Starting phenix.real_space_refine (version: dev) on Mon Dec 19 00:50:17 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt4_0967/12_2022/6lt4_0967_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt4_0967/12_2022/6lt4_0967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt4_0967/12_2022/6lt4_0967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt4_0967/12_2022/6lt4_0967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt4_0967/12_2022/6lt4_0967_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt4_0967/12_2022/6lt4_0967_updated_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.009 sd= 0.045 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 468": "OD1" <-> "OD2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 486": "OD1" <-> "OD2" Residue "A TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 272": "OD1" <-> "OD2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 468": "OD1" <-> "OD2" Residue "B PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 486": "OD1" <-> "OD2" Residue "B TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 272": "OD1" <-> "OD2" Residue "C GLU 331": "OE1" <-> "OE2" Residue "C PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 468": "OD1" <-> "OD2" Residue "C PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 486": "OD1" <-> "OD2" Residue "C TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 272": "OD1" <-> "OD2" Residue "D GLU 331": "OE1" <-> "OE2" Residue "D PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 468": "OD1" <-> "OD2" Residue "D PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 486": "OD1" <-> "OD2" Residue "D TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 654": "OE1" <-> "OE2" Residue "E PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 272": "OD1" <-> "OD2" Residue "E GLU 331": "OE1" <-> "OE2" Residue "E PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 468": "OD1" <-> "OD2" Residue "E PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 486": "OD1" <-> "OD2" Residue "E TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 654": "OE1" <-> "OE2" Residue "F PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 272": "OD1" <-> "OD2" Residue "F GLU 331": "OE1" <-> "OE2" Residue "F PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 468": "OD1" <-> "OD2" Residue "F PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 486": "OD1" <-> "OD2" Residue "F TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 654": "OE1" <-> "OE2" Residue "G PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 272": "OD1" <-> "OD2" Residue "G GLU 331": "OE1" <-> "OE2" Residue "G PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 468": "OD1" <-> "OD2" Residue "G PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 486": "OD1" <-> "OD2" Residue "G TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 654": "OE1" <-> "OE2" Residue "H PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 272": "OD1" <-> "OD2" Residue "H GLU 331": "OE1" <-> "OE2" Residue "H PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 468": "OD1" <-> "OD2" Residue "H PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 486": "OD1" <-> "OD2" Residue "H TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 654": "OE1" <-> "OE2" Residue "I PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 272": "OD1" <-> "OD2" Residue "I GLU 331": "OE1" <-> "OE2" Residue "I PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 468": "OD1" <-> "OD2" Residue "I PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 486": "OD1" <-> "OD2" Residue "I TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 654": "OE1" <-> "OE2" Residue "J PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 272": "OD1" <-> "OD2" Residue "J GLU 331": "OE1" <-> "OE2" Residue "J PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 468": "OD1" <-> "OD2" Residue "J PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 486": "OD1" <-> "OD2" Residue "J TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 654": "OE1" <-> "OE2" Residue "K PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 272": "OD1" <-> "OD2" Residue "K GLU 331": "OE1" <-> "OE2" Residue "K PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 468": "OD1" <-> "OD2" Residue "K PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 486": "OD1" <-> "OD2" Residue "K TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 654": "OE1" <-> "OE2" Residue "L PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 272": "OD1" <-> "OD2" Residue "L GLU 331": "OE1" <-> "OE2" Residue "L PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 468": "OD1" <-> "OD2" Residue "L PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 486": "OD1" <-> "OD2" Residue "L TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 654": "OE1" <-> "OE2" Residue "M PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 272": "OD1" <-> "OD2" Residue "M GLU 331": "OE1" <-> "OE2" Residue "M PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 468": "OD1" <-> "OD2" Residue "M PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 486": "OD1" <-> "OD2" Residue "M TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 654": "OE1" <-> "OE2" Residue "N PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 272": "OD1" <-> "OD2" Residue "N GLU 331": "OE1" <-> "OE2" Residue "N PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 468": "OD1" <-> "OD2" Residue "N PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 486": "OD1" <-> "OD2" Residue "N TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 654": "OE1" <-> "OE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 68432 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "B" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "C" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "D" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "E" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "F" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "G" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "H" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "I" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "J" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "K" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "L" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "M" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "N" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4824 Classifications: {'peptide': 623} Link IDs: {'CIS': 4, 'PTRANS': 17, 'TRANS': 601} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "M" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 27.79, per 1000 atoms: 0.41 Number of scatterers: 68432 At special positions: 0 Unit cell: (165.2, 165.2, 226.8, 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 182 16.00 P 84 15.00 Mg 28 11.99 O 13748 8.00 N 12040 7.00 C 42350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.24 Conformation dependent library (CDL) restraints added in 7.6 seconds 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16268 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 406 helices and 70 sheets defined 51.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.30 Creating SS restraints... Processing helix chain 'A' and resid 83 through 89 Processing helix chain 'A' and resid 99 through 109 removed outlier: 4.017A pdb=" N ALA A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 140 removed outlier: 4.366A pdb=" N VAL A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 167 through 180 removed outlier: 3.627A pdb=" N VAL A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 212 through 221 removed outlier: 5.256A pdb=" N LYS A 217 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 233 through 242 removed outlier: 4.506A pdb=" N LEU A 241 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 262 through 277 removed outlier: 4.639A pdb=" N ASP A 272 " --> pdb=" O GLN A 268 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 297 removed outlier: 3.616A pdb=" N GLN A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 371 Processing helix chain 'A' and resid 380 through 391 Processing helix chain 'A' and resid 402 through 416 removed outlier: 3.645A pdb=" N LYS A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 436 Processing helix chain 'A' and resid 460 through 470 removed outlier: 3.788A pdb=" N LEU A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 484 No H-bonds generated for 'chain 'A' and resid 481 through 484' Processing helix chain 'A' and resid 497 through 506 removed outlier: 3.858A pdb=" N VAL A 501 " --> pdb=" O THR A 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 536 through 544 removed outlier: 3.905A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Proline residue: A 591 - end of helix Processing helix chain 'A' and resid 595 through 599 Processing helix chain 'A' and resid 613 through 633 removed outlier: 4.091A pdb=" N SER A 616 " --> pdb=" O GLU A 613 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 617 " --> pdb=" O ASP A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 651 Processing helix chain 'A' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 89 Processing helix chain 'B' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER B 106 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 167 through 180 removed outlier: 3.626A pdb=" N VAL B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 197 No H-bonds generated for 'chain 'B' and resid 194 through 197' Processing helix chain 'B' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS B 217 " --> pdb=" O ASP B 214 " (cutoff:3.500A) Proline residue: B 218 - end of helix Processing helix chain 'B' and resid 233 through 242 removed outlier: 4.505A pdb=" N LEU B 241 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 262 through 277 removed outlier: 4.639A pdb=" N ASP B 272 " --> pdb=" O GLN B 268 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLN B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 297 removed outlier: 3.616A pdb=" N GLN B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 319 Processing helix chain 'B' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 371 Processing helix chain 'B' and resid 380 through 391 Processing helix chain 'B' and resid 402 through 416 removed outlier: 3.644A pdb=" N LYS B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 416 " --> pdb=" O ARG B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 436 Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.788A pdb=" N LEU B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 484 No H-bonds generated for 'chain 'B' and resid 481 through 484' Processing helix chain 'B' and resid 497 through 506 removed outlier: 3.859A pdb=" N VAL B 501 " --> pdb=" O THR B 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 516 Processing helix chain 'B' and resid 536 through 544 removed outlier: 3.906A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) Proline residue: B 591 - end of helix Processing helix chain 'B' and resid 595 through 599 Processing helix chain 'B' and resid 613 through 633 removed outlier: 4.092A pdb=" N SER B 616 " --> pdb=" O GLU B 613 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS B 617 " --> pdb=" O ASP B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 651 Processing helix chain 'B' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL B 665 " --> pdb=" O LEU B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 89 Processing helix chain 'C' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER C 106 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL C 131 " --> pdb=" O LYS C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 167 through 180 removed outlier: 3.626A pdb=" N VAL C 178 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 197 No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS C 217 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Proline residue: C 218 - end of helix Processing helix chain 'C' and resid 233 through 242 removed outlier: 4.505A pdb=" N LEU C 241 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 248 Processing helix chain 'C' and resid 262 through 277 removed outlier: 4.639A pdb=" N ASP C 272 " --> pdb=" O GLN C 268 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR C 274 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN C 275 " --> pdb=" O ARG C 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS C 277 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN C 296 " --> pdb=" O ASP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 319 Processing helix chain 'C' and resid 325 through 346 removed outlier: 5.368A pdb=" N VAL C 330 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 371 Processing helix chain 'C' and resid 380 through 391 Processing helix chain 'C' and resid 402 through 416 removed outlier: 3.645A pdb=" N LYS C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS C 411 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 416 " --> pdb=" O ARG C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 436 Processing helix chain 'C' and resid 460 through 470 removed outlier: 3.788A pdb=" N LEU C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 484 No H-bonds generated for 'chain 'C' and resid 481 through 484' Processing helix chain 'C' and resid 497 through 506 removed outlier: 3.858A pdb=" N VAL C 501 " --> pdb=" O THR C 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 516 Processing helix chain 'C' and resid 536 through 544 removed outlier: 3.906A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) Proline residue: C 591 - end of helix Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'C' and resid 613 through 633 removed outlier: 4.090A pdb=" N SER C 616 " --> pdb=" O GLU C 613 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS C 617 " --> pdb=" O ASP C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 651 Processing helix chain 'C' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL C 665 " --> pdb=" O LEU C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 89 Processing helix chain 'D' and resid 99 through 109 removed outlier: 4.019A pdb=" N ALA D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER D 106 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU D 107 " --> pdb=" O GLN D 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE D 108 " --> pdb=" O GLU D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL D 131 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 167 through 180 removed outlier: 3.626A pdb=" N VAL D 178 " --> pdb=" O VAL D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 197 No H-bonds generated for 'chain 'D' and resid 194 through 197' Processing helix chain 'D' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS D 217 " --> pdb=" O ASP D 214 " (cutoff:3.500A) Proline residue: D 218 - end of helix Processing helix chain 'D' and resid 233 through 242 removed outlier: 4.505A pdb=" N LEU D 241 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 262 through 277 removed outlier: 4.639A pdb=" N ASP D 272 " --> pdb=" O GLN D 268 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 325 through 346 removed outlier: 5.366A pdb=" N VAL D 330 " --> pdb=" O ASP D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 371 Processing helix chain 'D' and resid 380 through 391 Processing helix chain 'D' and resid 402 through 416 removed outlier: 3.644A pdb=" N LYS D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA D 410 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS D 411 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS D 416 " --> pdb=" O ARG D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 436 Processing helix chain 'D' and resid 460 through 470 removed outlier: 3.788A pdb=" N LEU D 465 " --> pdb=" O LEU D 461 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA D 466 " --> pdb=" O ALA D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 484 No H-bonds generated for 'chain 'D' and resid 481 through 484' Processing helix chain 'D' and resid 497 through 506 removed outlier: 3.857A pdb=" N VAL D 501 " --> pdb=" O THR D 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY D 502 " --> pdb=" O ALA D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 516 Processing helix chain 'D' and resid 536 through 544 removed outlier: 3.906A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 592 removed outlier: 4.842A pdb=" N ARG D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) Proline residue: D 591 - end of helix Processing helix chain 'D' and resid 595 through 599 Processing helix chain 'D' and resid 613 through 633 removed outlier: 4.091A pdb=" N SER D 616 " --> pdb=" O GLU D 613 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS D 617 " --> pdb=" O ASP D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 651 Processing helix chain 'D' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL D 665 " --> pdb=" O LEU D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 89 Processing helix chain 'E' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA E 105 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER E 106 " --> pdb=" O ILE E 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU E 107 " --> pdb=" O GLN E 103 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL E 131 " --> pdb=" O LYS E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 147 No H-bonds generated for 'chain 'E' and resid 145 through 147' Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 167 through 180 removed outlier: 3.626A pdb=" N VAL E 178 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 197 No H-bonds generated for 'chain 'E' and resid 194 through 197' Processing helix chain 'E' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS E 217 " --> pdb=" O ASP E 214 " (cutoff:3.500A) Proline residue: E 218 - end of helix Processing helix chain 'E' and resid 233 through 242 removed outlier: 4.506A pdb=" N LEU E 241 " --> pdb=" O ARG E 237 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS E 242 " --> pdb=" O ASN E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 248 Processing helix chain 'E' and resid 262 through 277 removed outlier: 4.640A pdb=" N ASP E 272 " --> pdb=" O GLN E 268 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU E 273 " --> pdb=" O GLY E 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN E 275 " --> pdb=" O ARG E 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN E 276 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 297 removed outlier: 3.616A pdb=" N GLN E 296 " --> pdb=" O ASP E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 319 Processing helix chain 'E' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 371 Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 402 through 416 removed outlier: 3.644A pdb=" N LYS E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA E 410 " --> pdb=" O LEU E 406 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS E 411 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS E 416 " --> pdb=" O ARG E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 436 Processing helix chain 'E' and resid 460 through 470 removed outlier: 3.788A pdb=" N LEU E 465 " --> pdb=" O LEU E 461 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 481 through 484 No H-bonds generated for 'chain 'E' and resid 481 through 484' Processing helix chain 'E' and resid 497 through 506 removed outlier: 3.858A pdb=" N VAL E 501 " --> pdb=" O THR E 497 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY E 502 " --> pdb=" O ALA E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 516 Processing helix chain 'E' and resid 536 through 544 removed outlier: 3.906A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL E 541 " --> pdb=" O LEU E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 592 removed outlier: 4.842A pdb=" N ARG E 588 " --> pdb=" O GLU E 584 " (cutoff:3.500A) Proline residue: E 591 - end of helix Processing helix chain 'E' and resid 595 through 599 Processing helix chain 'E' and resid 613 through 633 removed outlier: 4.090A pdb=" N SER E 616 " --> pdb=" O GLU E 613 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS E 617 " --> pdb=" O ASP E 614 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 651 Processing helix chain 'E' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL E 665 " --> pdb=" O LEU E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 678 removed outlier: 3.503A pdb=" N ASP E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 89 Processing helix chain 'F' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA F 105 " --> pdb=" O GLU F 101 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER F 106 " --> pdb=" O ILE F 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL F 131 " --> pdb=" O LYS F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 147 No H-bonds generated for 'chain 'F' and resid 145 through 147' Processing helix chain 'F' and resid 160 through 163 Processing helix chain 'F' and resid 167 through 180 removed outlier: 3.626A pdb=" N VAL F 178 " --> pdb=" O VAL F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 197 No H-bonds generated for 'chain 'F' and resid 194 through 197' Processing helix chain 'F' and resid 212 through 221 removed outlier: 5.256A pdb=" N LYS F 217 " --> pdb=" O ASP F 214 " (cutoff:3.500A) Proline residue: F 218 - end of helix Processing helix chain 'F' and resid 233 through 242 removed outlier: 4.505A pdb=" N LEU F 241 " --> pdb=" O ARG F 237 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS F 242 " --> pdb=" O ASN F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 248 Processing helix chain 'F' and resid 262 through 277 removed outlier: 4.640A pdb=" N ASP F 272 " --> pdb=" O GLN F 268 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU F 273 " --> pdb=" O GLY F 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR F 274 " --> pdb=" O ILE F 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN F 275 " --> pdb=" O ARG F 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN F 276 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN F 296 " --> pdb=" O ASP F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL F 330 " --> pdb=" O ASP F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 371 Processing helix chain 'F' and resid 380 through 391 Processing helix chain 'F' and resid 402 through 416 removed outlier: 3.645A pdb=" N LYS F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA F 410 " --> pdb=" O LEU F 406 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS F 411 " --> pdb=" O LYS F 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS F 416 " --> pdb=" O ARG F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 436 Processing helix chain 'F' and resid 460 through 470 removed outlier: 3.788A pdb=" N LEU F 465 " --> pdb=" O LEU F 461 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA F 466 " --> pdb=" O ALA F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 481 through 484 No H-bonds generated for 'chain 'F' and resid 481 through 484' Processing helix chain 'F' and resid 497 through 506 removed outlier: 3.858A pdb=" N VAL F 501 " --> pdb=" O THR F 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY F 502 " --> pdb=" O ALA F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 516 Processing helix chain 'F' and resid 536 through 544 removed outlier: 3.907A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) Proline residue: F 591 - end of helix Processing helix chain 'F' and resid 595 through 599 Processing helix chain 'F' and resid 613 through 633 removed outlier: 4.091A pdb=" N SER F 616 " --> pdb=" O GLU F 613 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS F 617 " --> pdb=" O ASP F 614 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 651 Processing helix chain 'F' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL F 665 " --> pdb=" O LEU F 661 " (cutoff:3.500A) Processing helix chain 'F' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 89 Processing helix chain 'G' and resid 99 through 109 removed outlier: 4.019A pdb=" N ALA G 105 " --> pdb=" O GLU G 101 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER G 106 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU G 107 " --> pdb=" O GLN G 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE G 108 " --> pdb=" O GLU G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 140 removed outlier: 4.366A pdb=" N VAL G 131 " --> pdb=" O LYS G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 147 No H-bonds generated for 'chain 'G' and resid 145 through 147' Processing helix chain 'G' and resid 160 through 163 Processing helix chain 'G' and resid 167 through 180 removed outlier: 3.627A pdb=" N VAL G 178 " --> pdb=" O VAL G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 197 No H-bonds generated for 'chain 'G' and resid 194 through 197' Processing helix chain 'G' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS G 217 " --> pdb=" O ASP G 214 " (cutoff:3.500A) Proline residue: G 218 - end of helix Processing helix chain 'G' and resid 233 through 242 removed outlier: 4.505A pdb=" N LEU G 241 " --> pdb=" O ARG G 237 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS G 242 " --> pdb=" O ASN G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 248 Processing helix chain 'G' and resid 262 through 277 removed outlier: 4.640A pdb=" N ASP G 272 " --> pdb=" O GLN G 268 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU G 273 " --> pdb=" O GLY G 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR G 274 " --> pdb=" O ILE G 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN G 275 " --> pdb=" O ARG G 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN G 276 " --> pdb=" O ASP G 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS G 277 " --> pdb=" O LEU G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN G 296 " --> pdb=" O ASP G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 319 Processing helix chain 'G' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL G 330 " --> pdb=" O ASP G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 371 Processing helix chain 'G' and resid 380 through 391 Processing helix chain 'G' and resid 402 through 416 removed outlier: 3.645A pdb=" N LYS G 407 " --> pdb=" O ILE G 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA G 410 " --> pdb=" O LEU G 406 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS G 411 " --> pdb=" O LYS G 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS G 416 " --> pdb=" O ARG G 412 " (cutoff:3.500A) Processing helix chain 'G' and resid 421 through 436 Processing helix chain 'G' and resid 460 through 470 removed outlier: 3.789A pdb=" N LEU G 465 " --> pdb=" O LEU G 461 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA G 466 " --> pdb=" O ALA G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 481 through 484 No H-bonds generated for 'chain 'G' and resid 481 through 484' Processing helix chain 'G' and resid 497 through 506 removed outlier: 3.859A pdb=" N VAL G 501 " --> pdb=" O THR G 497 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY G 502 " --> pdb=" O ALA G 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 516 Processing helix chain 'G' and resid 536 through 544 removed outlier: 3.906A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL G 541 " --> pdb=" O LEU G 537 " (cutoff:3.500A) Processing helix chain 'G' and resid 583 through 592 removed outlier: 4.842A pdb=" N ARG G 588 " --> pdb=" O GLU G 584 " (cutoff:3.500A) Proline residue: G 591 - end of helix Processing helix chain 'G' and resid 595 through 599 Processing helix chain 'G' and resid 613 through 633 removed outlier: 4.091A pdb=" N SER G 616 " --> pdb=" O GLU G 613 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS G 617 " --> pdb=" O ASP G 614 " (cutoff:3.500A) Processing helix chain 'G' and resid 641 through 651 Processing helix chain 'G' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL G 665 " --> pdb=" O LEU G 661 " (cutoff:3.500A) Processing helix chain 'G' and resid 668 through 678 removed outlier: 3.503A pdb=" N ASP G 675 " --> pdb=" O ASP G 671 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 89 Processing helix chain 'H' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA H 105 " --> pdb=" O GLU H 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER H 106 " --> pdb=" O ILE H 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU H 107 " --> pdb=" O GLN H 103 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE H 108 " --> pdb=" O GLU H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL H 131 " --> pdb=" O LYS H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 147 No H-bonds generated for 'chain 'H' and resid 145 through 147' Processing helix chain 'H' and resid 160 through 163 Processing helix chain 'H' and resid 167 through 180 removed outlier: 3.626A pdb=" N VAL H 178 " --> pdb=" O VAL H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 197 No H-bonds generated for 'chain 'H' and resid 194 through 197' Processing helix chain 'H' and resid 212 through 221 removed outlier: 5.256A pdb=" N LYS H 217 " --> pdb=" O ASP H 214 " (cutoff:3.500A) Proline residue: H 218 - end of helix Processing helix chain 'H' and resid 233 through 242 removed outlier: 4.506A pdb=" N LEU H 241 " --> pdb=" O ARG H 237 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS H 242 " --> pdb=" O ASN H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 248 Processing helix chain 'H' and resid 262 through 277 removed outlier: 4.640A pdb=" N ASP H 272 " --> pdb=" O GLN H 268 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU H 273 " --> pdb=" O GLY H 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR H 274 " --> pdb=" O ILE H 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN H 275 " --> pdb=" O ARG H 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN H 276 " --> pdb=" O ASP H 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS H 277 " --> pdb=" O LEU H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN H 296 " --> pdb=" O ASP H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 319 Processing helix chain 'H' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL H 330 " --> pdb=" O ASP H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 371 Processing helix chain 'H' and resid 380 through 391 Processing helix chain 'H' and resid 402 through 416 removed outlier: 3.645A pdb=" N LYS H 407 " --> pdb=" O ILE H 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA H 410 " --> pdb=" O LEU H 406 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS H 411 " --> pdb=" O LYS H 407 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS H 416 " --> pdb=" O ARG H 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 421 through 436 Processing helix chain 'H' and resid 460 through 470 removed outlier: 3.789A pdb=" N LEU H 465 " --> pdb=" O LEU H 461 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA H 466 " --> pdb=" O ALA H 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 481 through 484 No H-bonds generated for 'chain 'H' and resid 481 through 484' Processing helix chain 'H' and resid 497 through 506 removed outlier: 3.858A pdb=" N VAL H 501 " --> pdb=" O THR H 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY H 502 " --> pdb=" O ALA H 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 511 through 516 Processing helix chain 'H' and resid 536 through 544 removed outlier: 3.906A pdb=" N GLN H 540 " --> pdb=" O THR H 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL H 541 " --> pdb=" O LEU H 537 " (cutoff:3.500A) Processing helix chain 'H' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG H 588 " --> pdb=" O GLU H 584 " (cutoff:3.500A) Proline residue: H 591 - end of helix Processing helix chain 'H' and resid 595 through 599 Processing helix chain 'H' and resid 613 through 633 removed outlier: 4.090A pdb=" N SER H 616 " --> pdb=" O GLU H 613 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS H 617 " --> pdb=" O ASP H 614 " (cutoff:3.500A) Processing helix chain 'H' and resid 641 through 651 Processing helix chain 'H' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL H 665 " --> pdb=" O LEU H 661 " (cutoff:3.500A) Processing helix chain 'H' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP H 675 " --> pdb=" O ASP H 671 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 89 Processing helix chain 'I' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER I 106 " --> pdb=" O ILE I 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU I 107 " --> pdb=" O GLN I 103 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE I 108 " --> pdb=" O GLU I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL I 131 " --> pdb=" O LYS I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 147 No H-bonds generated for 'chain 'I' and resid 145 through 147' Processing helix chain 'I' and resid 160 through 163 Processing helix chain 'I' and resid 167 through 180 removed outlier: 3.626A pdb=" N VAL I 178 " --> pdb=" O VAL I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 197 No H-bonds generated for 'chain 'I' and resid 194 through 197' Processing helix chain 'I' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS I 217 " --> pdb=" O ASP I 214 " (cutoff:3.500A) Proline residue: I 218 - end of helix Processing helix chain 'I' and resid 233 through 242 removed outlier: 4.505A pdb=" N LEU I 241 " --> pdb=" O ARG I 237 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS I 242 " --> pdb=" O ASN I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 244 through 248 Processing helix chain 'I' and resid 262 through 277 removed outlier: 4.640A pdb=" N ASP I 272 " --> pdb=" O GLN I 268 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU I 273 " --> pdb=" O GLY I 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR I 274 " --> pdb=" O ILE I 270 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN I 275 " --> pdb=" O ARG I 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN I 276 " --> pdb=" O ASP I 272 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS I 277 " --> pdb=" O LEU I 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN I 296 " --> pdb=" O ASP I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 319 Processing helix chain 'I' and resid 325 through 346 removed outlier: 5.368A pdb=" N VAL I 330 " --> pdb=" O ASP I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 371 Processing helix chain 'I' and resid 380 through 391 Processing helix chain 'I' and resid 402 through 416 removed outlier: 3.645A pdb=" N LYS I 407 " --> pdb=" O ILE I 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA I 410 " --> pdb=" O LEU I 406 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS I 411 " --> pdb=" O LYS I 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS I 416 " --> pdb=" O ARG I 412 " (cutoff:3.500A) Processing helix chain 'I' and resid 421 through 436 Processing helix chain 'I' and resid 460 through 470 removed outlier: 3.789A pdb=" N LEU I 465 " --> pdb=" O LEU I 461 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA I 466 " --> pdb=" O ALA I 462 " (cutoff:3.500A) Processing helix chain 'I' and resid 481 through 484 No H-bonds generated for 'chain 'I' and resid 481 through 484' Processing helix chain 'I' and resid 497 through 506 removed outlier: 3.859A pdb=" N VAL I 501 " --> pdb=" O THR I 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY I 502 " --> pdb=" O ALA I 498 " (cutoff:3.500A) Processing helix chain 'I' and resid 511 through 516 Processing helix chain 'I' and resid 536 through 544 removed outlier: 3.905A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL I 541 " --> pdb=" O LEU I 537 " (cutoff:3.500A) Processing helix chain 'I' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG I 588 " --> pdb=" O GLU I 584 " (cutoff:3.500A) Proline residue: I 591 - end of helix Processing helix chain 'I' and resid 595 through 599 Processing helix chain 'I' and resid 613 through 633 removed outlier: 4.092A pdb=" N SER I 616 " --> pdb=" O GLU I 613 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS I 617 " --> pdb=" O ASP I 614 " (cutoff:3.500A) Processing helix chain 'I' and resid 641 through 651 Processing helix chain 'I' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL I 665 " --> pdb=" O LEU I 661 " (cutoff:3.500A) Processing helix chain 'I' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP I 675 " --> pdb=" O ASP I 671 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 89 Processing helix chain 'J' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA J 105 " --> pdb=" O GLU J 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER J 106 " --> pdb=" O ILE J 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU J 107 " --> pdb=" O GLN J 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE J 108 " --> pdb=" O GLU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL J 131 " --> pdb=" O LYS J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 147 No H-bonds generated for 'chain 'J' and resid 145 through 147' Processing helix chain 'J' and resid 160 through 163 Processing helix chain 'J' and resid 167 through 180 removed outlier: 3.627A pdb=" N VAL J 178 " --> pdb=" O VAL J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 197 No H-bonds generated for 'chain 'J' and resid 194 through 197' Processing helix chain 'J' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS J 217 " --> pdb=" O ASP J 214 " (cutoff:3.500A) Proline residue: J 218 - end of helix Processing helix chain 'J' and resid 233 through 242 removed outlier: 4.506A pdb=" N LEU J 241 " --> pdb=" O ARG J 237 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LYS J 242 " --> pdb=" O ASN J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 244 through 248 Processing helix chain 'J' and resid 262 through 277 removed outlier: 4.640A pdb=" N ASP J 272 " --> pdb=" O GLN J 268 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU J 273 " --> pdb=" O GLY J 269 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR J 274 " --> pdb=" O ILE J 270 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN J 275 " --> pdb=" O ARG J 271 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLN J 276 " --> pdb=" O ASP J 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS J 277 " --> pdb=" O LEU J 273 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 297 removed outlier: 3.616A pdb=" N GLN J 296 " --> pdb=" O ASP J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 319 Processing helix chain 'J' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL J 330 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 371 Processing helix chain 'J' and resid 380 through 391 Processing helix chain 'J' and resid 402 through 416 removed outlier: 3.644A pdb=" N LYS J 407 " --> pdb=" O ILE J 403 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA J 410 " --> pdb=" O LEU J 406 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS J 411 " --> pdb=" O LYS J 407 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS J 416 " --> pdb=" O ARG J 412 " (cutoff:3.500A) Processing helix chain 'J' and resid 421 through 436 Processing helix chain 'J' and resid 460 through 470 removed outlier: 3.788A pdb=" N LEU J 465 " --> pdb=" O LEU J 461 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA J 466 " --> pdb=" O ALA J 462 " (cutoff:3.500A) Processing helix chain 'J' and resid 481 through 484 No H-bonds generated for 'chain 'J' and resid 481 through 484' Processing helix chain 'J' and resid 497 through 506 removed outlier: 3.858A pdb=" N VAL J 501 " --> pdb=" O THR J 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY J 502 " --> pdb=" O ALA J 498 " (cutoff:3.500A) Processing helix chain 'J' and resid 511 through 516 Processing helix chain 'J' and resid 536 through 544 removed outlier: 3.907A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL J 541 " --> pdb=" O LEU J 537 " (cutoff:3.500A) Processing helix chain 'J' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG J 588 " --> pdb=" O GLU J 584 " (cutoff:3.500A) Proline residue: J 591 - end of helix Processing helix chain 'J' and resid 595 through 599 Processing helix chain 'J' and resid 613 through 633 removed outlier: 4.091A pdb=" N SER J 616 " --> pdb=" O GLU J 613 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS J 617 " --> pdb=" O ASP J 614 " (cutoff:3.500A) Processing helix chain 'J' and resid 641 through 651 Processing helix chain 'J' and resid 659 through 666 removed outlier: 4.349A pdb=" N VAL J 665 " --> pdb=" O LEU J 661 " (cutoff:3.500A) Processing helix chain 'J' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP J 675 " --> pdb=" O ASP J 671 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 89 Processing helix chain 'K' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER K 106 " --> pdb=" O ILE K 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU K 107 " --> pdb=" O GLN K 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE K 108 " --> pdb=" O GLU K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL K 131 " --> pdb=" O LYS K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 147 No H-bonds generated for 'chain 'K' and resid 145 through 147' Processing helix chain 'K' and resid 160 through 163 Processing helix chain 'K' and resid 167 through 180 removed outlier: 3.627A pdb=" N VAL K 178 " --> pdb=" O VAL K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 197 No H-bonds generated for 'chain 'K' and resid 194 through 197' Processing helix chain 'K' and resid 212 through 221 removed outlier: 5.256A pdb=" N LYS K 217 " --> pdb=" O ASP K 214 " (cutoff:3.500A) Proline residue: K 218 - end of helix Processing helix chain 'K' and resid 233 through 242 removed outlier: 4.505A pdb=" N LEU K 241 " --> pdb=" O ARG K 237 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS K 242 " --> pdb=" O ASN K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 248 Processing helix chain 'K' and resid 262 through 277 removed outlier: 4.639A pdb=" N ASP K 272 " --> pdb=" O GLN K 268 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU K 273 " --> pdb=" O GLY K 269 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N TYR K 274 " --> pdb=" O ILE K 270 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN K 275 " --> pdb=" O ARG K 271 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLN K 276 " --> pdb=" O ASP K 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS K 277 " --> pdb=" O LEU K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN K 296 " --> pdb=" O ASP K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 303 through 319 Processing helix chain 'K' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL K 330 " --> pdb=" O ASP K 326 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 371 Processing helix chain 'K' and resid 380 through 391 Processing helix chain 'K' and resid 402 through 416 removed outlier: 3.644A pdb=" N LYS K 407 " --> pdb=" O ILE K 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA K 410 " --> pdb=" O LEU K 406 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS K 411 " --> pdb=" O LYS K 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS K 416 " --> pdb=" O ARG K 412 " (cutoff:3.500A) Processing helix chain 'K' and resid 421 through 436 Processing helix chain 'K' and resid 460 through 470 removed outlier: 3.789A pdb=" N LEU K 465 " --> pdb=" O LEU K 461 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA K 466 " --> pdb=" O ALA K 462 " (cutoff:3.500A) Processing helix chain 'K' and resid 481 through 484 No H-bonds generated for 'chain 'K' and resid 481 through 484' Processing helix chain 'K' and resid 497 through 506 removed outlier: 3.857A pdb=" N VAL K 501 " --> pdb=" O THR K 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY K 502 " --> pdb=" O ALA K 498 " (cutoff:3.500A) Processing helix chain 'K' and resid 511 through 516 Processing helix chain 'K' and resid 536 through 544 removed outlier: 3.905A pdb=" N GLN K 540 " --> pdb=" O THR K 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL K 541 " --> pdb=" O LEU K 537 " (cutoff:3.500A) Processing helix chain 'K' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG K 588 " --> pdb=" O GLU K 584 " (cutoff:3.500A) Proline residue: K 591 - end of helix Processing helix chain 'K' and resid 595 through 599 Processing helix chain 'K' and resid 613 through 633 removed outlier: 4.091A pdb=" N SER K 616 " --> pdb=" O GLU K 613 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS K 617 " --> pdb=" O ASP K 614 " (cutoff:3.500A) Processing helix chain 'K' and resid 641 through 651 Processing helix chain 'K' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL K 665 " --> pdb=" O LEU K 661 " (cutoff:3.500A) Processing helix chain 'K' and resid 668 through 678 removed outlier: 3.503A pdb=" N ASP K 675 " --> pdb=" O ASP K 671 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 89 Processing helix chain 'L' and resid 99 through 109 removed outlier: 4.017A pdb=" N ALA L 105 " --> pdb=" O GLU L 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER L 106 " --> pdb=" O ILE L 102 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU L 107 " --> pdb=" O GLN L 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 140 removed outlier: 4.364A pdb=" N VAL L 131 " --> pdb=" O LYS L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 147 No H-bonds generated for 'chain 'L' and resid 145 through 147' Processing helix chain 'L' and resid 160 through 163 Processing helix chain 'L' and resid 167 through 180 removed outlier: 3.626A pdb=" N VAL L 178 " --> pdb=" O VAL L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 194 through 197 No H-bonds generated for 'chain 'L' and resid 194 through 197' Processing helix chain 'L' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS L 217 " --> pdb=" O ASP L 214 " (cutoff:3.500A) Proline residue: L 218 - end of helix Processing helix chain 'L' and resid 233 through 242 removed outlier: 4.506A pdb=" N LEU L 241 " --> pdb=" O ARG L 237 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS L 242 " --> pdb=" O ASN L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 248 Processing helix chain 'L' and resid 262 through 277 removed outlier: 4.640A pdb=" N ASP L 272 " --> pdb=" O GLN L 268 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU L 273 " --> pdb=" O GLY L 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR L 274 " --> pdb=" O ILE L 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN L 275 " --> pdb=" O ARG L 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN L 276 " --> pdb=" O ASP L 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS L 277 " --> pdb=" O LEU L 273 " (cutoff:3.500A) Processing helix chain 'L' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN L 296 " --> pdb=" O ASP L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 303 through 319 Processing helix chain 'L' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL L 330 " --> pdb=" O ASP L 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 371 Processing helix chain 'L' and resid 380 through 391 Processing helix chain 'L' and resid 402 through 416 removed outlier: 3.645A pdb=" N LYS L 407 " --> pdb=" O ILE L 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA L 410 " --> pdb=" O LEU L 406 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS L 411 " --> pdb=" O LYS L 407 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS L 416 " --> pdb=" O ARG L 412 " (cutoff:3.500A) Processing helix chain 'L' and resid 421 through 436 Processing helix chain 'L' and resid 460 through 470 removed outlier: 3.789A pdb=" N LEU L 465 " --> pdb=" O LEU L 461 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA L 466 " --> pdb=" O ALA L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 481 through 484 No H-bonds generated for 'chain 'L' and resid 481 through 484' Processing helix chain 'L' and resid 497 through 506 removed outlier: 3.858A pdb=" N VAL L 501 " --> pdb=" O THR L 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY L 502 " --> pdb=" O ALA L 498 " (cutoff:3.500A) Processing helix chain 'L' and resid 511 through 516 Processing helix chain 'L' and resid 536 through 544 removed outlier: 3.906A pdb=" N GLN L 540 " --> pdb=" O THR L 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL L 541 " --> pdb=" O LEU L 537 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG L 588 " --> pdb=" O GLU L 584 " (cutoff:3.500A) Proline residue: L 591 - end of helix Processing helix chain 'L' and resid 595 through 599 Processing helix chain 'L' and resid 613 through 633 removed outlier: 4.091A pdb=" N SER L 616 " --> pdb=" O GLU L 613 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS L 617 " --> pdb=" O ASP L 614 " (cutoff:3.500A) Processing helix chain 'L' and resid 641 through 651 Processing helix chain 'L' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL L 665 " --> pdb=" O LEU L 661 " (cutoff:3.500A) Processing helix chain 'L' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP L 675 " --> pdb=" O ASP L 671 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 89 Processing helix chain 'M' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA M 105 " --> pdb=" O GLU M 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER M 106 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU M 107 " --> pdb=" O GLN M 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE M 108 " --> pdb=" O GLU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL M 131 " --> pdb=" O LYS M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 147 No H-bonds generated for 'chain 'M' and resid 145 through 147' Processing helix chain 'M' and resid 160 through 163 Processing helix chain 'M' and resid 167 through 180 removed outlier: 3.626A pdb=" N VAL M 178 " --> pdb=" O VAL M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 197 No H-bonds generated for 'chain 'M' and resid 194 through 197' Processing helix chain 'M' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS M 217 " --> pdb=" O ASP M 214 " (cutoff:3.500A) Proline residue: M 218 - end of helix Processing helix chain 'M' and resid 233 through 242 removed outlier: 4.505A pdb=" N LEU M 241 " --> pdb=" O ARG M 237 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS M 242 " --> pdb=" O ASN M 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 244 through 248 Processing helix chain 'M' and resid 262 through 277 removed outlier: 4.640A pdb=" N ASP M 272 " --> pdb=" O GLN M 268 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU M 273 " --> pdb=" O GLY M 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR M 274 " --> pdb=" O ILE M 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN M 275 " --> pdb=" O ARG M 271 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLN M 276 " --> pdb=" O ASP M 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS M 277 " --> pdb=" O LEU M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN M 296 " --> pdb=" O ASP M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 303 through 319 Processing helix chain 'M' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL M 330 " --> pdb=" O ASP M 326 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 371 Processing helix chain 'M' and resid 380 through 391 Processing helix chain 'M' and resid 402 through 416 removed outlier: 3.644A pdb=" N LYS M 407 " --> pdb=" O ILE M 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA M 410 " --> pdb=" O LEU M 406 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS M 411 " --> pdb=" O LYS M 407 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS M 416 " --> pdb=" O ARG M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 421 through 436 Processing helix chain 'M' and resid 460 through 470 removed outlier: 3.789A pdb=" N LEU M 465 " --> pdb=" O LEU M 461 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA M 466 " --> pdb=" O ALA M 462 " (cutoff:3.500A) Processing helix chain 'M' and resid 481 through 484 No H-bonds generated for 'chain 'M' and resid 481 through 484' Processing helix chain 'M' and resid 497 through 506 removed outlier: 3.857A pdb=" N VAL M 501 " --> pdb=" O THR M 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY M 502 " --> pdb=" O ALA M 498 " (cutoff:3.500A) Processing helix chain 'M' and resid 511 through 516 Processing helix chain 'M' and resid 536 through 544 removed outlier: 3.906A pdb=" N GLN M 540 " --> pdb=" O THR M 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL M 541 " --> pdb=" O LEU M 537 " (cutoff:3.500A) Processing helix chain 'M' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG M 588 " --> pdb=" O GLU M 584 " (cutoff:3.500A) Proline residue: M 591 - end of helix Processing helix chain 'M' and resid 595 through 599 Processing helix chain 'M' and resid 613 through 633 removed outlier: 4.090A pdb=" N SER M 616 " --> pdb=" O GLU M 613 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS M 617 " --> pdb=" O ASP M 614 " (cutoff:3.500A) Processing helix chain 'M' and resid 641 through 651 Processing helix chain 'M' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL M 665 " --> pdb=" O LEU M 661 " (cutoff:3.500A) Processing helix chain 'M' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP M 675 " --> pdb=" O ASP M 671 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 89 Processing helix chain 'N' and resid 99 through 109 removed outlier: 4.018A pdb=" N ALA N 105 " --> pdb=" O GLU N 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER N 106 " --> pdb=" O ILE N 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU N 107 " --> pdb=" O GLN N 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE N 108 " --> pdb=" O GLU N 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 140 removed outlier: 4.365A pdb=" N VAL N 131 " --> pdb=" O LYS N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 147 No H-bonds generated for 'chain 'N' and resid 145 through 147' Processing helix chain 'N' and resid 160 through 163 Processing helix chain 'N' and resid 167 through 180 removed outlier: 3.627A pdb=" N VAL N 178 " --> pdb=" O VAL N 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 197 No H-bonds generated for 'chain 'N' and resid 194 through 197' Processing helix chain 'N' and resid 212 through 221 removed outlier: 5.255A pdb=" N LYS N 217 " --> pdb=" O ASP N 214 " (cutoff:3.500A) Proline residue: N 218 - end of helix Processing helix chain 'N' and resid 233 through 242 removed outlier: 4.506A pdb=" N LEU N 241 " --> pdb=" O ARG N 237 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS N 242 " --> pdb=" O ASN N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 244 through 248 Processing helix chain 'N' and resid 262 through 277 removed outlier: 4.640A pdb=" N ASP N 272 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU N 273 " --> pdb=" O GLY N 269 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR N 274 " --> pdb=" O ILE N 270 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN N 275 " --> pdb=" O ARG N 271 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN N 276 " --> pdb=" O ASP N 272 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS N 277 " --> pdb=" O LEU N 273 " (cutoff:3.500A) Processing helix chain 'N' and resid 284 through 297 removed outlier: 3.615A pdb=" N GLN N 296 " --> pdb=" O ASP N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 303 through 319 Processing helix chain 'N' and resid 325 through 346 removed outlier: 5.367A pdb=" N VAL N 330 " --> pdb=" O ASP N 326 " (cutoff:3.500A) Processing helix chain 'N' and resid 350 through 371 Processing helix chain 'N' and resid 380 through 391 Processing helix chain 'N' and resid 402 through 416 removed outlier: 3.645A pdb=" N LYS N 407 " --> pdb=" O ILE N 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA N 410 " --> pdb=" O LEU N 406 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS N 411 " --> pdb=" O LYS N 407 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS N 416 " --> pdb=" O ARG N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 421 through 436 Processing helix chain 'N' and resid 460 through 470 removed outlier: 3.788A pdb=" N LEU N 465 " --> pdb=" O LEU N 461 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA N 466 " --> pdb=" O ALA N 462 " (cutoff:3.500A) Processing helix chain 'N' and resid 481 through 484 No H-bonds generated for 'chain 'N' and resid 481 through 484' Processing helix chain 'N' and resid 497 through 506 removed outlier: 3.859A pdb=" N VAL N 501 " --> pdb=" O THR N 497 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY N 502 " --> pdb=" O ALA N 498 " (cutoff:3.500A) Processing helix chain 'N' and resid 511 through 516 Processing helix chain 'N' and resid 536 through 544 removed outlier: 3.906A pdb=" N GLN N 540 " --> pdb=" O THR N 536 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL N 541 " --> pdb=" O LEU N 537 " (cutoff:3.500A) Processing helix chain 'N' and resid 583 through 592 removed outlier: 4.841A pdb=" N ARG N 588 " --> pdb=" O GLU N 584 " (cutoff:3.500A) Proline residue: N 591 - end of helix Processing helix chain 'N' and resid 595 through 599 Processing helix chain 'N' and resid 613 through 633 removed outlier: 4.090A pdb=" N SER N 616 " --> pdb=" O GLU N 613 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS N 617 " --> pdb=" O ASP N 614 " (cutoff:3.500A) Processing helix chain 'N' and resid 641 through 651 Processing helix chain 'N' and resid 659 through 666 removed outlier: 4.350A pdb=" N VAL N 665 " --> pdb=" O LEU N 661 " (cutoff:3.500A) Processing helix chain 'N' and resid 668 through 678 removed outlier: 3.504A pdb=" N ASP N 675 " --> pdb=" O ASP N 671 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 80 through 82 Processing sheet with id= B, first strand: chain 'A' and resid 116 through 120 Processing sheet with id= C, first strand: chain 'A' and resid 603 through 607 removed outlier: 3.987A pdb=" N ALA A 603 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 546 through 548 Processing sheet with id= E, first strand: chain 'A' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU A 686 " --> pdb=" O VAL A 638 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 80 through 82 Processing sheet with id= G, first strand: chain 'B' and resid 116 through 120 Processing sheet with id= H, first strand: chain 'B' and resid 603 through 607 removed outlier: 3.986A pdb=" N ALA B 603 " --> pdb=" O ASN B 447 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 546 through 548 Processing sheet with id= J, first strand: chain 'B' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU B 686 " --> pdb=" O VAL B 638 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 80 through 82 Processing sheet with id= L, first strand: chain 'C' and resid 116 through 120 Processing sheet with id= M, first strand: chain 'C' and resid 603 through 607 removed outlier: 3.986A pdb=" N ALA C 603 " --> pdb=" O ASN C 447 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 546 through 548 Processing sheet with id= O, first strand: chain 'C' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU C 686 " --> pdb=" O VAL C 638 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 80 through 82 Processing sheet with id= Q, first strand: chain 'D' and resid 116 through 120 Processing sheet with id= R, first strand: chain 'D' and resid 603 through 607 removed outlier: 3.986A pdb=" N ALA D 603 " --> pdb=" O ASN D 447 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 546 through 548 Processing sheet with id= T, first strand: chain 'D' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU D 686 " --> pdb=" O VAL D 638 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 80 through 82 Processing sheet with id= V, first strand: chain 'E' and resid 116 through 120 Processing sheet with id= W, first strand: chain 'E' and resid 603 through 607 removed outlier: 3.986A pdb=" N ALA E 603 " --> pdb=" O ASN E 447 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 546 through 548 Processing sheet with id= Y, first strand: chain 'E' and resid 637 through 639 removed outlier: 6.726A pdb=" N LEU E 686 " --> pdb=" O VAL E 638 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 80 through 82 Processing sheet with id= AA, first strand: chain 'F' and resid 116 through 120 Processing sheet with id= AB, first strand: chain 'F' and resid 603 through 607 removed outlier: 3.987A pdb=" N ALA F 603 " --> pdb=" O ASN F 447 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 546 through 548 Processing sheet with id= AD, first strand: chain 'F' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU F 686 " --> pdb=" O VAL F 638 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 80 through 82 Processing sheet with id= AF, first strand: chain 'G' and resid 116 through 120 Processing sheet with id= AG, first strand: chain 'G' and resid 603 through 607 removed outlier: 3.986A pdb=" N ALA G 603 " --> pdb=" O ASN G 447 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 546 through 548 Processing sheet with id= AI, first strand: chain 'G' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU G 686 " --> pdb=" O VAL G 638 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 80 through 82 Processing sheet with id= AK, first strand: chain 'H' and resid 116 through 120 Processing sheet with id= AL, first strand: chain 'H' and resid 603 through 607 removed outlier: 3.987A pdb=" N ALA H 603 " --> pdb=" O ASN H 447 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 546 through 548 Processing sheet with id= AN, first strand: chain 'H' and resid 637 through 639 removed outlier: 6.726A pdb=" N LEU H 686 " --> pdb=" O VAL H 638 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 80 through 82 Processing sheet with id= AP, first strand: chain 'I' and resid 116 through 120 Processing sheet with id= AQ, first strand: chain 'I' and resid 603 through 607 removed outlier: 3.985A pdb=" N ALA I 603 " --> pdb=" O ASN I 447 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'I' and resid 546 through 548 Processing sheet with id= AS, first strand: chain 'I' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU I 686 " --> pdb=" O VAL I 638 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'J' and resid 80 through 82 Processing sheet with id= AU, first strand: chain 'J' and resid 116 through 120 Processing sheet with id= AV, first strand: chain 'J' and resid 603 through 607 removed outlier: 3.986A pdb=" N ALA J 603 " --> pdb=" O ASN J 447 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'J' and resid 546 through 548 Processing sheet with id= AX, first strand: chain 'J' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU J 686 " --> pdb=" O VAL J 638 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'K' and resid 80 through 82 Processing sheet with id= AZ, first strand: chain 'K' and resid 116 through 120 Processing sheet with id= BA, first strand: chain 'K' and resid 603 through 607 removed outlier: 3.987A pdb=" N ALA K 603 " --> pdb=" O ASN K 447 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'K' and resid 546 through 548 Processing sheet with id= BC, first strand: chain 'K' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU K 686 " --> pdb=" O VAL K 638 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'L' and resid 80 through 82 Processing sheet with id= BE, first strand: chain 'L' and resid 116 through 120 Processing sheet with id= BF, first strand: chain 'L' and resid 603 through 607 removed outlier: 3.986A pdb=" N ALA L 603 " --> pdb=" O ASN L 447 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'L' and resid 546 through 548 Processing sheet with id= BH, first strand: chain 'L' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU L 686 " --> pdb=" O VAL L 638 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'M' and resid 80 through 82 Processing sheet with id= BJ, first strand: chain 'M' and resid 116 through 120 Processing sheet with id= BK, first strand: chain 'M' and resid 603 through 607 removed outlier: 3.986A pdb=" N ALA M 603 " --> pdb=" O ASN M 447 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'M' and resid 546 through 548 Processing sheet with id= BM, first strand: chain 'M' and resid 637 through 639 removed outlier: 6.726A pdb=" N LEU M 686 " --> pdb=" O VAL M 638 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'N' and resid 80 through 82 Processing sheet with id= BO, first strand: chain 'N' and resid 116 through 120 Processing sheet with id= BP, first strand: chain 'N' and resid 603 through 607 removed outlier: 3.986A pdb=" N ALA N 603 " --> pdb=" O ASN N 447 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'N' and resid 546 through 548 Processing sheet with id= BR, first strand: chain 'N' and resid 637 through 639 removed outlier: 6.725A pdb=" N LEU N 686 " --> pdb=" O VAL N 638 " (cutoff:3.500A) 2898 hydrogen bonds defined for protein. 7812 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: 23.57 Time building geometry restraints manager: 23.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 24125 1.37 - 1.51: 20691 1.51 - 1.66: 24148 1.66 - 1.80: 256 1.80 - 1.95: 66 Bond restraints: 69286 Sorted by residual: bond pdb=" C ASP E 679 " pdb=" N HIS E 680 " ideal model delta sigma weight residual 1.329 1.347 -0.018 1.40e-02 5.10e+03 1.71e+00 bond pdb=" CG ARG I 222 " pdb=" CD ARG I 222 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" CG ARG D 222 " pdb=" CD ARG D 222 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" CG ARG B 222 " pdb=" CD ARG B 222 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" CG ARG L 222 " pdb=" CD ARG L 222 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.65e+00 ... (remaining 69281 not shown) Histogram of bond angle deviations from ideal: 96.57 - 103.76: 700 103.76 - 110.94: 25261 110.94 - 118.13: 28273 118.13 - 125.31: 38992 125.31 - 132.50: 672 Bond angle restraints: 93898 Sorted by residual: angle pdb=" N LYS B 529 " pdb=" CA LYS B 529 " pdb=" C LYS B 529 " ideal model delta sigma weight residual 114.75 103.57 11.18 1.26e+00 6.30e-01 7.88e+01 angle pdb=" N LYS N 529 " pdb=" CA LYS N 529 " pdb=" C LYS N 529 " ideal model delta sigma weight residual 114.75 103.57 11.18 1.26e+00 6.30e-01 7.87e+01 angle pdb=" N LYS E 529 " pdb=" CA LYS E 529 " pdb=" C LYS E 529 " ideal model delta sigma weight residual 114.75 103.58 11.17 1.26e+00 6.30e-01 7.87e+01 angle pdb=" N LYS M 529 " pdb=" CA LYS M 529 " pdb=" C LYS M 529 " ideal model delta sigma weight residual 114.75 103.58 11.17 1.26e+00 6.30e-01 7.86e+01 angle pdb=" N LYS D 529 " pdb=" CA LYS D 529 " pdb=" C LYS D 529 " ideal model delta sigma weight residual 114.75 103.58 11.17 1.26e+00 6.30e-01 7.85e+01 ... (remaining 93893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.87: 41295 32.87 - 65.74: 915 65.74 - 98.61: 98 98.61 - 131.48: 14 131.48 - 164.35: 28 Dihedral angle restraints: 42350 sinusoidal: 17192 harmonic: 25158 Sorted by residual: dihedral pdb=" CA GLU D 528 " pdb=" C GLU D 528 " pdb=" N LYS D 529 " pdb=" CA LYS D 529 " ideal model delta harmonic sigma weight residual -180.00 -46.70 -133.30 0 5.00e+00 4.00e-02 7.11e+02 dihedral pdb=" CA GLU G 528 " pdb=" C GLU G 528 " pdb=" N LYS G 529 " pdb=" CA LYS G 529 " ideal model delta harmonic sigma weight residual -180.00 -46.71 -133.29 0 5.00e+00 4.00e-02 7.11e+02 dihedral pdb=" CA GLU E 528 " pdb=" C GLU E 528 " pdb=" N LYS E 529 " pdb=" CA LYS E 529 " ideal model delta harmonic sigma weight residual -180.00 -46.71 -133.29 0 5.00e+00 4.00e-02 7.11e+02 ... (remaining 42347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 6303 0.034 - 0.068: 2956 0.068 - 0.103: 1226 0.103 - 0.137: 398 0.137 - 0.171: 79 Chirality restraints: 10962 Sorted by residual: chirality pdb=" CG LEU J 225 " pdb=" CB LEU J 225 " pdb=" CD1 LEU J 225 " pdb=" CD2 LEU J 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CG LEU N 225 " pdb=" CB LEU N 225 " pdb=" CD1 LEU N 225 " pdb=" CD2 LEU N 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CG LEU A 225 " pdb=" CB LEU A 225 " pdb=" CD1 LEU A 225 " pdb=" CD2 LEU A 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 10959 not shown) Planarity restraints: 12306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 100 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.41e+00 pdb=" C LYS D 100 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS D 100 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU D 101 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 100 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C LYS F 100 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS F 100 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU F 101 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 100 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" C LYS A 100 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS A 100 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU A 101 " 0.012 2.00e-02 2.50e+03 ... (remaining 12303 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 708 2.47 - 3.08: 53887 3.08 - 3.69: 107629 3.69 - 4.29: 154992 4.29 - 4.90: 235434 Nonbonded interactions: 552650 Sorted by model distance: nonbonded pdb="MG MG I 801 " pdb=" O3A AGS I 802 " model vdw 1.863 2.170 nonbonded pdb="MG MG H 801 " pdb=" O3A AGS H 802 " model vdw 1.863 2.170 nonbonded pdb="MG MG C 801 " pdb=" O3A AGS C 802 " model vdw 1.863 2.170 nonbonded pdb="MG MG K 801 " pdb=" O3A AGS K 802 " model vdw 1.863 2.170 nonbonded pdb="MG MG F 801 " pdb=" O3A AGS F 802 " model vdw 1.864 2.170 ... (remaining 552645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set refine NCS operators NCS operators will be refined. Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 84 5.49 5 Mg 28 5.21 5 S 182 5.16 5 C 42350 2.51 5 N 12040 2.21 5 O 13748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 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: 0.050 Extract box with map and model: 7.120 Check model and map are aligned: 0.750 Convert atoms to be neutral: 0.460 Process input model: 130.510 Find NCS groups from input model: 3.970 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.030 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 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 : 0.006 0.039 69286 Z= 0.371 Angle : 0.922 11.184 93898 Z= 0.546 Chirality : 0.048 0.171 10962 Planarity : 0.004 0.036 12306 Dihedral : 15.212 164.351 26082 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 25.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -0.98 (0.09), residues: 8694 helix: -0.23 (0.08), residues: 3990 sheet: -1.02 (0.16), residues: 1050 loop : -0.85 (0.10), residues: 3654 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 178 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 181 average time/residue: 0.1712 time to fit residues: 37.0675 Evaluate side-chains 74 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.431 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0355 time to fit residues: 0.6576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 770, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.5298 > 50: distance: 0 - 1: 38.854 distance: 1 - 2: 41.004 distance: 1 - 4: 40.618 distance: 2 - 8: 39.906 distance: 4 - 5: 11.268 distance: 5 - 6: 57.084 distance: 5 - 7: 31.325 distance: 8 - 9: 40.007 distance: 9 - 10: 16.345 distance: 9 - 12: 4.359 distance: 10 - 11: 44.859 distance: 10 - 19: 41.433 distance: 12 - 13: 17.259 distance: 13 - 14: 46.184 distance: 13 - 15: 16.797 distance: 14 - 16: 57.906 distance: 15 - 17: 56.285 distance: 16 - 18: 40.650 distance: 17 - 18: 68.449 distance: 19 - 20: 28.719 distance: 20 - 21: 15.563 distance: 20 - 23: 34.840 distance: 21 - 22: 40.435 distance: 21 - 29: 34.909 distance: 23 - 24: 14.488 distance: 24 - 25: 40.979 distance: 24 - 26: 40.910 distance: 25 - 27: 37.631 distance: 27 - 28: 40.935 distance: 29 - 30: 39.790 distance: 30 - 31: 39.998 distance: 30 - 33: 58.081 distance: 31 - 32: 20.915 distance: 31 - 37: 39.942 distance: 33 - 34: 46.626 distance: 34 - 35: 20.962 distance: 34 - 36: 18.806 distance: 38 - 39: 40.435 distance: 38 - 41: 40.508 distance: 39 - 45: 4.093 distance: 41 - 42: 39.690 distance: 42 - 43: 56.976 distance: 42 - 44: 48.326 distance: 45 - 46: 37.767 distance: 46 - 47: 57.157 distance: 46 - 49: 39.789 distance: 47 - 48: 39.922 distance: 47 - 55: 46.276 distance: 49 - 50: 41.267 distance: 50 - 51: 43.471 distance: 50 - 52: 32.418 distance: 51 - 53: 28.480 distance: 52 - 54: 39.333 distance: 53 - 54: 57.426 distance: 55 - 56: 62.480 distance: 56 - 57: 13.153 distance: 57 - 58: 43.738 distance: 57 - 63: 61.814 distance: 59 - 60: 36.649 distance: 60 - 61: 55.127 distance: 63 - 64: 40.703 distance: 64 - 65: 41.097 distance: 64 - 67: 56.687 distance: 65 - 71: 4.808 distance: 67 - 68: 56.797 distance: 68 - 70: 56.672 distance: 72 - 73: 43.531 distance: 72 - 75: 40.857 distance: 73 - 74: 12.041 distance: 73 - 76: 41.619 distance: 76 - 77: 12.726 distance: 77 - 78: 22.777 distance: 77 - 80: 44.191 distance: 78 - 79: 39.723 distance: 80 - 81: 3.211 distance: 81 - 82: 37.137 distance: 82 - 83: 37.838 distance: 83 - 84: 41.116