlier: 3.688A pdb=" N GLU F 457 " --> pdb=" O CYS F 453 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 30 Processing helix chain 'N' and resid 60 through 75 removed outlier: 4.165A pdb=" N VAL N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET N 65 " --> pdb=" O PRO N 61 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU N 67 " --> pdb=" O GLY N 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 25 Processing helix chain 'G' and resid 51 through 63 removed outlier: 3.548A pdb=" N SER G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 76 removed outlier: 3.599A pdb=" N ASP G 74 " --> pdb=" O VAL G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 3.805A pdb=" N TYR G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 114 through 123 removed outlier: 3.677A pdb=" N LEU G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 148 removed outlier: 3.536A pdb=" N LYS G 148 " --> pdb=" O VAL G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 165 removed outlier: 3.673A pdb=" N GLY G 159 " --> pdb=" O THR G 155 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG G 163 " --> pdb=" O GLY G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 198 removed outlier: 3.599A pdb=" N GLY G 188 " --> pdb=" O GLY G 184 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG G 189 " --> pdb=" O LYS G 185 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY G 198 " --> pdb=" O GLY G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 235 removed outlier: 3.600A pdb=" N LEU G 221 " --> pdb=" O ARG G 217 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET G 224 " --> pdb=" O PHE G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 263 removed outlier: 3.507A pdb=" N ARG G 254 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 287 removed outlier: 3.586A pdb=" N SER G 280 " --> pdb=" O THR G 276 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE G 281 " --> pdb=" O ALA G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 323 removed outlier: 3.609A pdb=" N ILE G 315 " --> pdb=" O SER G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 352 removed outlier: 3.530A pdb=" N TYR G 346 " --> pdb=" O THR G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 384 through 386 No H-bonds generated for 'chain 'G' and resid 384 through 386' Processing helix chain 'G' and resid 387 through 395 removed outlier: 3.512A pdb=" N SER G 393 " --> pdb=" O HIS G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 409 removed outlier: 4.019A pdb=" N ILE G 408 " --> pdb=" O GLY G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 435 Processing helix chain 'G' and resid 441 through 450 Processing helix chain 'G' and resid 453 through 463 removed outlier: 3.693A pdb=" N GLU G 457 " --> pdb=" O CYS G 453 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 30 Processing helix chain 'O' and resid 60 through 75 removed outlier: 4.168A pdb=" N VAL O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET O 65 " --> pdb=" O PRO O 61 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU O 67 " --> pdb=" O GLY O 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 51 through 63 removed outlier: 3.541A pdb=" N SER H 63 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 76 removed outlier: 3.600A pdb=" N ASP H 74 " --> pdb=" O VAL H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 3.799A pdb=" N TYR H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 110 No H-bonds generated for 'chain 'H' and resid 108 through 110' Processing helix chain 'H' and resid 114 through 123 removed outlier: 3.686A pdb=" N LEU H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 148 removed outlier: 3.528A pdb=" N LYS H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 165 removed outlier: 3.660A pdb=" N GLY H 159 " --> pdb=" O THR H 155 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG H 163 " --> pdb=" O GLY H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 198 removed outlier: 3.599A pdb=" N GLY H 188 " --> pdb=" O GLY H 184 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG H 189 " --> pdb=" O LYS H 185 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY H 198 " --> pdb=" O GLY H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 235 removed outlier: 3.605A pdb=" N LEU H 221 " --> pdb=" O ARG H 217 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET H 224 " --> pdb=" O PHE H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 263 Processing helix chain 'H' and resid 274 through 287 removed outlier: 3.585A pdb=" N SER H 280 " --> pdb=" O THR H 276 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE H 281 " --> pdb=" O ALA H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 323 removed outlier: 3.608A pdb=" N ILE H 315 " --> pdb=" O SER H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 352 removed outlier: 3.543A pdb=" N TYR H 346 " --> pdb=" O THR H 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 386 No H-bonds generated for 'chain 'H' and resid 384 through 386' Processing helix chain 'H' and resid 387 through 395 removed outlier: 3.509A pdb=" N SER H 393 " --> pdb=" O HIS H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 409 removed outlier: 4.022A pdb=" N ILE H 408 " --> pdb=" O GLY H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 435 Processing helix chain 'H' and resid 441 through 450 Processing helix chain 'H' and resid 453 through 463 removed outlier: 3.683A pdb=" N GLU H 457 " --> pdb=" O CYS H 453 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 30 Processing helix chain 'P' and resid 61 through 75 removed outlier: 3.649A pdb=" N MET P 65 " --> pdb=" O PRO P 61 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU P 67 " --> pdb=" O GLY P 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 91 removed outlier: 5.492A pdb=" N ALA A 86 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA A 104 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG A 88 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 39 " --> pdb=" O MET A 140 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N MET A 140 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 41 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 175 removed outlier: 6.692A pdb=" N LEU A 172 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N KCX A 203 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA A 174 " --> pdb=" O KCX A 203 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N MET A 202 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN A 243 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N HIS A 240 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N MET A 268 " --> pdb=" O HIS A 240 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU A 242 " --> pdb=" O MET A 268 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ASP A 270 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 267 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N HIS A 295 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 269 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU A 292 " --> pdb=" O HIS A 326 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N HIS A 328 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N MET A 294 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 327 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N SER A 380 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 354 through 355 Processing sheet with id=AA4, first strand: chain 'I' and resid 49 through 50 removed outlier: 7.189A pdb=" N ILE I 80 " --> pdb=" O ILE I 99 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE I 99 " --> pdb=" O ILE I 80 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE I 82 " --> pdb=" O SER I 97 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER I 97 " --> pdb=" O ILE I 82 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA I 84 " --> pdb=" O THR I 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 109 through 115 removed outlier: 4.348A pdb=" N TYR I 123 " --> pdb=" O GLU J 115 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS I 125 " --> pdb=" O ARG J 113 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG J 113 " --> pdb=" O HIS I 125 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE I 127 " --> pdb=" O MET J 111 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N MET J 111 " --> pdb=" O ILE I 127 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR J 123 " --> pdb=" O GLU K 115 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS J 125 " --> pdb=" O ARG K 113 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG K 113 " --> pdb=" O HIS J 125 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE J 127 " --> pdb=" O MET K 111 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N MET K 111 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR K 123 " --> pdb=" O GLU L 115 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS K 125 " --> pdb=" O ARG L 113 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ARG L 113 " --> pdb=" O HIS K 125 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE K 127 " --> pdb=" O MET L 111 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N MET L 111 " --> pdb=" O ILE K 127 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR L 123 " --> pdb=" O GLU I 115 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N HIS L 125 " --> pdb=" O ARG I 113 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG I 113 " --> pdb=" O HIS L 125 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE L 127 " --> pdb=" O MET I 111 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N MET I 111 " --> pdb=" O ILE L 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 85 through 91 removed outlier: 5.491A pdb=" N ALA B 86 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA B 104 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG B 88 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 39 " --> pdb=" O MET B 140 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N MET B 140 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU B 41 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 171 through 175 removed outlier: 6.684A pdb=" N LEU B 172 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N KCX B 203 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA B 174 " --> pdb=" O KCX B 203 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N MET B 202 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ASN B 243 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N HIS B 240 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET B 268 " --> pdb=" O HIS B 240 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU B 242 " --> pdb=" O MET B 268 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ASP B 270 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 267 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N HIS B 295 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL B 269 " --> pdb=" O HIS B 295 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU B 292 " --> pdb=" O HIS B 326 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N HIS B 328 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N MET B 294 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 327 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N SER B 380 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 355 Processing sheet with id=AA9, first strand: chain 'J' and resid 49 through 50 removed outlier: 7.191A pdb=" N ILE J 80 " --> pdb=" O ILE J 99 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE J 99 " --> pdb=" O ILE J 80 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE J 82 " --> pdb=" O SER J 97 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER J 97 " --> pdb=" O ILE J 82 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA J 84 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 85 through 91 removed outlier: 5.494A pdb=" N ALA C 86 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA C 104 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG C 88 " --> pdb=" O TYR C 102 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU C 39 " --> pdb=" O MET C 140 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N MET C 140 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU C 41 " --> pdb=" O GLU C 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 171 through 175 removed outlier: 6.693A pdb=" N LEU C 172 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N KCX C 203 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA C 174 " --> pdb=" O KCX C 203 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N MET C 202 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ASN C 243 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N HIS C 240 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N MET C 268 " --> pdb=" O HIS C 240 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU C 242 " --> pdb=" O MET C 268 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ASP C 270 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL C 267 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N HIS C 295 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL C 269 " --> pdb=" O HIS C 295 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU C 292 " --> pdb=" O HIS C 326 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N HIS C 328 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N MET C 294 " --> pdb=" O HIS C 328 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU C 327 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N SER C 380 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AB4, first strand: chain 'K' and resid 49 through 50 removed outlier: 7.198A pdb=" N ILE K 80 " --> pdb=" O ILE K 99 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE K 99 " --> pdb=" O ILE K 80 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE K 82 " --> pdb=" O SER K 97 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER K 97 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA K 84 " --> pdb=" O THR K 95 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 85 through 91 removed outlier: 5.485A pdb=" N ALA D 86 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA D 104 " --> pdb=" O ALA D 86 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG D 88 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU D 39 " --> pdb=" O MET D 140 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N MET D 140 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU D 41 " --> pdb=" O GLU D 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 171 through 175 removed outlier: 6.690A pdb=" N LEU D 172 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N KCX D 203 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ALA D 174 " --> pdb=" O KCX D 203 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N MET D 202 " --> pdb=" O TYR D 241 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ASN D 243 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N HIS D 240 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N MET D 268 " --> pdb=" O HIS D 240 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU D 242 " --> pdb=" O MET D 268 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP D 270 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL D 267 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N HIS D 295 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL D 269 " --> pdb=" O HIS D 295 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU D 292 " --> pdb=" O HIS D 326 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N HIS D 328 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N MET D 294 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU D 327 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N SER D 380 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 354 through 355 Processing sheet with id=AB8, first strand: chain 'L' and resid 49 through 50 removed outlier: 7.183A pdb=" N ILE L 80 " --> pdb=" O ILE L 99 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE L 99 " --> pdb=" O ILE L 80 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE L 82 " --> pdb=" O SER L 97 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER L 97 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA L 84 " --> pdb=" O THR L 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 85 through 91 removed outlier: 5.510A pdb=" N ALA E 86 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA E 104 " --> pdb=" O ALA E 86 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG E 88 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU E 39 " --> pdb=" O MET E 140 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N MET E 140 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU E 41 " --> pdb=" O GLU E 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 171 through 175 removed outlier: 6.692A pdb=" N LEU E 172 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N KCX E 203 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA E 174 " --> pdb=" O KCX E 203 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N MET E 202 " --> pdb=" O TYR E 241 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ASN E 243 " --> pdb=" O MET E 202 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N HIS E 240 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N MET E 268 " --> pdb=" O HIS E 240 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU E 242 " --> pdb=" O MET E 268 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASP E 270 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL E 267 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N HIS E 295 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL E 269 " --> pdb=" O HIS E 295 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU E 292 " --> pdb=" O HIS E 326 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N HIS E 328 " --> pdb=" O LEU E 292 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N MET E 294 " --> pdb=" O HIS E 328 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU E 327 " --> pdb=" O VAL E 378 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N SER E 380 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 354 through 355 Processing sheet with id=AC3, first strand: chain 'M' and resid 49 through 50 removed outlier: 7.195A pdb=" N ILE M 80 " --> pdb=" O ILE M 99 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE M 99 " --> pdb=" O ILE M 80 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE M 82 " --> pdb=" O SER M 97 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER M 97 " --> pdb=" O ILE M 82 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA M 84 " --> pdb=" O THR M 95 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 109 through 115 removed outlier: 4.323A pdb=" N TYR M 123 " --> pdb=" O GLU P 115 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS M 125 " --> pdb=" O ARG P 113 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG P 113 " --> pdb=" O HIS M 125 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE M 127 " --> pdb=" O MET P 111 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N MET P 111 " --> pdb=" O ILE M 127 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR P 123 " --> pdb=" O GLU O 115 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS P 125 " --> pdb=" O ARG O 113 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG O 113 " --> pdb=" O HIS P 125 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE P 127 " --> pdb=" O MET O 111 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N MET O 111 " --> pdb=" O ILE P 127 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR O 123 " --> pdb=" O GLU N 115 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS O 125 " --> pdb=" O ARG N 113 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ARG N 113 " --> pdb=" O HIS O 125 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE O 127 " --> pdb=" O MET N 111 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N MET N 111 " --> pdb=" O ILE O 127 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR N 123 " --> pdb=" O GLU M 115 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS N 125 " --> pdb=" O ARG M 113 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG M 113 " --> pdb=" O HIS N 125 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE N 127 " --> pdb=" O MET M 111 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N MET M 111 " --> pdb=" O ILE N 127 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 85 through 91 removed outlier: 5.506A pdb=" N ALA F 86 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA F 104 " --> pdb=" O ALA F 86 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG F 88 " --> pdb=" O TYR F 102 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU F 39 " --> pdb=" O MET F 140 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N MET F 140 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU F 41 " --> pdb=" O GLU F 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 171 through 175 removed outlier: 6.685A pdb=" N LEU F 172 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N KCX F 203 " --> pdb=" O LEU F 172 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA F 174 " --> pdb=" O KCX F 203 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N MET F 202 " --> pdb=" O TYR F 241 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N ASN F 243 " --> pdb=" O MET F 202 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N HIS F 240 " --> pdb=" O ILE F 266 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N MET F 268 " --> pdb=" O HIS F 240 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU F 242 " --> pdb=" O MET F 268 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP F 270 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL F 267 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N HIS F 295 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL F 269 " --> pdb=" O HIS F 295 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU F 292 " --> pdb=" O HIS F 326 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N HIS F 328 " --> pdb=" O LEU F 292 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N MET F 294 " --> pdb=" O HIS F 328 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU F 327 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N SER F 380 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 354 through 355 Processing sheet with id=AC8, first strand: chain 'N' and resid 49 through 50 removed outlier: 7.193A pdb=" N ILE N 80 " --> pdb=" O ILE N 99 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE N 99 " --> pdb=" O ILE N 80 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE N 82 " --> pdb=" O SER N 97 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER N 97 " --> pdb=" O ILE N 82 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA N 84 " --> pdb=" O THR N 95 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 85 through 91 removed outlier: 5.509A pdb=" N ALA G 86 " --> pdb=" O ALA G 104 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA G 104 " --> pdb=" O ALA G 86 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG G 88 " --> pdb=" O TYR G 102 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU G 39 " --> pdb=" O MET G 140 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N MET G 140 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU G 41 " --> pdb=" O GLU G 138 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 171 through 175 removed outlier: 6.690A pdb=" N LEU G 172 " --> pdb=" O PHE G 201 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N KCX G 203 " --> pdb=" O LEU G 172 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA G 174 " --> pdb=" O KCX G 203 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N MET G 202 " --> pdb=" O TYR G 241 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ASN G 243 " --> pdb=" O MET G 202 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N HIS G 240 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N MET G 268 " --> pdb=" O HIS G 240 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU G 242 " --> pdb=" O MET G 268 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASP G 270 " --> pdb=" O LEU G 242 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL G 267 " --> pdb=" O HIS G 293 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N HIS G 295 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL G 269 " --> pdb=" O HIS G 295 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU G 292 " --> pdb=" O HIS G 326 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N HIS G 328 " --> pdb=" O LEU G 292 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N MET G 294 " --> pdb=" O HIS G 328 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU G 327 " --> pdb=" O VAL G 378 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N SER G 380 " --> pdb=" O LEU G 327 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 354 through 355 Processing sheet with id=AD3, first strand: chain 'O' and resid 49 through 50 removed outlier: 7.186A pdb=" N ILE O 80 " --> pdb=" O ILE O 99 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE O 99 " --> pdb=" O ILE O 80 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE O 82 " --> pdb=" O SER O 97 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER O 97 " --> pdb=" O ILE O 82 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA O 84 " --> pdb=" O THR O 95 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 85 through 91 removed outlier: 5.499A pdb=" N ALA H 86 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA H 104 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG H 88 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU H 39 " --> pdb=" O MET H 140 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET H 140 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU H 41 " --> pdb=" O GLU H 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 171 through 175 removed outlier: 6.693A pdb=" N LEU H 172 " --> pdb=" O PHE H 201 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N KCX H 203 " --> pdb=" O LEU H 172 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA H 174 " --> pdb=" O KCX H 203 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N MET H 202 " --> pdb=" O TYR H 241 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ASN H 243 " --> pdb=" O MET H 202 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N HIS H 240 " --> pdb=" O ILE H 266 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N MET H 268 " --> pdb=" O HIS H 240 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU H 242 " --> pdb=" O MET H 268 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ASP H 270 " --> pdb=" O LEU H 242 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL H 267 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N HIS H 295 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL H 269 " --> pdb=" O HIS H 295 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU H 292 " --> pdb=" O HIS H 326 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N HIS H 328 " --> pdb=" O LEU H 292 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N MET H 294 " --> pdb=" O HIS H 328 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU H 327 " --> pdb=" O VAL H 378 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N SER H 380 " --> pdb=" O LEU H 327 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 354 through 355 Processing sheet with id=AD7, first strand: chain 'P' and resid 49 through 50 removed outlier: 7.187A pdb=" N ILE P 80 " --> pdb=" O ILE P 99 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE P 99 " --> pdb=" O ILE P 80 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE P 82 " --> pdb=" O SER P 97 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER P 97 " --> pdb=" O ILE P 82 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA P 84 " --> pdb=" O THR P 95 " (cutoff:3.500A) 1468 hydrogen bonds defined for protein. 4188 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: 8.66 Time building geometry restraints manager: 4.33 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: 12256 1.34 - 1.46: 4862 1.46 - 1.57: 21186 1.57 - 1.69: 16 1.69 - 1.81: 408 Bond restraints: 38728 Sorted by residual: bond pdb=" CX KCX G 203 " pdb=" OQ1 KCX G 203 " ideal model delta sigma weight residual 1.250 1.330 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" CX KCX F 203 " pdb=" OQ1 KCX F 203 " ideal model delta sigma weight residual 1.250 1.330 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" CX KCX E 203 " pdb=" OQ1 KCX E 203 " ideal model delta sigma weight residual 1.250 1.330 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" CX KCX B 203 " pdb=" OQ2 KCX B 203 " ideal model delta sigma weight residual 1.251 1.331 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" CX KCX H 203 " pdb=" OQ1 KCX H 203 " ideal model delta sigma weight residual 1.250 1.330 -0.080 2.00e-02 2.50e+03 1.59e+01 ... (remaining 38723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 47136 1.92 - 3.84: 4853 3.84 - 5.76: 460 5.76 - 7.68: 83 7.68 - 9.60: 12 Bond angle restraints: 52544 Sorted by residual: angle pdb=" C ASP C 339 " pdb=" N PRO C 340 " pdb=" CA PRO C 340 " ideal model delta sigma weight residual 119.84 125.45 -5.61 1.25e+00 6.40e-01 2.02e+01 angle pdb=" C ASP A 339 " pdb=" N PRO A 340 " pdb=" CA PRO A 340 " ideal model delta sigma weight residual 119.84 125.45 -5.61 1.25e+00 6.40e-01 2.02e+01 angle pdb=" C ASP G 339 " pdb=" N PRO G 340 " pdb=" CA PRO G 340 " ideal model delta sigma weight residual 119.84 125.42 -5.58 1.25e+00 6.40e-01 1.99e+01 angle pdb=" C ASP B 339 " pdb=" N PRO B 340 " pdb=" CA PRO B 340 " ideal model delta sigma weight residual 119.84 125.38 -5.54 1.25e+00 6.40e-01 1.97e+01 angle pdb=" C ASP H 339 " pdb=" N PRO H 340 " pdb=" CA PRO H 340 " ideal model delta sigma weight residual 119.84 125.34 -5.50 1.25e+00 6.40e-01 1.93e+01 ... (remaining 52539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 22336 35.40 - 70.79: 460 70.79 - 106.19: 4 106.19 - 141.58: 4 141.58 - 176.98: 4 Dihedral angle restraints: 22808 sinusoidal: 9200 harmonic: 13608 Sorted by residual: dihedral pdb=" C3 CAP A1001 " pdb=" C CAP A1001 " pdb=" C2 CAP A1001 " pdb=" O6 CAP A1001 " ideal model delta sinusoidal sigma weight residual 81.86 -101.16 -176.98 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C3 CAP C1001 " pdb=" C CAP C1001 " pdb=" C2 CAP C1001 " pdb=" O6 CAP C1001 " ideal model delta sinusoidal sigma weight residual 81.86 -101.18 -176.95 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C3 CAP B1001 " pdb=" C CAP B1001 " pdb=" C2 CAP B1001 " pdb=" O6 CAP B1001 " ideal model delta sinusoidal sigma weight residual 81.86 -101.57 -176.57 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 22805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4468 0.079 - 0.158: 981 0.158 - 0.237: 137 0.237 - 0.316: 14 0.316 - 0.394: 16 Chirality restraints: 5616 Sorted by residual: chirality pdb=" CA TYR G 87 " pdb=" N TYR G 87 " pdb=" C TYR G 87 " pdb=" CB TYR G 87 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CA TYR A 87 " pdb=" N TYR A 87 " pdb=" C TYR A 87 " pdb=" CB TYR A 87 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA TYR F 87 " pdb=" N TYR F 87 " pdb=" C TYR F 87 " pdb=" CB TYR F 87 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 5613 not shown) Planarity restraints: 6800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 359 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO C 360 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 360 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 360 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 359 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A 360 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 359 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.59e+00 pdb=" N PRO D 360 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 360 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 360 " 0.018 5.00e-02 4.00e+02 ... (remaining 6797 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 288 2.71 - 3.26: 33127 3.26 - 3.81: 59653 3.81 - 4.35: 85034 4.35 - 4.90: 136612 Nonbonded interactions: 314714 Sorted by model distance: nonbonded pdb=" OQ2 KCX A 203 " pdb="MG MG A1002 " model vdw 2.164 2.170 nonbonded pdb=" OQ2 KCX C 203 " pdb="MG MG C1002 " model vdw 2.169 2.170 nonbonded pdb=" OQ2 KCX D 203 " pdb="MG MG D1002 " model vdw 2.199 2.170 nonbonded pdb=" OQ1 KCX H 203 " pdb="MG MG H1002 " model vdw 2.202 2.170 nonbonded pdb=" OQ1 KCX G 203 " pdb="MG MG G1002 " model vdw 2.211 2.170 ... (remaining 314709 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 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' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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=0.40 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 33.330 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.100 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1481 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 : 0.007 0.080 38728 Z= 0.486 Angle : 1.218 9.597 52544 Z= 0.793 Chirality : 0.068 0.394 5616 Planarity : 0.004 0.033 6800 Dihedral : 14.589 176.981 14152 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 0.94 % Allowed : 5.36 % Favored : 93.70 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.82 (0.10), residues: 4712 helix: -2.40 (0.08), residues: 1688 sheet: -0.28 (0.17), residues: 784 loop : -1.97 (0.11), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 119 TYR 0.015 0.001 TYR E 87 PHE 0.014 0.002 PHE A 213 TRP 0.012 0.001 TRP K 48 HIS 0.005 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00731 (38728) covalent geometry : angle 1.21761 (52544) hydrogen bonds : bond 0.31273 ( 1468) hydrogen bonds : angle 8.45880 ( 4188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 648 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 THR cc_start: 0.3669 (p) cc_final: 0.3344 (p) REVERT: A 44 ILE cc_start: 0.2658 (mt) cc_final: 0.2416 (pt) REVERT: A 99 TYR cc_start: 0.3042 (m-80) cc_final: 0.2747 (m-80) REVERT: A 129 PHE cc_start: 0.1030 (m-80) cc_final: 0.0725 (m-80) REVERT: A 283 GLU cc_start: 0.2358 (tt0) cc_final: 0.2018 (mp0) REVERT: A 306 LYS cc_start: 0.3676 (ttpt) cc_final: 0.3265 (tptt) REVERT: I 50 MET cc_start: 0.4406 (mtt) cc_final: 0.3718 (mmt) REVERT: I 112 GLU cc_start: 0.2459 (mt-10) cc_final: 0.2081 (mp0) REVERT: B 36 THR cc_start: 0.3600 (p) cc_final: 0.3065 (p) REVERT: B 99 TYR cc_start: 0.2950 (m-80) cc_final: 0.2647 (m-80) REVERT: B 133 LYS cc_start: 0.3273 (tptp) cc_final: 0.3073 (mtmm) REVERT: B 283 GLU cc_start: 0.2370 (tt0) cc_final: 0.2023 (mp0) REVERT: B 306 LYS cc_start: 0.3622 (ttpt) cc_final: 0.3195 (tptt) REVERT: J 50 MET cc_start: 0.4543 (mtt) cc_final: 0.3812 (mmt) REVERT: J 112 GLU cc_start: 0.2467 (mt-10) cc_final: 0.2072 (mp0) REVERT: C 36 THR cc_start: 0.3589 (p) cc_final: 0.3026 (p) REVERT: C 44 ILE cc_start: 0.2675 (mt) cc_final: 0.2442 (pt) REVERT: C 99 TYR cc_start: 0.2972 (m-80) cc_final: 0.2683 (m-80) REVERT: C 129 PHE cc_start: 0.0985 (m-80) cc_final: 0.0678 (m-80) REVERT: C 133 LYS cc_start: 0.3270 (tptp) cc_final: 0.3068 (mtmm) REVERT: C 306 LYS cc_start: 0.3579 (ttpt) cc_final: 0.3185 (tptt) REVERT: C 457 GLU cc_start: 0.2482 (tt0) cc_final: 0.2277 (mt-10) REVERT: K 50 MET cc_start: 0.4560 (mtt) cc_final: 0.3851 (mmt) REVERT: K 112 GLU cc_start: 0.2461 (mt-10) cc_final: 0.2084 (mp0) REVERT: D 20 LYS cc_start: 0.1417 (mttt) cc_final: 0.1177 (ttpt) REVERT: D 36 THR cc_start: 0.3234 (p) cc_final: 0.2582 (p) REVERT: D 99 TYR cc_start: 0.2995 (m-80) cc_final: 0.2677 (m-80) REVERT: D 129 PHE cc_start: 0.1109 (m-80) cc_final: 0.0881 (m-80) REVERT: D 133 LYS cc_start: 0.3266 (tptp) cc_final: 0.3064 (mtmm) REVERT: D 283 GLU cc_start: 0.2389 (tt0) cc_final: 0.2040 (mp0) REVERT: D 306 LYS cc_start: 0.3616 (ttpt) cc_final: 0.3213 (tptt) REVERT: L 50 MET cc_start: 0.4508 (mtt) cc_final: 0.3803 (mmt) REVERT: L 112 GLU cc_start: 0.2467 (mt-10) cc_final: 0.2094 (mp0) REVERT: E 20 LYS cc_start: 0.1141 (mttt) cc_final: 0.0906 (ttpt) REVERT: E 36 THR cc_start: 0.3314 (p) cc_final: 0.2768 (p) REVERT: E 44 ILE cc_start: 0.2566 (mt) cc_final: 0.2364 (pt) REVERT: E 99 TYR cc_start: 0.2940 (m-80) cc_final: 0.2622 (m-80) REVERT: E 129 PHE cc_start: 0.0955 (m-80) cc_final: 0.0585 (m-80) REVERT: E 306 LYS cc_start: 0.3541 (ttpt) cc_final: 0.3125 (tptt) REVERT: E 457 GLU cc_start: 0.2702 (tt0) cc_final: 0.2486 (mt-10) REVERT: M 50 MET cc_start: 0.4404 (mtt) cc_final: 0.3698 (mmt) REVERT: M 112 GLU cc_start: 0.2454 (mt-10) cc_final: 0.2080 (mp0) REVERT: F 36 THR cc_start: 0.3452 (p) cc_final: 0.2922 (p) REVERT: F 99 TYR cc_start: 0.2944 (m-80) cc_final: 0.2640 (m-80) REVERT: F 129 PHE cc_start: 0.1039 (m-80) cc_final: 0.0668 (m-80) REVERT: F 306 LYS cc_start: 0.3576 (ttpt) cc_final: 0.3159 (tptt) REVERT: F 457 GLU cc_start: 0.2640 (tt0) cc_final: 0.2438 (mt-10) REVERT: N 50 MET cc_start: 0.4301 (mtt) cc_final: 0.3593 (mmt) REVERT: N 112 GLU cc_start: 0.2444 (mt-10) cc_final: 0.2072 (mp0) REVERT: G 36 THR cc_start: 0.3174 (p) cc_final: 0.2861 (p) REVERT: G 44 ILE cc_start: 0.2531 (mt) cc_final: 0.2322 (pt) REVERT: G 99 TYR cc_start: 0.2940 (m-80) cc_final: 0.2626 (m-80) REVERT: G 129 PHE cc_start: 0.1018 (m-80) cc_final: 0.0609 (m-80) REVERT: G 306 LYS cc_start: 0.3573 (ttpt) cc_final: 0.3157 (tptt) REVERT: G 457 GLU cc_start: 0.2884 (tt0) cc_final: 0.2637 (mt-10) REVERT: O 50 MET cc_start: 0.4314 (mtt) cc_final: 0.3611 (mmt) REVERT: O 112 GLU cc_start: 0.2415 (mt-10) cc_final: 0.2051 (mp0) REVERT: H 20 LYS cc_start: 0.1140 (mttt) cc_final: 0.0902 (ttpt) REVERT: H 36 THR cc_start: 0.3168 (p) cc_final: 0.2858 (p) REVERT: H 99 TYR cc_start: 0.3008 (m-80) cc_final: 0.2692 (m-80) REVERT: H 129 PHE cc_start: 0.1034 (m-80) cc_final: 0.0722 (m-80) REVERT: H 133 LYS cc_start: 0.3205 (tptp) cc_final: 0.2993 (mtmm) REVERT: H 306 LYS cc_start: 0.3555 (ttpt) cc_final: 0.3146 (tptt) REVERT: H 457 GLU cc_start: 0.2734 (tt0) cc_final: 0.2488 (mt-10) REVERT: P 50 MET cc_start: 0.4324 (mtt) cc_final: 0.3646 (mmt) REVERT: P 112 GLU cc_start: 0.2449 (mt-10) cc_final: 0.2055 (mp0) outliers start: 37 outliers final: 8 residues processed: 678 average time/residue: 0.2363 time to fit residues: 256.2606 Evaluate side-chains 441 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 433 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain H residue 281 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.6386 > 50: distance: 60 - 64: 10.023 distance: 61 - 237: 3.013 distance: 64 - 65: 5.193 distance: 65 - 66: 8.133 distance: 65 - 68: 18.925 distance: 66 - 67: 12.914 distance: 66 - 72: 13.197 distance: 68 - 69: 16.179 distance: 69 - 70: 17.465 distance: 69 - 71: 23.417 distance: 72 - 73: 28.239 distance: 72 - 239: 16.145 distance: 73 - 74: 12.220 distance: 74 - 75: 24.259 distance: 74 - 76: 19.540 distance: 76 - 77: 20.315 distance: 77 - 78: 11.536 distance: 77 - 80: 17.489 distance: 78 - 79: 35.664 distance: 78 - 81: 26.415 distance: 81 - 82: 6.297 distance: 82 - 83: 8.488 distance: 82 - 85: 16.451 distance: 83 - 84: 7.021 distance: 83 - 88: 20.648 distance: 85 - 86: 25.536 distance: 85 - 87: 17.243 distance: 88 - 89: 17.990 distance: 89 - 90: 5.544 distance: 89 - 92: 20.057 distance: 90 - 91: 24.761 distance: 90 - 95: 27.172 distance: 92 - 93: 39.422 distance: 92 - 94: 22.504 distance: 95 - 96: 6.719 distance: 96 - 97: 13.384 distance: 96 - 99: 9.859 distance: 97 - 98: 24.596 distance: 97 - 104: 22.137 distance: 99 - 100: 32.915 distance: 100 - 101: 36.092 distance: 101 - 102: 18.393 distance: 102 - 103: 28.281 distance: 104 - 105: 35.304 distance: 104 - 110: 28.541 distance: 105 - 106: 16.327 distance: 105 - 108: 25.530 distance: 106 - 107: 30.073 distance: 106 - 111: 22.183 distance: 108 - 109: 9.947 distance: 109 - 110: 35.875 distance: 111 - 112: 12.167 distance: 112 - 113: 27.124 distance: 112 - 115: 11.470 distance: 113 - 114: 20.284 distance: 113 - 120: 6.831 distance: 115 - 116: 17.908 distance: 116 - 117: 9.719 distance: 117 - 118: 8.286 distance: 118 - 119: 35.501 distance: 120 - 121: 21.961 distance: 121 - 122: 18.311 distance: 121 - 124: 27.326 distance: 122 - 123: 14.101 distance: 122 - 128: 11.026 distance: 124 - 125: 14.913 distance: 125 - 126: 12.702 distance: 125 - 127: 9.520 distance: 128 - 129: 10.823 distance: 129 - 130: 8.694 distance: 130 - 131: 23.995 distance: 130 - 132: 13.073