Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 27 13:13:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf9_25866/08_2023/7tf9_25866.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf9_25866/08_2023/7tf9_25866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf9_25866/08_2023/7tf9_25866.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf9_25866/08_2023/7tf9_25866.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf9_25866/08_2023/7tf9_25866.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf9_25866/08_2023/7tf9_25866.pdb" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.073 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 Mg 28 5.21 5 S 252 5.16 5 C 31920 2.51 5 N 8372 2.21 5 O 9156 1.98 5 H 140 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 49868 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "F" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "G" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "H" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "I" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "J" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "K" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "L" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "M" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "N" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "O" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "P" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "Q" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "R" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "S" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "T" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "U" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "V" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "W" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "X" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "Y" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "Z" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "a" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "N" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "O" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "P" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "Q" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "S" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "T" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 14 residue: pdb=" N LEU A 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU A 350 " occ=0.92 residue: pdb=" N LEU B 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU B 350 " occ=0.92 residue: pdb=" N LEU C 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU C 350 " occ=0.92 residue: pdb=" N LEU F 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU F 350 " occ=0.92 residue: pdb=" N LEU G 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU G 350 " occ=0.92 residue: pdb=" N LEU H 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU H 350 " occ=0.92 residue: pdb=" N LEU I 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU I 350 " occ=0.92 residue: pdb=" N LEU N 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU N 350 " occ=0.92 residue: pdb=" N LEU O 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU O 350 " occ=0.92 residue: pdb=" N LEU P 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU P 350 " occ=0.92 residue: pdb=" N LEU Q 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU Q 350 " occ=0.92 residue: pdb=" N LEU R 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU R 350 " occ=0.92 ... (remaining 2 not shown) Time building chain proxies: 23.75, per 1000 atoms: 0.48 Number of scatterers: 49868 At special positions: 0 Unit cell: (173.36, 169.84, 122.32, 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 252 16.00 Mg 28 11.99 O 9156 8.00 N 8372 7.00 C 31920 6.00 H 140 1.00 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: 19.25 Conformation dependent library (CDL) restraints added in 6.9 seconds 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11732 Finding SS restraints... Secondary structure from input PDB file: 265 helices and 56 sheets defined 46.0% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.17 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 55 through 62 removed outlier: 6.518A pdb=" N PHE A 60 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL A 61 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 62 " --> pdb=" O GLY A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 77 Processing helix chain 'A' and resid 107 through 123 Processing helix chain 'A' and resid 167 through 180 Processing helix chain 'A' and resid 203 through 225 Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 268 through 281 Processing helix chain 'A' and resid 281 through 290 removed outlier: 5.102A pdb=" N ALA A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 299 removed outlier: 3.642A pdb=" N ARG A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 294 through 299' Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.528A pdb=" N SER A 329 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 361 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 376 through 382 removed outlier: 3.638A pdb=" N ALA A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 402 Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 410 through 430 Processing helix chain 'A' and resid 433 through 441 removed outlier: 3.550A pdb=" N ARG A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 17 Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 55 through 62 removed outlier: 6.523A pdb=" N PHE B 60 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL B 61 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 62 " --> pdb=" O GLY B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 77 Processing helix chain 'B' and resid 107 through 123 Processing helix chain 'B' and resid 167 through 180 Processing helix chain 'B' and resid 203 through 225 Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 268 through 281 Processing helix chain 'B' and resid 281 through 290 removed outlier: 5.102A pdb=" N ALA B 287 " --> pdb=" O ARG B 283 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 299 removed outlier: 3.647A pdb=" N ARG B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 294 through 299' Processing helix chain 'B' and resid 326 through 330 removed outlier: 3.528A pdb=" N SER B 329 " --> pdb=" O ARG B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 361 Processing helix chain 'B' and resid 376 through 382 removed outlier: 3.639A pdb=" N ALA B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 410 through 430 Processing helix chain 'B' and resid 433 through 441 removed outlier: 3.550A pdb=" N ARG B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 17 Processing helix chain 'C' and resid 41 through 47 Processing helix chain 'C' and resid 55 through 62 removed outlier: 6.519A pdb=" N PHE C 60 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL C 61 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 62 " --> pdb=" O GLY C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 77 Processing helix chain 'C' and resid 107 through 123 Processing helix chain 'C' and resid 167 through 180 Processing helix chain 'C' and resid 203 through 225 Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 281 through 290 removed outlier: 5.102A pdb=" N ALA C 287 " --> pdb=" O ARG C 283 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 299 removed outlier: 3.644A pdb=" N ARG C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU C 299 " --> pdb=" O SER C 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 294 through 299' Processing helix chain 'C' and resid 326 through 330 removed outlier: 3.528A pdb=" N SER C 329 " --> pdb=" O ARG C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 361 Processing helix chain 'C' and resid 371 through 375 Processing helix chain 'C' and resid 376 through 382 removed outlier: 3.639A pdb=" N ALA C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 402 Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 410 through 430 Processing helix chain 'C' and resid 433 through 441 removed outlier: 3.550A pdb=" N ARG C 437 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 17 Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 55 through 62 removed outlier: 6.522A pdb=" N PHE F 60 " --> pdb=" O ILE F 57 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL F 61 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG F 62 " --> pdb=" O GLY F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 77 Processing helix chain 'F' and resid 107 through 123 Processing helix chain 'F' and resid 167 through 180 Processing helix chain 'F' and resid 203 through 225 Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 268 through 281 Processing helix chain 'F' and resid 281 through 290 removed outlier: 5.102A pdb=" N ALA F 287 " --> pdb=" O ARG F 283 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 removed outlier: 3.571A pdb=" N ARG F 298 " --> pdb=" O ASN F 294 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU F 299 " --> pdb=" O SER F 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 294 through 299' Processing helix chain 'F' and resid 326 through 330 removed outlier: 3.528A pdb=" N SER F 329 " --> pdb=" O ARG F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 361 Processing helix chain 'F' and resid 371 through 375 Processing helix chain 'F' and resid 376 through 382 removed outlier: 3.639A pdb=" N ALA F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 402 Processing helix chain 'F' and resid 403 through 410 Processing helix chain 'F' and resid 410 through 431 removed outlier: 3.524A pdb=" N ALA F 431 " --> pdb=" O MET F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 439 Processing helix chain 'G' and resid 5 through 17 Processing helix chain 'G' and resid 41 through 47 Processing helix chain 'G' and resid 55 through 62 removed outlier: 6.534A pdb=" N PHE G 60 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL G 61 " --> pdb=" O GLU G 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG G 62 " --> pdb=" O GLY G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 77 Processing helix chain 'G' and resid 107 through 123 Processing helix chain 'G' and resid 167 through 180 Processing helix chain 'G' and resid 203 through 225 Processing helix chain 'G' and resid 263 through 267 Processing helix chain 'G' and resid 268 through 281 Processing helix chain 'G' and resid 281 through 290 removed outlier: 5.102A pdb=" N ALA G 287 " --> pdb=" O ARG G 283 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL G 288 " --> pdb=" O GLY G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 299 removed outlier: 3.571A pdb=" N ARG G 298 " --> pdb=" O ASN G 294 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU G 299 " --> pdb=" O SER G 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 294 through 299' Processing helix chain 'G' and resid 326 through 330 removed outlier: 3.528A pdb=" N SER G 329 " --> pdb=" O ARG G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 361 Processing helix chain 'G' and resid 371 through 375 Processing helix chain 'G' and resid 376 through 382 removed outlier: 3.639A pdb=" N ALA G 382 " --> pdb=" O GLU G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 391 through 402 Processing helix chain 'G' and resid 403 through 410 Processing helix chain 'G' and resid 410 through 431 Processing helix chain 'G' and resid 435 through 439 Processing helix chain 'H' and resid 5 through 17 Processing helix chain 'H' and resid 41 through 47 Processing helix chain 'H' and resid 55 through 62 removed outlier: 6.517A pdb=" N PHE H 60 " --> pdb=" O ILE H 57 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL H 61 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG H 62 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 77 Processing helix chain 'H' and resid 107 through 123 Processing helix chain 'H' and resid 167 through 180 Processing helix chain 'H' and resid 203 through 225 Processing helix chain 'H' and resid 263 through 267 Processing helix chain 'H' and resid 268 through 281 Processing helix chain 'H' and resid 281 through 290 removed outlier: 5.102A pdb=" N ALA H 287 " --> pdb=" O ARG H 283 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL H 288 " --> pdb=" O GLY H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 299 removed outlier: 3.571A pdb=" N ARG H 298 " --> pdb=" O ASN H 294 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU H 299 " --> pdb=" O SER H 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 294 through 299' Processing helix chain 'H' and resid 326 through 330 removed outlier: 3.527A pdb=" N SER H 329 " --> pdb=" O ARG H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 361 Processing helix chain 'H' and resid 371 through 375 Processing helix chain 'H' and resid 376 through 382 removed outlier: 3.638A pdb=" N ALA H 382 " --> pdb=" O GLU H 378 " (cutoff:3.500A) Processing helix chain 'H' and resid 391 through 402 Processing helix chain 'H' and resid 403 through 410 Processing helix chain 'H' and resid 410 through 431 Processing helix chain 'H' and resid 435 through 439 Processing helix chain 'I' and resid 5 through 17 Processing helix chain 'I' and resid 41 through 47 Processing helix chain 'I' and resid 55 through 62 removed outlier: 6.534A pdb=" N PHE I 60 " --> pdb=" O ILE I 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL I 61 " --> pdb=" O GLU I 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG I 62 " --> pdb=" O GLY I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 77 Processing helix chain 'I' and resid 107 through 123 Processing helix chain 'I' and resid 167 through 180 Processing helix chain 'I' and resid 203 through 225 Processing helix chain 'I' and resid 263 through 267 Processing helix chain 'I' and resid 268 through 281 Processing helix chain 'I' and resid 281 through 290 removed outlier: 5.102A pdb=" N ALA I 287 " --> pdb=" O ARG I 283 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL I 288 " --> pdb=" O GLY I 284 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 299 removed outlier: 3.571A pdb=" N ARG I 298 " --> pdb=" O ASN I 294 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU I 299 " --> pdb=" O SER I 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 294 through 299' Processing helix chain 'I' and resid 326 through 330 removed outlier: 3.528A pdb=" N SER I 329 " --> pdb=" O ARG I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 361 Processing helix chain 'I' and resid 371 through 375 Processing helix chain 'I' and resid 376 through 382 removed outlier: 3.639A pdb=" N ALA I 382 " --> pdb=" O GLU I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 391 through 402 Processing helix chain 'I' and resid 403 through 410 Processing helix chain 'I' and resid 410 through 431 Processing helix chain 'I' and resid 433 through 441 removed outlier: 3.549A pdb=" N ARG I 437 " --> pdb=" O HIS I 433 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 17 Processing helix chain 'N' and resid 41 through 47 Processing helix chain 'N' and resid 55 through 62 removed outlier: 6.524A pdb=" N PHE N 60 " --> pdb=" O ILE N 57 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL N 61 " --> pdb=" O GLU N 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG N 62 " --> pdb=" O GLY N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 77 Processing helix chain 'N' and resid 107 through 123 Processing helix chain 'N' and resid 167 through 180 Processing helix chain 'N' and resid 203 through 225 Processing helix chain 'N' and resid 263 through 267 Processing helix chain 'N' and resid 268 through 281 Processing helix chain 'N' and resid 281 through 290 removed outlier: 5.102A pdb=" N ALA N 287 " --> pdb=" O ARG N 283 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL N 288 " --> pdb=" O GLY N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 299 removed outlier: 3.637A pdb=" N ARG N 298 " --> pdb=" O ASN N 294 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU N 299 " --> pdb=" O SER N 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 294 through 299' Processing helix chain 'N' and resid 326 through 330 removed outlier: 3.528A pdb=" N SER N 329 " --> pdb=" O ARG N 326 " (cutoff:3.500A) Processing helix chain 'N' and resid 342 through 361 Processing helix chain 'N' and resid 371 through 375 Processing helix chain 'N' and resid 376 through 382 removed outlier: 3.639A pdb=" N ALA N 382 " --> pdb=" O GLU N 378 " (cutoff:3.500A) Processing helix chain 'N' and resid 391 through 402 Processing helix chain 'N' and resid 403 through 410 Processing helix chain 'N' and resid 410 through 430 Processing helix chain 'N' and resid 433 through 441 removed outlier: 3.550A pdb=" N ARG N 437 " --> pdb=" O HIS N 433 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 17 Processing helix chain 'O' and resid 41 through 47 Processing helix chain 'O' and resid 55 through 62 removed outlier: 6.525A pdb=" N PHE O 60 " --> pdb=" O ILE O 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL O 61 " --> pdb=" O GLU O 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG O 62 " --> pdb=" O GLY O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 77 Processing helix chain 'O' and resid 107 through 123 Processing helix chain 'O' and resid 167 through 180 Processing helix chain 'O' and resid 203 through 225 Processing helix chain 'O' and resid 263 through 267 Processing helix chain 'O' and resid 268 through 281 Processing helix chain 'O' and resid 281 through 290 removed outlier: 5.102A pdb=" N ALA O 287 " --> pdb=" O ARG O 283 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL O 288 " --> pdb=" O GLY O 284 " (cutoff:3.500A) Processing helix chain 'O' and resid 294 through 299 removed outlier: 3.571A pdb=" N ARG O 298 " --> pdb=" O ASN O 294 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU O 299 " --> pdb=" O SER O 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 294 through 299' Processing helix chain 'O' and resid 326 through 330 removed outlier: 3.528A pdb=" N SER O 329 " --> pdb=" O ARG O 326 " (cutoff:3.500A) Processing helix chain 'O' and resid 342 through 361 Processing helix chain 'O' and resid 371 through 375 Processing helix chain 'O' and resid 376 through 382 removed outlier: 3.638A pdb=" N ALA O 382 " --> pdb=" O GLU O 378 " (cutoff:3.500A) Processing helix chain 'O' and resid 391 through 402 Processing helix chain 'O' and resid 403 through 410 Processing helix chain 'O' and resid 410 through 430 Processing helix chain 'O' and resid 433 through 441 removed outlier: 3.550A pdb=" N ARG O 437 " --> pdb=" O HIS O 433 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 17 Processing helix chain 'P' and resid 41 through 47 Processing helix chain 'P' and resid 55 through 62 removed outlier: 6.525A pdb=" N PHE P 60 " --> pdb=" O ILE P 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL P 61 " --> pdb=" O GLU P 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG P 62 " --> pdb=" O GLY P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 74 through 77 Processing helix chain 'P' and resid 107 through 123 Processing helix chain 'P' and resid 167 through 180 Processing helix chain 'P' and resid 203 through 225 Processing helix chain 'P' and resid 263 through 267 Processing helix chain 'P' and resid 268 through 281 Processing helix chain 'P' and resid 281 through 290 removed outlier: 5.102A pdb=" N ALA P 287 " --> pdb=" O ARG P 283 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL P 288 " --> pdb=" O GLY P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 294 through 299 removed outlier: 3.571A pdb=" N ARG P 298 " --> pdb=" O ASN P 294 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU P 299 " --> pdb=" O SER P 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 294 through 299' Processing helix chain 'P' and resid 326 through 330 removed outlier: 3.527A pdb=" N SER P 329 " --> pdb=" O ARG P 326 " (cutoff:3.500A) Processing helix chain 'P' and resid 342 through 361 Processing helix chain 'P' and resid 371 through 375 Processing helix chain 'P' and resid 376 through 382 removed outlier: 3.637A pdb=" N ALA P 382 " --> pdb=" O GLU P 378 " (cutoff:3.500A) Processing helix chain 'P' and resid 391 through 402 Processing helix chain 'P' and resid 403 through 410 Processing helix chain 'P' and resid 410 through 430 Processing helix chain 'P' and resid 433 through 441 removed outlier: 3.550A pdb=" N ARG P 437 " --> pdb=" O HIS P 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 17 Processing helix chain 'Q' and resid 41 through 47 Processing helix chain 'Q' and resid 55 through 62 removed outlier: 6.524A pdb=" N PHE Q 60 " --> pdb=" O ILE Q 57 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL Q 61 " --> pdb=" O GLU Q 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG Q 62 " --> pdb=" O GLY Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 77 Processing helix chain 'Q' and resid 107 through 123 Processing helix chain 'Q' and resid 167 through 180 Processing helix chain 'Q' and resid 203 through 225 Processing helix chain 'Q' and resid 263 through 267 Processing helix chain 'Q' and resid 268 through 281 Processing helix chain 'Q' and resid 281 through 290 removed outlier: 5.102A pdb=" N ALA Q 287 " --> pdb=" O ARG Q 283 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL Q 288 " --> pdb=" O GLY Q 284 " (cutoff:3.500A) Processing helix chain 'Q' and resid 294 through 299 removed outlier: 3.633A pdb=" N ARG Q 298 " --> pdb=" O ASN Q 294 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU Q 299 " --> pdb=" O SER Q 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 294 through 299' Processing helix chain 'Q' and resid 326 through 330 removed outlier: 3.528A pdb=" N SER Q 329 " --> pdb=" O ARG Q 326 " (cutoff:3.500A) Processing helix chain 'Q' and resid 342 through 361 Processing helix chain 'Q' and resid 371 through 375 Processing helix chain 'Q' and resid 376 through 382 removed outlier: 3.638A pdb=" N ALA Q 382 " --> pdb=" O GLU Q 378 " (cutoff:3.500A) Processing helix chain 'Q' and resid 391 through 402 Processing helix chain 'Q' and resid 403 through 410 Processing helix chain 'Q' and resid 410 through 430 Processing helix chain 'Q' and resid 433 through 441 removed outlier: 3.550A pdb=" N ARG Q 437 " --> pdb=" O HIS Q 433 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 17 Processing helix chain 'R' and resid 41 through 47 Processing helix chain 'R' and resid 55 through 62 removed outlier: 6.534A pdb=" N PHE R 60 " --> pdb=" O ILE R 57 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL R 61 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG R 62 " --> pdb=" O GLY R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 77 Processing helix chain 'R' and resid 107 through 123 Processing helix chain 'R' and resid 167 through 180 Processing helix chain 'R' and resid 203 through 225 Processing helix chain 'R' and resid 263 through 267 Processing helix chain 'R' and resid 268 through 281 Processing helix chain 'R' and resid 281 through 290 removed outlier: 5.102A pdb=" N ALA R 287 " --> pdb=" O ARG R 283 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL R 288 " --> pdb=" O GLY R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 299 removed outlier: 3.571A pdb=" N ARG R 298 " --> pdb=" O ASN R 294 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU R 299 " --> pdb=" O SER R 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 294 through 299' Processing helix chain 'R' and resid 326 through 330 removed outlier: 3.528A pdb=" N SER R 329 " --> pdb=" O ARG R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 342 through 361 Processing helix chain 'R' and resid 371 through 375 Processing helix chain 'R' and resid 376 through 382 removed outlier: 3.638A pdb=" N ALA R 382 " --> pdb=" O GLU R 378 " (cutoff:3.500A) Processing helix chain 'R' and resid 391 through 402 Processing helix chain 'R' and resid 403 through 410 Processing helix chain 'R' and resid 410 through 431 Processing helix chain 'R' and resid 435 through 439 Processing helix chain 'S' and resid 5 through 17 Processing helix chain 'S' and resid 41 through 47 Processing helix chain 'S' and resid 55 through 62 removed outlier: 6.534A pdb=" N PHE S 60 " --> pdb=" O ILE S 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL S 61 " --> pdb=" O GLU S 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG S 62 " --> pdb=" O GLY S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 77 Processing helix chain 'S' and resid 107 through 123 Processing helix chain 'S' and resid 167 through 180 Processing helix chain 'S' and resid 203 through 225 Processing helix chain 'S' and resid 263 through 267 Processing helix chain 'S' and resid 268 through 281 Processing helix chain 'S' and resid 281 through 290 removed outlier: 5.102A pdb=" N ALA S 287 " --> pdb=" O ARG S 283 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL S 288 " --> pdb=" O GLY S 284 " (cutoff:3.500A) Processing helix chain 'S' and resid 294 through 299 removed outlier: 3.571A pdb=" N ARG S 298 " --> pdb=" O ASN S 294 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU S 299 " --> pdb=" O SER S 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 294 through 299' Processing helix chain 'S' and resid 326 through 330 removed outlier: 3.528A pdb=" N SER S 329 " --> pdb=" O ARG S 326 " (cutoff:3.500A) Processing helix chain 'S' and resid 342 through 361 Processing helix chain 'S' and resid 371 through 375 Processing helix chain 'S' and resid 376 through 382 removed outlier: 3.639A pdb=" N ALA S 382 " --> pdb=" O GLU S 378 " (cutoff:3.500A) Processing helix chain 'S' and resid 391 through 402 Processing helix chain 'S' and resid 403 through 410 Processing helix chain 'S' and resid 410 through 431 Processing helix chain 'S' and resid 435 through 439 Processing helix chain 'T' and resid 5 through 17 Processing helix chain 'T' and resid 41 through 47 Processing helix chain 'T' and resid 55 through 62 removed outlier: 6.534A pdb=" N PHE T 60 " --> pdb=" O ILE T 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL T 61 " --> pdb=" O GLU T 58 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG T 62 " --> pdb=" O GLY T 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 77 Processing helix chain 'T' and resid 107 through 123 Processing helix chain 'T' and resid 167 through 180 Processing helix chain 'T' and resid 203 through 225 Processing helix chain 'T' and resid 263 through 267 Processing helix chain 'T' and resid 268 through 281 Processing helix chain 'T' and resid 281 through 290 removed outlier: 5.102A pdb=" N ALA T 287 " --> pdb=" O ARG T 283 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL T 288 " --> pdb=" O GLY T 284 " (cutoff:3.500A) Processing helix chain 'T' and resid 294 through 299 removed outlier: 3.570A pdb=" N ARG T 298 " --> pdb=" O ASN T 294 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU T 299 " --> pdb=" O SER T 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 294 through 299' Processing helix chain 'T' and resid 326 through 330 removed outlier: 3.527A pdb=" N SER T 329 " --> pdb=" O ARG T 326 " (cutoff:3.500A) Processing helix chain 'T' and resid 342 through 361 Processing helix chain 'T' and resid 371 through 375 Processing helix chain 'T' and resid 376 through 382 removed outlier: 3.639A pdb=" N ALA T 382 " --> pdb=" O GLU T 378 " (cutoff:3.500A) Processing helix chain 'T' and resid 391 through 402 Processing helix chain 'T' and resid 403 through 410 Processing helix chain 'T' and resid 410 through 431 Processing helix chain 'T' and resid 433 through 441 removed outlier: 3.551A pdb=" N ARG T 437 " --> pdb=" O HIS T 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS A 88 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 92 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR A 26 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE A 96 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 97 " --> pdb=" O TYR A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS A 88 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 92 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR A 26 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE A 96 " --> pdb=" O THR A 26 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU A 149 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 188 removed outlier: 3.860A pdb=" N ALA A 185 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 197 " --> pdb=" O PRO A 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 199 " --> pdb=" O PRO A 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 126 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS A 245 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS B 88 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET B 92 " --> pdb=" O ARG B 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR B 26 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE B 96 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B 97 " --> pdb=" O TYR B 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS B 88 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET B 92 " --> pdb=" O ARG B 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR B 26 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE B 96 " --> pdb=" O THR B 26 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU B 149 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 183 through 188 removed outlier: 3.870A pdb=" N ALA B 185 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 197 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE B 199 " --> pdb=" O PRO B 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 126 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS B 245 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS C 88 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET C 92 " --> pdb=" O ARG C 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR C 26 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE C 96 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR C 97 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS C 88 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET C 92 " --> pdb=" O ARG C 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR C 26 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE C 96 " --> pdb=" O THR C 26 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU C 149 " --> pdb=" O LYS C 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 183 through 188 removed outlier: 3.864A pdb=" N ALA C 185 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE C 197 " --> pdb=" O PRO C 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE C 199 " --> pdb=" O PRO C 131 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU C 126 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS C 245 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS F 88 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET F 92 " --> pdb=" O ARG F 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR F 26 " --> pdb=" O CYS F 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE F 96 " --> pdb=" O THR F 26 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR F 97 " --> pdb=" O TYR F 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS F 88 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET F 92 " --> pdb=" O ARG F 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR F 26 " --> pdb=" O CYS F 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE F 96 " --> pdb=" O THR F 26 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU F 149 " --> pdb=" O LYS F 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 183 through 188 removed outlier: 3.849A pdb=" N ALA F 185 " --> pdb=" O ASP F 198 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE F 197 " --> pdb=" O PRO F 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE F 199 " --> pdb=" O PRO F 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU F 126 " --> pdb=" O PHE F 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS F 245 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS G 88 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET G 92 " --> pdb=" O ARG G 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR G 26 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE G 96 " --> pdb=" O THR G 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR G 97 " --> pdb=" O TYR G 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS G 88 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET G 92 " --> pdb=" O ARG G 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR G 26 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE G 96 " --> pdb=" O THR G 26 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU G 149 " --> pdb=" O LYS G 139 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 183 through 188 removed outlier: 3.852A pdb=" N ALA G 185 " --> pdb=" O ASP G 198 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE G 197 " --> pdb=" O PRO G 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE G 199 " --> pdb=" O PRO G 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU G 126 " --> pdb=" O PHE G 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS G 245 " --> pdb=" O GLU G 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 32 through 38 removed outlier: 5.548A pdb=" N LYS H 88 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET H 92 " --> pdb=" O ARG H 22 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR H 26 " --> pdb=" O CYS H 94 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE H 96 " --> pdb=" O THR H 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR H 97 " --> pdb=" O TYR H 69 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 32 through 38 removed outlier: 5.548A pdb=" N LYS H 88 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET H 92 " --> pdb=" O ARG H 22 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR H 26 " --> pdb=" O CYS H 94 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE H 96 " --> pdb=" O THR H 26 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU H 149 " --> pdb=" O LYS H 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 183 through 188 removed outlier: 3.868A pdb=" N ALA H 185 " --> pdb=" O ASP H 198 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE H 197 " --> pdb=" O PRO H 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE H 199 " --> pdb=" O PRO H 131 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU H 126 " --> pdb=" O PHE H 251 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS H 245 " --> pdb=" O GLU H 132 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS I 88 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET I 92 " --> pdb=" O ARG I 22 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR I 26 " --> pdb=" O CYS I 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE I 96 " --> pdb=" O THR I 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR I 97 " --> pdb=" O TYR I 69 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS I 88 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET I 92 " --> pdb=" O ARG I 22 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR I 26 " --> pdb=" O CYS I 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE I 96 " --> pdb=" O THR I 26 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU I 149 " --> pdb=" O LYS I 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 183 through 188 removed outlier: 3.859A pdb=" N ALA I 185 " --> pdb=" O ASP I 198 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE I 197 " --> pdb=" O PRO I 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE I 199 " --> pdb=" O PRO I 131 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU I 126 " --> pdb=" O PHE I 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS I 245 " --> pdb=" O GLU I 132 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS N 88 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET N 92 " --> pdb=" O ARG N 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR N 26 " --> pdb=" O CYS N 94 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE N 96 " --> pdb=" O THR N 26 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR N 97 " --> pdb=" O TYR N 69 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS N 88 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET N 92 " --> pdb=" O ARG N 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR N 26 " --> pdb=" O CYS N 94 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE N 96 " --> pdb=" O THR N 26 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU N 149 " --> pdb=" O LYS N 139 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 183 through 188 removed outlier: 3.856A pdb=" N ALA N 185 " --> pdb=" O ASP N 198 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE N 197 " --> pdb=" O PRO N 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE N 199 " --> pdb=" O PRO N 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU N 126 " --> pdb=" O PHE N 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS N 245 " --> pdb=" O GLU N 132 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS O 88 " --> pdb=" O VAL O 18 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET O 92 " --> pdb=" O ARG O 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR O 26 " --> pdb=" O CYS O 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE O 96 " --> pdb=" O THR O 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR O 97 " --> pdb=" O TYR O 69 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS O 88 " --> pdb=" O VAL O 18 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET O 92 " --> pdb=" O ARG O 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR O 26 " --> pdb=" O CYS O 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE O 96 " --> pdb=" O THR O 26 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU O 149 " --> pdb=" O LYS O 139 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 183 through 188 removed outlier: 3.865A pdb=" N ALA O 185 " --> pdb=" O ASP O 198 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE O 197 " --> pdb=" O PRO O 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE O 199 " --> pdb=" O PRO O 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU O 126 " --> pdb=" O PHE O 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS O 245 " --> pdb=" O GLU O 132 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS P 88 " --> pdb=" O VAL P 18 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET P 92 " --> pdb=" O ARG P 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR P 26 " --> pdb=" O CYS P 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE P 96 " --> pdb=" O THR P 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR P 97 " --> pdb=" O TYR P 69 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS P 88 " --> pdb=" O VAL P 18 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET P 92 " --> pdb=" O ARG P 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR P 26 " --> pdb=" O CYS P 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE P 96 " --> pdb=" O THR P 26 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU P 149 " --> pdb=" O LYS P 139 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 183 through 188 removed outlier: 3.851A pdb=" N ALA P 185 " --> pdb=" O ASP P 198 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE P 197 " --> pdb=" O PRO P 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE P 199 " --> pdb=" O PRO P 131 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU P 126 " --> pdb=" O PHE P 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS P 245 " --> pdb=" O GLU P 132 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS Q 88 " --> pdb=" O VAL Q 18 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET Q 92 " --> pdb=" O ARG Q 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR Q 26 " --> pdb=" O CYS Q 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE Q 96 " --> pdb=" O THR Q 26 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR Q 97 " --> pdb=" O TYR Q 69 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS Q 88 " --> pdb=" O VAL Q 18 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET Q 92 " --> pdb=" O ARG Q 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR Q 26 " --> pdb=" O CYS Q 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE Q 96 " --> pdb=" O THR Q 26 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU Q 149 " --> pdb=" O LYS Q 139 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 183 through 188 removed outlier: 3.858A pdb=" N ALA Q 185 " --> pdb=" O ASP Q 198 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE Q 197 " --> pdb=" O PRO Q 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE Q 199 " --> pdb=" O PRO Q 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU Q 126 " --> pdb=" O PHE Q 251 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS Q 245 " --> pdb=" O GLU Q 132 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS R 88 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET R 92 " --> pdb=" O ARG R 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR R 26 " --> pdb=" O CYS R 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE R 96 " --> pdb=" O THR R 26 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR R 97 " --> pdb=" O TYR R 69 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'R' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS R 88 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET R 92 " --> pdb=" O ARG R 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR R 26 " --> pdb=" O CYS R 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE R 96 " --> pdb=" O THR R 26 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU R 149 " --> pdb=" O LYS R 139 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 183 through 188 removed outlier: 3.860A pdb=" N ALA R 185 " --> pdb=" O ASP R 198 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE R 197 " --> pdb=" O PRO R 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE R 199 " --> pdb=" O PRO R 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU R 126 " --> pdb=" O PHE R 251 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS R 245 " --> pdb=" O GLU R 132 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 32 through 38 removed outlier: 5.550A pdb=" N LYS S 88 " --> pdb=" O VAL S 18 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET S 92 " --> pdb=" O ARG S 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR S 26 " --> pdb=" O CYS S 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE S 96 " --> pdb=" O THR S 26 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR S 97 " --> pdb=" O TYR S 69 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 32 through 38 removed outlier: 5.550A pdb=" N LYS S 88 " --> pdb=" O VAL S 18 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET S 92 " --> pdb=" O ARG S 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR S 26 " --> pdb=" O CYS S 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE S 96 " --> pdb=" O THR S 26 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'S' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU S 149 " --> pdb=" O LYS S 139 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 183 through 188 removed outlier: 3.845A pdb=" N ALA S 185 " --> pdb=" O ASP S 198 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE S 197 " --> pdb=" O PRO S 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE S 199 " --> pdb=" O PRO S 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU S 126 " --> pdb=" O PHE S 251 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS S 245 " --> pdb=" O GLU S 132 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'T' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS T 88 " --> pdb=" O VAL T 18 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET T 92 " --> pdb=" O ARG T 22 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR T 26 " --> pdb=" O CYS T 94 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE T 96 " --> pdb=" O THR T 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR T 97 " --> pdb=" O TYR T 69 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS T 88 " --> pdb=" O VAL T 18 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET T 92 " --> pdb=" O ARG T 22 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR T 26 " --> pdb=" O CYS T 94 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE T 96 " --> pdb=" O THR T 26 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'T' and resid 146 through 150 removed outlier: 5.300A pdb=" N GLU T 149 " --> pdb=" O LYS T 139 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'T' and resid 183 through 188 removed outlier: 3.866A pdb=" N ALA T 185 " --> pdb=" O ASP T 198 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE T 197 " --> pdb=" O PRO T 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE T 199 " --> pdb=" O PRO T 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU T 126 " --> pdb=" O PHE T 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS T 245 " --> pdb=" O GLU T 132 " (cutoff:3.500A) 2500 hydrogen bonds defined for protein. 7056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 26.18 Time building geometry restraints manager: 20.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.14: 140 1.14 - 1.31: 8386 1.31 - 1.48: 19928 1.48 - 1.64: 22170 1.64 - 1.81: 434 Bond restraints: 51058 Sorted by residual: bond pdb=" NE2 GLN I 503 " pdb="HE21 GLN I 503 " ideal model delta sigma weight residual 0.860 1.017 -0.157 2.00e-02 2.50e+03 6.14e+01 bond pdb=" NE2 GLN Q 503 " pdb="HE21 GLN Q 503 " ideal model delta sigma weight residual 0.860 1.017 -0.157 2.00e-02 2.50e+03 6.14e+01 bond pdb=" NE2 GLN N 503 " pdb="HE22 GLN N 503 " ideal model delta sigma weight residual 0.860 1.017 -0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" NE2 GLN A 503 " pdb="HE21 GLN A 503 " ideal model delta sigma weight residual 0.860 1.017 -0.157 2.00e-02 2.50e+03 6.12e+01 bond pdb=" NE2 GLN N 503 " pdb="HE21 GLN N 503 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.12e+01 ... (remaining 51053 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.15: 1849 107.15 - 113.98: 28364 113.98 - 120.81: 22942 120.81 - 127.65: 15574 127.65 - 134.48: 515 Bond angle restraints: 69244 Sorted by residual: angle pdb=" O LEU W 7 " pdb=" C LEU W 7 " pdb=" N PRO W 8 " ideal model delta sigma weight residual 121.37 116.64 4.73 9.00e-01 1.23e+00 2.76e+01 angle pdb=" O LEU D 7 " pdb=" C LEU D 7 " pdb=" N PRO D 8 " ideal model delta sigma weight residual 121.37 116.74 4.63 9.00e-01 1.23e+00 2.65e+01 angle pdb=" O LEU Y 7 " pdb=" C LEU Y 7 " pdb=" N PRO Y 8 " ideal model delta sigma weight residual 121.37 116.81 4.56 9.00e-01 1.23e+00 2.57e+01 angle pdb=" O LEU X 7 " pdb=" C LEU X 7 " pdb=" N PRO X 8 " ideal model delta sigma weight residual 121.37 116.96 4.41 9.00e-01 1.23e+00 2.40e+01 angle pdb=" CA LEU E 7 " pdb=" C LEU E 7 " pdb=" N PRO E 8 " ideal model delta sigma weight residual 117.52 121.07 -3.55 7.90e-01 1.60e+00 2.02e+01 ... (remaining 69239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 27182 17.67 - 35.34: 2318 35.34 - 53.01: 788 53.01 - 70.68: 206 70.68 - 88.35: 40 Dihedral angle restraints: 30534 sinusoidal: 12362 harmonic: 18172 Sorted by residual: dihedral pdb=" CB GLU F 424 " pdb=" CG GLU F 424 " pdb=" CD GLU F 424 " pdb=" OE1 GLU F 424 " ideal model delta sinusoidal sigma weight residual 0.00 88.35 -88.35 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU G 438 " pdb=" CG GLU G 438 " pdb=" CD GLU G 438 " pdb=" OE1 GLU G 438 " ideal model delta sinusoidal sigma weight residual 0.00 87.06 -87.06 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CG ARG H 316 " pdb=" CD ARG H 316 " pdb=" NE ARG H 316 " pdb=" CZ ARG H 316 " ideal model delta sinusoidal sigma weight residual 180.00 136.61 43.39 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 30531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 5740 0.052 - 0.103: 1243 0.103 - 0.155: 401 0.155 - 0.207: 53 0.207 - 0.258: 25 Chirality restraints: 7462 Sorted by residual: chirality pdb=" CB VAL N 35 " pdb=" CA VAL N 35 " pdb=" CG1 VAL N 35 " pdb=" CG2 VAL N 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB VAL T 35 " pdb=" CA VAL T 35 " pdb=" CG1 VAL T 35 " pdb=" CG2 VAL T 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB VAL B 35 " pdb=" CA VAL B 35 " pdb=" CG1 VAL B 35 " pdb=" CG2 VAL B 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.27e+00 ... (remaining 7459 not shown) Planarity restraints: 9030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 503 " 0.264 2.00e-02 2.50e+03 2.65e-01 1.06e+03 pdb=" CD GLN B 503 " -0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN B 503 " -0.251 2.00e-02 2.50e+03 pdb=" NE2 GLN B 503 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 503 " 0.385 2.00e-02 2.50e+03 pdb="HE22 GLN B 503 " -0.376 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN T 503 " -0.262 2.00e-02 2.50e+03 2.63e-01 1.04e+03 pdb=" CD GLN T 503 " 0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN T 503 " 0.249 2.00e-02 2.50e+03 pdb=" NE2 GLN T 503 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN T 503 " -0.381 2.00e-02 2.50e+03 pdb="HE22 GLN T 503 " 0.372 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN O 503 " 0.231 2.00e-02 2.50e+03 2.28e-01 7.79e+02 pdb=" CD GLN O 503 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN O 503 " -0.219 2.00e-02 2.50e+03 pdb=" NE2 GLN O 503 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN O 503 " 0.328 2.00e-02 2.50e+03 pdb="HE22 GLN O 503 " -0.320 2.00e-02 2.50e+03 ... (remaining 9027 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.42: 342 2.42 - 2.96: 23994 2.96 - 3.51: 59870 3.51 - 4.05: 93150 4.05 - 4.60: 144831 Nonbonded interactions: 322187 Sorted by model distance: nonbonded pdb=" OE1 GLU O 196 " pdb="MG MG O 501 " model vdw 1.872 2.050 nonbonded pdb=" O GLY I 241 " pdb=" H1 GLN I 503 " model vdw 1.969 1.850 nonbonded pdb=" O GLY C 241 " pdb=" H1 GLN C 503 " model vdw 1.975 1.850 nonbonded pdb=" O GLY S 241 " pdb=" H1 GLN S 503 " model vdw 1.981 1.850 nonbonded pdb=" O GLY G 241 " pdb=" H1 GLN G 503 " model vdw 1.983 1.850 ... (remaining 322182 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } 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=0.92 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.420 Extract box with map and model: 18.370 Check model and map are aligned: 0.730 Set scattering table: 0.440 Process input model: 125.970 Find NCS groups from input model: 4.200 Set up NCS constraints: 0.760 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:15.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 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 : 0.005 0.037 50918 Z= 0.303 Angle : 0.683 8.899 68936 Z= 0.439 Chirality : 0.050 0.258 7462 Planarity : 0.004 0.033 9030 Dihedral : 15.757 88.346 18788 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 3.66 % 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: 0.50 (0.11), residues: 6216 helix: 1.79 (0.11), residues: 2338 sheet: -0.69 (0.16), residues: 1078 loop : -0.43 (0.12), residues: 2800 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1429 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1238 time to evaluate : 6.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 191 outliers final: 27 residues processed: 1355 average time/residue: 1.7003 time to fit residues: 2854.9166 Evaluate side-chains 782 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 755 time to evaluate : 5.877 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 19 residues processed: 8 average time/residue: 0.5569 time to fit residues: 15.5274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 520 optimal weight: 3.9990 chunk 466 optimal weight: 7.9990 chunk 259 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 314 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 482 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 293 optimal weight: 6.9990 chunk 359 optimal weight: 4.9990 chunk 559 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 17 ASN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 GLN ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN C 17 ASN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 ASN G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN H 34 ASN H 187 HIS ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 ASN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN ** I 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN N 17 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN O 34 ASN O 167 ASN O 187 HIS ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 41 GLN P 187 HIS P 281 HIS Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 187 HIS ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 187 HIS ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 41 GLN S 187 HIS S 281 HIS T 17 ASN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 GLN ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 315 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 50918 Z= 0.329 Angle : 0.582 5.810 68936 Z= 0.302 Chirality : 0.045 0.160 7462 Planarity : 0.005 0.038 9030 Dihedral : 5.142 66.101 6790 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 5.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.11), residues: 6216 helix: 1.91 (0.11), residues: 2352 sheet: -0.81 (0.15), residues: 1148 loop : -0.56 (0.12), residues: 2716 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 716 time to evaluate : 5.604 Fit side-chains outliers start: 301 outliers final: 85 residues processed: 943 average time/residue: 1.6196 time to fit residues: 1916.2984 Evaluate side-chains 754 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 669 time to evaluate : 5.852 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 67 residues processed: 18 average time/residue: 1.5806 time to fit residues: 43.6506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 310 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 465 optimal weight: 7.9990 chunk 380 optimal weight: 0.0570 chunk 154 optimal weight: 5.9990 chunk 560 optimal weight: 0.0020 chunk 605 optimal weight: 0.0670 chunk 499 optimal weight: 9.9990 chunk 555 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 449 optimal weight: 4.9990 overall best weight: 0.8246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 HIS A 225 HIS ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS B 225 HIS ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS C 225 HIS ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 HIS F 225 HIS ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN H 34 ASN H 225 HIS ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 ASN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 187 HIS I 225 HIS ** I 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN O 34 ASN O 225 HIS ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 225 HIS ** P 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 187 HIS T 225 HIS ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 50918 Z= 0.123 Angle : 0.424 5.291 68936 Z= 0.222 Chirality : 0.038 0.130 7462 Planarity : 0.003 0.029 9030 Dihedral : 4.622 64.245 6790 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 3.83 % 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: 0.90 (0.11), residues: 6216 helix: 2.19 (0.11), residues: 2394 sheet: -0.38 (0.16), residues: 1078 loop : -0.39 (0.12), residues: 2744 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 690 time to evaluate : 5.631 Fit side-chains revert: symmetry clash outliers start: 200 outliers final: 78 residues processed: 828 average time/residue: 1.6540 time to fit residues: 1710.1166 Evaluate side-chains 722 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 644 time to evaluate : 6.004 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 61 residues processed: 19 average time/residue: 1.0144 time to fit residues: 35.3284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 553 optimal weight: 0.0040 chunk 421 optimal weight: 0.4980 chunk 290 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 267 optimal weight: 5.9990 chunk 376 optimal weight: 10.0000 chunk 562 optimal weight: 0.6980 chunk 595 optimal weight: 4.9990 chunk 293 optimal weight: 0.9980 chunk 533 optimal weight: 0.4980 chunk 160 optimal weight: 5.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 439 GLN G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 187 HIS ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN H 34 ASN ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 HIS ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN O 34 ASN ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 50918 Z= 0.099 Angle : 0.391 3.896 68936 Z= 0.203 Chirality : 0.038 0.131 7462 Planarity : 0.003 0.028 9030 Dihedral : 4.215 60.492 6790 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.11), residues: 6216 helix: 2.49 (0.11), residues: 2394 sheet: -0.35 (0.17), residues: 1078 loop : -0.28 (0.12), residues: 2744 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 658 time to evaluate : 5.710 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 174 outliers final: 76 residues processed: 770 average time/residue: 1.6690 time to fit residues: 1608.2030 Evaluate side-chains 724 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 648 time to evaluate : 5.911 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 55 residues processed: 22 average time/residue: 1.0160 time to fit residues: 39.2412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 495 optimal weight: 6.9990 chunk 337 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 443 optimal weight: 0.0370 chunk 245 optimal weight: 7.9990 chunk 508 optimal weight: 10.0000 chunk 411 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 304 optimal weight: 5.9990 chunk 534 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 ASN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 ASN G 225 HIS ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN H 34 ASN ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 315 ASN ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 412 HIS ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN N 34 ASN N 151 ASN N 225 HIS ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN O 34 ASN ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 315 ASN ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 225 HIS ** S 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 342 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.083 50918 Z= 0.480 Angle : 0.646 7.319 68936 Z= 0.336 Chirality : 0.050 0.161 7462 Planarity : 0.006 0.050 9030 Dihedral : 5.692 75.457 6790 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 3.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.10), residues: 6216 helix: 1.63 (0.10), residues: 2366 sheet: -0.77 (0.17), residues: 868 loop : -0.75 (0.11), residues: 2982 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 582 time to evaluate : 6.424 Fit side-chains outliers start: 193 outliers final: 75 residues processed: 746 average time/residue: 1.7631 time to fit residues: 1633.2425 Evaluate side-chains 651 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 576 time to evaluate : 5.937 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 70 residues processed: 6 average time/residue: 1.7443 time to fit residues: 20.8464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 200 optimal weight: 2.9990 chunk 536 optimal weight: 9.9990 chunk 117 optimal weight: 0.6980 chunk 349 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 596 optimal weight: 5.9990 chunk 494 optimal weight: 3.9990 chunk 275 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 197 optimal weight: 0.7980 chunk 312 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 ASN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 342 ASN ** T 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 50918 Z= 0.143 Angle : 0.433 4.779 68936 Z= 0.228 Chirality : 0.039 0.133 7462 Planarity : 0.003 0.032 9030 Dihedral : 4.969 72.663 6790 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 2.82 % 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: 0.72 (0.11), residues: 6216 helix: 2.12 (0.11), residues: 2366 sheet: -0.55 (0.16), residues: 1176 loop : -0.50 (0.12), residues: 2674 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 615 time to evaluate : 5.897 Fit side-chains outliers start: 147 outliers final: 82 residues processed: 719 average time/residue: 1.7141 time to fit residues: 1534.3526 Evaluate side-chains 678 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 596 time to evaluate : 6.363 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 71 residues processed: 13 average time/residue: 1.4717 time to fit residues: 32.6159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 574 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 339 optimal weight: 4.9990 chunk 435 optimal weight: 9.9990 chunk 337 optimal weight: 1.9990 chunk 501 optimal weight: 2.9990 chunk 332 optimal weight: 9.9990 chunk 593 optimal weight: 6.9990 chunk 371 optimal weight: 1.9990 chunk 361 optimal weight: 4.9990 chunk 274 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 ASN ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 HIS ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 ASN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 151 ASN ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN O 34 ASN ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 50918 Z= 0.252 Angle : 0.495 5.123 68936 Z= 0.258 Chirality : 0.042 0.142 7462 Planarity : 0.004 0.039 9030 Dihedral : 5.135 71.855 6790 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 2.89 % 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: 0.61 (0.11), residues: 6216 helix: 2.01 (0.10), residues: 2366 sheet: -0.61 (0.16), residues: 1176 loop : -0.52 (0.12), residues: 2674 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 592 time to evaluate : 6.509 Fit side-chains outliers start: 151 outliers final: 81 residues processed: 716 average time/residue: 1.7696 time to fit residues: 1586.6405 Evaluate side-chains 668 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 587 time to evaluate : 5.835 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 72 residues processed: 9 average time/residue: 1.4973 time to fit residues: 24.8867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 367 optimal weight: 10.0000 chunk 237 optimal weight: 7.9990 chunk 354 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 377 optimal weight: 0.0770 chunk 404 optimal weight: 10.0000 chunk 293 optimal weight: 0.4980 chunk 55 optimal weight: 0.5980 chunk 466 optimal weight: 7.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 ASN ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 439 GLN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 HIS ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 50918 Z= 0.138 Angle : 0.429 5.517 68936 Z= 0.225 Chirality : 0.039 0.132 7462 Planarity : 0.003 0.033 9030 Dihedral : 4.786 69.608 6790 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 2.05 % 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: 0.81 (0.11), residues: 6216 helix: 2.24 (0.10), residues: 2394 sheet: -0.57 (0.16), residues: 1176 loop : -0.47 (0.12), residues: 2646 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 615 time to evaluate : 6.371 Fit side-chains outliers start: 107 outliers final: 84 residues processed: 700 average time/residue: 1.6889 time to fit residues: 1471.7782 Evaluate side-chains 669 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 585 time to evaluate : 5.308 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 72 residues processed: 12 average time/residue: 0.9534 time to fit residues: 24.2869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 540 optimal weight: 7.9990 chunk 568 optimal weight: 4.9990 chunk 518 optimal weight: 4.9990 chunk 553 optimal weight: 0.9990 chunk 333 optimal weight: 1.9990 chunk 241 optimal weight: 0.9990 chunk 434 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 499 optimal weight: 8.9990 chunk 523 optimal weight: 7.9990 chunk 551 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 HIS ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 ASN ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 151 ASN ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 50918 Z= 0.229 Angle : 0.478 5.180 68936 Z= 0.250 Chirality : 0.041 0.139 7462 Planarity : 0.004 0.038 9030 Dihedral : 4.989 69.659 6790 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 2.30 % 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: 0.69 (0.11), residues: 6216 helix: 2.10 (0.11), residues: 2366 sheet: -0.61 (0.16), residues: 1176 loop : -0.48 (0.12), residues: 2674 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 581 time to evaluate : 5.837 Fit side-chains outliers start: 120 outliers final: 79 residues processed: 685 average time/residue: 1.6931 time to fit residues: 1442.8271 Evaluate side-chains 666 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 587 time to evaluate : 4.803 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 72 residues processed: 7 average time/residue: 1.6975 time to fit residues: 21.9438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 363 optimal weight: 0.9980 chunk 585 optimal weight: 3.9990 chunk 357 optimal weight: 6.9990 chunk 277 optimal weight: 6.9990 chunk 406 optimal weight: 2.9990 chunk 613 optimal weight: 5.9990 chunk 564 optimal weight: 0.0470 chunk 488 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 377 optimal weight: 0.0670 chunk 299 optimal weight: 6.9990 overall best weight: 1.0218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 GLN ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 50918 Z= 0.139 Angle : 0.424 4.566 68936 Z= 0.222 Chirality : 0.039 0.131 7462 Planarity : 0.003 0.079 9030 Dihedral : 4.680 67.571 6790 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 1.67 % 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: 0.88 (0.11), residues: 6216 helix: 2.31 (0.10), residues: 2394 sheet: -0.56 (0.16), residues: 1176 loop : -0.44 (0.12), residues: 2646 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 616 time to evaluate : 5.780 Fit side-chains outliers start: 87 outliers final: 71 residues processed: 696 average time/residue: 1.6457 time to fit residues: 1428.3875 Evaluate side-chains 675 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 604 time to evaluate : 5.120 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 68 residues processed: 3 average time/residue: 1.6310 time to fit residues: 12.7131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 388 optimal weight: 0.5980 chunk 520 optimal weight: 0.0980 chunk 149 optimal weight: 4.9990 chunk 450 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 489 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 502 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 HIS ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 ASN ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 HIS ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 151 ASN ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 HIS ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.135645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.111873 restraints weight = 51777.697| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.45 r_work: 0.3194 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 50918 Z= 0.224 Angle : 0.475 5.076 68936 Z= 0.248 Chirality : 0.041 0.139 7462 Planarity : 0.004 0.068 9030 Dihedral : 4.927 68.348 6790 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.11), residues: 6216 helix: 2.15 (0.11), residues: 2366 sheet: -0.60 (0.16), residues: 1176 loop : -0.46 (0.12), residues: 2674 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22957.22 seconds wall clock time: 404 minutes 22.87 seconds (24262.87 seconds total)