Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 20 06:24:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfa_25867/10_2023/7tfa_25867.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfa_25867/10_2023/7tfa_25867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfa_25867/10_2023/7tfa_25867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfa_25867/10_2023/7tfa_25867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfa_25867/10_2023/7tfa_25867.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfa_25867/10_2023/7tfa_25867.pdb" } resolution = 2.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.082 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 24 5.21 5 S 228 5.16 5 C 27096 2.51 5 N 7296 2.21 5 O 7872 1.98 5 H 120 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 42636 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "F" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "G" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "K" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "L" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "M" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "R" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "S" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "T" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "U" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "X" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 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: "E" 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: "J" 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: "K" 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: "L" 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} Chain: "W" 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: "X" 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: 12 residue: pdb=" N LEU B 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU B 248 " occ=0.97 residue: pdb=" N LEU E 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU E 248 " occ=0.97 residue: pdb=" N LEU F 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU F 248 " occ=0.97 residue: pdb=" N LEU J 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU J 248 " occ=0.97 residue: pdb=" N LEU K 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU K 248 " occ=0.97 residue: pdb=" N LEU L 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU L 248 " occ=0.97 residue: pdb=" N LEU Q 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU Q 248 " occ=0.97 residue: pdb=" N LEU R 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU R 248 " occ=0.97 residue: pdb=" N LEU S 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU S 248 " occ=0.97 residue: pdb=" N LEU T 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU T 248 " occ=0.97 residue: pdb=" N LEU W 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU W 248 " occ=0.97 residue: pdb=" N LEU X 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU X 248 " occ=0.97 Time building chain proxies: 23.96, per 1000 atoms: 0.56 Number of scatterers: 42636 At special positions: 0 Unit cell: (157.52, 148.72, 122.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 228 16.00 Mg 24 11.99 O 7872 8.00 N 7296 7.00 C 27096 6.00 H 120 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: 17.48 Conformation dependent library (CDL) restraints added in 6.4 seconds 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10200 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 24 sheets defined 43.8% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 removed outlier: 4.202A pdb=" N ARG A 9 " --> pdb=" O GLU A 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 40 through 46 Processing helix chain 'B' and resid 53 through 61 removed outlier: 6.591A pdb=" N TYR B 59 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 119 Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 202 through 223 Processing helix chain 'B' and resid 266 through 279 Processing helix chain 'B' and resid 279 through 288 removed outlier: 4.506A pdb=" N ALA B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 removed outlier: 3.607A pdb=" N ARG B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 292 through 297' Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.808A pdb=" N THR B 328 " --> pdb=" O GLY B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 359 Processing helix chain 'B' and resid 374 through 381 Processing helix chain 'B' and resid 389 through 400 Processing helix chain 'B' and resid 401 through 408 removed outlier: 3.553A pdb=" N ASP B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 428 removed outlier: 3.577A pdb=" N ALA B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 414 " --> pdb=" O HIS B 410 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 438 Processing helix chain 'C' and resid 6 through 11 removed outlier: 4.234A pdb=" N ARG C 9 " --> pdb=" O GLU C 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 11 removed outlier: 4.077A pdb=" N ARG D 9 " --> pdb=" O GLU D 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 16 Processing helix chain 'E' and resid 40 through 46 Processing helix chain 'E' and resid 53 through 61 removed outlier: 6.739A pdb=" N TYR E 59 " --> pdb=" O ILE E 56 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL E 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG E 61 " --> pdb=" O GLY E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 119 Processing helix chain 'E' and resid 165 through 178 Processing helix chain 'E' and resid 202 through 223 Processing helix chain 'E' and resid 266 through 279 Processing helix chain 'E' and resid 279 through 288 removed outlier: 4.521A pdb=" N ALA E 285 " --> pdb=" O ARG E 281 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 297 removed outlier: 3.581A pdb=" N ARG E 296 " --> pdb=" O ASN E 292 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU E 297 " --> pdb=" O SER E 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 292 through 297' Processing helix chain 'E' and resid 324 through 328 removed outlier: 3.838A pdb=" N THR E 328 " --> pdb=" O GLY E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 359 Processing helix chain 'E' and resid 374 through 381 Processing helix chain 'E' and resid 389 through 400 Processing helix chain 'E' and resid 401 through 408 removed outlier: 3.580A pdb=" N ASP E 405 " --> pdb=" O GLU E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 428 removed outlier: 3.568A pdb=" N ALA E 413 " --> pdb=" O ASP E 409 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR E 414 " --> pdb=" O HIS E 410 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR E 428 " --> pdb=" O ASP E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 438 Processing helix chain 'F' and resid 4 through 16 Processing helix chain 'F' and resid 40 through 46 Processing helix chain 'F' and resid 53 through 61 removed outlier: 6.662A pdb=" N TYR F 59 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL F 60 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG F 61 " --> pdb=" O GLY F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 119 Processing helix chain 'F' and resid 165 through 178 Processing helix chain 'F' and resid 202 through 223 Processing helix chain 'F' and resid 266 through 279 Processing helix chain 'F' and resid 279 through 288 removed outlier: 4.522A pdb=" N ALA F 285 " --> pdb=" O ARG F 281 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 297 removed outlier: 3.602A pdb=" N ARG F 296 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU F 297 " --> pdb=" O SER F 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 292 through 297' Processing helix chain 'F' and resid 324 through 328 removed outlier: 3.796A pdb=" N THR F 328 " --> pdb=" O GLY F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 359 Processing helix chain 'F' and resid 374 through 381 Processing helix chain 'F' and resid 389 through 400 Processing helix chain 'F' and resid 401 through 408 removed outlier: 3.691A pdb=" N ASP F 405 " --> pdb=" O GLU F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 428 removed outlier: 3.554A pdb=" N ALA F 413 " --> pdb=" O ASP F 409 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR F 414 " --> pdb=" O HIS F 410 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR F 428 " --> pdb=" O ASP F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 438 Processing helix chain 'G' and resid 6 through 11 removed outlier: 4.263A pdb=" N ARG G 9 " --> pdb=" O GLU G 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 11 removed outlier: 4.274A pdb=" N ARG H 9 " --> pdb=" O GLU H 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 11 removed outlier: 4.099A pdb=" N ARG I 9 " --> pdb=" O GLU I 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 16 Processing helix chain 'J' and resid 40 through 46 Processing helix chain 'J' and resid 53 through 61 removed outlier: 6.590A pdb=" N TYR J 59 " --> pdb=" O ILE J 56 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL J 60 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG J 61 " --> pdb=" O GLY J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 119 Processing helix chain 'J' and resid 165 through 178 Processing helix chain 'J' and resid 202 through 223 Processing helix chain 'J' and resid 266 through 279 Processing helix chain 'J' and resid 279 through 288 removed outlier: 4.509A pdb=" N ALA J 285 " --> pdb=" O ARG J 281 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE J 286 " --> pdb=" O ALA J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.609A pdb=" N ARG J 296 " --> pdb=" O ASN J 292 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU J 297 " --> pdb=" O SER J 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 292 through 297' Processing helix chain 'J' and resid 324 through 328 removed outlier: 3.808A pdb=" N THR J 328 " --> pdb=" O GLY J 325 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 359 Processing helix chain 'J' and resid 374 through 381 Processing helix chain 'J' and resid 389 through 400 Processing helix chain 'J' and resid 401 through 408 removed outlier: 3.554A pdb=" N ASP J 405 " --> pdb=" O GLU J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 408 through 428 removed outlier: 3.582A pdb=" N ALA J 413 " --> pdb=" O ASP J 409 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR J 414 " --> pdb=" O HIS J 410 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR J 428 " --> pdb=" O ASP J 424 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 438 Processing helix chain 'K' and resid 4 through 16 Processing helix chain 'K' and resid 40 through 46 Processing helix chain 'K' and resid 53 through 61 removed outlier: 6.728A pdb=" N TYR K 59 " --> pdb=" O ILE K 56 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL K 60 " --> pdb=" O GLU K 57 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG K 61 " --> pdb=" O GLY K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 119 Processing helix chain 'K' and resid 165 through 178 Processing helix chain 'K' and resid 202 through 223 Processing helix chain 'K' and resid 266 through 279 Processing helix chain 'K' and resid 279 through 288 removed outlier: 4.512A pdb=" N ALA K 285 " --> pdb=" O ARG K 281 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ILE K 286 " --> pdb=" O ALA K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 292 through 297 removed outlier: 3.582A pdb=" N ARG K 296 " --> pdb=" O ASN K 292 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU K 297 " --> pdb=" O SER K 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 292 through 297' Processing helix chain 'K' and resid 324 through 328 removed outlier: 3.839A pdb=" N THR K 328 " --> pdb=" O GLY K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 359 Processing helix chain 'K' and resid 374 through 381 Processing helix chain 'K' and resid 389 through 400 Processing helix chain 'K' and resid 401 through 408 removed outlier: 3.607A pdb=" N ASP K 405 " --> pdb=" O GLU K 401 " (cutoff:3.500A) Processing helix chain 'K' and resid 408 through 428 removed outlier: 3.568A pdb=" N ALA K 413 " --> pdb=" O ASP K 409 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR K 414 " --> pdb=" O HIS K 410 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR K 428 " --> pdb=" O ASP K 424 " (cutoff:3.500A) Processing helix chain 'K' and resid 431 through 438 Processing helix chain 'L' and resid 4 through 16 Processing helix chain 'L' and resid 40 through 46 Processing helix chain 'L' and resid 53 through 61 removed outlier: 6.589A pdb=" N TYR L 59 " --> pdb=" O ILE L 56 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL L 60 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 119 Processing helix chain 'L' and resid 165 through 178 removed outlier: 3.541A pdb=" N GLU L 169 " --> pdb=" O ASN L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 223 Processing helix chain 'L' and resid 266 through 279 Processing helix chain 'L' and resid 279 through 288 removed outlier: 4.523A pdb=" N ALA L 285 " --> pdb=" O ARG L 281 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE L 286 " --> pdb=" O ALA L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 297 removed outlier: 3.602A pdb=" N ARG L 296 " --> pdb=" O ASN L 292 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU L 297 " --> pdb=" O SER L 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 292 through 297' Processing helix chain 'L' and resid 324 through 328 removed outlier: 3.796A pdb=" N THR L 328 " --> pdb=" O GLY L 325 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 359 Processing helix chain 'L' and resid 374 through 381 Processing helix chain 'L' and resid 389 through 400 Processing helix chain 'L' and resid 402 through 408 Processing helix chain 'L' and resid 408 through 428 removed outlier: 3.566A pdb=" N ALA L 413 " --> pdb=" O ASP L 409 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR L 414 " --> pdb=" O HIS L 410 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR L 428 " --> pdb=" O ASP L 424 " (cutoff:3.500A) Processing helix chain 'L' and resid 431 through 438 Processing helix chain 'M' and resid 6 through 11 removed outlier: 4.273A pdb=" N ARG M 9 " --> pdb=" O GLU M 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 11 removed outlier: 4.126A pdb=" N ARG N 9 " --> pdb=" O GLU N 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 11 removed outlier: 4.152A pdb=" N ARG O 9 " --> pdb=" O GLU O 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 11 removed outlier: 4.173A pdb=" N ARG P 9 " --> pdb=" O GLU P 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 16 Processing helix chain 'Q' and resid 40 through 46 Processing helix chain 'Q' and resid 53 through 61 removed outlier: 6.728A pdb=" N TYR Q 59 " --> pdb=" O ILE Q 56 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL Q 60 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG Q 61 " --> pdb=" O GLY Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 119 Processing helix chain 'Q' and resid 165 through 178 Processing helix chain 'Q' and resid 202 through 223 Processing helix chain 'Q' and resid 266 through 279 Processing helix chain 'Q' and resid 279 through 288 removed outlier: 4.520A pdb=" N ALA Q 285 " --> pdb=" O ARG Q 281 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE Q 286 " --> pdb=" O ALA Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 292 through 297 removed outlier: 3.581A pdb=" N ARG Q 296 " --> pdb=" O ASN Q 292 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU Q 297 " --> pdb=" O SER Q 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 292 through 297' Processing helix chain 'Q' and resid 324 through 328 removed outlier: 3.838A pdb=" N THR Q 328 " --> pdb=" O GLY Q 325 " (cutoff:3.500A) Processing helix chain 'Q' and resid 340 through 358 Processing helix chain 'Q' and resid 374 through 381 Processing helix chain 'Q' and resid 389 through 400 Processing helix chain 'Q' and resid 401 through 408 removed outlier: 3.579A pdb=" N ASP Q 405 " --> pdb=" O GLU Q 401 " (cutoff:3.500A) Processing helix chain 'Q' and resid 408 through 428 removed outlier: 3.570A pdb=" N ALA Q 413 " --> pdb=" O ASP Q 409 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR Q 414 " --> pdb=" O HIS Q 410 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR Q 428 " --> pdb=" O ASP Q 424 " (cutoff:3.500A) Processing helix chain 'Q' and resid 431 through 438 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 40 through 46 Processing helix chain 'R' and resid 53 through 61 removed outlier: 6.667A pdb=" N TYR R 59 " --> pdb=" O ILE R 56 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL R 60 " --> pdb=" O GLU R 57 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG R 61 " --> pdb=" O GLY R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 119 Processing helix chain 'R' and resid 165 through 178 removed outlier: 3.549A pdb=" N GLU R 169 " --> pdb=" O ASN R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 223 Processing helix chain 'R' and resid 266 through 279 Processing helix chain 'R' and resid 279 through 288 removed outlier: 4.525A pdb=" N ALA R 285 " --> pdb=" O ARG R 281 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE R 286 " --> pdb=" O ALA R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 297 removed outlier: 3.602A pdb=" N ARG R 296 " --> pdb=" O ASN R 292 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU R 297 " --> pdb=" O SER R 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 292 through 297' Processing helix chain 'R' and resid 324 through 328 removed outlier: 3.795A pdb=" N THR R 328 " --> pdb=" O GLY R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 340 through 359 Processing helix chain 'R' and resid 374 through 381 Processing helix chain 'R' and resid 389 through 400 Processing helix chain 'R' and resid 401 through 408 removed outlier: 3.691A pdb=" N ASP R 405 " --> pdb=" O GLU R 401 " (cutoff:3.500A) Processing helix chain 'R' and resid 408 through 428 removed outlier: 3.554A pdb=" N ALA R 413 " --> pdb=" O ASP R 409 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR R 414 " --> pdb=" O HIS R 410 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR R 428 " --> pdb=" O ASP R 424 " (cutoff:3.500A) Processing helix chain 'R' and resid 431 through 438 Processing helix chain 'S' and resid 4 through 16 Processing helix chain 'S' and resid 40 through 46 Processing helix chain 'S' and resid 53 through 61 removed outlier: 6.596A pdb=" N TYR S 59 " --> pdb=" O ILE S 56 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL S 60 " --> pdb=" O GLU S 57 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG S 61 " --> pdb=" O GLY S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 119 Processing helix chain 'S' and resid 165 through 178 Processing helix chain 'S' and resid 202 through 223 Processing helix chain 'S' and resid 266 through 279 Processing helix chain 'S' and resid 279 through 288 removed outlier: 4.492A pdb=" N ALA S 285 " --> pdb=" O ARG S 281 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE S 286 " --> pdb=" O ALA S 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 292 through 297 removed outlier: 3.609A pdb=" N ARG S 296 " --> pdb=" O ASN S 292 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU S 297 " --> pdb=" O SER S 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 292 through 297' Processing helix chain 'S' and resid 324 through 328 removed outlier: 3.790A pdb=" N THR S 328 " --> pdb=" O GLY S 325 " (cutoff:3.500A) Processing helix chain 'S' and resid 340 through 359 Processing helix chain 'S' and resid 374 through 381 Processing helix chain 'S' and resid 389 through 400 Processing helix chain 'S' and resid 401 through 408 removed outlier: 3.555A pdb=" N ASP S 405 " --> pdb=" O GLU S 401 " (cutoff:3.500A) Processing helix chain 'S' and resid 408 through 428 removed outlier: 3.576A pdb=" N ALA S 413 " --> pdb=" O ASP S 409 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR S 414 " --> pdb=" O HIS S 410 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR S 428 " --> pdb=" O ASP S 424 " (cutoff:3.500A) Processing helix chain 'S' and resid 431 through 438 Processing helix chain 'T' and resid 4 through 16 Processing helix chain 'T' and resid 40 through 46 Processing helix chain 'T' and resid 53 through 61 removed outlier: 6.589A pdb=" N TYR T 59 " --> pdb=" O ILE T 56 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL T 60 " --> pdb=" O GLU T 57 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG T 61 " --> pdb=" O GLY T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 119 Processing helix chain 'T' and resid 165 through 178 removed outlier: 3.542A pdb=" N GLU T 169 " --> pdb=" O ASN T 165 " (cutoff:3.500A) Processing helix chain 'T' and resid 202 through 223 Processing helix chain 'T' and resid 266 through 279 Processing helix chain 'T' and resid 279 through 288 removed outlier: 4.509A pdb=" N ALA T 285 " --> pdb=" O ARG T 281 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE T 286 " --> pdb=" O ALA T 282 " (cutoff:3.500A) Processing helix chain 'T' and resid 292 through 297 removed outlier: 3.597A pdb=" N ARG T 296 " --> pdb=" O ASN T 292 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU T 297 " --> pdb=" O SER T 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 292 through 297' Processing helix chain 'T' and resid 324 through 328 removed outlier: 3.795A pdb=" N THR T 328 " --> pdb=" O GLY T 325 " (cutoff:3.500A) Processing helix chain 'T' and resid 340 through 359 Processing helix chain 'T' and resid 374 through 381 Processing helix chain 'T' and resid 389 through 400 Processing helix chain 'T' and resid 402 through 408 Processing helix chain 'T' and resid 408 through 428 removed outlier: 3.568A pdb=" N ALA T 413 " --> pdb=" O ASP T 409 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR T 414 " --> pdb=" O HIS T 410 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR T 428 " --> pdb=" O ASP T 424 " (cutoff:3.500A) Processing helix chain 'T' and resid 431 through 438 Processing helix chain 'U' and resid 6 through 11 removed outlier: 4.293A pdb=" N ARG U 9 " --> pdb=" O GLU U 6 " (cutoff:3.500A) Processing helix chain 'V' and resid 6 through 11 removed outlier: 4.281A pdb=" N ARG V 9 " --> pdb=" O GLU V 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 16 Processing helix chain 'W' and resid 40 through 46 Processing helix chain 'W' and resid 53 through 61 removed outlier: 6.587A pdb=" N TYR W 59 " --> pdb=" O ILE W 56 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL W 60 " --> pdb=" O GLU W 57 " (cutoff:3.500A) Processing helix chain 'W' and resid 105 through 119 Processing helix chain 'W' and resid 165 through 178 Processing helix chain 'W' and resid 202 through 223 Processing helix chain 'W' and resid 266 through 279 Processing helix chain 'W' and resid 279 through 288 removed outlier: 4.496A pdb=" N ALA W 285 " --> pdb=" O ARG W 281 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ILE W 286 " --> pdb=" O ALA W 282 " (cutoff:3.500A) Processing helix chain 'W' and resid 292 through 297 removed outlier: 3.607A pdb=" N ARG W 296 " --> pdb=" O ASN W 292 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU W 297 " --> pdb=" O SER W 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 292 through 297' Processing helix chain 'W' and resid 324 through 328 removed outlier: 3.809A pdb=" N THR W 328 " --> pdb=" O GLY W 325 " (cutoff:3.500A) Processing helix chain 'W' and resid 340 through 359 Processing helix chain 'W' and resid 374 through 381 Processing helix chain 'W' and resid 389 through 400 Processing helix chain 'W' and resid 401 through 408 removed outlier: 3.555A pdb=" N ASP W 405 " --> pdb=" O GLU W 401 " (cutoff:3.500A) Processing helix chain 'W' and resid 408 through 428 removed outlier: 3.589A pdb=" N ALA W 413 " --> pdb=" O ASP W 409 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR W 414 " --> pdb=" O HIS W 410 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR W 428 " --> pdb=" O ASP W 424 " (cutoff:3.500A) Processing helix chain 'W' and resid 431 through 438 Processing helix chain 'X' and resid 4 through 16 Processing helix chain 'X' and resid 40 through 46 Processing helix chain 'X' and resid 53 through 61 removed outlier: 6.751A pdb=" N TYR X 59 " --> pdb=" O ILE X 56 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL X 60 " --> pdb=" O GLU X 57 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG X 61 " --> pdb=" O GLY X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 119 Processing helix chain 'X' and resid 165 through 178 Processing helix chain 'X' and resid 202 through 223 Processing helix chain 'X' and resid 266 through 279 Processing helix chain 'X' and resid 279 through 288 removed outlier: 4.478A pdb=" N ALA X 285 " --> pdb=" O ARG X 281 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ILE X 286 " --> pdb=" O ALA X 282 " (cutoff:3.500A) Processing helix chain 'X' and resid 292 through 297 removed outlier: 3.589A pdb=" N ARG X 296 " --> pdb=" O ASN X 292 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU X 297 " --> pdb=" O SER X 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 292 through 297' Processing helix chain 'X' and resid 324 through 328 removed outlier: 3.701A pdb=" N THR X 328 " --> pdb=" O GLY X 325 " (cutoff:3.500A) Processing helix chain 'X' and resid 340 through 359 Processing helix chain 'X' and resid 374 through 381 Processing helix chain 'X' and resid 389 through 400 Processing helix chain 'X' and resid 401 through 408 removed outlier: 3.595A pdb=" N ASP X 405 " --> pdb=" O GLU X 401 " (cutoff:3.500A) Processing helix chain 'X' and resid 408 through 428 removed outlier: 3.546A pdb=" N ALA X 413 " --> pdb=" O ASP X 409 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR X 414 " --> pdb=" O HIS X 410 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR X 428 " --> pdb=" O ASP X 424 " (cutoff:3.500A) Processing helix chain 'X' and resid 431 through 438 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 37 removed outlier: 4.829A pdb=" N VAL B 17 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ALA B 88 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE B 19 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU B 90 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ARG B 21 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N CYS B 92 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN B 23 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ILE B 94 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N THR B 25 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 11.856A pdb=" N VAL B 87 " --> pdb=" O TRP B 76 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N TRP B 76 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 10.234A pdb=" N ARG B 89 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ASP B 74 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE B 91 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N MET B 49 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 124 through 138 removed outlier: 7.190A pdb=" N LEU B 135 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLU B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LYS B 137 " --> pdb=" O THR B 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 144 through 148 current: chain 'B' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 192 through 197 current: chain 'B' and resid 318 through 319 Processing sheet with id=AA3, first strand: chain 'E' and resid 31 through 37 removed outlier: 4.793A pdb=" N VAL E 17 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ALA E 88 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE E 19 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU E 90 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ARG E 21 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N CYS E 92 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLN E 23 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ILE E 94 " --> pdb=" O GLN E 23 " (cutoff:3.500A) removed outlier: 10.364A pdb=" N THR E 25 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 11.868A pdb=" N VAL E 87 " --> pdb=" O TRP E 76 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N TRP E 76 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 10.271A pdb=" N ARG E 89 " --> pdb=" O ASP E 74 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ASP E 74 " --> pdb=" O ARG E 89 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE E 91 " --> pdb=" O ASP E 72 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N MET E 49 " --> pdb=" O LEU E 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 124 through 138 removed outlier: 7.237A pdb=" N LEU E 135 " --> pdb=" O GLU E 147 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLU E 147 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LYS E 137 " --> pdb=" O THR E 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 144 through 148 current: chain 'E' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 192 through 197 current: chain 'E' and resid 318 through 319 Processing sheet with id=AA5, first strand: chain 'F' and resid 31 through 37 removed outlier: 4.814A pdb=" N VAL F 17 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA F 88 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE F 19 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU F 90 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ARG F 21 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N CYS F 92 " --> pdb=" O ARG F 21 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN F 23 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE F 94 " --> pdb=" O GLN F 23 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N THR F 25 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 11.848A pdb=" N VAL F 87 " --> pdb=" O TRP F 76 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N TRP F 76 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N ARG F 89 " --> pdb=" O ASP F 74 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ASP F 74 " --> pdb=" O ARG F 89 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE F 91 " --> pdb=" O ASP F 72 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N MET F 49 " --> pdb=" O LEU F 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 124 through 138 removed outlier: 7.246A pdb=" N LEU F 135 " --> pdb=" O GLU F 147 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU F 147 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYS F 137 " --> pdb=" O THR F 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 144 through 148 current: chain 'F' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 192 through 197 current: chain 'F' and resid 318 through 319 Processing sheet with id=AA7, first strand: chain 'J' and resid 31 through 37 removed outlier: 4.828A pdb=" N VAL J 17 " --> pdb=" O ARG J 86 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ALA J 88 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE J 19 " --> pdb=" O ALA J 88 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU J 90 " --> pdb=" O PHE J 19 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ARG J 21 " --> pdb=" O LEU J 90 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N CYS J 92 " --> pdb=" O ARG J 21 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLN J 23 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ILE J 94 " --> pdb=" O GLN J 23 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N THR J 25 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 11.858A pdb=" N VAL J 87 " --> pdb=" O TRP J 76 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N TRP J 76 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N ARG J 89 " --> pdb=" O ASP J 74 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ASP J 74 " --> pdb=" O ARG J 89 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE J 91 " --> pdb=" O ASP J 72 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N MET J 49 " --> pdb=" O LEU J 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 124 through 138 removed outlier: 7.191A pdb=" N LEU J 135 " --> pdb=" O GLU J 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLU J 147 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LYS J 137 " --> pdb=" O THR J 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 144 through 148 current: chain 'J' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 192 through 197 current: chain 'J' and resid 318 through 319 Processing sheet with id=AA9, first strand: chain 'K' and resid 31 through 37 removed outlier: 4.812A pdb=" N VAL K 17 " --> pdb=" O ARG K 86 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA K 88 " --> pdb=" O VAL K 17 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE K 19 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU K 90 " --> pdb=" O PHE K 19 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG K 21 " --> pdb=" O LEU K 90 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N CYS K 92 " --> pdb=" O ARG K 21 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN K 23 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE K 94 " --> pdb=" O GLN K 23 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N THR K 25 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 11.865A pdb=" N VAL K 87 " --> pdb=" O TRP K 76 " (cutoff:3.500A) removed outlier: 10.525A pdb=" N TRP K 76 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 10.273A pdb=" N ARG K 89 " --> pdb=" O ASP K 74 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ASP K 74 " --> pdb=" O ARG K 89 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE K 91 " --> pdb=" O ASP K 72 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N MET K 49 " --> pdb=" O LEU K 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 124 through 138 removed outlier: 7.221A pdb=" N LEU K 135 " --> pdb=" O GLU K 147 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU K 147 " --> pdb=" O LEU K 135 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LYS K 137 " --> pdb=" O THR K 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 144 through 148 current: chain 'K' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 192 through 197 current: chain 'K' and resid 318 through 319 Processing sheet with id=AB2, first strand: chain 'L' and resid 31 through 37 removed outlier: 4.818A pdb=" N VAL L 17 " --> pdb=" O ARG L 86 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA L 88 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE L 19 " --> pdb=" O ALA L 88 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU L 90 " --> pdb=" O PHE L 19 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ARG L 21 " --> pdb=" O LEU L 90 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N CYS L 92 " --> pdb=" O ARG L 21 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN L 23 " --> pdb=" O CYS L 92 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ILE L 94 " --> pdb=" O GLN L 23 " (cutoff:3.500A) removed outlier: 10.374A pdb=" N THR L 25 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 11.850A pdb=" N VAL L 87 " --> pdb=" O TRP L 76 " (cutoff:3.500A) removed outlier: 10.504A pdb=" N TRP L 76 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N ARG L 89 " --> pdb=" O ASP L 74 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ASP L 74 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE L 91 " --> pdb=" O ASP L 72 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N MET L 49 " --> pdb=" O LEU L 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 124 through 138 removed outlier: 7.245A pdb=" N LEU L 135 " --> pdb=" O GLU L 147 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU L 147 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYS L 137 " --> pdb=" O THR L 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 144 through 148 current: chain 'L' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 192 through 197 current: chain 'L' and resid 318 through 319 Processing sheet with id=AB4, first strand: chain 'Q' and resid 31 through 37 removed outlier: 4.809A pdb=" N VAL Q 17 " --> pdb=" O ARG Q 86 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA Q 88 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE Q 19 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU Q 90 " --> pdb=" O PHE Q 19 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG Q 21 " --> pdb=" O LEU Q 90 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N CYS Q 92 " --> pdb=" O ARG Q 21 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN Q 23 " --> pdb=" O CYS Q 92 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE Q 94 " --> pdb=" O GLN Q 23 " (cutoff:3.500A) removed outlier: 10.359A pdb=" N THR Q 25 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) removed outlier: 11.861A pdb=" N VAL Q 87 " --> pdb=" O TRP Q 76 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N TRP Q 76 " --> pdb=" O VAL Q 87 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N ARG Q 89 " --> pdb=" O ASP Q 74 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N ASP Q 74 " --> pdb=" O ARG Q 89 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE Q 91 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N MET Q 49 " --> pdb=" O LEU Q 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 124 through 138 removed outlier: 7.236A pdb=" N LEU Q 135 " --> pdb=" O GLU Q 147 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLU Q 147 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LYS Q 137 " --> pdb=" O THR Q 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 144 through 148 current: chain 'Q' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 192 through 197 current: chain 'Q' and resid 318 through 319 Processing sheet with id=AB6, first strand: chain 'R' and resid 31 through 37 removed outlier: 4.815A pdb=" N VAL R 17 " --> pdb=" O ARG R 86 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ALA R 88 " --> pdb=" O VAL R 17 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE R 19 " --> pdb=" O ALA R 88 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU R 90 " --> pdb=" O PHE R 19 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ARG R 21 " --> pdb=" O LEU R 90 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N CYS R 92 " --> pdb=" O ARG R 21 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN R 23 " --> pdb=" O CYS R 92 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE R 94 " --> pdb=" O GLN R 23 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N THR R 25 " --> pdb=" O ILE R 94 " (cutoff:3.500A) removed outlier: 11.848A pdb=" N VAL R 87 " --> pdb=" O TRP R 76 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N TRP R 76 " --> pdb=" O VAL R 87 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N ARG R 89 " --> pdb=" O ASP R 74 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ASP R 74 " --> pdb=" O ARG R 89 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE R 91 " --> pdb=" O ASP R 72 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N MET R 49 " --> pdb=" O LEU R 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 124 through 138 removed outlier: 7.243A pdb=" N LEU R 135 " --> pdb=" O GLU R 147 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLU R 147 " --> pdb=" O LEU R 135 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS R 137 " --> pdb=" O THR R 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 144 through 148 current: chain 'R' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 192 through 197 current: chain 'R' and resid 318 through 319 Processing sheet with id=AB8, first strand: chain 'S' and resid 31 through 37 removed outlier: 4.835A pdb=" N VAL S 17 " --> pdb=" O ARG S 86 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA S 88 " --> pdb=" O VAL S 17 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE S 19 " --> pdb=" O ALA S 88 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU S 90 " --> pdb=" O PHE S 19 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ARG S 21 " --> pdb=" O LEU S 90 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N CYS S 92 " --> pdb=" O ARG S 21 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN S 23 " --> pdb=" O CYS S 92 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ILE S 94 " --> pdb=" O GLN S 23 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N THR S 25 " --> pdb=" O ILE S 94 " (cutoff:3.500A) removed outlier: 11.870A pdb=" N VAL S 87 " --> pdb=" O TRP S 76 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N TRP S 76 " --> pdb=" O VAL S 87 " (cutoff:3.500A) removed outlier: 10.238A pdb=" N ARG S 89 " --> pdb=" O ASP S 74 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ASP S 74 " --> pdb=" O ARG S 89 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE S 91 " --> pdb=" O ASP S 72 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N MET S 49 " --> pdb=" O LEU S 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 124 through 138 removed outlier: 7.182A pdb=" N LEU S 135 " --> pdb=" O GLU S 147 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLU S 147 " --> pdb=" O LEU S 135 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS S 137 " --> pdb=" O THR S 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 144 through 148 current: chain 'S' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 192 through 197 current: chain 'S' and resid 318 through 319 Processing sheet with id=AC1, first strand: chain 'T' and resid 31 through 37 removed outlier: 4.819A pdb=" N VAL T 17 " --> pdb=" O ARG T 86 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ALA T 88 " --> pdb=" O VAL T 17 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE T 19 " --> pdb=" O ALA T 88 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU T 90 " --> pdb=" O PHE T 19 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ARG T 21 " --> pdb=" O LEU T 90 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N CYS T 92 " --> pdb=" O ARG T 21 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN T 23 " --> pdb=" O CYS T 92 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE T 94 " --> pdb=" O GLN T 23 " (cutoff:3.500A) removed outlier: 10.372A pdb=" N THR T 25 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 11.850A pdb=" N VAL T 87 " --> pdb=" O TRP T 76 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N TRP T 76 " --> pdb=" O VAL T 87 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N ARG T 89 " --> pdb=" O ASP T 74 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ASP T 74 " --> pdb=" O ARG T 89 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE T 91 " --> pdb=" O ASP T 72 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N MET T 49 " --> pdb=" O LEU T 69 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 124 through 138 removed outlier: 7.247A pdb=" N LEU T 135 " --> pdb=" O GLU T 147 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLU T 147 " --> pdb=" O LEU T 135 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYS T 137 " --> pdb=" O THR T 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 144 through 148 current: chain 'T' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 192 through 197 current: chain 'T' and resid 318 through 319 Processing sheet with id=AC3, first strand: chain 'W' and resid 31 through 37 removed outlier: 4.828A pdb=" N VAL W 17 " --> pdb=" O ARG W 86 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ALA W 88 " --> pdb=" O VAL W 17 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE W 19 " --> pdb=" O ALA W 88 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU W 90 " --> pdb=" O PHE W 19 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ARG W 21 " --> pdb=" O LEU W 90 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N CYS W 92 " --> pdb=" O ARG W 21 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLN W 23 " --> pdb=" O CYS W 92 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ILE W 94 " --> pdb=" O GLN W 23 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N THR W 25 " --> pdb=" O ILE W 94 " (cutoff:3.500A) removed outlier: 11.857A pdb=" N VAL W 87 " --> pdb=" O TRP W 76 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N TRP W 76 " --> pdb=" O VAL W 87 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N ARG W 89 " --> pdb=" O ASP W 74 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ASP W 74 " --> pdb=" O ARG W 89 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE W 91 " --> pdb=" O ASP W 72 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N MET W 49 " --> pdb=" O LEU W 69 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'W' and resid 124 through 138 removed outlier: 7.193A pdb=" N LEU W 135 " --> pdb=" O GLU W 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLU W 147 " --> pdb=" O LEU W 135 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYS W 137 " --> pdb=" O THR W 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 144 through 148 current: chain 'W' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 192 through 197 current: chain 'W' and resid 318 through 319 Processing sheet with id=AC5, first strand: chain 'X' and resid 31 through 37 removed outlier: 4.813A pdb=" N VAL X 17 " --> pdb=" O ARG X 86 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ALA X 88 " --> pdb=" O VAL X 17 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N PHE X 19 " --> pdb=" O ALA X 88 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU X 90 " --> pdb=" O PHE X 19 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ARG X 21 " --> pdb=" O LEU X 90 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N CYS X 92 " --> pdb=" O ARG X 21 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLN X 23 " --> pdb=" O CYS X 92 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE X 94 " --> pdb=" O GLN X 23 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N THR X 25 " --> pdb=" O ILE X 94 " (cutoff:3.500A) removed outlier: 11.855A pdb=" N VAL X 87 " --> pdb=" O TRP X 76 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N TRP X 76 " --> pdb=" O VAL X 87 " (cutoff:3.500A) removed outlier: 10.258A pdb=" N ARG X 89 " --> pdb=" O ASP X 74 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ASP X 74 " --> pdb=" O ARG X 89 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE X 91 " --> pdb=" O ASP X 72 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N MET X 49 " --> pdb=" O LEU X 69 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 124 through 138 removed outlier: 7.228A pdb=" N LEU X 135 " --> pdb=" O GLU X 147 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU X 147 " --> pdb=" O LEU X 135 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LYS X 137 " --> pdb=" O THR X 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 144 through 148 current: chain 'X' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 192 through 197 current: chain 'X' and resid 318 through 319 1642 hydrogen bonds defined for protein. 4668 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: 14.45 Time building geometry restraints manager: 18.45 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: 120 1.14 - 1.30: 7140 1.30 - 1.47: 17363 1.47 - 1.64: 18553 1.64 - 1.81: 408 Bond restraints: 43584 Sorted by residual: bond pdb=" NE2 GLN X 503 " pdb="HE21 GLN X 503 " ideal model delta sigma weight residual 0.860 1.017 -0.157 2.00e-02 2.50e+03 6.15e+01 bond pdb=" NE2 GLN S 503 " pdb="HE22 GLN S 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 K 503 " pdb="HE21 GLN K 503 " ideal model delta sigma weight residual 0.860 1.017 -0.157 2.00e-02 2.50e+03 6.12e+01 bond pdb=" NE2 GLN W 503 " pdb="HE22 GLN W 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 L 503 " pdb="HE22 GLN L 503 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.11e+01 ... (remaining 43579 not shown) Histogram of bond angle deviations from ideal: 99.08 - 106.10: 1240 106.10 - 113.12: 23195 113.12 - 120.14: 15539 120.14 - 127.16: 18745 127.16 - 134.19: 513 Bond angle restraints: 59232 Sorted by residual: angle pdb=" N LEU F 162 " pdb=" CA LEU F 162 " pdb=" C LEU F 162 " ideal model delta sigma weight residual 114.75 109.79 4.96 1.26e+00 6.30e-01 1.55e+01 angle pdb=" C ASP T 161 " pdb=" CA ASP T 161 " pdb=" CB ASP T 161 " ideal model delta sigma weight residual 116.34 110.92 5.42 1.40e+00 5.10e-01 1.50e+01 angle pdb=" C ASP L 161 " pdb=" CA ASP L 161 " pdb=" CB ASP L 161 " ideal model delta sigma weight residual 116.34 110.92 5.42 1.40e+00 5.10e-01 1.50e+01 angle pdb=" N LEU L 162 " pdb=" CA LEU L 162 " pdb=" C LEU L 162 " ideal model delta sigma weight residual 114.31 109.35 4.96 1.29e+00 6.01e-01 1.48e+01 angle pdb=" N LEU T 162 " pdb=" CA LEU T 162 " pdb=" C LEU T 162 " ideal model delta sigma weight residual 114.31 109.40 4.91 1.29e+00 6.01e-01 1.45e+01 ... (remaining 59227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 22553 16.95 - 33.90: 2470 33.90 - 50.85: 873 50.85 - 67.80: 249 67.80 - 84.75: 87 Dihedral angle restraints: 26232 sinusoidal: 10404 harmonic: 15828 Sorted by residual: dihedral pdb=" CA TYR S 371 " pdb=" C TYR S 371 " pdb=" N VAL S 372 " pdb=" CA VAL S 372 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA TYR J 371 " pdb=" C TYR J 371 " pdb=" N VAL J 372 " pdb=" CA VAL J 372 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA TYR W 371 " pdb=" C TYR W 371 " pdb=" N VAL W 372 " pdb=" CA VAL W 372 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 26229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 5517 0.055 - 0.109: 752 0.109 - 0.164: 182 0.164 - 0.219: 4 0.219 - 0.274: 1 Chirality restraints: 6456 Sorted by residual: chirality pdb=" CA LEU F 157 " pdb=" N LEU F 157 " pdb=" C LEU F 157 " pdb=" CB LEU F 157 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ARG L 168 " pdb=" N ARG L 168 " pdb=" C ARG L 168 " pdb=" CB ARG L 168 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA ARG T 168 " pdb=" N ARG T 168 " pdb=" C ARG T 168 " pdb=" CB ARG T 168 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 6453 not shown) Planarity restraints: 7716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN W 503 " -0.314 2.00e-02 2.50e+03 3.32e-01 1.66e+03 pdb=" CD GLN W 503 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLN W 503 " 0.301 2.00e-02 2.50e+03 pdb=" NE2 GLN W 503 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN W 503 " 0.479 2.00e-02 2.50e+03 pdb="HE22 GLN W 503 " -0.493 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN J 503 " 0.299 2.00e-02 2.50e+03 3.10e-01 1.44e+03 pdb=" CD GLN J 503 " -0.024 2.00e-02 2.50e+03 pdb=" OE1 GLN J 503 " -0.286 2.00e-02 2.50e+03 pdb=" NE2 GLN J 503 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN J 503 " -0.443 2.00e-02 2.50e+03 pdb="HE22 GLN J 503 " 0.456 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN S 503 " 0.293 2.00e-02 2.50e+03 3.01e-01 1.36e+03 pdb=" CD GLN S 503 " -0.024 2.00e-02 2.50e+03 pdb=" OE1 GLN S 503 " -0.279 2.00e-02 2.50e+03 pdb=" NE2 GLN S 503 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN S 503 " -0.429 2.00e-02 2.50e+03 pdb="HE22 GLN S 503 " 0.442 2.00e-02 2.50e+03 ... (remaining 7713 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.39: 185 2.39 - 2.94: 19108 2.94 - 3.49: 51487 3.49 - 4.05: 84184 4.05 - 4.60: 126311 Nonbonded interactions: 281275 Sorted by model distance: nonbonded pdb=" O GLY Q 239 " pdb=" H1 GLN Q 503 " model vdw 1.836 1.850 nonbonded pdb=" O GLY X 239 " pdb=" H1 GLN X 503 " model vdw 1.838 1.850 nonbonded pdb=" O GLY K 239 " pdb=" H1 GLN K 503 " model vdw 1.840 1.850 nonbonded pdb=" O GLY E 239 " pdb=" H1 GLN E 503 " model vdw 1.841 1.850 nonbonded pdb=" O GLY T 239 " pdb=" H1 GLN T 503 " model vdw 1.848 1.850 ... (remaining 281270 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 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' } 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=0.97 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.770 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: 1.040 Extract box with map and model: 20.280 Check model and map are aligned: 0.610 Set scattering table: 0.370 Process input model: 106.150 Find NCS groups from input model: 2.870 Set up NCS constraints: 0.420 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:13.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43464 Z= 0.187 Angle : 0.566 7.929 58968 Z= 0.314 Chirality : 0.041 0.274 6456 Planarity : 0.003 0.034 7716 Dihedral : 17.351 84.748 16020 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.62 % Favored : 96.36 % Rotamer: Outliers : 2.16 % Allowed : 18.78 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.12), residues: 5364 helix: 1.31 (0.11), residues: 2136 sheet: -0.78 (0.17), residues: 876 loop : -0.33 (0.13), residues: 2352 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1023 time to evaluate : 4.813 Fit side-chains outliers start: 95 outliers final: 20 residues processed: 1075 average time/residue: 2.0455 time to fit residues: 2576.0209 Evaluate side-chains 756 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 736 time to evaluate : 5.278 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 8 average time/residue: 0.4768 time to fit residues: 13.9893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 455 optimal weight: 3.9990 chunk 409 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 276 optimal weight: 9.9990 chunk 218 optimal weight: 8.9990 chunk 423 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 315 optimal weight: 4.9990 chunk 490 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN B 33 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN E 33 ASN E 410 HIS F 33 ASN ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 GLN F 288 ASN H 4 GLN J 23 GLN ** J 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 210 GLN J 313 ASN K 33 ASN L 33 ASN L 210 GLN L 288 ASN Q 33 ASN R 33 ASN R 210 GLN R 288 ASN S 23 GLN S 33 ASN S 313 ASN T 33 ASN T 210 GLN T 288 ASN U 4 GLN W 23 GLN ** W 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 210 GLN ** W 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 313 ASN X 33 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 43464 Z= 0.365 Angle : 0.721 6.433 58968 Z= 0.389 Chirality : 0.049 0.187 6456 Planarity : 0.007 0.075 7716 Dihedral : 5.522 48.223 5976 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.69 % Allowed : 14.57 % Favored : 80.74 % 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: -0.14 (0.11), residues: 5364 helix: 0.95 (0.11), residues: 2184 sheet: -1.58 (0.16), residues: 756 loop : -0.45 (0.12), residues: 2424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 978 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 772 time to evaluate : 5.132 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 206 outliers final: 86 residues processed: 885 average time/residue: 1.8608 time to fit residues: 1959.7099 Evaluate side-chains 825 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 739 time to evaluate : 4.786 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 60 residues processed: 26 average time/residue: 1.0963 time to fit residues: 43.9480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 272 optimal weight: 0.1980 chunk 152 optimal weight: 1.9990 chunk 408 optimal weight: 2.9990 chunk 333 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 491 optimal weight: 1.9990 chunk 530 optimal weight: 8.9990 chunk 437 optimal weight: 3.9990 chunk 487 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 394 optimal weight: 0.0870 overall best weight: 1.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN B 313 ASN E 33 ASN E 165 ASN F 33 ASN F 126 ASN ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 223 HIS ** J 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 165 ASN J 210 GLN J 313 ASN K 33 ASN K 165 ASN L 33 ASN L 126 ASN L 223 HIS L 313 ASN O 4 GLN Q 33 ASN Q 165 ASN R 33 ASN R 126 ASN R 223 HIS S 33 ASN S 313 ASN T 33 ASN T 126 ASN T 223 HIS V 4 GLN ** W 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 210 GLN W 313 ASN X 33 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43464 Z= 0.167 Angle : 0.496 4.796 58968 Z= 0.265 Chirality : 0.040 0.142 6456 Planarity : 0.004 0.048 7716 Dihedral : 4.962 46.072 5976 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.80 % Allowed : 15.78 % Favored : 80.42 % 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 (0.11), residues: 5364 helix: 1.33 (0.11), residues: 2184 sheet: -1.11 (0.16), residues: 876 loop : -0.32 (0.13), residues: 2304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 781 time to evaluate : 4.764 Fit side-chains revert: symmetry clash outliers start: 167 outliers final: 88 residues processed: 878 average time/residue: 1.8762 time to fit residues: 1956.3566 Evaluate side-chains 847 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 759 time to evaluate : 4.936 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 60 residues processed: 28 average time/residue: 0.9374 time to fit residues: 42.6702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 485 optimal weight: 6.9990 chunk 369 optimal weight: 0.4980 chunk 254 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 234 optimal weight: 8.9990 chunk 329 optimal weight: 7.9990 chunk 493 optimal weight: 2.9990 chunk 521 optimal weight: 10.0000 chunk 257 optimal weight: 6.9990 chunk 467 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN B 313 ASN E 33 ASN E 410 HIS F 33 ASN F 210 GLN F 246 GLN J 33 ASN J 313 ASN K 33 ASN L 33 ASN L 210 GLN L 246 GLN L 313 ASN O 4 GLN Q 33 ASN R 33 ASN R 210 GLN R 246 GLN S 33 ASN S 313 ASN T 33 ASN T 126 ASN T 210 GLN T 246 GLN W 33 ASN W 313 ASN X 33 ASN X 165 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 43464 Z= 0.260 Angle : 0.603 6.256 58968 Z= 0.323 Chirality : 0.044 0.147 6456 Planarity : 0.005 0.057 7716 Dihedral : 5.295 44.751 5976 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.80 % Allowed : 15.80 % Favored : 80.40 % 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: -0.00 (0.11), residues: 5364 helix: 1.10 (0.11), residues: 2196 sheet: -1.62 (0.16), residues: 756 loop : -0.37 (0.12), residues: 2412 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 752 time to evaluate : 4.542 Fit side-chains revert: symmetry clash outliers start: 167 outliers final: 100 residues processed: 857 average time/residue: 1.8557 time to fit residues: 1898.7236 Evaluate side-chains 842 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 742 time to evaluate : 4.778 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 67 residues processed: 33 average time/residue: 0.9300 time to fit residues: 48.9219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 434 optimal weight: 3.9990 chunk 296 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.3980 chunk 445 optimal weight: 0.9980 chunk 360 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 266 optimal weight: 4.9990 chunk 468 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN B 313 ASN C 4 GLN E 33 ASN F 33 ASN F 210 GLN J 33 ASN J 313 ASN K 33 ASN L 33 ASN L 210 GLN M 4 GLN Q 33 ASN R 33 ASN R 126 ASN R 210 GLN S 33 ASN S 313 ASN T 33 ASN T 126 ASN T 210 GLN W 33 ASN W 313 ASN X 33 ASN X 165 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 43464 Z= 0.212 Angle : 0.544 5.597 58968 Z= 0.291 Chirality : 0.042 0.143 6456 Planarity : 0.005 0.051 7716 Dihedral : 5.113 44.119 5976 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.33 % Allowed : 15.51 % Favored : 80.17 % 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: 0.11 (0.11), residues: 5364 helix: 1.26 (0.11), residues: 2196 sheet: -1.63 (0.16), residues: 756 loop : -0.36 (0.12), residues: 2412 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 745 time to evaluate : 4.867 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 190 outliers final: 104 residues processed: 860 average time/residue: 1.8963 time to fit residues: 1953.9936 Evaluate side-chains 836 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 732 time to evaluate : 4.779 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 77 residues processed: 27 average time/residue: 1.2518 time to fit residues: 50.4561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 175 optimal weight: 0.9980 chunk 470 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 306 optimal weight: 4.9990 chunk 128 optimal weight: 0.2980 chunk 522 optimal weight: 7.9990 chunk 433 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 274 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN B 165 ASN B 313 ASN E 33 ASN F 33 ASN F 313 ASN J 33 ASN J 313 ASN K 33 ASN L 33 ASN Q 33 ASN R 33 ASN R 126 ASN R 313 ASN S 33 ASN S 165 ASN S 313 ASN T 33 ASN T 126 ASN ** T 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 313 ASN W 33 ASN W 313 ASN X 33 ASN X 165 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 43464 Z= 0.153 Angle : 0.474 5.162 58968 Z= 0.252 Chirality : 0.039 0.138 6456 Planarity : 0.004 0.043 7716 Dihedral : 4.815 43.538 5976 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.67 % Allowed : 16.35 % Favored : 79.99 % 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 (0.11), residues: 5364 helix: 1.53 (0.11), residues: 2208 sheet: -1.18 (0.16), residues: 900 loop : -0.29 (0.13), residues: 2256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 734 time to evaluate : 5.325 Fit side-chains revert: symmetry clash outliers start: 161 outliers final: 94 residues processed: 853 average time/residue: 1.8612 time to fit residues: 1894.5783 Evaluate side-chains 830 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 736 time to evaluate : 4.678 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 82 residues processed: 12 average time/residue: 0.6377 time to fit residues: 17.9422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 503 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 297 optimal weight: 5.9990 chunk 381 optimal weight: 10.0000 chunk 295 optimal weight: 4.9990 chunk 439 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 chunk 520 optimal weight: 6.9990 chunk 325 optimal weight: 0.0670 chunk 317 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN E 33 ASN F 33 ASN F 313 ASN I 4 GLN J 33 ASN J 165 ASN J 313 ASN K 33 ASN L 33 ASN Q 33 ASN R 33 ASN R 313 ASN S 33 ASN ** S 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 313 ASN T 33 ASN T 126 ASN T 288 ASN T 313 ASN W 33 ASN W 165 ASN W 313 ASN X 33 ASN X 165 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43464 Z= 0.194 Angle : 0.527 5.001 58968 Z= 0.280 Chirality : 0.041 0.139 6456 Planarity : 0.004 0.045 7716 Dihedral : 5.004 43.608 5976 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.55 % Allowed : 16.48 % Favored : 79.96 % 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 (0.11), residues: 5364 helix: 1.42 (0.11), residues: 2208 sheet: -1.64 (0.16), residues: 756 loop : -0.30 (0.12), residues: 2400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 736 time to evaluate : 4.810 Fit side-chains outliers start: 156 outliers final: 111 residues processed: 850 average time/residue: 1.9136 time to fit residues: 1934.1173 Evaluate side-chains 846 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 735 time to evaluate : 5.353 Switching outliers to nearest non-outliers outliers start: 111 outliers final: 91 residues processed: 20 average time/residue: 0.9954 time to fit residues: 34.1679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 321 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 310 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 330 optimal weight: 5.9990 chunk 354 optimal weight: 8.9990 chunk 257 optimal weight: 0.0770 chunk 48 optimal weight: 10.0000 chunk 409 optimal weight: 0.0020 overall best weight: 2.6152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN E 33 ASN F 33 ASN F 313 ASN I 4 GLN J 33 ASN J 313 ASN K 33 ASN L 33 ASN Q 33 ASN R 33 ASN R 313 ASN S 33 ASN ** S 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 313 ASN T 33 ASN T 126 ASN T 313 ASN W 33 ASN W 313 ASN X 33 ASN ** X 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 43464 Z= 0.255 Angle : 0.598 5.631 58968 Z= 0.320 Chirality : 0.044 0.146 6456 Planarity : 0.005 0.058 7716 Dihedral : 5.252 43.635 5976 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.51 % Allowed : 16.37 % Favored : 80.12 % 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: 0.08 (0.11), residues: 5364 helix: 1.22 (0.11), residues: 2196 sheet: -1.71 (0.16), residues: 756 loop : -0.32 (0.12), residues: 2412 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 723 time to evaluate : 4.902 Fit side-chains revert: symmetry clash outliers start: 154 outliers final: 100 residues processed: 836 average time/residue: 1.6627 time to fit residues: 1654.5764 Evaluate side-chains 817 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 717 time to evaluate : 4.955 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 85 residues processed: 16 average time/residue: 0.9194 time to fit residues: 27.3824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 473 optimal weight: 4.9990 chunk 498 optimal weight: 0.9990 chunk 454 optimal weight: 0.6980 chunk 485 optimal weight: 1.9990 chunk 291 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 chunk 380 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 438 optimal weight: 8.9990 chunk 458 optimal weight: 3.9990 chunk 483 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: