Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 21 23:35:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfc_25869/10_2023/7tfc_25869.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfc_25869/10_2023/7tfc_25869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfc_25869/10_2023/7tfc_25869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfc_25869/10_2023/7tfc_25869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfc_25869/10_2023/7tfc_25869.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfc_25869/10_2023/7tfc_25869.pdb" } resolution = 1.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.120 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 224 5.16 5 C 32130 2.51 5 N 8484 2.21 5 O 9450 1.98 5 H 140 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 50456 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "O" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "P" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "Q" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "S" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "T" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "U" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 24.59, per 1000 atoms: 0.49 Number of scatterers: 50456 At special positions: 0 Unit cell: (170.72, 168.96, 124.08, 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 224 16.00 Mg 28 11.99 O 9450 8.00 N 8484 7.00 C 32130 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: 19.38 Conformation dependent library (CDL) restraints added in 6.8 seconds 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11900 Finding SS restraints... Secondary structure from input PDB file: 262 helices and 44 sheets defined 45.0% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.73 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: 6.472A pdb=" N PHE A 60 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A 61 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 121 Processing helix chain 'A' and resid 167 through 179 Processing helix chain 'A' and resid 204 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: 3.513A pdb=" N THR A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ALA A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 299 removed outlier: 3.719A pdb=" N ARG A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) removed outlier: 3.621A 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: 3.669A 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 376 through 382 removed outlier: 4.061A pdb=" N GLU A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 402 removed outlier: 3.507A pdb=" N SER A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 409 through 430 removed outlier: 4.148A pdb=" N LEU A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 441 removed outlier: 3.545A 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: 6.487A pdb=" N PHE B 60 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 61 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 204 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: 5.234A pdb=" N ALA B 287 " --> pdb=" O THR B 283 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 299 removed outlier: 3.710A pdb=" N ARG B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) removed outlier: 3.614A 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: 3.613A 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: 4.117A pdb=" N GLU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 402 removed outlier: 3.502A pdb=" N SER B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 409 through 430 removed outlier: 4.128A pdb=" N LEU B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 441 removed outlier: 3.569A 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: 6.411A pdb=" N PHE C 60 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL C 61 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 62 " --> pdb=" O GLY C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 167 through 179 Processing helix chain 'C' and resid 204 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: 3.524A pdb=" N THR C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ALA C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N VAL C 288 " --> pdb=" O SER C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 299 removed outlier: 3.705A pdb=" N ARG C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) removed outlier: 3.553A 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: 3.686A 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 377 through 382 removed outlier: 4.277A pdb=" N GLU C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 402 removed outlier: 3.511A pdb=" N ASN C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 408 removed outlier: 3.537A pdb=" N LYS C 407 " --> pdb=" O GLU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 430 removed outlier: 4.127A pdb=" N LEU C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 441 removed outlier: 3.543A pdb=" N ARG C 437 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 10 removed outlier: 4.247A pdb=" N ARG D 9 " --> pdb=" O ASP D 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 10 removed outlier: 3.551A pdb=" N SER E 8 " --> pdb=" O GLY E 5 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG E 9 " --> pdb=" O ASP E 6 " (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: 6.458A pdb=" N PHE F 60 " --> pdb=" O ILE F 57 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL F 61 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG F 62 " --> pdb=" O GLY F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 77 Processing helix chain 'F' and resid 107 through 121 Processing helix chain 'F' and resid 167 through 179 Processing helix chain 'F' and resid 204 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: 3.517A pdb=" N THR F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ALA F 287 " --> pdb=" O THR F 283 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL F 288 " --> pdb=" O SER F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 removed outlier: 3.660A pdb=" N ARG F 298 " --> pdb=" O ASN F 294 " (cutoff:3.500A) removed outlier: 3.588A 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: 3.622A 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 376 through 382 removed outlier: 4.116A pdb=" N GLU 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 402 through 408 Processing helix chain 'F' and resid 409 through 430 removed outlier: 4.190A pdb=" N LEU F 413 " --> pdb=" O LEU F 409 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR F 430 " --> pdb=" O ASP F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 441 removed outlier: 3.526A pdb=" N ARG F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) 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: 6.422A pdb=" N PHE G 60 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL G 61 " --> pdb=" O GLU G 58 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG G 62 " --> pdb=" O GLY G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 77 Processing helix chain 'G' and resid 107 through 121 Processing helix chain 'G' and resid 167 through 179 Processing helix chain 'G' and resid 204 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: 3.531A pdb=" N THR G 286 " --> pdb=" O ALA G 282 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ALA G 287 " --> pdb=" O THR G 283 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL G 288 " --> pdb=" O SER G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 299 removed outlier: 3.705A pdb=" N ARG G 298 " --> pdb=" O ASN G 294 " (cutoff:3.500A) removed outlier: 3.579A 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: 3.627A 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 376 through 382 removed outlier: 4.069A pdb=" N GLU 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 402 through 408 removed outlier: 3.524A pdb=" N LYS G 407 " --> pdb=" O GLU G 403 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 430 removed outlier: 4.163A pdb=" N LEU G 413 " --> pdb=" O LEU G 409 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 441 removed outlier: 3.553A pdb=" N ARG G 437 " --> pdb=" O HIS G 433 " (cutoff:3.500A) 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: 6.453A pdb=" N PHE H 60 " --> pdb=" O ILE H 57 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL H 61 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG H 62 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 Processing helix chain 'H' and resid 107 through 121 Processing helix chain 'H' and resid 167 through 179 Processing helix chain 'H' and resid 204 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: 5.263A pdb=" N ALA H 287 " --> pdb=" O THR H 283 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL H 288 " --> pdb=" O SER H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 299 removed outlier: 3.739A pdb=" N ARG H 298 " --> pdb=" O ASN H 294 " (cutoff:3.500A) removed outlier: 3.641A 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: 3.601A 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 377 through 382 removed outlier: 4.190A pdb=" N GLU 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 402 through 408 Processing helix chain 'H' and resid 409 through 430 removed outlier: 4.153A pdb=" N LEU H 413 " --> pdb=" O LEU H 409 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 441 removed outlier: 3.544A pdb=" N ARG H 437 " --> pdb=" O HIS H 433 " (cutoff:3.500A) 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: 6.491A pdb=" N PHE I 60 " --> pdb=" O ILE I 57 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL I 61 " --> pdb=" O GLU I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 77 Processing helix chain 'I' and resid 107 through 122 Processing helix chain 'I' and resid 167 through 179 Processing helix chain 'I' and resid 204 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: 5.233A pdb=" N ALA I 287 " --> pdb=" O THR I 283 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL I 288 " --> pdb=" O SER I 284 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 299 removed outlier: 3.693A pdb=" N ARG I 298 " --> pdb=" O ASN I 294 " (cutoff:3.500A) removed outlier: 3.578A 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: 3.566A 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 376 through 382 removed outlier: 4.113A pdb=" N GLU I 382 " --> pdb=" O GLU I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 391 through 402 removed outlier: 3.500A pdb=" N SER I 401 " --> pdb=" O GLU I 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN I 402 " --> pdb=" O GLU I 398 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 408 Processing helix chain 'I' and resid 409 through 430 removed outlier: 4.104A pdb=" N LEU I 413 " --> pdb=" O LEU I 409 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR I 430 " --> pdb=" O ASP I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 441 removed outlier: 3.567A pdb=" N ARG I 437 " --> pdb=" O HIS I 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 10 removed outlier: 4.166A pdb=" N ARG J 9 " --> pdb=" O ASP J 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.636A pdb=" N SER K 8 " --> pdb=" O GLY K 5 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG K 9 " --> pdb=" O ASP K 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 10 removed outlier: 3.525A pdb=" N SER L 8 " --> pdb=" O GLY L 5 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG L 9 " --> pdb=" O ASP L 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 10 removed outlier: 3.559A pdb=" N SER M 8 " --> pdb=" O GLY M 5 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG M 9 " --> pdb=" O ASP M 6 " (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: 6.448A pdb=" N PHE N 60 " --> pdb=" O ILE N 57 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL N 61 " --> pdb=" O GLU N 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG N 62 " --> pdb=" O GLY N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 77 Processing helix chain 'N' and resid 107 through 121 Processing helix chain 'N' and resid 167 through 179 Processing helix chain 'N' and resid 204 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: 3.516A pdb=" N THR N 286 " --> pdb=" O ALA N 282 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ALA N 287 " --> pdb=" O THR N 283 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL N 288 " --> pdb=" O SER N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 299 removed outlier: 3.660A pdb=" N ARG N 298 " --> pdb=" O ASN N 294 " (cutoff:3.500A) removed outlier: 3.591A 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: 3.628A 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 376 through 382 removed outlier: 4.114A pdb=" N GLU 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 402 through 408 removed outlier: 3.512A pdb=" N LYS N 407 " --> pdb=" O GLU N 403 " (cutoff:3.500A) Processing helix chain 'N' and resid 409 through 430 removed outlier: 4.156A pdb=" N LEU N 413 " --> pdb=" O LEU N 409 " (cutoff:3.500A) Processing helix chain 'N' and resid 433 through 441 removed outlier: 3.524A 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: 6.422A pdb=" N PHE O 60 " --> pdb=" O ILE O 57 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL O 61 " --> pdb=" O GLU O 58 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG O 62 " --> pdb=" O GLY O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 77 Processing helix chain 'O' and resid 107 through 121 Processing helix chain 'O' and resid 167 through 179 Processing helix chain 'O' and resid 204 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: 3.545A pdb=" N THR O 286 " --> pdb=" O ALA O 282 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ALA O 287 " --> pdb=" O THR O 283 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N VAL O 288 " --> pdb=" O SER O 284 " (cutoff:3.500A) Processing helix chain 'O' and resid 294 through 299 removed outlier: 3.711A pdb=" N ARG O 298 " --> pdb=" O ASN O 294 " (cutoff:3.500A) removed outlier: 3.585A 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: 3.649A 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 376 through 382 removed outlier: 4.149A pdb=" N GLU 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 402 through 408 removed outlier: 3.576A pdb=" N VAL O 406 " --> pdb=" O ASN O 402 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS O 407 " --> pdb=" O GLU O 403 " (cutoff:3.500A) Processing helix chain 'O' and resid 409 through 430 removed outlier: 4.147A pdb=" N LEU O 413 " --> pdb=" O LEU O 409 " (cutoff:3.500A) Processing helix chain 'O' and resid 433 through 441 removed outlier: 3.553A 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: 6.453A pdb=" N PHE P 60 " --> pdb=" O ILE P 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL P 61 " --> pdb=" O GLU P 58 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG P 62 " --> pdb=" O GLY P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 77 Processing helix chain 'P' and resid 107 through 121 Processing helix chain 'P' and resid 167 through 179 Processing helix chain 'P' and resid 204 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: 5.270A pdb=" N ALA P 287 " --> pdb=" O THR P 283 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL P 288 " --> pdb=" O SER P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 294 through 299 removed outlier: 3.735A pdb=" N ARG P 298 " --> pdb=" O ASN P 294 " (cutoff:3.500A) removed outlier: 3.638A 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: 3.577A 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 376 through 382 removed outlier: 4.196A pdb=" N GLU 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 402 through 408 removed outlier: 3.539A pdb=" N VAL P 406 " --> pdb=" O ASN P 402 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS P 407 " --> pdb=" O GLU P 403 " (cutoff:3.500A) Processing helix chain 'P' and resid 409 through 430 removed outlier: 4.158A pdb=" N LEU P 413 " --> pdb=" O LEU P 409 " (cutoff:3.500A) Processing helix chain 'P' and resid 433 through 441 removed outlier: 3.542A 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: 6.494A pdb=" N PHE Q 60 " --> pdb=" O ILE Q 57 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL Q 61 " --> pdb=" O GLU Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 77 Processing helix chain 'Q' and resid 107 through 122 Processing helix chain 'Q' and resid 167 through 179 Processing helix chain 'Q' and resid 204 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: 5.229A pdb=" N ALA Q 287 " --> pdb=" O THR Q 283 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL Q 288 " --> pdb=" O SER Q 284 " (cutoff:3.500A) Processing helix chain 'Q' and resid 294 through 299 removed outlier: 3.692A pdb=" N ARG Q 298 " --> pdb=" O ASN Q 294 " (cutoff:3.500A) removed outlier: 3.578A 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: 3.567A 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 376 through 382 removed outlier: 4.119A pdb=" N GLU 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 402 through 408 Processing helix chain 'Q' and resid 409 through 430 removed outlier: 4.114A pdb=" N LEU Q 413 " --> pdb=" O LEU Q 409 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR Q 430 " --> pdb=" O ASP Q 426 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 441 removed outlier: 3.566A 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: 6.467A pdb=" N PHE R 60 " --> pdb=" O ILE R 57 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL R 61 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG R 62 " --> pdb=" O GLY R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 121 Processing helix chain 'R' and resid 167 through 179 Processing helix chain 'R' and resid 204 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: 3.514A pdb=" N THR R 286 " --> pdb=" O ALA R 282 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ALA R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N VAL R 288 " --> pdb=" O SER R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 299 removed outlier: 3.729A pdb=" N ARG R 298 " --> pdb=" O ASN R 294 " (cutoff:3.500A) removed outlier: 3.642A 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: 3.857A 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 376 through 382 removed outlier: 4.063A pdb=" N GLU R 382 " --> pdb=" O GLU R 378 " (cutoff:3.500A) Processing helix chain 'R' and resid 391 through 402 removed outlier: 3.528A pdb=" N ASN R 402 " --> pdb=" O GLU R 398 " (cutoff:3.500A) Processing helix chain 'R' and resid 402 through 408 removed outlier: 3.654A pdb=" N LYS R 407 " --> pdb=" O GLU R 403 " (cutoff:3.500A) Processing helix chain 'R' and resid 409 through 430 removed outlier: 4.159A pdb=" N LEU R 413 " --> pdb=" O LEU R 409 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR R 430 " --> pdb=" O ASP R 426 " (cutoff:3.500A) Processing helix chain 'R' and resid 433 through 441 removed outlier: 3.530A pdb=" N ARG R 437 " --> pdb=" O HIS R 433 " (cutoff:3.500A) 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: 6.498A pdb=" N PHE S 60 " --> pdb=" O ILE S 57 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL S 61 " --> pdb=" O GLU S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 121 Processing helix chain 'S' and resid 167 through 179 Processing helix chain 'S' and resid 204 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: 3.502A pdb=" N THR S 286 " --> pdb=" O ALA S 282 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA S 287 " --> pdb=" O THR S 283 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N VAL S 288 " --> pdb=" O SER S 284 " (cutoff:3.500A) Processing helix chain 'S' and resid 294 through 299 removed outlier: 3.712A pdb=" N ARG S 298 " --> pdb=" O ASN S 294 " (cutoff:3.500A) removed outlier: 3.613A 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: 3.614A 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 376 through 382 removed outlier: 4.130A pdb=" N GLU S 382 " --> pdb=" O GLU S 378 " (cutoff:3.500A) Processing helix chain 'S' and resid 391 through 402 removed outlier: 3.524A pdb=" N ASN S 402 " --> pdb=" O GLU S 398 " (cutoff:3.500A) Processing helix chain 'S' and resid 402 through 408 Processing helix chain 'S' and resid 409 through 430 removed outlier: 4.121A pdb=" N LEU S 413 " --> pdb=" O LEU S 409 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR S 430 " --> pdb=" O ASP S 426 " (cutoff:3.500A) Processing helix chain 'S' and resid 433 through 441 removed outlier: 3.567A pdb=" N ARG S 437 " --> pdb=" O HIS S 433 " (cutoff:3.500A) 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: 6.411A pdb=" N PHE T 60 " --> pdb=" O ILE T 57 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL T 61 " --> pdb=" O GLU T 58 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG T 62 " --> pdb=" O GLY T 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 107 through 122 Processing helix chain 'T' and resid 167 through 179 Processing helix chain 'T' and resid 204 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: 3.545A pdb=" N THR T 286 " --> pdb=" O ALA T 282 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ALA T 287 " --> pdb=" O THR T 283 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N VAL T 288 " --> pdb=" O SER T 284 " (cutoff:3.500A) Processing helix chain 'T' and resid 294 through 299 removed outlier: 3.706A pdb=" N ARG T 298 " --> pdb=" O ASN T 294 " (cutoff:3.500A) removed outlier: 3.552A 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: 3.658A 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 377 through 382 removed outlier: 4.263A pdb=" N GLU 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 402 through 408 removed outlier: 3.841A pdb=" N LYS T 407 " --> pdb=" O GLU T 403 " (cutoff:3.500A) Processing helix chain 'T' and resid 409 through 430 removed outlier: 4.113A pdb=" N LEU T 413 " --> pdb=" O LEU T 409 " (cutoff:3.500A) Processing helix chain 'T' and resid 433 through 441 removed outlier: 3.539A pdb=" N ARG T 437 " --> pdb=" O HIS T 433 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 10 removed outlier: 4.152A pdb=" N ARG U 9 " --> pdb=" O ASP U 6 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 10 removed outlier: 3.579A pdb=" N SER V 8 " --> pdb=" O GLY V 5 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG V 9 " --> pdb=" O ASP V 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 10 removed outlier: 4.264A pdb=" N ARG W 9 " --> pdb=" O ASP W 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 6 through 10 removed outlier: 4.237A pdb=" N ARG X 9 " --> pdb=" O ASP X 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 10 removed outlier: 4.135A pdb=" N ARG Y 9 " --> pdb=" O ASP Y 6 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 10 removed outlier: 4.216A pdb=" N ARG Z 9 " --> pdb=" O ASP Z 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 10 removed outlier: 3.616A pdb=" N SER a 8 " --> pdb=" O GLY a 5 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG a 9 " --> pdb=" O ASP a 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 10 removed outlier: 4.161A pdb=" N ARG b 9 " --> pdb=" O ASP b 6 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 removed outlier: 3.514A pdb=" N VAL A 35 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL A 18 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ALA A 90 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TYR A 20 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N PHE A 92 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ARG A 22 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N CYS A 94 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLN A 24 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE A 93 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR A 76 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 140 removed outlier: 5.419A pdb=" N GLU A 149 " --> pdb=" O LYS A 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 146 through 150 current: chain 'A' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 194 through 199 current: chain 'A' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 255 through 256 current: chain 'A' and resid 320 through 321 Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 309 removed outlier: 4.192A pdb=" N VAL A 386 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 32 through 38 removed outlier: 5.528A pdb=" N LYS B 88 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR B 26 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ILE B 93 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N THR B 76 " --> pdb=" O ILE B 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA7, first strand: chain 'B' and resid 126 through 140 removed outlier: 5.420A pdb=" N GLU B 149 " --> pdb=" O LYS B 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 146 through 150 current: chain 'B' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 194 through 199 current: chain 'B' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 255 through 256 current: chain 'B' and resid 320 through 321 Processing sheet with id=AA8, first strand: chain 'C' and resid 32 through 38 removed outlier: 5.523A pdb=" N LYS C 88 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N THR C 26 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE C 93 " --> pdb=" O THR C 76 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR C 76 " --> pdb=" O ILE C 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AB1, first strand: chain 'C' and resid 126 through 140 removed outlier: 5.410A pdb=" N GLU C 149 " --> pdb=" O LYS C 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 146 through 150 current: chain 'C' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 194 through 199 current: chain 'C' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 255 through 256 current: chain 'C' and resid 320 through 321 Processing sheet with id=AB2, first strand: chain 'F' and resid 32 through 38 removed outlier: 3.511A pdb=" N VAL F 35 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LYS F 88 " --> pdb=" O VAL F 18 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 51 through 53 Processing sheet with id=AB4, first strand: chain 'F' and resid 126 through 140 removed outlier: 5.391A pdb=" N GLU F 149 " --> pdb=" O LYS F 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 146 through 150 current: chain 'F' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 194 through 199 current: chain 'F' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 255 through 256 current: chain 'F' and resid 320 through 321 Processing sheet with id=AB5, first strand: chain 'G' and resid 32 through 38 removed outlier: 5.507A pdb=" N LYS G 88 " --> pdb=" O VAL G 18 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 51 through 53 Processing sheet with id=AB7, first strand: chain 'G' and resid 126 through 140 removed outlier: 5.406A pdb=" N GLU G 149 " --> pdb=" O LYS G 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 146 through 150 current: chain 'G' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 194 through 199 current: chain 'G' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 255 through 256 current: chain 'G' and resid 320 through 321 Processing sheet with id=AB8, first strand: chain 'H' and resid 32 through 38 removed outlier: 4.764A pdb=" N VAL H 18 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ALA H 90 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR H 20 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N PHE H 92 " --> pdb=" O TYR H 20 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG H 22 " --> pdb=" O PHE H 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 51 through 53 Processing sheet with id=AC1, first strand: chain 'H' and resid 126 through 140 removed outlier: 5.399A pdb=" N GLU H 149 " --> pdb=" O LYS H 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 146 through 150 current: chain 'H' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 194 through 199 current: chain 'H' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 255 through 256 current: chain 'H' and resid 320 through 321 Processing sheet with id=AC2, first strand: chain 'I' and resid 32 through 38 removed outlier: 5.587A pdb=" N LYS I 88 " --> pdb=" O VAL I 18 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 51 through 53 Processing sheet with id=AC4, first strand: chain 'I' and resid 126 through 140 removed outlier: 5.388A pdb=" N GLU I 149 " --> pdb=" O LYS I 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 146 through 150 current: chain 'I' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 194 through 199 current: chain 'I' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 255 through 256 current: chain 'I' and resid 320 through 321 Processing sheet with id=AC5, first strand: chain 'N' and resid 32 through 38 removed outlier: 5.645A pdb=" N LYS N 88 " --> pdb=" O VAL N 18 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 51 through 53 Processing sheet with id=AC7, first strand: chain 'N' and resid 126 through 140 removed outlier: 5.390A pdb=" N GLU N 149 " --> pdb=" O LYS N 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 146 through 150 current: chain 'N' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 194 through 199 current: chain 'N' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 255 through 256 current: chain 'N' and resid 320 through 321 Processing sheet with id=AC8, first strand: chain 'O' and resid 32 through 38 removed outlier: 5.530A pdb=" N LYS O 88 " --> pdb=" O VAL O 18 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 51 through 53 Processing sheet with id=AD1, first strand: chain 'O' and resid 126 through 140 removed outlier: 5.420A pdb=" N GLU O 149 " --> pdb=" O LYS O 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 146 through 150 current: chain 'O' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 194 through 199 current: chain 'O' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 255 through 256 current: chain 'O' and resid 320 through 321 Processing sheet with id=AD2, first strand: chain 'P' and resid 32 through 38 removed outlier: 5.542A pdb=" N LYS P 88 " --> pdb=" O VAL P 18 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 51 through 53 Processing sheet with id=AD4, first strand: chain 'P' and resid 126 through 140 removed outlier: 5.393A pdb=" N GLU P 149 " --> pdb=" O LYS P 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 146 through 150 current: chain 'P' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 194 through 199 current: chain 'P' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 255 through 256 current: chain 'P' and resid 320 through 321 Processing sheet with id=AD5, first strand: chain 'Q' and resid 32 through 38 removed outlier: 4.816A pdb=" N VAL Q 18 " --> pdb=" O LYS Q 88 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ALA Q 90 " --> pdb=" O VAL Q 18 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR Q 20 " --> pdb=" O ALA Q 90 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE Q 92 " --> pdb=" O TYR Q 20 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG Q 22 " --> pdb=" O PHE Q 92 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 51 through 53 Processing sheet with id=AD7, first strand: chain 'Q' and resid 126 through 140 removed outlier: 5.390A pdb=" N GLU Q 149 " --> pdb=" O LYS Q 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 146 through 150 current: chain 'Q' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 194 through 199 current: chain 'Q' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 255 through 256 current: chain 'Q' and resid 320 through 321 Processing sheet with id=AD8, first strand: chain 'R' and resid 32 through 38 removed outlier: 3.516A pdb=" N VAL R 35 " --> pdb=" O LEU R 23 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL R 18 " --> pdb=" O LYS R 88 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ALA R 90 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR R 20 " --> pdb=" O ALA R 90 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N PHE R 92 " --> pdb=" O TYR R 20 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ARG R 22 " --> pdb=" O PHE R 92 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N CYS R 94 " --> pdb=" O ARG R 22 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN R 24 " --> pdb=" O CYS R 94 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE R 93 " --> pdb=" O THR R 76 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N THR R 76 " --> pdb=" O ILE R 93 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 51 through 53 Processing sheet with id=AE1, first strand: chain 'R' and resid 126 through 140 removed outlier: 5.420A pdb=" N GLU R 149 " --> pdb=" O LYS R 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 146 through 150 current: chain 'R' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 194 through 199 current: chain 'R' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 255 through 256 current: chain 'R' and resid 320 through 321 Processing sheet with id=AE2, first strand: chain 'R' and resid 308 through 309 removed outlier: 4.205A pdb=" N VAL R 386 " --> pdb=" O VAL R 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 32 through 38 removed outlier: 5.523A pdb=" N LYS S 88 " --> pdb=" O VAL S 18 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR S 26 " --> pdb=" O CYS S 94 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE S 93 " --> pdb=" O THR S 76 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N THR S 76 " --> pdb=" O ILE S 93 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 51 through 53 Processing sheet with id=AE5, first strand: chain 'S' and resid 126 through 140 removed outlier: 5.421A pdb=" N GLU S 149 " --> pdb=" O LYS S 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 146 through 150 current: chain 'S' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 194 through 199 current: chain 'S' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 255 through 256 current: chain 'S' and resid 320 through 321 Processing sheet with id=AE6, first strand: chain 'T' and resid 32 through 38 removed outlier: 5.514A pdb=" N LYS T 88 " --> pdb=" O VAL T 18 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N THR T 26 " --> pdb=" O CYS T 94 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE T 93 " --> pdb=" O THR T 76 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR T 76 " --> pdb=" O ILE T 93 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 51 through 53 Processing sheet with id=AE8, first strand: chain 'T' and resid 126 through 140 removed outlier: 5.407A pdb=" N GLU T 149 " --> pdb=" O LYS T 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 146 through 150 current: chain 'T' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 194 through 199 current: chain 'T' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 255 through 256 current: chain 'T' and resid 320 through 321 1909 hydrogen bonds defined for protein. 5367 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: 18.24 Time building geometry restraints manager: 20.79 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: 8680 1.31 - 1.48: 20394 1.48 - 1.65: 21998 1.65 - 1.82: 378 Bond restraints: 51590 Sorted by residual: bond pdb=" NE2 GLN N 503 " pdb="HE21 GLN N 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 O 503 " pdb="HE21 GLN O 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 T 503 " pdb="HE22 GLN T 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 I 503 " pdb="HE22 GLN I 503 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.12e+01 bond pdb=" NE2 GLN F 503 " pdb="HE22 GLN F 503 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.12e+01 ... (remaining 51585 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.30: 1501 106.30 - 113.22: 27156 113.22 - 120.15: 18514 120.15 - 127.07: 22201 127.07 - 133.99: 586 Bond angle restraints: 69958 Sorted by residual: angle pdb=" CA ARG T 370 " pdb=" CB ARG T 370 " pdb=" CG ARG T 370 " ideal model delta sigma weight residual 114.10 121.46 -7.36 2.00e+00 2.50e-01 1.36e+01 angle pdb=" CA ARG P 370 " pdb=" CB ARG P 370 " pdb=" CG ARG P 370 " ideal model delta sigma weight residual 114.10 121.41 -7.31 2.00e+00 2.50e-01 1.34e+01 angle pdb=" N GLU O 15 " pdb=" CA GLU O 15 " pdb=" CB GLU O 15 " ideal model delta sigma weight residual 110.20 115.60 -5.40 1.49e+00 4.50e-01 1.31e+01 angle pdb=" CA ARG H 370 " pdb=" CB ARG H 370 " pdb=" CG ARG H 370 " ideal model delta sigma weight residual 114.10 121.16 -7.06 2.00e+00 2.50e-01 1.24e+01 angle pdb=" CA ARG B 370 " pdb=" CB ARG B 370 " pdb=" CG ARG B 370 " ideal model delta sigma weight residual 114.10 121.11 -7.01 2.00e+00 2.50e-01 1.23e+01 ... (remaining 69953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 26758 17.98 - 35.95: 2965 35.95 - 53.93: 935 53.93 - 71.90: 173 71.90 - 89.88: 95 Dihedral angle restraints: 30926 sinusoidal: 12516 harmonic: 18410 Sorted by residual: dihedral pdb=" CA ASN C 34 " pdb=" C ASN C 34 " pdb=" N VAL C 35 " pdb=" CA VAL C 35 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASN F 34 " pdb=" C ASN F 34 " pdb=" N VAL F 35 " pdb=" CA VAL F 35 " ideal model delta harmonic sigma weight residual 180.00 162.16 17.84 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASN T 34 " pdb=" C ASN T 34 " pdb=" N VAL T 35 " pdb=" CA VAL T 35 " ideal model delta harmonic sigma weight residual 180.00 162.37 17.63 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 30923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 5070 0.035 - 0.070: 1790 0.070 - 0.105: 498 0.105 - 0.140: 181 0.140 - 0.176: 7 Chirality restraints: 7546 Sorted by residual: chirality pdb=" CA GLU H 15 " pdb=" N GLU H 15 " pdb=" C GLU H 15 " pdb=" CB GLU H 15 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA GLU B 15 " pdb=" N GLU B 15 " pdb=" C GLU B 15 " pdb=" CB GLU B 15 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA GLU I 15 " pdb=" N GLU I 15 " pdb=" C GLU I 15 " pdb=" CB GLU I 15 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.19e-01 ... (remaining 7543 not shown) Planarity restraints: 9184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN R 503 " -0.319 2.00e-02 2.50e+03 3.39e-01 1.73e+03 pdb=" CD GLN R 503 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLN R 503 " 0.305 2.00e-02 2.50e+03 pdb=" NE2 GLN R 503 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN R 503 " 0.491 2.00e-02 2.50e+03 pdb="HE22 GLN R 503 " -0.504 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 503 " -0.307 2.00e-02 2.50e+03 3.21e-01 1.54e+03 pdb=" CD GLN A 503 " 0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN A 503 " 0.293 2.00e-02 2.50e+03 pdb=" NE2 GLN A 503 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 503 " 0.461 2.00e-02 2.50e+03 pdb="HE22 GLN A 503 " -0.473 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN T 503 " -0.305 2.00e-02 2.50e+03 3.18e-01 1.52e+03 pdb=" CD GLN T 503 " 0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN T 503 " 0.292 2.00e-02 2.50e+03 pdb=" NE2 GLN T 503 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN T 503 " 0.457 2.00e-02 2.50e+03 pdb="HE22 GLN T 503 " -0.469 2.00e-02 2.50e+03 ... (remaining 9181 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 290 2.37 - 2.93: 22227 2.93 - 3.49: 59513 3.49 - 4.04: 100686 4.04 - 4.60: 149099 Nonbonded interactions: 331815 Sorted by model distance: nonbonded pdb=" O GLY I 241 " pdb=" H1 GLN I 503 " model vdw 1.813 1.850 nonbonded pdb=" O GLY Q 241 " pdb=" H1 GLN Q 503 " model vdw 1.816 1.850 nonbonded pdb=" O GLY F 241 " pdb=" H1 GLN F 503 " model vdw 1.827 1.850 nonbonded pdb=" O GLY N 241 " pdb=" H1 GLN N 503 " model vdw 1.834 1.850 nonbonded pdb=" O GLY T 241 " pdb=" H1 GLN T 503 " model vdw 1.851 1.850 ... (remaining 331810 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: 2.900 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: 1.340 Extract box with map and model: 16.520 Check model and map are aligned: 0.700 Set scattering table: 0.490 Process input model: 117.420 Find NCS groups from input model: 3.440 Set up NCS constraints: 0.660 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 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 : 0.002 0.038 51450 Z= 0.163 Angle : 0.532 7.362 69650 Z= 0.288 Chirality : 0.041 0.176 7546 Planarity : 0.004 0.037 9184 Dihedral : 17.585 89.876 19012 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.74 % Allowed : 21.93 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.11), residues: 6286 helix: 1.64 (0.11), residues: 2338 sheet: -0.37 (0.17), residues: 980 loop : 0.09 (0.12), residues: 2968 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1194 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1101 time to evaluate : 5.636 Fit side-chains revert: symmetry clash outliers start: 93 outliers final: 25 residues processed: 1160 average time/residue: 1.8212 time to fit residues: 2582.0182 Evaluate side-chains 779 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 754 time to evaluate : 5.210 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 24 residues processed: 1 average time/residue: 0.4070 time to fit residues: 8.1189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 531 optimal weight: 7.9990 chunk 477 optimal weight: 0.0670 chunk 264 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 322 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 chunk 493 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 300 optimal weight: 8.9990 chunk 367 optimal weight: 10.0000 chunk 572 optimal weight: 9.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 41 GLN A 212 GLN A 443 GLN B 34 ASN B 41 GLN B 212 GLN B 443 GLN C 34 ASN C 75 ASN C 443 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN G 34 ASN G 75 ASN G 212 GLN G 314 GLN G 443 GLN H 17 ASN H 34 ASN H 212 GLN H 228 HIS ** H 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 443 GLN I 17 ASN I 34 ASN I 41 GLN I 75 ASN I 212 GLN N 34 ASN O 17 ASN O 34 ASN O 75 ASN O 212 GLN O 443 GLN P 17 ASN P 34 ASN P 212 GLN P 443 GLN Q 34 ASN Q 41 GLN Q 75 ASN Q 212 GLN Q 412 HIS R 34 ASN R 41 GLN R 212 GLN S 34 ASN S 41 GLN S 212 GLN S 443 GLN T 34 ASN T 75 ASN T 439 GLN T 443 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 51450 Z= 0.352 Angle : 0.725 10.099 69650 Z= 0.393 Chirality : 0.049 0.190 7546 Planarity : 0.007 0.099 9184 Dihedral : 5.668 56.076 6846 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.17 % Allowed : 17.87 % Favored : 78.97 % 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: 0.58 (0.10), residues: 6286 helix: 1.52 (0.10), residues: 2296 sheet: -0.29 (0.17), residues: 840 loop : -0.20 (0.11), residues: 3150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 868 time to evaluate : 6.141 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 169 outliers final: 56 residues processed: 977 average time/residue: 1.8450 time to fit residues: 2205.5097 Evaluate side-chains 820 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 764 time to evaluate : 5.333 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 43 residues processed: 13 average time/residue: 0.8442 time to fit residues: 23.5168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 317 optimal weight: 8.9990 chunk 177 optimal weight: 0.0010 chunk 476 optimal weight: 0.2980 chunk 389 optimal weight: 6.9990 chunk 157 optimal weight: 0.6980 chunk 573 optimal weight: 4.9990 chunk 619 optimal weight: 7.9990 chunk 510 optimal weight: 4.9990 chunk 568 optimal weight: 0.9990 chunk 195 optimal weight: 7.9990 chunk 459 optimal weight: 1.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN A 314 GLN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN C 34 ASN C 75 ASN C 315 ASN C 443 GLN F 24 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 167 ASN F 443 GLN G 24 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN G 167 ASN G 314 GLN G 443 GLN H 34 ASN H 315 ASN H 443 GLN I 34 ASN I 75 ASN I 167 ASN I 266 GLN N 24 GLN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 ASN N 167 ASN O 24 GLN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 ASN O 443 GLN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 443 GLN Q 34 ASN Q 75 ASN Q 266 GLN R 24 GLN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN R 314 GLN R 315 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 ASN S 266 GLN S 314 GLN S 443 GLN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 ASN T 443 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5936 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 51450 Z= 0.123 Angle : 0.440 4.344 69650 Z= 0.241 Chirality : 0.040 0.134 7546 Planarity : 0.003 0.031 9184 Dihedral : 4.881 50.531 6846 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.87 % Allowed : 18.07 % Favored : 80.05 % 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: 1.03 (0.11), residues: 6286 helix: 2.09 (0.10), residues: 2324 sheet: -0.39 (0.17), residues: 980 loop : 0.00 (0.12), residues: 2982 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 823 time to evaluate : 5.843 Fit side-chains outliers start: 100 outliers final: 41 residues processed: 885 average time/residue: 1.8630 time to fit residues: 2008.4575 Evaluate side-chains 815 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 774 time to evaluate : 5.537 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 28 residues processed: 13 average time/residue: 1.2422 time to fit residues: 28.9075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 566 optimal weight: 4.9990 chunk 430 optimal weight: 8.9990 chunk 297 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 273 optimal weight: 7.9990 chunk 384 optimal weight: 0.9980 chunk 575 optimal weight: 3.9990 chunk 608 optimal weight: 6.9990 chunk 300 optimal weight: 2.9990 chunk 545 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 24 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN A 315 ASN B 24 GLN B 34 ASN ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 34 ASN C 75 ASN C 167 ASN C 439 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 98 ASN F 443 GLN G 17 ASN G 34 ASN G 75 ASN H 34 ASN ** H 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 443 GLN I 24 GLN I 34 ASN I 266 GLN J 4 GLN N 24 GLN N 34 ASN N 75 ASN N 98 ASN O 34 ASN O 75 ASN P 34 ASN P 443 GLN Q 17 ASN Q 24 GLN Q 34 ASN Q 266 GLN R 17 ASN R 24 GLN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN S 24 GLN S 34 ASN T 24 GLN T 34 ASN T 75 ASN T 167 ASN X 4 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 51450 Z= 0.275 Angle : 0.623 6.967 69650 Z= 0.340 Chirality : 0.046 0.167 7546 Planarity : 0.005 0.088 9184 Dihedral : 5.562 55.899 6846 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.50 % Favored : 95.37 % Rotamer: Outliers : 2.17 % Allowed : 17.44 % Favored : 80.39 % 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: 0.65 (0.10), residues: 6286 helix: 1.75 (0.10), residues: 2310 sheet: -0.23 (0.17), residues: 812 loop : -0.34 (0.11), residues: 3164 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 797 time to evaluate : 5.621 Fit side-chains revert: symmetry clash outliers start: 116 outliers final: 53 residues processed: 871 average time/residue: 1.7538 time to fit residues: 1866.4459 Evaluate side-chains 839 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 786 time to evaluate : 5.229 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 32 residues processed: 21 average time/residue: 0.9366 time to fit residues: 35.2628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 507 optimal weight: 6.9990 chunk 345 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 453 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 519 optimal weight: 2.9990 chunk 420 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 310 optimal weight: 7.9990 chunk 546 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 A 315 ASN B 17 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN C 17 ASN C 34 ASN C 75 ASN C 167 ASN F 24 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN G 24 GLN G 34 ASN G 75 ASN H 34 ASN ** H 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 443 GLN I 34 ASN I 266 GLN N 24 GLN N 34 ASN N 75 ASN O 24 GLN O 34 ASN O 75 ASN P 34 ASN P 315 ASN P 443 GLN Q 34 ASN Q 266 GLN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 ASN T 17 ASN T 34 ASN T 75 ASN T 167 ASN V 4 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 51450 Z= 0.314 Angle : 0.664 6.637 69650 Z= 0.364 Chirality : 0.048 0.160 7546 Planarity : 0.006 0.106 9184 Dihedral : 5.873 56.928 6846 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.61 % Favored : 95.23 % Rotamer: Outliers : 2.16 % Allowed : 17.17 % Favored : 80.67 % 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: 0.25 (0.10), residues: 6286 helix: 1.40 (0.10), residues: 2310 sheet: -0.39 (0.17), residues: 812 loop : -0.57 (0.11), residues: 3164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 805 time to evaluate : 4.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 56 residues processed: 874 average time/residue: 1.7650 time to fit residues: 1874.5641 Evaluate side-chains 851 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 795 time to evaluate : 5.371 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 35 residues processed: 21 average time/residue: 1.0138 time to fit residues: 37.3388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 204 optimal weight: 9.9990 chunk 548 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 357 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 609 optimal weight: 4.9990 chunk 506 optimal weight: 6.9990 chunk 282 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 320 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 A 315 ASN B 34 ASN ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN C 75 ASN C 167 ASN F 17 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 167 ASN F 443 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN G 439 GLN H 34 ASN ** H 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 443 GLN I 34 ASN I 266 GLN N 24 GLN N 34 ASN N 75 ASN N 167 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 ASN O 167 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 167 ASN P 315 ASN P 443 GLN Q 34 ASN Q 266 GLN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN S 34 ASN ** S 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 ASN T 75 ASN T 167 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5964 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 51450 Z= 0.242 Angle : 0.579 6.186 69650 Z= 0.318 Chirality : 0.044 0.155 7546 Planarity : 0.005 0.085 9184 Dihedral : 5.650 55.332 6846 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.33 % Favored : 95.50 % Rotamer: Outliers : 2.02 % Allowed : 17.02 % Favored : 80.95 % 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: 0.42 (0.10), residues: 6286 helix: 1.61 (0.10), residues: 2324 sheet: -0.30 (0.17), residues: 812 loop : -0.55 (0.11), residues: 3150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 814 time to evaluate : 4.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 52 residues processed: 881 average time/residue: 1.7419 time to fit residues: 1864.1762 Evaluate side-chains 850 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 798 time to evaluate : 4.941 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 41 residues processed: 11 average time/residue: 0.9761 time to fit residues: 21.5008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 587 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 347 optimal weight: 6.9990 chunk 445 optimal weight: 3.9990 chunk 344 optimal weight: 2.9990 chunk 513 optimal weight: 5.9990 chunk 340 optimal weight: 2.9990 chunk 607 optimal weight: 2.9990 chunk 380 optimal weight: 10.0000 chunk 370 optimal weight: 7.9990 chunk 280 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 A 315 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN C 75 ASN C 167 ASN F 24 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 167 ASN F 443 GLN G 34 ASN G 75 ASN H 34 ASN ** H 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 443 GLN I 34 ASN I 266 GLN N 17 ASN N 24 GLN N 34 ASN N 75 ASN N 167 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 ASN P 34 ASN P 167 ASN P 315 ASN P 443 GLN Q 34 ASN Q 167 ASN Q 266 GLN R 34 ASN R 167 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 ASN T 75 ASN T 167 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5966 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 51450 Z= 0.245 Angle : 0.596 6.380 69650 Z= 0.326 Chirality : 0.045 0.158 7546 Planarity : 0.005 0.088 9184 Dihedral : 5.689 55.928 6846 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.79 % Favored : 95.02 % Rotamer: Outliers : 1.69 % Allowed : 17.17 % Favored : 81.14 % 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: 0.39 (0.10), residues: 6286 helix: 1.59 (0.10), residues: 2324 sheet: -0.23 (0.17), residues: 784 loop : -0.60 (0.11), residues: 3178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 812 time to evaluate : 4.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 50 residues processed: 868 average time/residue: 1.7016 time to fit residues: 1797.3031 Evaluate side-chains 851 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 801 time to evaluate : 4.371 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 34 residues processed: 16 average time/residue: 1.0054 time to fit residues: 27.5426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 375 optimal weight: 9.9990 chunk 242 optimal weight: 0.7980 chunk 362 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 119 optimal weight: 0.0000 chunk 117 optimal weight: 0.3980 chunk 386 optimal weight: 7.9990 chunk 413 optimal weight: 10.0000 chunk 300 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 477 optimal weight: 0.8980 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 A 315 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN C 75 ASN C 167 ASN F 24 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 167 ASN F 443 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 315 ASN H 443 GLN I 34 ASN I 266 GLN N 24 GLN N 34 ASN N 75 ASN N 167 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 ASN O 315 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 167 ASN P 315 ASN P 443 GLN Q 34 ASN Q 167 ASN Q 266 GLN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN R 315 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 ASN S 266 GLN T 34 ASN T 75 ASN T 167 ASN T 315 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 51450 Z= 0.114 Angle : 0.431 4.292 69650 Z= 0.235 Chirality : 0.039 0.127 7546 Planarity : 0.003 0.047 9184 Dihedral : 4.915 50.135 6846 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.04 % Favored : 95.83 % Rotamer: Outliers : 1.27 % Allowed : 17.29 % Favored : 81.44 % 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: 0.97 (0.11), residues: 6286 helix: 2.19 (0.10), residues: 2338 sheet: -0.29 (0.15), residues: 1092 loop : -0.22 (0.12), residues: 2856 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 827 time to evaluate : 4.571 Fit side-chains outliers start: 68 outliers final: 33 residues processed: 870 average time/residue: 1.6508 time to fit residues: 1755.5217 Evaluate side-chains 841 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 808 time to evaluate : 4.382 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 25 residues processed: 8 average time/residue: 1.2210 time to fit residues: 18.8138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 552 optimal weight: 0.4980 chunk 581 optimal weight: 8.9990 chunk 530 optimal weight: 8.9990 chunk 565 optimal weight: 0.0050 chunk 340 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 444 optimal weight: 5.9990 chunk 173 optimal weight: 0.9990 chunk 511 optimal weight: 2.9990 chunk 535 optimal weight: 0.0980 chunk 563 optimal weight: 5.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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 A 315 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN C 75 ASN C 167 ASN F 24 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 443 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN G 167 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 315 ASN H 443 GLN I 34 ASN I 167 ASN I 266 GLN N 24 GLN N 34 ASN N 75 ASN O 24 GLN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 ASN O 167 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 167 ASN P 315 ASN P 443 GLN Q 34 ASN Q 266 GLN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN R 315 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 266 GLN T 34 ASN T 75 ASN T 167 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 51450 Z= 0.129 Angle : 0.452 4.639 69650 Z= 0.245 Chirality : 0.040 0.139 7546 Planarity : 0.003 0.058 9184 Dihedral : 4.917 49.558 6846 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.20 % Favored : 95.67 % Rotamer: Outliers : 1.07 % Allowed : 17.59 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.10), residues: 6286 helix: 2.29 (0.10), residues: 2324 sheet: -0.45 (0.16), residues: 952 loop : -0.25 (0.11), residues: 3010 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 808 time to evaluate : 4.551 Fit side-chains outliers start: 57 outliers final: 30 residues processed: 849 average time/residue: 1.6266 time to fit residues: 1696.3098 Evaluate side-chains 832 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 802 time to evaluate : 4.309 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 26 residues processed: 4 average time/residue: 0.8623 time to fit residues: 10.7241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 371 optimal weight: 2.9990 chunk 598 optimal weight: 0.7980 chunk 365 optimal weight: 6.9990 chunk 283 optimal weight: 5.9990 chunk 415 optimal weight: 5.9990 chunk 627 optimal weight: 10.0000 chunk 577 optimal weight: 0.9980 chunk 499 optimal weight: 0.0970 chunk 51 optimal weight: 0.0370 chunk 386 optimal weight: 8.9990 chunk 306 optimal weight: 6.9990 overall best weight: 0.9858 ------------------------------------------------------------------------------- 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 A 315 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN C 75 ASN C 167 ASN F 24 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 167 ASN F 443 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN G 167 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 315 ASN H 443 GLN I 34 ASN I 266 GLN N 24 GLN N 34 ASN N 75 ASN N 167 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 ASN O 315 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 167 ASN P 315 ASN P 443 GLN Q 34 ASN Q 167 ASN Q 266 GLN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN R 315 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 266 GLN T 34 ASN T 75 ASN T 167 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 51450 Z= 0.131 Angle : 0.453 5.014 69650 Z= 0.246 Chirality : 0.040 0.137 7546 Planarity : 0.003 0.055 9184 Dihedral : 4.893 49.302 6846 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.98 % Favored : 95.90 % Rotamer: Outliers : 0.97 % Allowed : 17.75 % Favored : 81.27 % 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: 1.02 (0.11), residues: 6286 helix: 2.32 (0.10), residues: 2324 sheet: -0.44 (0.17), residues: 952 loop : -0.21 (0.11), residues: 3010 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 805 time to evaluate : 5.825 Fit side-chains outliers start: 52 outliers final: 29 residues processed: 839 average time/residue: 1.5480 time to fit residues: 1577.6850 Evaluate side-chains 831 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 802 time to evaluate : 4.225 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 23 residues processed: 6 average time/residue: 0.7539 time to fit residues: 12.2372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 396 optimal weight: 0.0980 chunk 532 optimal weight: 9.9990 chunk 153 optimal weight: 0.3980 chunk 460 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 500 optimal weight: 0.8980 chunk 209 optimal weight: 4.9990 chunk 514 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 92 optimal weight: 0.0470 overall best weight: 1.2880 ------------------------------------------------------------------------------- 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 315 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN C 75 ASN C 167 ASN F 24 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 443 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** G 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 315 ASN H 443 GLN I 34 ASN I 167 ASN I 266 GLN N 24 GLN N 34 ASN N 75 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 ASN O 167 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 167 ASN P 315 ASN P 443 GLN Q 34 ASN Q 266 GLN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN R 315 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 266 GLN T 34 ASN T 75 ASN T 167 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.192528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.170995 restraints weight = 30600.025| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 0.50 r_work: 0.3642 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work: 0.3462 rms_B_bonded: 4.09 restraints_weight: 0.1250 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 51450 Z= 0.149 Angle : 0.480 5.318 69650 Z= 0.260 Chirality : 0.041 0.144 7546 Planarity : 0.004 0.059 9184 Dihedral : 5.021 50.566 6846 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.34 % Favored : 95.53 % Rotamer: Outliers : 0.75 % Allowed : 18.17 % Favored : 81.08 % 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 (0.10), residues: 6286 helix: 2.21 (0.10), residues: 2338 sheet: -0.28 (0.17), residues: 854 loop : -0.38 (0.11), residues: 3094 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25586.52 seconds wall clock time: 445 minutes 23.10 seconds (26723.10 seconds total)