Starting phenix.real_space_refine on Tue Jun 25 16:44:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qys_18761/06_2024/8qys_18761.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qys_18761/06_2024/8qys_18761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qys_18761/06_2024/8qys_18761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qys_18761/06_2024/8qys_18761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qys_18761/06_2024/8qys_18761.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qys_18761/06_2024/8qys_18761.pdb" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.139 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 370 5.16 5 C 36728 2.51 5 N 9884 2.21 5 O 10880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 225": "OE1" <-> "OE2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H GLU 115": "OE1" <-> "OE2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "N GLU 126": "OE1" <-> "OE2" Residue "O GLU 229": "OE1" <-> "OE2" Residue "Q GLU 106": "OE1" <-> "OE2" Residue "Q GLU 126": "OE1" <-> "OE2" Residue "R GLU 225": "OE1" <-> "OE2" Residue "S GLU 26": "OE1" <-> "OE2" Residue "T GLU 90": "OE1" <-> "OE2" Residue "T GLU 182": "OE1" <-> "OE2" Residue "U GLU 51": "OE1" <-> "OE2" Residue "V GLU 173": "OE1" <-> "OE2" Residue "V GLU 234": "OE1" <-> "OE2" Residue "Y GLU 82": "OE1" <-> "OE2" Residue "Y GLU 115": "OE1" <-> "OE2" Residue "Y GLU 125": "OE1" <-> "OE2" Residue "c GLU 106": "OE1" <-> "OE2" Residue "d GLU 58": "OE1" <-> "OE2" Residue "e GLU 126": "OE1" <-> "OE2" Residue "f GLU 229": "OE1" <-> "OE2" Residue "h GLU 106": "OE1" <-> "OE2" Residue "h GLU 126": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 57862 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1720 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1808 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 242} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 105 Chain: "C" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1744 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 6, 'TRANS': 227} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "D" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1760 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 8, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1863 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 230} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "F" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1847 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 235} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1846 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 235} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2040 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 55 Chain: "J" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1885 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 15, 'TRANS': 232} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "K" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1980 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 249} Chain: "L" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1585 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "M" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1568 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1607 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 205} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1643 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "P" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1623 Classifications: {'peptide': 208} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 201} Chain: "Q" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1475 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 190} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1720 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "S" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1808 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 242} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 105 Chain: "T" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1744 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 6, 'TRANS': 227} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "U" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1760 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 8, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "V" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1863 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 230} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "W" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1847 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 235} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "X" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1846 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 235} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "Y" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 2040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2040 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 55 Chain: "a" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1885 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 15, 'TRANS': 232} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "b" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1980 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 249} Chain: "c" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1585 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "d" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1568 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "e" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1607 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 205} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "f" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1643 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "g" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1623 Classifications: {'peptide': 208} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 201} Chain: "h" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1475 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 190} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 22.03, per 1000 atoms: 0.38 Number of scatterers: 57862 At special positions: 0 Unit cell: (235.625, 216.775, 143.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 370 16.00 O 10880 8.00 N 9884 7.00 C 36728 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: 17.10 Conformation dependent library (CDL) restraints added in 7.9 seconds 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14048 Finding SS restraints... Secondary structure from input PDB file: 211 helices and 104 sheets defined 36.7% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.30 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 79 through 82 Processing helix chain 'A' and resid 83 through 100 removed outlier: 3.850A pdb=" N VAL A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 124 removed outlier: 3.657A pdb=" N LEU A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 removed outlier: 3.600A pdb=" N GLY A 170 " --> pdb=" O ASN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 198 removed outlier: 3.622A pdb=" N HIS A 189 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.689A pdb=" N GLU B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 31 removed outlier: 3.939A pdb=" N ALA B 31 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 82 through 101 removed outlier: 3.961A pdb=" N LEU B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 removed outlier: 4.482A pdb=" N ALA B 113 " --> pdb=" O GLN B 109 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 178 Processing helix chain 'B' and resid 185 through 200 Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 233 through 246 Processing helix chain 'C' and resid 16 through 27 removed outlier: 3.775A pdb=" N GLU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 98 removed outlier: 3.566A pdb=" N ALA C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 118 removed outlier: 3.592A pdb=" N ILE C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 174 removed outlier: 4.165A pdb=" N VAL C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 184 through 196 removed outlier: 3.671A pdb=" N ILE C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'D' and resid 21 through 30 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 60 through 64 removed outlier: 3.903A pdb=" N ILE D 64 " --> pdb=" O PRO D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 104 Processing helix chain 'D' and resid 108 through 121 removed outlier: 3.991A pdb=" N ALA D 115 " --> pdb=" O SER D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.606A pdb=" N SER D 180 " --> pdb=" O GLY D 176 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 203 removed outlier: 3.560A pdb=" N ALA D 194 " --> pdb=" O THR D 190 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS D 196 " --> pdb=" O LYS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 239 removed outlier: 3.808A pdb=" N GLU D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 removed outlier: 4.040A pdb=" N ASP E 7 " --> pdb=" O ASN E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 29 removed outlier: 3.637A pdb=" N GLU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 99 removed outlier: 4.365A pdb=" N ARG E 82 " --> pdb=" O THR E 78 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE E 87 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 3.840A pdb=" N SER E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 175 Processing helix chain 'E' and resid 177 through 181 removed outlier: 4.158A pdb=" N MET E 180 " --> pdb=" O SER E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 removed outlier: 3.674A pdb=" N GLU E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 199 " --> pdb=" O LEU E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 230 Processing helix chain 'F' and resid 21 through 31 removed outlier: 3.569A pdb=" N VAL F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 104 removed outlier: 3.562A pdb=" N ASN F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY F 104 " --> pdb=" O ARG F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 123 removed outlier: 4.039A pdb=" N TYR F 123 " --> pdb=" O TYR F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 126 No H-bonds generated for 'chain 'F' and resid 124 through 126' Processing helix chain 'F' and resid 170 through 179 removed outlier: 3.972A pdb=" N LYS F 179 " --> pdb=" O THR F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 201 Processing helix chain 'F' and resid 229 through 244 removed outlier: 3.666A pdb=" N LEU F 244 " --> pdb=" O ALA F 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 36 removed outlier: 3.762A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY G 36 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 removed outlier: 4.290A pdb=" N SER G 89 " --> pdb=" O ALA G 85 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN G 92 " --> pdb=" O ARG G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 124 removed outlier: 3.632A pdb=" N LEU G 114 " --> pdb=" O PRO G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 127 No H-bonds generated for 'chain 'G' and resid 125 through 127' Processing helix chain 'G' and resid 171 through 184 removed outlier: 3.544A pdb=" N LYS G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 231 through 242 Processing helix chain 'H' and resid 55 through 71 Processing helix chain 'H' and resid 73 through 88 removed outlier: 3.893A pdb=" N LEU H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 107 Processing helix chain 'H' and resid 120 through 124 Processing helix chain 'H' and resid 129 through 138 Processing helix chain 'I' and resid 31 through 46 removed outlier: 3.679A pdb=" N GLU I 36 " --> pdb=" O PRO I 32 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL I 37 " --> pdb=" O GLU I 33 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG I 38 " --> pdb=" O ASP I 34 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU I 39 " --> pdb=" O ARG I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 86 Processing helix chain 'I' and resid 144 through 154 removed outlier: 4.280A pdb=" N GLN I 148 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 226 Processing helix chain 'I' and resid 244 through 249 Processing helix chain 'I' and resid 250 through 254 Processing helix chain 'I' and resid 265 through 279 removed outlier: 3.621A pdb=" N SER I 269 " --> pdb=" O ASN I 265 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 25 No H-bonds generated for 'chain 'J' and resid 23 through 25' Processing helix chain 'J' and resid 26 through 40 Processing helix chain 'J' and resid 98 through 114 removed outlier: 3.542A pdb=" N PHE J 102 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 134 Processing helix chain 'J' and resid 147 through 159 removed outlier: 6.143A pdb=" N ASN J 153 " --> pdb=" O LYS J 149 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LYS J 154 " --> pdb=" O SER J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 196 removed outlier: 3.900A pdb=" N SER J 196 " --> pdb=" O ASP J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 229 removed outlier: 3.901A pdb=" N TRP J 227 " --> pdb=" O TYR J 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 31 removed outlier: 3.826A pdb=" N VAL K 24 " --> pdb=" O ARG K 20 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 114 removed outlier: 3.757A pdb=" N MET K 97 " --> pdb=" O ALA K 93 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE K 102 " --> pdb=" O THR K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 133 removed outlier: 3.789A pdb=" N ALA K 122 " --> pdb=" O ARG K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 185 Processing helix chain 'K' and resid 190 through 208 Processing helix chain 'L' and resid 56 through 79 removed outlier: 4.154A pdb=" N THR L 62 " --> pdb=" O THR L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 97 removed outlier: 3.786A pdb=" N LEU L 87 " --> pdb=" O LYS L 83 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET L 88 " --> pdb=" O PRO L 84 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER L 89 " --> pdb=" O TYR L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 154 removed outlier: 4.065A pdb=" N SER L 152 " --> pdb=" O GLY L 148 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU L 153 " --> pdb=" O MET L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 173 removed outlier: 3.699A pdb=" N MET L 171 " --> pdb=" O ILE L 167 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN L 173 " --> pdb=" O GLN L 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 62 Processing helix chain 'M' and resid 63 through 72 removed outlier: 3.779A pdb=" N TYR M 67 " --> pdb=" O ASN M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 95 removed outlier: 3.761A pdb=" N ARG M 86 " --> pdb=" O ASN M 82 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG M 95 " --> pdb=" O CYS M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 147 removed outlier: 4.175A pdb=" N LEU M 138 " --> pdb=" O TYR M 134 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER M 141 " --> pdb=" O PHE M 137 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE M 142 " --> pdb=" O LEU M 138 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR M 146 " --> pdb=" O ILE M 142 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR M 147 " --> pdb=" O LEU M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 171 removed outlier: 3.642A pdb=" N VAL M 157 " --> pdb=" O ARG M 153 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU M 158 " --> pdb=" O GLU M 154 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU M 167 " --> pdb=" O CYS M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 130 Processing helix chain 'N' and resid 134 through 149 removed outlier: 4.092A pdb=" N TYR N 149 " --> pdb=" O MET N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 192 removed outlier: 4.236A pdb=" N VAL N 192 " --> pdb=" O SER N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 202 Processing helix chain 'N' and resid 207 through 226 removed outlier: 3.688A pdb=" N ARG N 225 " --> pdb=" O GLN N 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 251 through 258 Processing helix chain 'O' and resid 88 through 108 removed outlier: 3.573A pdb=" N THR O 93 " --> pdb=" O CYS O 89 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU O 97 " --> pdb=" O THR O 93 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA O 98 " --> pdb=" O LYS O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 126 removed outlier: 3.505A pdb=" N ILE O 116 " --> pdb=" O THR O 112 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA O 117 " --> pdb=" O THR O 113 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA O 118 " --> pdb=" O GLY O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 181 removed outlier: 4.336A pdb=" N LEU O 176 " --> pdb=" O MET O 172 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU O 177 " --> pdb=" O LEU O 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 214 removed outlier: 3.836A pdb=" N MET O 200 " --> pdb=" O LEU O 196 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG O 201 " --> pdb=" O ASP O 197 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU O 212 " --> pdb=" O ILE O 208 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG O 213 " --> pdb=" O SER O 209 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP O 214 " --> pdb=" O ALA O 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 123 removed outlier: 3.746A pdb=" N GLY P 123 " --> pdb=" O GLU P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 147 Processing helix chain 'P' and resid 186 through 202 removed outlier: 4.277A pdb=" N LEU P 190 " --> pdb=" O TYR P 186 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLN P 192 " --> pdb=" O ALA P 188 " (cutoff:3.500A) Proline residue: P 193 - end of helix Processing helix chain 'P' and resid 206 through 224 Processing helix chain 'Q' and resid 84 through 105 Processing helix chain 'Q' and resid 109 through 124 removed outlier: 3.550A pdb=" N ALA Q 113 " --> pdb=" O LEU Q 109 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG Q 123 " --> pdb=" O GLU Q 119 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR Q 124 " --> pdb=" O MET Q 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 169 through 177 Processing helix chain 'Q' and resid 182 through 200 removed outlier: 3.719A pdb=" N ALA Q 197 " --> pdb=" O ALA Q 193 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU Q 199 " --> pdb=" O ALA Q 195 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG Q 200 " --> pdb=" O LEU Q 196 " (cutoff:3.500A) Processing helix chain 'Q' and resid 224 through 228 Processing helix chain 'R' and resid 19 through 31 Processing helix chain 'R' and resid 79 through 82 Processing helix chain 'R' and resid 83 through 100 removed outlier: 3.848A pdb=" N VAL R 100 " --> pdb=" O GLN R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 124 removed outlier: 3.656A pdb=" N LEU R 110 " --> pdb=" O PRO R 106 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR R 122 " --> pdb=" O MET R 118 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN R 123 " --> pdb=" O GLN R 119 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER R 124 " --> pdb=" O GLU R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 175 removed outlier: 3.602A pdb=" N GLY R 170 " --> pdb=" O ASN R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 198 removed outlier: 3.622A pdb=" N HIS R 189 " --> pdb=" O GLU R 185 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER R 198 " --> pdb=" O THR R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 232 Processing helix chain 'S' and resid 18 through 26 removed outlier: 3.688A pdb=" N GLU S 26 " --> pdb=" O GLU S 22 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 31 removed outlier: 3.939A pdb=" N ALA S 31 " --> pdb=" O ILE S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 81 No H-bonds generated for 'chain 'S' and resid 79 through 81' Processing helix chain 'S' and resid 82 through 101 removed outlier: 3.959A pdb=" N LEU S 86 " --> pdb=" O ASP S 82 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN S 88 " --> pdb=" O ASN S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 121 removed outlier: 4.480A pdb=" N ALA S 113 " --> pdb=" O GLN S 109 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE S 117 " --> pdb=" O ALA S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 167 through 178 Processing helix chain 'S' and resid 185 through 200 Processing helix chain 'S' and resid 229 through 232 Processing helix chain 'S' and resid 233 through 246 Processing helix chain 'T' and resid 16 through 27 removed outlier: 3.775A pdb=" N GLU T 20 " --> pdb=" O LEU T 16 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 98 removed outlier: 3.568A pdb=" N ALA T 80 " --> pdb=" O LEU T 76 " (cutoff:3.500A) Processing helix chain 'T' and resid 103 through 118 removed outlier: 3.588A pdb=" N ILE T 107 " --> pdb=" O THR T 103 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR T 118 " --> pdb=" O LEU T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 174 removed outlier: 4.168A pdb=" N VAL T 168 " --> pdb=" O GLY T 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 177 through 182 Processing helix chain 'T' and resid 184 through 196 removed outlier: 3.669A pdb=" N ILE T 188 " --> pdb=" O ASP T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 221 through 233 Processing helix chain 'U' and resid 21 through 30 Processing helix chain 'U' and resid 31 through 33 No H-bonds generated for 'chain 'U' and resid 31 through 33' Processing helix chain 'U' and resid 60 through 64 removed outlier: 3.902A pdb=" N ILE U 64 " --> pdb=" O PRO U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 104 Processing helix chain 'U' and resid 108 through 121 removed outlier: 3.991A pdb=" N ALA U 115 " --> pdb=" O SER U 111 " (cutoff:3.500A) Processing helix chain 'U' and resid 175 through 185 removed outlier: 3.605A pdb=" N SER U 180 " --> pdb=" O GLY U 176 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU U 181 " --> pdb=" O ALA U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 190 through 204 removed outlier: 3.559A pdb=" N ALA U 194 " --> pdb=" O THR U 190 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE U 195 " --> pdb=" O LEU U 191 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS U 196 " --> pdb=" O LYS U 192 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN U 204 " --> pdb=" O ILE U 200 " (cutoff:3.500A) Processing helix chain 'U' and resid 230 through 239 removed outlier: 3.808A pdb=" N GLU U 236 " --> pdb=" O GLU U 232 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL U 237 " --> pdb=" O GLU U 233 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 7 removed outlier: 4.040A pdb=" N ASP V 7 " --> pdb=" O ASN V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 19 through 29 removed outlier: 3.637A pdb=" N GLU V 23 " --> pdb=" O ILE V 19 " (cutoff:3.500A) Processing helix chain 'V' and resid 78 through 99 removed outlier: 4.365A pdb=" N ARG V 82 " --> pdb=" O THR V 78 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU V 83 " --> pdb=" O ALA V 79 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE V 87 " --> pdb=" O LEU V 83 " (cutoff:3.500A) Processing helix chain 'V' and resid 104 through 118 removed outlier: 3.840A pdb=" N SER V 110 " --> pdb=" O SER V 106 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE V 118 " --> pdb=" O SER V 114 " (cutoff:3.500A) Processing helix chain 'V' and resid 165 through 175 Processing helix chain 'V' and resid 177 through 181 removed outlier: 4.157A pdb=" N MET V 180 " --> pdb=" O SER V 177 " (cutoff:3.500A) Processing helix chain 'V' and resid 183 through 199 removed outlier: 3.674A pdb=" N GLU V 197 " --> pdb=" O ARG V 193 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR V 198 " --> pdb=" O ALA V 194 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU V 199 " --> pdb=" O LEU V 195 " (cutoff:3.500A) Processing helix chain 'V' and resid 225 through 230 Processing helix chain 'W' and resid 21 through 31 removed outlier: 3.570A pdb=" N VAL W 31 " --> pdb=" O ALA W 27 " (cutoff:3.500A) Processing helix chain 'W' and resid 81 through 104 removed outlier: 3.563A pdb=" N ASN W 102 " --> pdb=" O ASN W 98 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY W 104 " --> pdb=" O ARG W 100 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 123 removed outlier: 4.039A pdb=" N TYR W 123 " --> pdb=" O TYR W 119 " (cutoff:3.500A) Processing helix chain 'W' and resid 124 through 126 No H-bonds generated for 'chain 'W' and resid 124 through 126' Processing helix chain 'W' and resid 170 through 179 removed outlier: 3.972A pdb=" N LYS W 179 " --> pdb=" O THR W 175 " (cutoff:3.500A) Processing helix chain 'W' and resid 189 through 201 Processing helix chain 'W' and resid 229 through 244 removed outlier: 3.666A pdb=" N LEU W 244 " --> pdb=" O ALA W 240 " (cutoff:3.500A) Processing helix chain 'X' and resid 22 through 36 removed outlier: 3.762A pdb=" N ILE X 32 " --> pdb=" O ALA X 28 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASN X 33 " --> pdb=" O PHE X 29 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN X 34 " --> pdb=" O LYS X 30 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY X 35 " --> pdb=" O ALA X 31 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY X 36 " --> pdb=" O ILE X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 106 removed outlier: 4.290A pdb=" N SER X 89 " --> pdb=" O ALA X 85 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN X 92 " --> pdb=" O ARG X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 110 through 124 removed outlier: 3.632A pdb=" N LEU X 114 " --> pdb=" O PRO X 110 " (cutoff:3.500A) Processing helix chain 'X' and resid 125 through 127 No H-bonds generated for 'chain 'X' and resid 125 through 127' Processing helix chain 'X' and resid 171 through 184 removed outlier: 3.544A pdb=" N LYS X 184 " --> pdb=" O GLU X 180 " (cutoff:3.500A) Processing helix chain 'X' and resid 190 through 207 Processing helix chain 'X' and resid 231 through 242 Processing helix chain 'Y' and resid 55 through 71 Processing helix chain 'Y' and resid 73 through 88 removed outlier: 3.893A pdb=" N LEU Y 77 " --> pdb=" O LEU Y 73 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN Y 88 " --> pdb=" O LYS Y 84 " (cutoff:3.500A) Processing helix chain 'Y' and resid 102 through 107 Processing helix chain 'Y' and resid 120 through 124 Processing helix chain 'Y' and resid 129 through 138 Processing helix chain 'Z' and resid 31 through 46 removed outlier: 3.679A pdb=" N GLU Z 36 " --> pdb=" O PRO Z 32 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL Z 37 " --> pdb=" O GLU Z 33 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG Z 38 " --> pdb=" O ASP Z 34 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU Z 39 " --> pdb=" O ARG Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 86 Processing helix chain 'Z' and resid 144 through 154 removed outlier: 4.280A pdb=" N GLN Z 148 " --> pdb=" O ASP Z 144 " (cutoff:3.500A) Processing helix chain 'Z' and resid 214 through 226 Processing helix chain 'Z' and resid 244 through 249 Processing helix chain 'Z' and resid 250 through 254 Processing helix chain 'Z' and resid 265 through 279 removed outlier: 3.621A pdb=" N SER Z 269 " --> pdb=" O ASN Z 265 " (cutoff:3.500A) Processing helix chain 'a' and resid 23 through 25 No H-bonds generated for 'chain 'a' and resid 23 through 25' Processing helix chain 'a' and resid 26 through 40 Processing helix chain 'a' and resid 98 through 114 removed outlier: 3.542A pdb=" N PHE a 102 " --> pdb=" O LYS a 98 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 134 Processing helix chain 'a' and resid 147 through 159 removed outlier: 6.144A pdb=" N ASN a 153 " --> pdb=" O LYS a 149 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LYS a 154 " --> pdb=" O SER a 150 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 196 removed outlier: 3.899A pdb=" N SER a 196 " --> pdb=" O ASP a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 213 through 229 removed outlier: 3.901A pdb=" N TRP a 227 " --> pdb=" O TYR a 223 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 31 removed outlier: 3.827A pdb=" N VAL b 24 " --> pdb=" O ARG b 20 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS b 31 " --> pdb=" O ALA b 27 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 114 removed outlier: 3.756A pdb=" N MET b 97 " --> pdb=" O ALA b 93 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE b 102 " --> pdb=" O THR b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 118 through 133 removed outlier: 3.790A pdb=" N ALA b 122 " --> pdb=" O ARG b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 174 through 185 Processing helix chain 'b' and resid 190 through 208 Processing helix chain 'c' and resid 56 through 79 removed outlier: 4.157A pdb=" N THR c 62 " --> pdb=" O THR c 58 " (cutoff:3.500A) Processing helix chain 'c' and resid 83 through 97 removed outlier: 3.786A pdb=" N LEU c 87 " --> pdb=" O LYS c 83 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET c 88 " --> pdb=" O PRO c 84 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER c 89 " --> pdb=" O TYR c 85 " (cutoff:3.500A) Processing helix chain 'c' and resid 143 through 145 No H-bonds generated for 'chain 'c' and resid 143 through 145' Processing helix chain 'c' and resid 146 through 154 removed outlier: 4.066A pdb=" N SER c 152 " --> pdb=" O GLY c 148 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU c 153 " --> pdb=" O MET c 149 " (cutoff:3.500A) Processing helix chain 'c' and resid 159 through 173 removed outlier: 3.698A pdb=" N MET c 171 " --> pdb=" O ILE c 167 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASN c 173 " --> pdb=" O GLN c 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 62 Processing helix chain 'd' and resid 63 through 72 removed outlier: 3.774A pdb=" N TYR d 67 " --> pdb=" O ASN d 63 " (cutoff:3.500A) Processing helix chain 'd' and resid 76 through 95 removed outlier: 3.759A pdb=" N ARG d 86 " --> pdb=" O ASN d 82 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG d 95 " --> pdb=" O CYS d 91 " (cutoff:3.500A) Processing helix chain 'd' and resid 134 through 147 removed outlier: 4.177A pdb=" N LEU d 138 " --> pdb=" O TYR d 134 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER d 141 " --> pdb=" O PHE d 137 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE d 142 " --> pdb=" O LEU d 138 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR d 146 " --> pdb=" O ILE d 142 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR d 147 " --> pdb=" O LEU d 143 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 171 removed outlier: 3.643A pdb=" N VAL d 157 " --> pdb=" O ARG d 153 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU d 158 " --> pdb=" O GLU d 154 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU d 167 " --> pdb=" O CYS d 163 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 130 Processing helix chain 'e' and resid 134 through 149 removed outlier: 4.092A pdb=" N TYR e 149 " --> pdb=" O MET e 145 " (cutoff:3.500A) Processing helix chain 'e' and resid 188 through 192 removed outlier: 4.238A pdb=" N VAL e 192 " --> pdb=" O SER e 189 " (cutoff:3.500A) Processing helix chain 'e' and resid 194 through 202 Processing helix chain 'e' and resid 207 through 226 removed outlier: 3.689A pdb=" N ARG e 225 " --> pdb=" O GLN e 221 " (cutoff:3.500A) Processing helix chain 'e' and resid 251 through 258 Processing helix chain 'f' and resid 88 through 108 removed outlier: 3.578A pdb=" N THR f 93 " --> pdb=" O CYS f 89 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU f 97 " --> pdb=" O THR f 93 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA f 98 " --> pdb=" O LYS f 94 " (cutoff:3.500A) Processing helix chain 'f' and resid 112 through 126 removed outlier: 3.506A pdb=" N ILE f 116 " --> pdb=" O THR f 112 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA f 117 " --> pdb=" O THR f 113 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA f 118 " --> pdb=" O GLY f 114 " (cutoff:3.500A) Processing helix chain 'f' and resid 172 through 181 removed outlier: 4.332A pdb=" N LEU f 176 " --> pdb=" O MET f 172 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU f 177 " --> pdb=" O LEU f 173 " (cutoff:3.500A) Processing helix chain 'f' and resid 195 through 214 removed outlier: 3.825A pdb=" N MET f 200 " --> pdb=" O LEU f 196 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG f 201 " --> pdb=" O ASP f 197 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU f 212 " --> pdb=" O ILE f 208 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG f 213 " --> pdb=" O SER f 209 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP f 214 " --> pdb=" O ALA f 210 " (cutoff:3.500A) Processing helix chain 'g' and resid 102 through 123 removed outlier: 3.745A pdb=" N GLY g 123 " --> pdb=" O GLU g 119 " (cutoff:3.500A) Processing helix chain 'g' and resid 129 through 147 Processing helix chain 'g' and resid 186 through 202 removed outlier: 4.277A pdb=" N LEU g 190 " --> pdb=" O TYR g 186 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN g 192 " --> pdb=" O ALA g 188 " (cutoff:3.500A) Proline residue: g 193 - end of helix Processing helix chain 'g' and resid 206 through 224 Processing helix chain 'h' and resid 84 through 105 Processing helix chain 'h' and resid 109 through 124 removed outlier: 3.550A pdb=" N ALA h 113 " --> pdb=" O LEU h 109 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG h 123 " --> pdb=" O GLU h 119 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR h 124 " --> pdb=" O MET h 120 " (cutoff:3.500A) Processing helix chain 'h' and resid 169 through 177 Processing helix chain 'h' and resid 182 through 200 removed outlier: 3.717A pdb=" N ALA h 197 " --> pdb=" O ALA h 193 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU h 199 " --> pdb=" O ALA h 195 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG h 200 " --> pdb=" O LEU h 196 " (cutoff:3.500A) Processing helix chain 'h' and resid 224 through 228 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA3, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.511A pdb=" N ILE B 137 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY B 138 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN B 146 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 214 through 215 removed outlier: 3.820A pdb=" N ARG B 226 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 218 through 219 removed outlier: 4.282A pdb=" N GLU B 219 " --> pdb=" O LYS B 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 32 through 33 removed outlier: 3.530A pdb=" N ALA C 32 " --> pdb=" O ILE C 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 35 through 36 removed outlier: 3.501A pdb=" N VAL C 35 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 46 Processing sheet with id=AA9, first strand: chain 'C' and resid 62 through 64 removed outlier: 3.889A pdb=" N VAL C 134 " --> pdb=" O CYS C 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 209 through 210 Processing sheet with id=AB2, first strand: chain 'D' and resid 37 through 42 Processing sheet with id=AB3, first strand: chain 'D' and resid 67 through 71 removed outlier: 3.646A pdb=" N CYS D 76 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 77 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA D 140 " --> pdb=" O SER D 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 67 through 71 removed outlier: 3.646A pdb=" N CYS D 76 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 77 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 218 through 220 Processing sheet with id=AB6, first strand: chain 'E' and resid 44 through 46 removed outlier: 3.905A pdb=" N VAL E 215 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR E 222 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 135 through 136 removed outlier: 3.547A pdb=" N GLY E 136 " --> pdb=" O HIS E 143 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE E 144 " --> pdb=" O CYS E 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 163 through 167 removed outlier: 4.816A pdb=" N THR F 36 " --> pdb=" O GLU F 51 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY F 45 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU F 213 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 163 through 167 removed outlier: 4.816A pdb=" N THR F 36 " --> pdb=" O GLU F 51 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY F 45 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 217 " --> pdb=" O VAL F 46 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER F 215 " --> pdb=" O PHE F 48 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP F 216 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU F 226 " --> pdb=" O TRP F 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 69 through 71 removed outlier: 6.512A pdb=" N VAL F 74 " --> pdb=" O VAL F 70 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 140 through 141 removed outlier: 3.609A pdb=" N GLN F 148 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 5 through 6 removed outlier: 5.616A pdb=" N SER G 5 " --> pdb=" O VAL I 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 165 through 169 removed outlier: 3.586A pdb=" N ARG G 228 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 70 through 73 removed outlier: 3.507A pdb=" N CYS G 78 " --> pdb=" O PHE G 70 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY G 77 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE G 141 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY G 142 " --> pdb=" O GLN G 150 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 70 through 73 removed outlier: 3.507A pdb=" N CYS G 78 " --> pdb=" O PHE G 70 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY G 77 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE G 141 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR G 152 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS G 153 " --> pdb=" O CYS G 161 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 48 through 49 removed outlier: 4.155A pdb=" N ARG I 48 " --> pdb=" O LYS I 100 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS I 100 " --> pdb=" O ARG I 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'I' and resid 135 through 137 removed outlier: 6.535A pdb=" N ALA I 74 " --> pdb=" O CYS I 137 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS I 169 " --> pdb=" O ILE I 75 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 93 through 95 Processing sheet with id=AD1, first strand: chain 'I' and resid 212 through 213 Processing sheet with id=AD2, first strand: chain 'J' and resid 2 through 4 Processing sheet with id=AD3, first strand: chain 'J' and resid 77 through 79 removed outlier: 6.146A pdb=" N THR J 16 " --> pdb=" O VAL J 86 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LEU J 88 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU J 18 " --> pdb=" O LEU J 88 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU J 17 " --> pdb=" O ILE J 119 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU J 121 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N MET J 19 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 124 through 125 removed outlier: 5.388A pdb=" N SER J 124 " --> pdb=" O VAL J 208 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'K' and resid 167 through 170 removed outlier: 3.744A pdb=" N ALA K 59 " --> pdb=" O ASP K 217 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP K 217 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE K 216 " --> pdb=" O TYR K 232 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LEU K 218 " --> pdb=" O ARG K 230 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ARG K 230 " --> pdb=" O LEU K 218 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 63 through 64 removed outlier: 3.672A pdb=" N ALA K 63 " --> pdb=" O ASP K 71 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 143 through 144 Processing sheet with id=AD8, first strand: chain 'K' and resid 256 through 261 removed outlier: 3.588A pdb=" N THR K 256 " --> pdb=" O THR L 199 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA L 23 " --> pdb=" O MET L 12 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP L 25 " --> pdb=" O ALA L 10 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ALA L 10 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 49 through 51 Processing sheet with id=AE1, first strand: chain 'M' and resid 5 through 7 removed outlier: 3.500A pdb=" N GLY M 6 " --> pdb=" O ALA M 130 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA M 130 " --> pdb=" O GLY M 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'M' and resid 15 through 16 removed outlier: 3.582A pdb=" N ILE M 182 " --> pdb=" O HIS M 189 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP M 184 " --> pdb=" O GLY M 187 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY M 187 " --> pdb=" O ASP M 184 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 36 through 37 removed outlier: 3.523A pdb=" N PHE M 36 " --> pdb=" O LEU M 44 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU M 102 " --> pdb=" O MET M 118 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET M 118 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR M 116 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 177 through 178 Processing sheet with id=AE5, first strand: chain 'N' and resid 184 through 186 removed outlier: 3.609A pdb=" N PHE N 65 " --> pdb=" O ILE N 72 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL N 233 " --> pdb=" O SER N 248 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER N 248 " --> pdb=" O VAL N 233 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU N 235 " --> pdb=" O VAL N 246 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 94 through 97 removed outlier: 4.493A pdb=" N ILE N 96 " --> pdb=" O LEU N 100 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU N 100 " --> pdb=" O ILE N 96 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 157 through 158 Processing sheet with id=AE8, first strand: chain 'O' and resid 166 through 167 removed outlier: 5.153A pdb=" N THR O 39 " --> pdb=" O ASP O 54 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP O 54 " --> pdb=" O THR O 39 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA O 220 " --> pdb=" O THR O 55 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.973A pdb=" N LEU O 57 " --> pdb=" O HIS O 64 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU O 59 " --> pdb=" O SER O 62 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 72 through 75 removed outlier: 6.818A pdb=" N THR O 78 " --> pdb=" O LEU O 74 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR O 135 " --> pdb=" O SER O 83 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 226 through 227 Processing sheet with id=AF3, first strand: chain 'P' and resid 181 through 182 removed outlier: 3.517A pdb=" N VAL P 59 " --> pdb=" O VAL P 66 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL P 66 " --> pdb=" O VAL P 59 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR P 236 " --> pdb=" O GLU P 243 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 73 through 75 removed outlier: 7.088A pdb=" N GLY P 73 " --> pdb=" O ARG P 80 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU P 78 " --> pdb=" O TYR P 75 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 87 through 88 removed outlier: 3.757A pdb=" N GLY P 158 " --> pdb=" O MET P 95 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR P 154 " --> pdb=" O SER P 99 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE P 157 " --> pdb=" O GLY P 168 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR P 177 " --> pdb=" O TYR P 169 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 159 through 162 removed outlier: 3.973A pdb=" N MET Q 38 " --> pdb=" O GLY Q 49 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL Q 40 " --> pdb=" O VAL Q 47 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY Q 45 " --> pdb=" O PHE Q 42 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 76 through 77 Processing sheet with id=AF8, first strand: chain 'R' and resid 35 through 39 Processing sheet with id=AF9, first strand: chain 'R' and resid 67 through 68 Processing sheet with id=AG1, first strand: chain 'S' and resid 73 through 75 removed outlier: 3.501A pdb=" N ALA S 73 " --> pdb=" O ILE S 137 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE S 137 " --> pdb=" O ALA S 73 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY S 138 " --> pdb=" O GLN S 146 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN S 146 " --> pdb=" O GLY S 138 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 214 through 215 removed outlier: 3.822A pdb=" N ARG S 226 " --> pdb=" O THR S 215 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 218 through 219 removed outlier: 4.278A pdb=" N GLU S 219 " --> pdb=" O LYS S 222 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'T' and resid 32 through 33 removed outlier: 3.520A pdb=" N ALA T 32 " --> pdb=" O ILE T 161 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 35 through 36 Processing sheet with id=AG6, first strand: chain 'T' and resid 45 through 46 Processing sheet with id=AG7, first strand: chain 'T' and resid 62 through 64 removed outlier: 3.888A pdb=" N VAL T 134 " --> pdb=" O CYS T 70 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'T' and resid 209 through 210 Processing sheet with id=AG9, first strand: chain 'U' and resid 37 through 42 Processing sheet with id=AH1, first strand: chain 'U' and resid 67 through 69 removed outlier: 3.654A pdb=" N CYS U 76 " --> pdb=" O VAL U 68 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA U 77 " --> pdb=" O LEU U 142 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA U 140 " --> pdb=" O SER U 79 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'U' and resid 67 through 69 removed outlier: 3.654A pdb=" N CYS U 76 " --> pdb=" O VAL U 68 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA U 77 " --> pdb=" O LEU U 142 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'U' and resid 218 through 220 Processing sheet with id=AH4, first strand: chain 'V' and resid 44 through 46 removed outlier: 3.905A pdb=" N VAL V 215 " --> pdb=" O ALA V 44 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR V 222 " --> pdb=" O ILE V 214 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'V' and resid 135 through 136 removed outlier: 3.546A pdb=" N GLY V 136 " --> pdb=" O HIS V 143 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE V 144 " --> pdb=" O CYS V 156 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'W' and resid 163 through 167 removed outlier: 4.816A pdb=" N THR W 36 " --> pdb=" O GLU W 51 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY W 45 " --> pdb=" O CYS W 42 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU W 213 " --> pdb=" O VAL W 50 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'W' and resid 163 through 167 removed outlier: 4.816A pdb=" N THR W 36 " --> pdb=" O GLU W 51 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY W 45 " --> pdb=" O CYS W 42 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL W 217 " --> pdb=" O VAL W 46 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER W 215 " --> pdb=" O PHE W 48 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP W 216 " --> pdb=" O GLU W 226 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU W 226 " --> pdb=" O TRP W 216 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'W' and resid 69 through 71 removed outlier: 6.513A pdb=" N VAL W 74 " --> pdb=" O VAL W 70 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'W' and resid 140 through 141 removed outlier: 3.610A pdb=" N GLN W 148 " --> pdb=" O SER W 140 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'X' and resid 5 through 6 removed outlier: 5.616A pdb=" N SER X 5 " --> pdb=" O VAL Z 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'X' and resid 165 through 169 removed outlier: 3.586A pdb=" N ARG X 228 " --> pdb=" O VAL X 219 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'X' and resid 70 through 73 removed outlier: 3.506A pdb=" N CYS X 78 " --> pdb=" O PHE X 70 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE X 76 " --> pdb=" O ILE X 72 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY X 77 " --> pdb=" O ILE X 141 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE X 141 " --> pdb=" O GLY X 77 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY X 142 " --> pdb=" O GLN X 150 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'X' and resid 70 through 73 removed outlier: 3.506A pdb=" N CYS X 78 " --> pdb=" O PHE X 70 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE X 76 " --> pdb=" O ILE X 72 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY X 77 " --> pdb=" O ILE X 141 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE X 141 " --> pdb=" O GLY X 77 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR X 152 " --> pdb=" O LEU X 140 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS X 153 " --> pdb=" O CYS X 161 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Z' and resid 48 through 49 removed outlier: 4.155A pdb=" N ARG Z 48 " --> pdb=" O LYS Z 100 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS Z 100 " --> pdb=" O ARG Z 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'Z' and resid 135 through 137 removed outlier: 6.538A pdb=" N ALA Z 74 " --> pdb=" O CYS Z 137 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS Z 169 " --> pdb=" O ILE Z 75 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Z' and resid 93 through 95 Processing sheet with id=AI8, first strand: chain 'Z' and resid 212 through 213 Processing sheet with id=AI9, first strand: chain 'a' and resid 2 through 4 Processing sheet with id=AJ1, first strand: chain 'a' and resid 77 through 79 removed outlier: 6.147A pdb=" N THR a 16 " --> pdb=" O VAL a 86 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LEU a 88 " --> pdb=" O THR a 16 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU a 18 " --> pdb=" O LEU a 88 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU a 17 " --> pdb=" O ILE a 119 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU a 121 " --> pdb=" O LEU a 17 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N MET a 19 " --> pdb=" O LEU a 121 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'a' and resid 124 through 125 removed outlier: 5.389A pdb=" N SER a 124 " --> pdb=" O VAL a 208 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'b' and resid 167 through 170 removed outlier: 3.744A pdb=" N ALA b 59 " --> pdb=" O ASP b 217 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP b 217 " --> pdb=" O ALA b 59 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE b 216 " --> pdb=" O TYR b 232 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N LEU b 218 " --> pdb=" O ARG b 230 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ARG b 230 " --> pdb=" O LEU b 218 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'b' and resid 63 through 64 removed outlier: 3.673A pdb=" N ALA b 63 " --> pdb=" O ASP b 71 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'b' and resid 143 through 144 Processing sheet with id=AJ6, first strand: chain 'b' and resid 256 through 261 removed outlier: 3.589A pdb=" N THR b 256 " --> pdb=" O THR c 199 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA c 23 " --> pdb=" O MET c 12 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP c 25 " --> pdb=" O ALA c 10 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ALA c 10 " --> pdb=" O ASP c 25 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'c' and resid 49 through 51 Processing sheet with id=AJ8, first strand: chain 'd' and resid 5 through 7 removed outlier: 3.525A pdb=" N ALA d 130 " --> pdb=" O GLY d 6 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'd' and resid 15 through 16 removed outlier: 3.582A pdb=" N ILE d 182 " --> pdb=" O HIS d 189 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP d 184 " --> pdb=" O GLY d 187 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY d 187 " --> pdb=" O ASP d 184 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'd' and resid 36 through 37 removed outlier: 3.520A pdb=" N LEU d 102 " --> pdb=" O MET d 118 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET d 118 " --> pdb=" O LEU d 102 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR d 116 " --> pdb=" O LEU d 104 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'd' and resid 177 through 178 Processing sheet with id=AK3, first strand: chain 'e' and resid 184 through 186 removed outlier: 3.597A pdb=" N PHE e 65 " --> pdb=" O ILE e 72 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL e 71 " --> pdb=" O VAL e 238 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL e 233 " --> pdb=" O SER e 248 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER e 248 " --> pdb=" O VAL e 233 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU e 235 " --> pdb=" O VAL e 246 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'e' and resid 94 through 97 removed outlier: 4.493A pdb=" N ILE e 96 " --> pdb=" O LEU e 100 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU e 100 " --> pdb=" O ILE e 96 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'e' and resid 157 through 158 Processing sheet with id=AK6, first strand: chain 'f' and resid 166 through 167 removed outlier: 5.146A pdb=" N THR f 39 " --> pdb=" O ASP f 54 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP f 54 " --> pdb=" O THR f 39 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA f 220 " --> pdb=" O THR f 55 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'f' and resid 57 through 59 removed outlier: 6.974A pdb=" N LEU f 57 " --> pdb=" O HIS f 64 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU f 59 " --> pdb=" O SER f 62 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'f' and resid 72 through 75 removed outlier: 6.822A pdb=" N THR f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR f 135 " --> pdb=" O SER f 83 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE f 138 " --> pdb=" O TYR f 150 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'f' and resid 226 through 227 Processing sheet with id=AL1, first strand: chain 'g' and resid 181 through 182 removed outlier: 3.516A pdb=" N VAL g 59 " --> pdb=" O VAL g 66 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL g 66 " --> pdb=" O VAL g 59 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR g 236 " --> pdb=" O GLU g 243 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'g' and resid 73 through 75 removed outlier: 7.089A pdb=" N GLY g 73 " --> pdb=" O ARG g 80 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU g 78 " --> pdb=" O TYR g 75 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'g' and resid 87 through 88 removed outlier: 3.766A pdb=" N GLY g 158 " --> pdb=" O MET g 95 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR g 154 " --> pdb=" O SER g 99 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE g 157 " --> pdb=" O GLY g 168 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR g 177 " --> pdb=" O TYR g 169 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'h' and resid 159 through 162 removed outlier: 3.971A pdb=" N MET h 38 " --> pdb=" O GLY h 49 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL h 40 " --> pdb=" O VAL h 47 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY h 45 " --> pdb=" O PHE h 42 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'h' and resid 76 through 77 2300 hydrogen bonds defined for protein. 6474 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: 19.28 Time building geometry restraints manager: 19.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18365 1.34 - 1.46: 8838 1.46 - 1.58: 31137 1.58 - 1.70: 0 1.70 - 1.82: 596 Bond restraints: 58936 Sorted by residual: bond pdb=" CA SER d 17 " pdb=" CB SER d 17 " ideal model delta sigma weight residual 1.538 1.451 0.087 1.22e-02 6.72e+03 5.05e+01 bond pdb=" CA SER M 17 " pdb=" CB SER M 17 " ideal model delta sigma weight residual 1.538 1.453 0.085 1.22e-02 6.72e+03 4.86e+01 bond pdb=" CA SER M 179 " pdb=" CB SER M 179 " ideal model delta sigma weight residual 1.532 1.466 0.066 1.74e-02 3.30e+03 1.45e+01 bond pdb=" N LEU M 121 " pdb=" CA LEU M 121 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.16e-02 7.43e+03 1.28e+01 bond pdb=" N LEU d 121 " pdb=" CA LEU d 121 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.16e-02 7.43e+03 1.27e+01 ... (remaining 58931 not shown) Histogram of bond angle deviations from ideal: 98.70 - 105.78: 1157 105.78 - 112.85: 31500 112.85 - 119.93: 19633 119.93 - 127.00: 27075 127.00 - 134.07: 473 Bond angle restraints: 79838 Sorted by residual: angle pdb=" N GLU D 18 " pdb=" CA GLU D 18 " pdb=" C GLU D 18 " ideal model delta sigma weight residual 112.59 120.67 -8.08 1.22e+00 6.72e-01 4.38e+01 angle pdb=" C PRO D 17 " pdb=" CA PRO D 17 " pdb=" CB PRO D 17 " ideal model delta sigma weight residual 111.56 121.93 -10.37 1.65e+00 3.67e-01 3.95e+01 angle pdb=" N GLU U 18 " pdb=" CA GLU U 18 " pdb=" C GLU U 18 " ideal model delta sigma weight residual 112.59 119.97 -7.38 1.22e+00 6.72e-01 3.66e+01 angle pdb=" C PRO U 17 " pdb=" CA PRO U 17 " pdb=" CB PRO U 17 " ideal model delta sigma weight residual 111.56 121.03 -9.47 1.65e+00 3.67e-01 3.30e+01 angle pdb=" N GLU D 18 " pdb=" CA GLU D 18 " pdb=" CB GLU D 18 " ideal model delta sigma weight residual 110.92 102.06 8.86 1.60e+00 3.91e-01 3.06e+01 ... (remaining 79833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 31834 18.10 - 36.20: 2961 36.20 - 54.29: 427 54.29 - 72.39: 85 72.39 - 90.49: 63 Dihedral angle restraints: 35370 sinusoidal: 13444 harmonic: 21926 Sorted by residual: dihedral pdb=" C PRO D 17 " pdb=" N PRO D 17 " pdb=" CA PRO D 17 " pdb=" CB PRO D 17 " ideal model delta harmonic sigma weight residual -120.70 -132.02 11.32 0 2.50e+00 1.60e-01 2.05e+01 dihedral pdb=" C PRO U 17 " pdb=" N PRO U 17 " pdb=" CA PRO U 17 " pdb=" CB PRO U 17 " ideal model delta harmonic sigma weight residual -120.70 -131.23 10.53 0 2.50e+00 1.60e-01 1.77e+01 dihedral pdb=" CA MET N 56 " pdb=" C MET N 56 " pdb=" N LEU N 57 " pdb=" CA LEU N 57 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 35367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 8392 0.079 - 0.158: 732 0.158 - 0.237: 10 0.237 - 0.316: 0 0.316 - 0.396: 2 Chirality restraints: 9136 Sorted by residual: chirality pdb=" CA PRO D 17 " pdb=" N PRO D 17 " pdb=" C PRO D 17 " pdb=" CB PRO D 17 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CA PRO U 17 " pdb=" N PRO U 17 " pdb=" C PRO U 17 " pdb=" CB PRO U 17 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA ILE M 151 " pdb=" N ILE M 151 " pdb=" C ILE M 151 " pdb=" CB ILE M 151 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.46e-01 ... (remaining 9133 not shown) Planarity restraints: 10240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 148 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO C 149 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP T 148 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO T 149 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO T 149 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO T 149 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER d 76 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.57e+00 pdb=" N PRO d 77 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO d 77 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO d 77 " 0.030 5.00e-02 4.00e+02 ... (remaining 10237 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 9029 2.76 - 3.29: 56111 3.29 - 3.83: 90701 3.83 - 4.36: 98316 4.36 - 4.90: 175913 Nonbonded interactions: 430070 Sorted by model distance: nonbonded pdb=" O ARG K 118 " pdb=" OG1 THR K 121 " model vdw 2.222 2.440 nonbonded pdb=" O ARG b 118 " pdb=" OG1 THR b 121 " model vdw 2.223 2.440 nonbonded pdb=" O ARG Z 51 " pdb=" OG1 THR Z 56 " model vdw 2.227 2.440 nonbonded pdb=" O ARG I 51 " pdb=" OG1 THR I 56 " model vdw 2.227 2.440 nonbonded pdb=" O GLY M 135 " pdb=" OG1 THR M 139 " model vdw 2.241 2.440 ... (remaining 430065 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 'R' } ncs_group { reference = chain 'B' selection = chain 'S' } ncs_group { reference = chain 'C' selection = chain 'T' } ncs_group { reference = chain 'D' selection = chain 'U' } ncs_group { reference = chain 'E' selection = chain 'V' } ncs_group { reference = chain 'F' selection = chain 'W' } ncs_group { reference = chain 'G' selection = chain 'X' } ncs_group { reference = chain 'H' selection = chain 'Y' } ncs_group { reference = chain 'I' selection = chain 'Z' } ncs_group { reference = chain 'J' selection = chain 'a' } ncs_group { reference = chain 'K' selection = chain 'b' } ncs_group { reference = chain 'L' selection = chain 'c' } ncs_group { reference = chain 'M' selection = chain 'd' } ncs_group { reference = chain 'N' selection = chain 'e' } ncs_group { reference = chain 'O' selection = chain 'f' } ncs_group { reference = chain 'P' selection = chain 'g' } ncs_group { reference = chain 'Q' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.290 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: 2.540 Check model and map are aligned: 0.310 Set scattering table: 0.400 Process input model: 110.200 Find NCS groups from input model: 5.570 Set up NCS constraints: 0.610 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 58936 Z= 0.185 Angle : 0.569 10.375 79838 Z= 0.303 Chirality : 0.042 0.396 9136 Planarity : 0.004 0.054 10240 Dihedral : 14.289 90.488 21322 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.10), residues: 7490 helix: 1.72 (0.11), residues: 2434 sheet: -1.69 (0.14), residues: 1342 loop : -2.12 (0.10), residues: 3714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 216 HIS 0.004 0.001 HIS W 121 PHE 0.023 0.001 PHE X 191 TYR 0.020 0.001 TYR G 159 ARG 0.005 0.000 ARG Z 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14980 Ramachandran restraints generated. 7490 Oldfield, 0 Emsley, 7490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 6392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 659 time to evaluate : 4.993 Fit side-chains revert: symmetry clash REVERT: A 81 PRO cc_start: 0.9223 (Cg_endo) cc_final: 0.8874 (Cg_exo) REVERT: A 123 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7677 (tm-30) REVERT: B 88 ASN cc_start: 0.8915 (t0) cc_final: 0.8539 (t0) REVERT: G 1 MET cc_start: 0.8065 (ppp) cc_final: 0.7437 (ppp) REVERT: G 15 ILE cc_start: 0.9537 (mt) cc_final: 0.9257 (mt) REVERT: H 39 LYS cc_start: 0.7886 (tptp) cc_final: 0.7531 (tptt) REVERT: H 68 ARG cc_start: 0.8736 (tmt-80) cc_final: 0.8269 (tpt170) REVERT: H 84 LYS cc_start: 0.6755 (ttmt) cc_final: 0.6535 (tptp) REVERT: H 133 MET cc_start: 0.8105 (mtp) cc_final: 0.7394 (mtp) REVERT: I 213 HIS cc_start: 0.7957 (p90) cc_final: 0.7753 (p90) REVERT: I 265 ASN cc_start: 0.7204 (t0) cc_final: 0.6973 (t0) REVERT: J 19 MET cc_start: 0.8587 (ppp) cc_final: 0.8109 (ppp) REVERT: J 55 MET cc_start: 0.8449 (tmm) cc_final: 0.8120 (tmm) REVERT: J 223 TYR cc_start: 0.8344 (t80) cc_final: 0.7602 (t80) REVERT: K 125 MET cc_start: 0.8853 (mtm) cc_final: 0.8295 (mtt) REVERT: L 12 MET cc_start: 0.8353 (mtt) cc_final: 0.7956 (mtt) REVERT: L 149 MET cc_start: 0.8576 (tpp) cc_final: 0.7532 (tpp) REVERT: L 158 MET cc_start: 0.7976 (mtp) cc_final: 0.6956 (mtp) REVERT: N 198 MET cc_start: 0.9350 (tmm) cc_final: 0.8770 (tmm) REVERT: O 188 ASN cc_start: 0.8593 (m110) cc_final: 0.8387 (m110) REVERT: P 115 MET cc_start: 0.8958 (ttm) cc_final: 0.8234 (ttp) REVERT: P 171 ASP cc_start: 0.8741 (t70) cc_final: 0.8324 (t0) REVERT: Q 105 ASN cc_start: 0.8727 (t0) cc_final: 0.8438 (t0) REVERT: R 81 PRO cc_start: 0.9228 (Cg_endo) cc_final: 0.8882 (Cg_exo) REVERT: R 123 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7682 (tm-30) REVERT: S 88 ASN cc_start: 0.8909 (t0) cc_final: 0.8530 (t0) REVERT: T 46 GLU cc_start: 0.8643 (pp20) cc_final: 0.8251 (pp20) REVERT: X 1 MET cc_start: 0.8064 (ppp) cc_final: 0.7436 (ppp) REVERT: X 15 ILE cc_start: 0.9540 (mt) cc_final: 0.9257 (mt) REVERT: Y 39 LYS cc_start: 0.7882 (tptp) cc_final: 0.7524 (tptt) REVERT: Y 68 ARG cc_start: 0.8738 (tmt-80) cc_final: 0.8269 (tpt170) REVERT: Y 84 LYS cc_start: 0.6755 (ttmt) cc_final: 0.6541 (tptp) REVERT: Y 133 MET cc_start: 0.8108 (mtp) cc_final: 0.7400 (mtp) REVERT: Z 213 HIS cc_start: 0.7953 (p90) cc_final: 0.7744 (p90) REVERT: Z 265 ASN cc_start: 0.7198 (t0) cc_final: 0.6970 (t0) REVERT: a 19 MET cc_start: 0.8541 (ppp) cc_final: 0.8040 (ppp) REVERT: a 55 MET cc_start: 0.8468 (tmm) cc_final: 0.8127 (tmm) REVERT: a 223 TYR cc_start: 0.8352 (t80) cc_final: 0.7611 (t80) REVERT: b 125 MET cc_start: 0.8850 (mtm) cc_final: 0.8290 (mtt) REVERT: c 12 MET cc_start: 0.8339 (mtt) cc_final: 0.7941 (mtt) REVERT: c 149 MET cc_start: 0.8585 (tpp) cc_final: 0.7530 (tpp) REVERT: c 158 MET cc_start: 0.7991 (mtp) cc_final: 0.6972 (mtp) REVERT: e 198 MET cc_start: 0.9333 (tmm) cc_final: 0.8777 (tmm) REVERT: g 115 MET cc_start: 0.8967 (ttm) cc_final: 0.8239 (ttp) REVERT: g 171 ASP cc_start: 0.8740 (t70) cc_final: 0.8328 (t0) REVERT: h 105 ASN cc_start: 0.8730 (t0) cc_final: 0.8446 (t0) outliers start: 0 outliers final: 0 residues processed: 659 average time/residue: 0.5226 time to fit residues: 587.3252 Evaluate side-chains 557 residues out of total 6392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 557 time to evaluate : 4.879 ------------------------------------------------------------------------------- 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-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.8985 > 50: distance: 17 - 158: 3.046 distance: 21 - 25: 34.901 distance: 25 - 26: 21.215 distance: 25 - 161: 31.750 distance: 26 - 27: 26.885 distance: 26 - 29: 44.435 distance: 27 - 28: 22.246 distance: 27 - 36: 48.332 distance: 28 - 172: 33.514 distance: 32 - 33: 39.952 distance: 33 - 34: 39.267 distance: 33 - 35: 57.610 distance: 36 - 37: 24.484 distance: 37 - 38: 43.132 distance: 37 - 40: 16.491 distance: 38 - 39: 19.688 distance: 40 - 41: 43.308 distance: 41 - 42: 45.362 distance: 41 - 43: 17.570 distance: 42 - 44: 40.220 distance: 43 - 45: 12.269 distance: 44 - 45: 28.422 distance: 47 - 48: 5.576 distance: 47 - 50: 40.080 distance: 48 - 49: 3.667 distance: 48 - 53: 34.686 distance: 50 - 51: 39.594 distance: 53 - 54: 56.690 distance: 54 - 55: 55.071 distance: 54 - 57: 36.309 distance: 55 - 56: 41.006 distance: 55 - 60: 41.706 distance: 57 - 58: 40.695 distance: 57 - 59: 40.176 distance: 60 - 61: 31.041 distance: 61 - 62: 4.395 distance: 61 - 64: 41.397 distance: 62 - 63: 35.845 distance: 62 - 68: 4.022 distance: 65 - 66: 39.736 distance: 65 - 67: 40.033 distance: 70 - 71: 36.062 distance: 70 - 80: 5.289 distance: 73 - 75: 38.614 distance: 74 - 76: 25.606 distance: 76 - 78: 41.077 distance: 77 - 78: 12.411 distance: 78 - 79: 13.676 distance: 81 - 82: 40.276 distance: 81 - 84: 18.506 distance: 82 - 89: 59.921 distance: 84 - 85: 20.638 distance: 86 - 87: 3.226 distance: 87 - 88: 54.233 distance: 89 - 90: 46.328 distance: 90 - 91: 39.392 distance: 90 - 93: 39.246 distance: 91 - 96: 40.918 distance: 93 - 94: 56.867 distance: 97 - 98: 41.839 distance: 97 - 100: 40.808 distance: 98 - 99: 30.059 distance: 98 - 102: 11.983 distance: 102 - 103: 27.683 distance: 103 - 104: 11.604 distance: 103 - 106: 27.693 distance: 104 - 105: 10.967 distance: 104 - 111: 35.359 distance: 106 - 107: 56.527 distance: 107 - 108: 15.833 distance: 108 - 109: 25.215 distance: 108 - 110: 6.856