Starting phenix.real_space_refine on Fri Jan 19 06:52:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jsi_9882/01_2024/6jsi_9882.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jsi_9882/01_2024/6jsi_9882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jsi_9882/01_2024/6jsi_9882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jsi_9882/01_2024/6jsi_9882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jsi_9882/01_2024/6jsi_9882.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jsi_9882/01_2024/6jsi_9882.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 144 5.16 5 C 39015 2.51 5 N 11361 2.21 5 O 12300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 46": "OE1" <-> "OE2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 403": "OD1" <-> "OD2" Residue "B PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1754": "OE1" <-> "OE2" Residue "B PHE 1764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1820": "OD1" <-> "OD2" Residue "B TYR 1833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1894": "OE1" <-> "OE2" Residue "B TYR 1898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1926": "OE1" <-> "OE2" Residue "B PHE 1941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 754": "OD1" <-> "OD2" Residue "A PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 841": "OE1" <-> "OE2" Residue "A GLU 915": "OE1" <-> "OE2" Residue "A PHE 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1016": "OE1" <-> "OE2" Residue "A GLU 1040": "OE1" <-> "OE2" Residue "A TYR 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1082": "OE1" <-> "OE2" Residue "A ASP 1085": "OD1" <-> "OD2" Residue "A TYR 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1099": "OE1" <-> "OE2" Residue "A GLU 1117": "OE1" <-> "OE2" Residue "A TYR 1163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1221": "OE1" <-> "OE2" Residue "A PHE 1223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1263": "OD1" <-> "OD2" Residue "A GLU 1317": "OE1" <-> "OE2" Residue "A GLU 1342": "OE1" <-> "OE2" Residue "A GLU 1357": "OE1" <-> "OE2" Residue "A TYR 1401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1473": "OE1" <-> "OE2" Residue "C TYR 1513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 329": "OE1" <-> "OE2" Residue "F GLU 347": "OE1" <-> "OE2" Residue "F TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 403": "OD1" <-> "OD2" Residue "F PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 467": "OD1" <-> "OD2" Residue "F PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1754": "OE1" <-> "OE2" Residue "F PHE 1764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 1820": "OD1" <-> "OD2" Residue "F TYR 1833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1894": "OE1" <-> "OE2" Residue "F TYR 1898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1926": "OE1" <-> "OE2" Residue "F PHE 1941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 754": "OD1" <-> "OD2" Residue "D PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 841": "OE1" <-> "OE2" Residue "D GLU 915": "OE1" <-> "OE2" Residue "D PHE 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1016": "OE1" <-> "OE2" Residue "D GLU 1040": "OE1" <-> "OE2" Residue "D TYR 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1082": "OE1" <-> "OE2" Residue "D ASP 1085": "OD1" <-> "OD2" Residue "D TYR 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1099": "OE1" <-> "OE2" Residue "D GLU 1117": "OE1" <-> "OE2" Residue "D TYR 1163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1221": "OE1" <-> "OE2" Residue "D PHE 1223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1263": "OD1" <-> "OD2" Residue "D GLU 1317": "OE1" <-> "OE2" Residue "D GLU 1342": "OE1" <-> "OE2" Residue "D GLU 1357": "OE1" <-> "OE2" Residue "D TYR 1401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 1473": "OE1" <-> "OE2" Residue "H TYR 1513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G GLU 121": "OE1" <-> "OE2" Residue "G TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 329": "OE1" <-> "OE2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 403": "OD1" <-> "OD2" Residue "G PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 467": "OD1" <-> "OD2" Residue "G PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1754": "OE1" <-> "OE2" Residue "G PHE 1764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1820": "OD1" <-> "OD2" Residue "G TYR 1833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1894": "OE1" <-> "OE2" Residue "G TYR 1898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1926": "OE1" <-> "OE2" Residue "G PHE 1941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 754": "OD1" <-> "OD2" Residue "E PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 841": "OE1" <-> "OE2" Residue "E GLU 915": "OE1" <-> "OE2" Residue "E PHE 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1016": "OE1" <-> "OE2" Residue "E GLU 1040": "OE1" <-> "OE2" Residue "E TYR 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1082": "OE1" <-> "OE2" Residue "E ASP 1085": "OD1" <-> "OD2" Residue "E TYR 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1099": "OE1" <-> "OE2" Residue "E GLU 1117": "OE1" <-> "OE2" Residue "E TYR 1163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1221": "OE1" <-> "OE2" Residue "E PHE 1223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1263": "OD1" <-> "OD2" Residue "E GLU 1317": "OE1" <-> "OE2" Residue "E GLU 1342": "OE1" <-> "OE2" Residue "E GLU 1357": "OE1" <-> "OE2" Residue "E TYR 1401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1473": "OE1" <-> "OE2" Residue "I TYR 1513": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 62820 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 11746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1904, 11746 Classifications: {'peptide': 1904} Incomplete info: {'truncation_to_alanine': 1086} Link IDs: {'PTRANS': 47, 'TRANS': 1856} Chain breaks: 4 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 2451 Unresolved non-hydrogen angles: 3534 Unresolved non-hydrogen dihedrals: 1438 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 5, 'UNK:plan-1': 912, 'TYR:plan': 6, 'ASN:plan1': 12, 'TRP:plan': 2, 'ASP:plan': 7, 'ARG:plan': 5, 'PHE:plan': 10, 'GLU:plan': 17, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 1217 Chain: "A" Number of atoms: 8587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1321, 8587 Classifications: {'peptide': 1321} Incomplete info: {'truncation_to_alanine': 571} Link IDs: {'PCIS': 4, 'PTRANS': 33, 'TRANS': 1283} Chain breaks: 6 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1327 Unresolved non-hydrogen angles: 1880 Unresolved non-hydrogen dihedrals: 812 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 4, 'UNK:plan-1': 436, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 660 Chain: "C" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 607 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "F" Number of atoms: 11746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1904, 11746 Classifications: {'peptide': 1904} Incomplete info: {'truncation_to_alanine': 1086} Link IDs: {'PTRANS': 47, 'TRANS': 1856} Chain breaks: 4 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 2451 Unresolved non-hydrogen angles: 3534 Unresolved non-hydrogen dihedrals: 1438 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 5, 'UNK:plan-1': 912, 'TYR:plan': 6, 'ASN:plan1': 12, 'TRP:plan': 2, 'ASP:plan': 7, 'ARG:plan': 5, 'PHE:plan': 10, 'GLU:plan': 17, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 1217 Chain: "D" Number of atoms: 8587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1321, 8587 Classifications: {'peptide': 1321} Incomplete info: {'truncation_to_alanine': 571} Link IDs: {'PCIS': 4, 'PTRANS': 33, 'TRANS': 1283} Chain breaks: 6 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1327 Unresolved non-hydrogen angles: 1880 Unresolved non-hydrogen dihedrals: 812 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 4, 'UNK:plan-1': 436, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 660 Chain: "H" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 607 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "G" Number of atoms: 11746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1904, 11746 Classifications: {'peptide': 1904} Incomplete info: {'truncation_to_alanine': 1086} Link IDs: {'PTRANS': 47, 'TRANS': 1856} Chain breaks: 4 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 2451 Unresolved non-hydrogen angles: 3534 Unresolved non-hydrogen dihedrals: 1438 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 5, 'UNK:plan-1': 912, 'TYR:plan': 6, 'ASN:plan1': 12, 'TRP:plan': 2, 'ASP:plan': 7, 'ARG:plan': 5, 'PHE:plan': 10, 'GLU:plan': 17, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 1217 Chain: "E" Number of atoms: 8587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1321, 8587 Classifications: {'peptide': 1321} Incomplete info: {'truncation_to_alanine': 571} Link IDs: {'PCIS': 4, 'PTRANS': 33, 'TRANS': 1283} Chain breaks: 6 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1327 Unresolved non-hydrogen angles: 1880 Unresolved non-hydrogen dihedrals: 812 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 4, 'UNK:plan-1': 436, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 660 Chain: "I" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 607 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Time building chain proxies: 26.07, per 1000 atoms: 0.41 Number of scatterers: 62820 At special positions: 0 Unit cell: (279.45, 272.7, 174.15, 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 144 16.00 O 12300 8.00 N 11361 7.00 C 39015 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: 20.36 Conformation dependent library (CDL) restraints added in 6.3 seconds 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18918 Finding SS restraints... Secondary structure from input PDB file: 315 helices and 45 sheets defined 52.7% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.23 Creating SS restraints... Processing helix chain 'B' and resid 22 through 27 removed outlier: 4.238A pdb=" N PHE B 27 " --> pdb=" O PRO B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 54 through 68 removed outlier: 3.921A pdb=" N ALA B 58 " --> pdb=" O PRO B 54 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 93 removed outlier: 4.048A pdb=" N VAL B 83 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU B 84 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE B 91 " --> pdb=" O CYS B 87 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 removed outlier: 3.504A pdb=" N ALA B 106 " --> pdb=" O HIS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 132 removed outlier: 3.537A pdb=" N LEU B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 184 through 197 removed outlier: 4.024A pdb=" N LYS B 189 " --> pdb=" O GLY B 185 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 221 Processing helix chain 'B' and resid 233 through 256 Proline residue: B 239 - end of helix removed outlier: 3.938A pdb=" N GLY B 242 " --> pdb=" O CYS B 238 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N TYR B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 266 removed outlier: 3.832A pdb=" N TYR B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 285 removed outlier: 4.411A pdb=" N VAL B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N THR B 279 " --> pdb=" O GLN B 275 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 283 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU B 285 " --> pdb=" O VAL B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 314 removed outlier: 3.585A pdb=" N ARG B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL B 302 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU B 312 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.759A pdb=" N LEU B 324 " --> pdb=" O PRO B 320 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B 325 " --> pdb=" O PRO B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 320 through 325' Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.708A pdb=" N GLU B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 325 through 330' Processing helix chain 'B' and resid 347 through 360 removed outlier: 3.720A pdb=" N ASP B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 removed outlier: 4.025A pdb=" N GLN B 365 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 395 removed outlier: 3.622A pdb=" N ASN B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 391 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 4.069A pdb=" N GLU B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG B 412 " --> pdb=" O PRO B 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 407 through 412' Processing helix chain 'B' and resid 433 through 446 removed outlier: 3.721A pdb=" N ASP B 437 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN B 440 " --> pdb=" O SER B 436 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS B 441 " --> pdb=" O ASP B 437 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 482 removed outlier: 4.176A pdb=" N ASP B 481 " --> pdb=" O GLU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 495 removed outlier: 3.798A pdb=" N THR B 494 " --> pdb=" O TRP B 490 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 490 through 495' Processing helix chain 'B' and resid 507 through 511 removed outlier: 3.939A pdb=" N SER B 510 " --> pdb=" O GLY B 507 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY B 511 " --> pdb=" O GLY B 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 507 through 511' Processing helix chain 'B' and resid 513 through 518 removed outlier: 4.015A pdb=" N ARG B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 605 removed outlier: 3.580A pdb=" N UNK B 603 " --> pdb=" O UNK B 599 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N UNK B 605 " --> pdb=" O UNK B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.721A pdb=" N UNK B 622 " --> pdb=" O UNK B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 628 Processing helix chain 'B' and resid 649 through 664 removed outlier: 4.407A pdb=" N UNK B 656 " --> pdb=" O UNK B 652 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N UNK B 661 " --> pdb=" O UNK B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 686 removed outlier: 3.824A pdb=" N UNK B 683 " --> pdb=" O UNK B 679 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N UNK B 684 " --> pdb=" O UNK B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 710 removed outlier: 3.940A pdb=" N UNK B 708 " --> pdb=" O UNK B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 771 removed outlier: 3.706A pdb=" N UNK B 769 " --> pdb=" O UNK B 765 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N UNK B 771 " --> pdb=" O UNK B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 803 Processing helix chain 'B' and resid 828 through 832 Processing helix chain 'B' and resid 841 through 847 removed outlier: 3.624A pdb=" N UNK B 845 " --> pdb=" O UNK B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 864 removed outlier: 4.480A pdb=" N UNK B 862 " --> pdb=" O UNK B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 871 Processing helix chain 'B' and resid 897 through 906 removed outlier: 3.863A pdb=" N UNK B 901 " --> pdb=" O UNK B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 930 removed outlier: 3.837A pdb=" N UNK B 925 " --> pdb=" O UNK B 921 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N UNK B 927 " --> pdb=" O UNK B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 979 Processing helix chain 'B' and resid 1105 through 1112 Processing helix chain 'B' and resid 1250 through 1255 Processing helix chain 'B' and resid 1279 through 1283 Processing helix chain 'B' and resid 1395 through 1401 Processing helix chain 'B' and resid 1415 through 1420 removed outlier: 3.543A pdb=" N UNK B1420 " --> pdb=" O UNK B1417 " (cutoff:3.500A) Processing helix chain 'B' and resid 1473 through 1477 Processing helix chain 'B' and resid 1512 through 1516 Processing helix chain 'B' and resid 1526 through 1531 removed outlier: 3.610A pdb=" N UNK B1531 " --> pdb=" O UNK B1528 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1555 removed outlier: 3.943A pdb=" N UNK B1545 " --> pdb=" O UNK B1541 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N UNK B1546 " --> pdb=" O UNK B1542 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N UNK B1548 " --> pdb=" O UNK B1544 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N UNK B1551 " --> pdb=" O UNK B1547 " (cutoff:3.500A) Processing helix chain 'B' and resid 1677 through 1682 removed outlier: 3.686A pdb=" N LYS B1682 " --> pdb=" O MET B1678 " (cutoff:3.500A) Processing helix chain 'B' and resid 1684 through 1700 removed outlier: 3.822A pdb=" N VAL B1690 " --> pdb=" O ALA B1686 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP B1691 " --> pdb=" O ALA B1687 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA B1694 " --> pdb=" O VAL B1690 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASP B1695 " --> pdb=" O TRP B1691 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS B1699 " --> pdb=" O ASP B1695 " (cutoff:3.500A) Processing helix chain 'B' and resid 1705 through 1711 removed outlier: 3.543A pdb=" N ILE B1711 " --> pdb=" O LEU B1707 " (cutoff:3.500A) Processing helix chain 'B' and resid 1776 through 1795 removed outlier: 3.620A pdb=" N GLU B1785 " --> pdb=" O LEU B1781 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B1786 " --> pdb=" O THR B1782 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP B1791 " --> pdb=" O ALA B1787 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU B1792 " --> pdb=" O ALA B1788 " (cutoff:3.500A) Processing helix chain 'B' and resid 1823 through 1838 removed outlier: 3.575A pdb=" N VAL B1830 " --> pdb=" O SER B1826 " (cutoff:3.500A) Processing helix chain 'B' and resid 1839 through 1842 removed outlier: 4.487A pdb=" N VAL B1842 " --> pdb=" O GLN B1839 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1839 through 1842' Processing helix chain 'B' and resid 1869 through 1875 Processing helix chain 'B' and resid 1897 through 1909 removed outlier: 3.756A pdb=" N ALA B1901 " --> pdb=" O GLN B1897 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU B1904 " --> pdb=" O ALA B1900 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG B1905 " --> pdb=" O ALA B1901 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA B1906 " --> pdb=" O GLY B1902 " (cutoff:3.500A) Processing helix chain 'B' and resid 1928 through 1933 removed outlier: 4.138A pdb=" N LEU B1933 " --> pdb=" O LYS B1929 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1973 Processing helix chain 'B' and resid 2002 through 2006 removed outlier: 3.541A pdb=" N ARG B2005 " --> pdb=" O LYS B2002 " (cutoff:3.500A) Processing helix chain 'B' and resid 2030 through 2044 removed outlier: 3.645A pdb=" N SER B2035 " --> pdb=" O ASP B2031 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLU B2036 " --> pdb=" O LEU B2032 " (cutoff:3.500A) Proline residue: B2037 - end of helix Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.782A pdb=" N UNK A 18 " --> pdb=" O UNK A 14 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N UNK A 19 " --> pdb=" O UNK A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 46 removed outlier: 4.296A pdb=" N UNK A 41 " --> pdb=" O UNK A 37 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N UNK A 42 " --> pdb=" O UNK A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.769A pdb=" N UNK A 288 " --> pdb=" O UNK A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 390 removed outlier: 3.702A pdb=" N UNK A 376 " --> pdb=" O UNK A 372 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N UNK A 378 " --> pdb=" O UNK A 374 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N UNK A 379 " --> pdb=" O UNK A 375 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N UNK A 383 " --> pdb=" O UNK A 379 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N UNK A 385 " --> pdb=" O UNK A 381 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N UNK A 387 " --> pdb=" O UNK A 383 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N UNK A 388 " --> pdb=" O UNK A 384 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N UNK A 390 " --> pdb=" O UNK A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 412 removed outlier: 3.601A pdb=" N UNK A 401 " --> pdb=" O UNK A 397 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N UNK A 403 " --> pdb=" O UNK A 399 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N UNK A 404 " --> pdb=" O UNK A 400 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N UNK A 405 " --> pdb=" O UNK A 401 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N UNK A 406 " --> pdb=" O UNK A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 538 Proline residue: A 534 - end of helix removed outlier: 3.905A pdb=" N GLU A 538 " --> pdb=" O PRO A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 550 removed outlier: 3.833A pdb=" N LEU A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 548 " --> pdb=" O GLU A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 578 removed outlier: 3.915A pdb=" N GLU A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 627 removed outlier: 4.053A pdb=" N THR A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 665 removed outlier: 4.004A pdb=" N LEU A 658 " --> pdb=" O GLN A 654 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 700 removed outlier: 4.089A pdb=" N GLU A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 726 removed outlier: 3.990A pdb=" N TYR A 717 " --> pdb=" O GLN A 713 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR A 718 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 720 " --> pdb=" O ASP A 716 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 721 " --> pdb=" O TYR A 717 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N TYR A 722 " --> pdb=" O TYR A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 744 through 752 removed outlier: 3.923A pdb=" N LEU A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 749 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 796 removed outlier: 3.907A pdb=" N ARG A 793 " --> pdb=" O GLU A 789 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 796 " --> pdb=" O HIS A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 814 removed outlier: 3.630A pdb=" N ARG A 801 " --> pdb=" O THR A 797 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 807 " --> pdb=" O MET A 803 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 813 " --> pdb=" O GLN A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 844 Processing helix chain 'A' and resid 847 through 853 removed outlier: 4.230A pdb=" N ASN A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 901 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 929 through 933 removed outlier: 3.685A pdb=" N PHE A 932 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 933 " --> pdb=" O LEU A 930 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 929 through 933' Processing helix chain 'A' and resid 935 through 967 removed outlier: 3.629A pdb=" N PHE A 939 " --> pdb=" O GLU A 935 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 943 " --> pdb=" O PHE A 939 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 948 " --> pdb=" O ARG A 944 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU A 949 " --> pdb=" O LYS A 945 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A 954 " --> pdb=" O THR A 950 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 959 " --> pdb=" O LYS A 955 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1042 removed outlier: 3.986A pdb=" N GLU A1038 " --> pdb=" O ARG A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1056 removed outlier: 3.595A pdb=" N ILE A1056 " --> pdb=" O GLU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1149 Processing helix chain 'A' and resid 1208 through 1226 removed outlier: 4.108A pdb=" N THR A1212 " --> pdb=" O VAL A1208 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A1213 " --> pdb=" O ASP A1209 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE A1214 " --> pdb=" O PRO A1210 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A1215 " --> pdb=" O ILE A1211 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A1220 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A1221 " --> pdb=" O VAL A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1237 removed outlier: 3.570A pdb=" N MET A1234 " --> pdb=" O PRO A1231 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A1236 " --> pdb=" O GLU A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1262 Processing helix chain 'A' and resid 1275 through 1279 removed outlier: 3.797A pdb=" N PHE A1279 " --> pdb=" O GLN A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1290 removed outlier: 4.040A pdb=" N ASN A1288 " --> pdb=" O SER A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1321 removed outlier: 3.622A pdb=" N ILE A1319 " --> pdb=" O GLY A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1340 Processing helix chain 'A' and resid 1752 through 1762 removed outlier: 3.668A pdb=" N UNK A1756 " --> pdb=" O UNK A1752 " (cutoff:3.500A) Processing helix chain 'A' and resid 1778 through 1783 removed outlier: 4.330A pdb=" N UNK A1782 " --> pdb=" O UNK A1779 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N UNK A1783 " --> pdb=" O UNK A1780 " (cutoff:3.500A) Processing helix chain 'A' and resid 1814 through 1818 Processing helix chain 'A' and resid 1820 through 1825 Processing helix chain 'C' and resid 1448 through 1453 Processing helix chain 'C' and resid 1457 through 1473 removed outlier: 3.812A pdb=" N VAL C1463 " --> pdb=" O ILE C1459 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU C1464 " --> pdb=" O LYS C1460 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU C1466 " --> pdb=" O TRP C1462 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C1467 " --> pdb=" O VAL C1463 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU C1468 " --> pdb=" O GLU C1464 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA C1469 " --> pdb=" O ASN C1465 " (cutoff:3.500A) Processing helix chain 'C' and resid 1481 through 1505 removed outlier: 4.748A pdb=" N ARG C1491 " --> pdb=" O LEU C1487 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN C1495 " --> pdb=" O ARG C1491 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU C1501 " --> pdb=" O ALA C1497 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 27 removed outlier: 4.239A pdb=" N PHE F 27 " --> pdb=" O PRO F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 36 Processing helix chain 'F' and resid 54 through 68 removed outlier: 3.922A pdb=" N ALA F 58 " --> pdb=" O PRO F 54 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY F 66 " --> pdb=" O GLY F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 93 removed outlier: 4.049A pdb=" N VAL F 83 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU F 84 " --> pdb=" O PHE F 80 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE F 91 " --> pdb=" O CYS F 87 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN F 93 " --> pdb=" O THR F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 109 removed outlier: 3.504A pdb=" N ALA F 106 " --> pdb=" O HIS F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 132 removed outlier: 3.538A pdb=" N LEU F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR F 126 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA F 129 " --> pdb=" O ASN F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 178 Processing helix chain 'F' and resid 184 through 197 removed outlier: 4.025A pdb=" N LYS F 189 " --> pdb=" O GLY F 185 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE F 190 " --> pdb=" O ASP F 186 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU F 193 " --> pdb=" O LYS F 189 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER F 196 " --> pdb=" O ALA F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 221 Processing helix chain 'F' and resid 233 through 256 Proline residue: F 239 - end of helix removed outlier: 3.937A pdb=" N GLY F 242 " --> pdb=" O CYS F 238 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N TYR F 249 " --> pdb=" O GLN F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 266 removed outlier: 3.831A pdb=" N TYR F 266 " --> pdb=" O GLU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 285 removed outlier: 4.410A pdb=" N VAL F 278 " --> pdb=" O SER F 274 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N THR F 279 " --> pdb=" O GLN F 275 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA F 282 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE F 283 " --> pdb=" O THR F 279 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA F 284 " --> pdb=" O ALA F 280 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU F 285 " --> pdb=" O VAL F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 314 removed outlier: 3.584A pdb=" N ARG F 297 " --> pdb=" O PHE F 293 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS F 298 " --> pdb=" O VAL F 294 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA F 299 " --> pdb=" O SER F 295 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL F 302 " --> pdb=" O LYS F 298 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU F 303 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE F 305 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU F 312 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 325 removed outlier: 3.759A pdb=" N LEU F 324 " --> pdb=" O PRO F 320 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU F 325 " --> pdb=" O PRO F 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 320 through 325' Processing helix chain 'F' and resid 325 through 330 removed outlier: 3.707A pdb=" N GLU F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN F 330 " --> pdb=" O ASP F 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 325 through 330' Processing helix chain 'F' and resid 347 through 360 removed outlier: 3.720A pdb=" N ASP F 351 " --> pdb=" O GLU F 347 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 365 removed outlier: 4.025A pdb=" N GLN F 365 " --> pdb=" O ALA F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 395 removed outlier: 3.622A pdb=" N ASN F 390 " --> pdb=" O LEU F 386 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU F 391 " --> pdb=" O TYR F 387 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR F 392 " --> pdb=" O GLY F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 412 removed outlier: 4.069A pdb=" N GLU F 411 " --> pdb=" O ILE F 407 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG F 412 " --> pdb=" O PRO F 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 407 through 412' Processing helix chain 'F' and resid 433 through 446 removed outlier: 3.721A pdb=" N ASP F 437 " --> pdb=" O VAL F 433 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN F 440 " --> pdb=" O SER F 436 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS F 441 " --> pdb=" O ASP F 437 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN F 446 " --> pdb=" O ASP F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 482 removed outlier: 4.176A pdb=" N ASP F 481 " --> pdb=" O GLU F 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 495 removed outlier: 3.798A pdb=" N THR F 494 " --> pdb=" O TRP F 490 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 490 through 495' Processing helix chain 'F' and resid 507 through 511 removed outlier: 3.939A pdb=" N SER F 510 " --> pdb=" O GLY F 507 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY F 511 " --> pdb=" O GLY F 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 507 through 511' Processing helix chain 'F' and resid 513 through 518 removed outlier: 4.014A pdb=" N ARG F 518 " --> pdb=" O VAL F 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 605 removed outlier: 3.579A pdb=" N UNK F 603 " --> pdb=" O UNK F 599 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N UNK F 605 " --> pdb=" O UNK F 601 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 623 removed outlier: 3.721A pdb=" N UNK F 622 " --> pdb=" O UNK F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 624 through 628 Processing helix chain 'F' and resid 649 through 664 removed outlier: 4.406A pdb=" N UNK F 656 " --> pdb=" O UNK F 652 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N UNK F 661 " --> pdb=" O UNK F 657 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 686 removed outlier: 3.825A pdb=" N UNK F 683 " --> pdb=" O UNK F 679 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N UNK F 684 " --> pdb=" O UNK F 680 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 710 removed outlier: 3.942A pdb=" N UNK F 708 " --> pdb=" O UNK F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 763 through 771 removed outlier: 3.705A pdb=" N UNK F 769 " --> pdb=" O UNK F 765 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N UNK F 771 " --> pdb=" O UNK F 767 " (cutoff:3.500A) Processing helix chain 'F' and resid 797 through 803 Processing helix chain 'F' and resid 828 through 832 Processing helix chain 'F' and resid 841 through 847 removed outlier: 3.624A pdb=" N UNK F 845 " --> pdb=" O UNK F 841 " (cutoff:3.500A) Processing helix chain 'F' and resid 858 through 864 removed outlier: 4.480A pdb=" N UNK F 862 " --> pdb=" O UNK F 858 " (cutoff:3.500A) Processing helix chain 'F' and resid 867 through 871 Processing helix chain 'F' and resid 897 through 906 removed outlier: 3.863A pdb=" N UNK F 901 " --> pdb=" O UNK F 897 " (cutoff:3.500A) Processing helix chain 'F' and resid 921 through 930 removed outlier: 3.837A pdb=" N UNK F 925 " --> pdb=" O UNK F 921 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N UNK F 927 " --> pdb=" O UNK F 923 " (cutoff:3.500A) Processing helix chain 'F' and resid 974 through 979 Processing helix chain 'F' and resid 1105 through 1112 Processing helix chain 'F' and resid 1250 through 1255 Processing helix chain 'F' and resid 1279 through 1283 Processing helix chain 'F' and resid 1395 through 1401 Processing helix chain 'F' and resid 1415 through 1420 removed outlier: 3.543A pdb=" N UNK F1420 " --> pdb=" O UNK F1417 " (cutoff:3.500A) Processing helix chain 'F' and resid 1473 through 1477 Processing helix chain 'F' and resid 1512 through 1516 Processing helix chain 'F' and resid 1526 through 1531 removed outlier: 3.611A pdb=" N UNK F1531 " --> pdb=" O UNK F1528 " (cutoff:3.500A) Processing helix chain 'F' and resid 1540 through 1555 removed outlier: 3.944A pdb=" N UNK F1545 " --> pdb=" O UNK F1541 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N UNK F1546 " --> pdb=" O UNK F1542 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N UNK F1548 " --> pdb=" O UNK F1544 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N UNK F1551 " --> pdb=" O UNK F1547 " (cutoff:3.500A) Processing helix chain 'F' and resid 1677 through 1682 removed outlier: 3.685A pdb=" N LYS F1682 " --> pdb=" O MET F1678 " (cutoff:3.500A) Processing helix chain 'F' and resid 1684 through 1700 removed outlier: 3.823A pdb=" N VAL F1690 " --> pdb=" O ALA F1686 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP F1691 " --> pdb=" O ALA F1687 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA F1694 " --> pdb=" O VAL F1690 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP F1695 " --> pdb=" O TRP F1691 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS F1699 " --> pdb=" O ASP F1695 " (cutoff:3.500A) Processing helix chain 'F' and resid 1705 through 1711 removed outlier: 3.544A pdb=" N ILE F1711 " --> pdb=" O LEU F1707 " (cutoff:3.500A) Processing helix chain 'F' and resid 1776 through 1795 removed outlier: 3.621A pdb=" N GLU F1785 " --> pdb=" O LEU F1781 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS F1786 " --> pdb=" O THR F1782 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP F1791 " --> pdb=" O ALA F1787 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU F1792 " --> pdb=" O ALA F1788 " (cutoff:3.500A) Processing helix chain 'F' and resid 1823 through 1838 removed outlier: 3.575A pdb=" N VAL F1830 " --> pdb=" O SER F1826 " (cutoff:3.500A) Processing helix chain 'F' and resid 1839 through 1842 removed outlier: 4.487A pdb=" N VAL F1842 " --> pdb=" O GLN F1839 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1839 through 1842' Processing helix chain 'F' and resid 1869 through 1875 Processing helix chain 'F' and resid 1897 through 1909 removed outlier: 3.757A pdb=" N ALA F1901 " --> pdb=" O GLN F1897 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU F1904 " --> pdb=" O ALA F1900 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG F1905 " --> pdb=" O ALA F1901 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA F1906 " --> pdb=" O GLY F1902 " (cutoff:3.500A) Processing helix chain 'F' and resid 1928 through 1933 removed outlier: 4.139A pdb=" N LEU F1933 " --> pdb=" O LYS F1929 " (cutoff:3.500A) Processing helix chain 'F' and resid 1968 through 1973 Processing helix chain 'F' and resid 2002 through 2006 removed outlier: 3.541A pdb=" N ARG F2005 " --> pdb=" O LYS F2002 " (cutoff:3.500A) Processing helix chain 'F' and resid 2030 through 2044 removed outlier: 3.644A pdb=" N SER F2035 " --> pdb=" O ASP F2031 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLU F2036 " --> pdb=" O LEU F2032 " (cutoff:3.500A) Proline residue: F2037 - end of helix Processing helix chain 'D' and resid 12 through 21 removed outlier: 3.781A pdb=" N UNK D 18 " --> pdb=" O UNK D 14 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N UNK D 19 " --> pdb=" O UNK D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 46 removed outlier: 4.295A pdb=" N UNK D 41 " --> pdb=" O UNK D 37 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N UNK D 42 " --> pdb=" O UNK D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 67 Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 182 through 190 Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 241 through 248 Processing helix chain 'D' and resid 284 through 288 removed outlier: 3.769A pdb=" N UNK D 288 " --> pdb=" O UNK D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 390 removed outlier: 3.702A pdb=" N UNK D 376 " --> pdb=" O UNK D 372 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N UNK D 378 " --> pdb=" O UNK D 374 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N UNK D 379 " --> pdb=" O UNK D 375 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N UNK D 383 " --> pdb=" O UNK D 379 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N UNK D 385 " --> pdb=" O UNK D 381 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N UNK D 387 " --> pdb=" O UNK D 383 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N UNK D 388 " --> pdb=" O UNK D 384 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N UNK D 390 " --> pdb=" O UNK D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 412 removed outlier: 3.601A pdb=" N UNK D 401 " --> pdb=" O UNK D 397 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N UNK D 403 " --> pdb=" O UNK D 399 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N UNK D 404 " --> pdb=" O UNK D 400 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N UNK D 405 " --> pdb=" O UNK D 401 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N UNK D 406 " --> pdb=" O UNK D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 538 Proline residue: D 534 - end of helix removed outlier: 3.905A pdb=" N GLU D 538 " --> pdb=" O PRO D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 550 removed outlier: 3.833A pdb=" N LEU D 547 " --> pdb=" O ILE D 543 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 578 removed outlier: 3.915A pdb=" N GLU D 570 " --> pdb=" O SER D 566 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR D 575 " --> pdb=" O PHE D 571 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER D 576 " --> pdb=" O GLU D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 627 removed outlier: 4.053A pdb=" N THR D 625 " --> pdb=" O THR D 621 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 665 removed outlier: 4.004A pdb=" N LEU D 658 " --> pdb=" O GLN D 654 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU D 660 " --> pdb=" O SER D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 700 removed outlier: 4.089A pdb=" N GLU D 691 " --> pdb=" O SER D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 726 removed outlier: 3.991A pdb=" N TYR D 717 " --> pdb=" O GLN D 713 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR D 718 " --> pdb=" O VAL D 714 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER D 720 " --> pdb=" O ASP D 716 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE D 721 " --> pdb=" O TYR D 717 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TYR D 722 " --> pdb=" O TYR D 718 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 744 through 752 removed outlier: 3.923A pdb=" N LEU D 748 " --> pdb=" O ASP D 744 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE D 749 " --> pdb=" O VAL D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 796 removed outlier: 3.906A pdb=" N ARG D 793 " --> pdb=" O GLU D 789 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 796 " --> pdb=" O HIS D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 814 removed outlier: 3.629A pdb=" N ARG D 801 " --> pdb=" O THR D 797 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS D 807 " --> pdb=" O MET D 803 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG D 813 " --> pdb=" O GLN D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 838 through 844 Processing helix chain 'D' and resid 847 through 853 removed outlier: 4.230A pdb=" N ASN D 851 " --> pdb=" O GLU D 847 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 901 through 908 Processing helix chain 'D' and resid 913 through 918 Processing helix chain 'D' and resid 929 through 933 removed outlier: 3.684A pdb=" N PHE D 932 " --> pdb=" O GLY D 929 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 933 " --> pdb=" O LEU D 930 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 929 through 933' Processing helix chain 'D' and resid 935 through 967 removed outlier: 3.629A pdb=" N PHE D 939 " --> pdb=" O GLU D 935 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU D 943 " --> pdb=" O PHE D 939 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 948 " --> pdb=" O ARG D 944 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU D 949 " --> pdb=" O LYS D 945 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG D 954 " --> pdb=" O THR D 950 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 959 " --> pdb=" O LYS D 955 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU D 960 " --> pdb=" O ALA D 956 " (cutoff:3.500A) Processing helix chain 'D' and resid 1034 through 1042 removed outlier: 3.986A pdb=" N GLU D1038 " --> pdb=" O ARG D1034 " (cutoff:3.500A) Processing helix chain 'D' and resid 1049 through 1056 removed outlier: 3.595A pdb=" N ILE D1056 " --> pdb=" O GLU D1052 " (cutoff:3.500A) Processing helix chain 'D' and resid 1144 through 1149 Processing helix chain 'D' and resid 1208 through 1226 removed outlier: 4.109A pdb=" N THR D1212 " --> pdb=" O VAL D1208 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D1213 " --> pdb=" O ASP D1209 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE D1214 " --> pdb=" O PRO D1210 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL D1215 " --> pdb=" O ILE D1211 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL D1220 " --> pdb=" O LEU D1216 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU D1221 " --> pdb=" O VAL D1217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1230 through 1237 removed outlier: 3.570A pdb=" N MET D1234 " --> pdb=" O PRO D1231 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS D1236 " --> pdb=" O GLU D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1256 through 1262 Processing helix chain 'D' and resid 1275 through 1279 removed outlier: 3.798A pdb=" N PHE D1279 " --> pdb=" O GLN D1276 " (cutoff:3.500A) Processing helix chain 'D' and resid 1281 through 1290 removed outlier: 4.041A pdb=" N ASN D1288 " --> pdb=" O SER D1284 " (cutoff:3.500A) Processing helix chain 'D' and resid 1309 through 1321 removed outlier: 3.622A pdb=" N ILE D1319 " --> pdb=" O GLY D1315 " (cutoff:3.500A) Processing helix chain 'D' and resid 1336 through 1340 Processing helix chain 'D' and resid 1752 through 1762 removed outlier: 3.668A pdb=" N UNK D1756 " --> pdb=" O UNK D1752 " (cutoff:3.500A) Processing helix chain 'D' and resid 1778 through 1783 removed outlier: 4.330A pdb=" N UNK D1782 " --> pdb=" O UNK D1779 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N UNK D1783 " --> pdb=" O UNK D1780 " (cutoff:3.500A) Processing helix chain 'D' and resid 1814 through 1818 Processing helix chain 'D' and resid 1820 through 1825 Processing helix chain 'H' and resid 1448 through 1453 Processing helix chain 'H' and resid 1457 through 1473 removed outlier: 3.813A pdb=" N VAL H1463 " --> pdb=" O ILE H1459 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU H1464 " --> pdb=" O LYS H1460 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU H1466 " --> pdb=" O TRP H1462 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU H1467 " --> pdb=" O VAL H1463 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU H1468 " --> pdb=" O GLU H1464 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA H1469 " --> pdb=" O ASN H1465 " (cutoff:3.500A) Processing helix chain 'H' and resid 1481 through 1505 removed outlier: 4.748A pdb=" N ARG H1491 " --> pdb=" O LEU H1487 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN H1495 " --> pdb=" O ARG H1491 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU H1501 " --> pdb=" O ALA H1497 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 27 removed outlier: 4.238A pdb=" N PHE G 27 " --> pdb=" O PRO G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 36 Processing helix chain 'G' and resid 54 through 68 removed outlier: 3.922A pdb=" N ALA G 58 " --> pdb=" O PRO G 54 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY G 66 " --> pdb=" O GLY G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 93 removed outlier: 4.049A pdb=" N VAL G 83 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE G 91 " --> pdb=" O CYS G 87 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN G 93 " --> pdb=" O THR G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 109 removed outlier: 3.504A pdb=" N ALA G 106 " --> pdb=" O HIS G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 132 removed outlier: 3.537A pdb=" N LEU G 122 " --> pdb=" O LYS G 118 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR G 126 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA G 129 " --> pdb=" O ASN G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 178 Processing helix chain 'G' and resid 184 through 197 removed outlier: 4.024A pdb=" N LYS G 189 " --> pdb=" O GLY G 185 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE G 190 " --> pdb=" O ASP G 186 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU G 193 " --> pdb=" O LYS G 189 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER G 196 " --> pdb=" O ALA G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 221 Processing helix chain 'G' and resid 233 through 256 Proline residue: G 239 - end of helix removed outlier: 3.938A pdb=" N GLY G 242 " --> pdb=" O CYS G 238 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N TYR G 249 " --> pdb=" O GLN G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 266 removed outlier: 3.831A pdb=" N TYR G 266 " --> pdb=" O GLU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 285 removed outlier: 4.411A pdb=" N VAL G 278 " --> pdb=" O SER G 274 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N THR G 279 " --> pdb=" O GLN G 275 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA G 282 " --> pdb=" O VAL G 278 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE G 283 " --> pdb=" O THR G 279 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU G 285 " --> pdb=" O VAL G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 314 removed outlier: 3.584A pdb=" N ARG G 297 " --> pdb=" O PHE G 293 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS G 298 " --> pdb=" O VAL G 294 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA G 299 " --> pdb=" O SER G 295 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL G 302 " --> pdb=" O LYS G 298 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU G 303 " --> pdb=" O ALA G 299 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE G 305 " --> pdb=" O THR G 301 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU G 312 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 325 removed outlier: 3.759A pdb=" N LEU G 324 " --> pdb=" O PRO G 320 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU G 325 " --> pdb=" O PRO G 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 320 through 325' Processing helix chain 'G' and resid 325 through 330 removed outlier: 3.708A pdb=" N GLU G 329 " --> pdb=" O GLU G 325 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN G 330 " --> pdb=" O ASP G 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 325 through 330' Processing helix chain 'G' and resid 347 through 360 removed outlier: 3.720A pdb=" N ASP G 351 " --> pdb=" O GLU G 347 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 365 removed outlier: 4.025A pdb=" N GLN G 365 " --> pdb=" O ALA G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 395 removed outlier: 3.622A pdb=" N ASN G 390 " --> pdb=" O LEU G 386 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU G 391 " --> pdb=" O TYR G 387 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR G 392 " --> pdb=" O GLY G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 407 through 412 removed outlier: 4.070A pdb=" N GLU G 411 " --> pdb=" O ILE G 407 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG G 412 " --> pdb=" O PRO G 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 407 through 412' Processing helix chain 'G' and resid 433 through 446 removed outlier: 3.722A pdb=" N ASP G 437 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN G 440 " --> pdb=" O SER G 436 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS G 441 " --> pdb=" O ASP G 437 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN G 446 " --> pdb=" O ASP G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 4.176A pdb=" N ASP G 481 " --> pdb=" O GLU G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 495 removed outlier: 3.798A pdb=" N THR G 494 " --> pdb=" O TRP G 490 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN G 495 " --> pdb=" O GLU G 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 490 through 495' Processing helix chain 'G' and resid 507 through 511 removed outlier: 3.939A pdb=" N SER G 510 " --> pdb=" O GLY G 507 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY G 511 " --> pdb=" O GLY G 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 507 through 511' Processing helix chain 'G' and resid 513 through 518 removed outlier: 4.014A pdb=" N ARG G 518 " --> pdb=" O VAL G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 605 removed outlier: 3.580A pdb=" N UNK G 603 " --> pdb=" O UNK G 599 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N UNK G 605 " --> pdb=" O UNK G 601 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 623 removed outlier: 3.721A pdb=" N UNK G 622 " --> pdb=" O UNK G 619 " (cutoff:3.500A) Processing helix chain 'G' and resid 624 through 628 Processing helix chain 'G' and resid 649 through 664 removed outlier: 4.406A pdb=" N UNK G 656 " --> pdb=" O UNK G 652 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N UNK G 661 " --> pdb=" O UNK G 657 " (cutoff:3.500A) Processing helix chain 'G' and resid 678 through 686 removed outlier: 3.824A pdb=" N UNK G 683 " --> pdb=" O UNK G 679 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N UNK G 684 " --> pdb=" O UNK G 680 " (cutoff:3.500A) Processing helix chain 'G' and resid 701 through 710 removed outlier: 3.942A pdb=" N UNK G 708 " --> pdb=" O UNK G 704 " (cutoff:3.500A) Processing helix chain 'G' and resid 763 through 771 removed outlier: 3.705A pdb=" N UNK G 769 " --> pdb=" O UNK G 765 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N UNK G 771 " --> pdb=" O UNK G 767 " (cutoff:3.500A) Processing helix chain 'G' and resid 797 through 803 Processing helix chain 'G' and resid 828 through 832 Processing helix chain 'G' and resid 841 through 847 removed outlier: 3.625A pdb=" N UNK G 845 " --> pdb=" O UNK G 841 " (cutoff:3.500A) Processing helix chain 'G' and resid 858 through 864 removed outlier: 4.481A pdb=" N UNK G 862 " --> pdb=" O UNK G 858 " (cutoff:3.500A) Processing helix chain 'G' and resid 867 through 871 Processing helix chain 'G' and resid 897 through 906 removed outlier: 3.864A pdb=" N UNK G 901 " --> pdb=" O UNK G 897 " (cutoff:3.500A) Processing helix chain 'G' and resid 921 through 930 removed outlier: 3.836A pdb=" N UNK G 925 " --> pdb=" O UNK G 921 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N UNK G 927 " --> pdb=" O UNK G 923 " (cutoff:3.500A) Processing helix chain 'G' and resid 974 through 979 Processing helix chain 'G' and resid 1105 through 1112 Processing helix chain 'G' and resid 1250 through 1255 Processing helix chain 'G' and resid 1279 through 1283 Processing helix chain 'G' and resid 1395 through 1401 Processing helix chain 'G' and resid 1415 through 1420 removed outlier: 3.543A pdb=" N UNK G1420 " --> pdb=" O UNK G1417 " (cutoff:3.500A) Processing helix chain 'G' and resid 1473 through 1477 Processing helix chain 'G' and resid 1512 through 1516 Processing helix chain 'G' and resid 1526 through 1531 removed outlier: 3.610A pdb=" N UNK G1531 " --> pdb=" O UNK G1528 " (cutoff:3.500A) Processing helix chain 'G' and resid 1540 through 1555 removed outlier: 3.943A pdb=" N UNK G1545 " --> pdb=" O UNK G1541 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N UNK G1546 " --> pdb=" O UNK G1542 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N UNK G1548 " --> pdb=" O UNK G1544 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N UNK G1551 " --> pdb=" O UNK G1547 " (cutoff:3.500A) Processing helix chain 'G' and resid 1677 through 1682 removed outlier: 3.685A pdb=" N LYS G1682 " --> pdb=" O MET G1678 " (cutoff:3.500A) Processing helix chain 'G' and resid 1684 through 1700 removed outlier: 3.822A pdb=" N VAL G1690 " --> pdb=" O ALA G1686 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP G1691 " --> pdb=" O ALA G1687 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA G1694 " --> pdb=" O VAL G1690 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASP G1695 " --> pdb=" O TRP G1691 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS G1699 " --> pdb=" O ASP G1695 " (cutoff:3.500A) Processing helix chain 'G' and resid 1705 through 1711 removed outlier: 3.544A pdb=" N ILE G1711 " --> pdb=" O LEU G1707 " (cutoff:3.500A) Processing helix chain 'G' and resid 1776 through 1795 removed outlier: 3.621A pdb=" N GLU G1785 " --> pdb=" O LEU G1781 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS G1786 " --> pdb=" O THR G1782 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP G1791 " --> pdb=" O ALA G1787 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU G1792 " --> pdb=" O ALA G1788 " (cutoff:3.500A) Processing helix chain 'G' and resid 1823 through 1838 removed outlier: 3.575A pdb=" N VAL G1830 " --> pdb=" O SER G1826 " (cutoff:3.500A) Processing helix chain 'G' and resid 1839 through 1842 removed outlier: 4.487A pdb=" N VAL G1842 " --> pdb=" O GLN G1839 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1839 through 1842' Processing helix chain 'G' and resid 1869 through 1875 Processing helix chain 'G' and resid 1897 through 1909 removed outlier: 3.758A pdb=" N ALA G1901 " --> pdb=" O GLN G1897 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU G1904 " --> pdb=" O ALA G1900 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG G1905 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA G1906 " --> pdb=" O GLY G1902 " (cutoff:3.500A) Processing helix chain 'G' and resid 1928 through 1933 removed outlier: 4.139A pdb=" N LEU G1933 " --> pdb=" O LYS G1929 " (cutoff:3.500A) Processing helix chain 'G' and resid 1968 through 1973 Processing helix chain 'G' and resid 2002 through 2006 removed outlier: 3.542A pdb=" N ARG G2005 " --> pdb=" O LYS G2002 " (cutoff:3.500A) Processing helix chain 'G' and resid 2030 through 2044 removed outlier: 3.645A pdb=" N SER G2035 " --> pdb=" O ASP G2031 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLU G2036 " --> pdb=" O LEU G2032 " (cutoff:3.500A) Proline residue: G2037 - end of helix Processing helix chain 'E' and resid 12 through 21 removed outlier: 3.782A pdb=" N UNK E 18 " --> pdb=" O UNK E 14 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N UNK E 19 " --> pdb=" O UNK E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 46 removed outlier: 4.294A pdb=" N UNK E 41 " --> pdb=" O UNK E 37 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N UNK E 42 " --> pdb=" O UNK E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 153 through 159 Processing helix chain 'E' and resid 182 through 190 Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 241 through 248 Processing helix chain 'E' and resid 284 through 288 removed outlier: 3.769A pdb=" N UNK E 288 " --> pdb=" O UNK E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 390 removed outlier: 3.702A pdb=" N UNK E 376 " --> pdb=" O UNK E 372 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N UNK E 378 " --> pdb=" O UNK E 374 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N UNK E 379 " --> pdb=" O UNK E 375 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N UNK E 383 " --> pdb=" O UNK E 379 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N UNK E 385 " --> pdb=" O UNK E 381 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N UNK E 387 " --> pdb=" O UNK E 383 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N UNK E 388 " --> pdb=" O UNK E 384 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N UNK E 390 " --> pdb=" O UNK E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 412 removed outlier: 3.601A pdb=" N UNK E 401 " --> pdb=" O UNK E 397 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N UNK E 403 " --> pdb=" O UNK E 399 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N UNK E 404 " --> pdb=" O UNK E 400 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N UNK E 405 " --> pdb=" O UNK E 401 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N UNK E 406 " --> pdb=" O UNK E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 538 Proline residue: E 534 - end of helix removed outlier: 3.905A pdb=" N GLU E 538 " --> pdb=" O PRO E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 550 removed outlier: 3.833A pdb=" N LEU E 547 " --> pdb=" O ILE E 543 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR E 548 " --> pdb=" O GLU E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 578 removed outlier: 3.915A pdb=" N GLU E 570 " --> pdb=" O SER E 566 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR E 575 " --> pdb=" O PHE E 571 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER E 576 " --> pdb=" O GLU E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 627 removed outlier: 4.053A pdb=" N THR E 625 " --> pdb=" O THR E 621 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 652 through 665 removed outlier: 4.004A pdb=" N LEU E 658 " --> pdb=" O GLN E 654 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE E 659 " --> pdb=" O LEU E 655 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU E 660 " --> pdb=" O SER E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 700 removed outlier: 4.089A pdb=" N GLU E 691 " --> pdb=" O SER E 687 " (cutoff:3.500A) Processing helix chain 'E' and resid 711 through 726 removed outlier: 3.990A pdb=" N TYR E 717 " --> pdb=" O GLN E 713 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR E 718 " --> pdb=" O VAL E 714 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER E 720 " --> pdb=" O ASP E 716 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE E 721 " --> pdb=" O TYR E 717 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N TYR E 722 " --> pdb=" O TYR E 718 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 743 No H-bonds generated for 'chain 'E' and resid 741 through 743' Processing helix chain 'E' and resid 744 through 752 removed outlier: 3.923A pdb=" N LEU E 748 " --> pdb=" O ASP E 744 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE E 749 " --> pdb=" O VAL E 745 " (cutoff:3.500A) Processing helix chain 'E' and resid 789 through 796 removed outlier: 3.906A pdb=" N ARG E 793 " --> pdb=" O GLU E 789 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU E 796 " --> pdb=" O HIS E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 796 through 814 removed outlier: 3.630A pdb=" N ARG E 801 " --> pdb=" O THR E 797 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY E 804 " --> pdb=" O LEU E 800 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 807 " --> pdb=" O MET E 803 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG E 813 " --> pdb=" O GLN E 809 " (cutoff:3.500A) Processing helix chain 'E' and resid 838 through 844 Processing helix chain 'E' and resid 847 through 853 removed outlier: 4.230A pdb=" N ASN E 851 " --> pdb=" O GLU E 847 " (cutoff:3.500A) Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 901 through 908 Processing helix chain 'E' and resid 913 through 918 Processing helix chain 'E' and resid 929 through 933 removed outlier: 3.684A pdb=" N PHE E 932 " --> pdb=" O GLY E 929 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL E 933 " --> pdb=" O LEU E 930 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 929 through 933' Processing helix chain 'E' and resid 935 through 967 removed outlier: 3.629A pdb=" N PHE E 939 " --> pdb=" O GLU E 935 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU E 943 " --> pdb=" O PHE E 939 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL E 948 " --> pdb=" O ARG E 944 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU E 949 " --> pdb=" O LYS E 945 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG E 954 " --> pdb=" O THR E 950 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE E 959 " --> pdb=" O LYS E 955 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU E 960 " --> pdb=" O ALA E 956 " (cutoff:3.500A) Processing helix chain 'E' and resid 1034 through 1042 removed outlier: 3.986A pdb=" N GLU E1038 " --> pdb=" O ARG E1034 " (cutoff:3.500A) Processing helix chain 'E' and resid 1049 through 1056 removed outlier: 3.595A pdb=" N ILE E1056 " --> pdb=" O GLU E1052 " (cutoff:3.500A) Processing helix chain 'E' and resid 1144 through 1149 Processing helix chain 'E' and resid 1208 through 1226 removed outlier: 4.108A pdb=" N THR E1212 " --> pdb=" O VAL E1208 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E1213 " --> pdb=" O ASP E1209 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N PHE E1214 " --> pdb=" O PRO E1210 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL E1215 " --> pdb=" O ILE E1211 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL E1220 " --> pdb=" O LEU E1216 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU E1221 " --> pdb=" O VAL E1217 " (cutoff:3.500A) Processing helix chain 'E' and resid 1230 through 1237 removed outlier: 3.570A pdb=" N MET E1234 " --> pdb=" O PRO E1231 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS E1236 " --> pdb=" O GLU E1233 " (cutoff:3.500A) Processing helix chain 'E' and resid 1256 through 1262 Processing helix chain 'E' and resid 1275 through 1279 removed outlier: 3.797A pdb=" N PHE E1279 " --> pdb=" O GLN E1276 " (cutoff:3.500A) Processing helix chain 'E' and resid 1281 through 1290 removed outlier: 4.041A pdb=" N ASN E1288 " --> pdb=" O SER E1284 " (cutoff:3.500A) Processing helix chain 'E' and resid 1309 through 1321 removed outlier: 3.621A pdb=" N ILE E1319 " --> pdb=" O GLY E1315 " (cutoff:3.500A) Processing helix chain 'E' and resid 1336 through 1340 Processing helix chain 'E' and resid 1752 through 1762 removed outlier: 3.670A pdb=" N UNK E1756 " --> pdb=" O UNK E1752 " (cutoff:3.500A) Processing helix chain 'E' and resid 1778 through 1783 removed outlier: 4.330A pdb=" N UNK E1782 " --> pdb=" O UNK E1779 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N UNK E1783 " --> pdb=" O UNK E1780 " (cutoff:3.500A) Processing helix chain 'E' and resid 1814 through 1818 Processing helix chain 'E' and resid 1820 through 1825 Processing helix chain 'I' and resid 1448 through 1453 Processing helix chain 'I' and resid 1457 through 1473 removed outlier: 3.812A pdb=" N VAL I1463 " --> pdb=" O ILE I1459 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU I1464 " --> pdb=" O LYS I1460 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU I1466 " --> pdb=" O TRP I1462 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU I1467 " --> pdb=" O VAL I1463 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU I1468 " --> pdb=" O GLU I1464 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA I1469 " --> pdb=" O ASN I1465 " (cutoff:3.500A) Processing helix chain 'I' and resid 1481 through 1505 removed outlier: 4.748A pdb=" N ARG I1491 " --> pdb=" O LEU I1487 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN I1495 " --> pdb=" O ARG I1491 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU I1501 " --> pdb=" O ALA I1497 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.544A pdb=" N ASP B 503 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 338 through 341 removed outlier: 3.636A pdb=" N LEU B 377 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL B 378 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B 367 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 641 through 642 removed outlier: 5.643A pdb=" N UNK B 670 " --> pdb=" O UNK B 642 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N UNK B 693 " --> pdb=" O UNK B 718 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1146 through 1148 Processing sheet with id=AA5, first strand: chain 'B' and resid 1182 through 1183 Processing sheet with id=AA6, first strand: chain 'B' and resid 1348 through 1350 removed outlier: 3.561A pdb=" N UNK B1358 " --> pdb=" O UNK B1350 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N UNK B1314 " --> pdb=" O UNK B1359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1342 through 1345 removed outlier: 3.680A pdb=" N UNK B1342 " --> pdb=" O UNK B1366 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1625 through 1628 removed outlier: 3.633A pdb=" N ILE B1626 " --> pdb=" O GLU B1641 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B1641 " --> pdb=" O ILE B1626 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1662 through 1663 Processing sheet with id=AB1, first strand: chain 'B' and resid 1741 through 1742 removed outlier: 3.857A pdb=" N GLU B1749 " --> pdb=" O VAL B1742 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1881 through 1882 removed outlier: 3.544A pdb=" N ILE B1855 " --> pdb=" O VAL B1893 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 597 through 600 removed outlier: 5.680A pdb=" N MET A 599 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 732 through 736 removed outlier: 7.072A pdb=" N VAL A 703 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL A 735 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL A 705 " --> pdb=" O VAL A 735 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE A 680 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 679 " --> pdb=" O ILE A 769 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1020 through 1024 removed outlier: 6.549A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY A1023 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN A1385 " --> pdb=" O VAL A1329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1060 through 1061 removed outlier: 3.944A pdb=" N SER A1078 " --> pdb=" O SER A1061 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 158 through 159 removed outlier: 3.543A pdb=" N ASP F 503 " --> pdb=" O VAL F 527 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 338 through 341 removed outlier: 3.636A pdb=" N LEU F 377 " --> pdb=" O ILE F 341 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL F 378 " --> pdb=" O SER F 369 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU F 367 " --> pdb=" O SER F 380 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 641 through 642 removed outlier: 5.644A pdb=" N UNK F 670 " --> pdb=" O UNK F 642 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N UNK F 693 " --> pdb=" O UNK F 718 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 1146 through 1148 Processing sheet with id=AC2, first strand: chain 'F' and resid 1182 through 1183 Processing sheet with id=AC3, first strand: chain 'F' and resid 1348 through 1350 removed outlier: 3.561A pdb=" N UNK F1358 " --> pdb=" O UNK F1350 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N UNK F1314 " --> pdb=" O UNK F1359 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 1342 through 1345 removed outlier: 3.681A pdb=" N UNK F1342 " --> pdb=" O UNK F1366 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 1625 through 1628 removed outlier: 3.633A pdb=" N ILE F1626 " --> pdb=" O GLU F1641 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU F1641 " --> pdb=" O ILE F1626 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 1662 through 1663 Processing sheet with id=AC7, first strand: chain 'F' and resid 1741 through 1742 removed outlier: 3.858A pdb=" N GLU F1749 " --> pdb=" O VAL F1742 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 1881 through 1882 removed outlier: 3.544A pdb=" N ILE F1855 " --> pdb=" O VAL F1893 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 597 through 600 removed outlier: 5.679A pdb=" N MET D 599 " --> pdb=" O ASP D 608 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 732 through 736 removed outlier: 7.072A pdb=" N VAL D 703 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N VAL D 735 " --> pdb=" O VAL D 703 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL D 705 " --> pdb=" O VAL D 735 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE D 680 " --> pdb=" O THR D 706 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU D 679 " --> pdb=" O ILE D 769 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 1020 through 1024 removed outlier: 6.549A pdb=" N VAL D1021 " --> pdb=" O MET D1388 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N MET D1388 " --> pdb=" O VAL D1021 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY D1023 " --> pdb=" O ILE D1386 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN D1385 " --> pdb=" O VAL D1329 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 1060 through 1061 removed outlier: 3.945A pdb=" N SER D1078 " --> pdb=" O SER D1061 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 158 through 159 removed outlier: 3.542A pdb=" N ASP G 503 " --> pdb=" O VAL G 527 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 338 through 341 removed outlier: 3.636A pdb=" N LEU G 377 " --> pdb=" O ILE G 341 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL G 378 " --> pdb=" O SER G 369 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU G 367 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 641 through 642 removed outlier: 5.643A pdb=" N UNK G 670 " --> pdb=" O UNK G 642 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N UNK G 693 " --> pdb=" O UNK G 718 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 1146 through 1148 Processing sheet with id=AD8, first strand: chain 'G' and resid 1182 through 1183 Processing sheet with id=AD9, first strand: chain 'G' and resid 1348 through 1350 removed outlier: 3.562A pdb=" N UNK G1358 " --> pdb=" O UNK G1350 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N UNK G1314 " --> pdb=" O UNK G1359 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 1342 through 1345 removed outlier: 3.681A pdb=" N UNK G1342 " --> pdb=" O UNK G1366 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 1625 through 1628 removed outlier: 3.633A pdb=" N ILE G1626 " --> pdb=" O GLU G1641 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU G1641 " --> pdb=" O ILE G1626 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 1662 through 1663 Processing sheet with id=AE4, first strand: chain 'G' and resid 1741 through 1742 removed outlier: 3.858A pdb=" N GLU G1749 " --> pdb=" O VAL G1742 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 1881 through 1882 removed outlier: 3.544A pdb=" N ILE G1855 " --> pdb=" O VAL G1893 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 597 through 600 removed outlier: 5.680A pdb=" N MET E 599 " --> pdb=" O ASP E 608 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 732 through 736 removed outlier: 7.071A pdb=" N VAL E 703 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL E 735 " --> pdb=" O VAL E 703 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL E 705 " --> pdb=" O VAL E 735 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE E 680 " --> pdb=" O THR E 706 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU E 679 " --> pdb=" O ILE E 769 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 1020 through 1024 removed outlier: 6.550A pdb=" N VAL E1021 " --> pdb=" O MET E1388 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N MET E1388 " --> pdb=" O VAL E1021 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY E1023 " --> pdb=" O ILE E1386 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN E1385 " --> pdb=" O VAL E1329 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 1060 through 1061 removed outlier: 3.945A pdb=" N SER E1078 " --> pdb=" O SER E1061 " (cutoff:3.500A) 1461 hydrogen bonds defined for protein. 4023 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: 20.95 Time building geometry restraints manager: 22.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 20507 1.33 - 1.46: 11542 1.46 - 1.58: 31224 1.58 - 1.70: 3 1.70 - 1.83: 252 Bond restraints: 63528 Sorted by residual: bond pdb=" C GLU E1268 " pdb=" N PRO E1269 " ideal model delta sigma weight residual 1.332 1.379 -0.047 1.12e-02 7.97e+03 1.76e+01 bond pdb=" C GLU D1268 " pdb=" N PRO D1269 " ideal model delta sigma weight residual 1.332 1.379 -0.047 1.12e-02 7.97e+03 1.76e+01 bond pdb=" C GLU A1268 " pdb=" N PRO A1269 " ideal model delta sigma weight residual 1.332 1.379 -0.047 1.12e-02 7.97e+03 1.76e+01 bond pdb=" C ARG E1017 " pdb=" N VAL E1018 " ideal model delta sigma weight residual 1.334 1.296 0.038 1.24e-02 6.50e+03 9.19e+00 bond pdb=" C ARG A1017 " pdb=" N VAL A1018 " ideal model delta sigma weight residual 1.334 1.296 0.037 1.24e-02 6.50e+03 9.02e+00 ... (remaining 63523 not shown) Histogram of bond angle deviations from ideal: 97.25 - 106.25: 1214 106.25 - 115.25: 38499 115.25 - 124.24: 44934 124.24 - 133.24: 2362 133.24 - 142.24: 102 Bond angle restraints: 87111 Sorted by residual: angle pdb=" N PRO B1987 " pdb=" CA PRO B1987 " pdb=" CB PRO B1987 " ideal model delta sigma weight residual 101.83 111.31 -9.48 8.40e-01 1.42e+00 1.27e+02 angle pdb=" N PRO F1987 " pdb=" CA PRO F1987 " pdb=" CB PRO F1987 " ideal model delta sigma weight residual 101.83 111.29 -9.46 8.40e-01 1.42e+00 1.27e+02 angle pdb=" N PRO G1987 " pdb=" CA PRO G1987 " pdb=" CB PRO G1987 " ideal model delta sigma weight residual 101.83 111.28 -9.45 8.40e-01 1.42e+00 1.26e+02 angle pdb=" N PRO B1975 " pdb=" CA PRO B1975 " pdb=" CB PRO B1975 " ideal model delta sigma weight residual 103.19 111.58 -8.39 9.50e-01 1.11e+00 7.81e+01 angle pdb=" N PRO G1975 " pdb=" CA PRO G1975 " pdb=" CB PRO G1975 " ideal model delta sigma weight residual 103.19 111.58 -8.39 9.50e-01 1.11e+00 7.80e+01 ... (remaining 87106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 34416 17.74 - 35.47: 2933 35.47 - 53.21: 604 53.21 - 70.95: 108 70.95 - 88.68: 33 Dihedral angle restraints: 38094 sinusoidal: 9183 harmonic: 28911 Sorted by residual: dihedral pdb=" CA ILE C1477 " pdb=" C ILE C1477 " pdb=" N PRO C1478 " pdb=" CA PRO C1478 " ideal model delta harmonic sigma weight residual 180.00 122.02 57.98 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA ILE H1477 " pdb=" C ILE H1477 " pdb=" N PRO H1478 " pdb=" CA PRO H1478 " ideal model delta harmonic sigma weight residual 180.00 122.08 57.92 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA ILE I1477 " pdb=" C ILE I1477 " pdb=" N PRO I1478 " pdb=" CA PRO I1478 " ideal model delta harmonic sigma weight residual 180.00 122.12 57.88 0 5.00e+00 4.00e-02 1.34e+02 ... (remaining 38091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 10124 0.115 - 0.229: 703 0.229 - 0.344: 48 0.344 - 0.458: 3 0.458 - 0.573: 3 Chirality restraints: 10881 Sorted by residual: chirality pdb=" CB ILE B1924 " pdb=" CA ILE B1924 " pdb=" CG1 ILE B1924 " pdb=" CG2 ILE B1924 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.57 2.00e-01 2.50e+01 8.20e+00 chirality pdb=" CB ILE F1924 " pdb=" CA ILE F1924 " pdb=" CG1 ILE F1924 " pdb=" CG2 ILE F1924 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.57 2.00e-01 2.50e+01 8.18e+00 chirality pdb=" CB ILE G1924 " pdb=" CA ILE G1924 " pdb=" CG1 ILE G1924 " pdb=" CG2 ILE G1924 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.57 2.00e-01 2.50e+01 8.15e+00 ... (remaining 10878 not shown) Planarity restraints: 11748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE I1477 " 0.098 5.00e-02 4.00e+02 1.48e-01 3.51e+01 pdb=" N PRO I1478 " -0.256 5.00e-02 4.00e+02 pdb=" CA PRO I1478 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO I1478 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE H1477 " -0.097 5.00e-02 4.00e+02 1.48e-01 3.48e+01 pdb=" N PRO H1478 " 0.255 5.00e-02 4.00e+02 pdb=" CA PRO H1478 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO H1478 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C1477 " -0.097 5.00e-02 4.00e+02 1.47e-01 3.48e+01 pdb=" N PRO C1478 " 0.255 5.00e-02 4.00e+02 pdb=" CA PRO C1478 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO C1478 " -0.075 5.00e-02 4.00e+02 ... (remaining 11745 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 13722 2.77 - 3.30: 64217 3.30 - 3.83: 96498 3.83 - 4.37: 105526 4.37 - 4.90: 166693 Nonbonded interactions: 446656 Sorted by model distance: nonbonded pdb=" O SER F 400 " pdb=" OG SER F 400 " model vdw 2.231 2.440 nonbonded pdb=" O SER B 400 " pdb=" OG SER B 400 " model vdw 2.231 2.440 nonbonded pdb=" O SER G 400 " pdb=" OG SER G 400 " model vdw 2.232 2.440 nonbonded pdb=" O PHE F1721 " pdb=" OH TYR F1733 " model vdw 2.238 2.440 nonbonded pdb=" O PHE G1721 " pdb=" OH TYR G1733 " model vdw 2.238 2.440 ... (remaining 446651 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 'D' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'I' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'G' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'I' } Set refine NCS operators NCS operators will be refined. 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: 2.310 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: 0.060 Extract box with map and model: 10.250 Check model and map are aligned: 0.730 Set scattering table: 0.460 Process input model: 122.180 Find NCS groups from input model: 3.280 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 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 : 0.007 0.073 63528 Z= 0.474 Angle : 1.479 16.353 87111 Z= 0.809 Chirality : 0.064 0.573 10881 Planarity : 0.007 0.148 11748 Dihedral : 15.333 88.684 19176 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 4.50 % Allowed : 23.18 % Favored : 72.32 % Rotamer: Outliers : 2.42 % Allowed : 16.32 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 8.24 % Twisted General : 2.14 % 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: -6.05 (0.08), residues: 5802 helix: -4.02 (0.07), residues: 1830 sheet: -3.02 (0.25), residues: 294 loop : -4.39 (0.08), residues: 3678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP D1193 HIS 0.014 0.003 HIS A1433 PHE 0.036 0.003 PHE E1376 TYR 0.063 0.003 TYR B 541 ARG 0.036 0.002 ARG B 478 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 712 LYS cc_start: 0.8419 (tttt) cc_final: 0.8204 (tttt) REVERT: A 838 MET cc_start: 0.8234 (mtp) cc_final: 0.7873 (mtt) REVERT: A 847 GLU cc_start: 0.8122 (mp0) cc_final: 0.7866 (mp0) REVERT: A 871 TRP cc_start: 0.8728 (t-100) cc_final: 0.8484 (t-100) REVERT: A 923 MET cc_start: 0.4801 (mtm) cc_final: 0.4293 (mtm) REVERT: A 932 PHE cc_start: 0.8522 (m-80) cc_final: 0.7819 (m-80) REVERT: A 942 LYS cc_start: 0.8796 (tttt) cc_final: 0.8547 (ttmm) REVERT: A 1024 PHE cc_start: 0.8544 (p90) cc_final: 0.8319 (p90) REVERT: A 1090 LYS cc_start: 0.7067 (mttm) cc_final: 0.6342 (pttp) REVERT: A 1111 PHE cc_start: 0.8365 (m-10) cc_final: 0.7852 (m-10) REVERT: A 1189 ILE cc_start: 0.7485 (mm) cc_final: 0.6844 (mt) REVERT: A 1283 MET cc_start: 0.8989 (mpp) cc_final: 0.8682 (mpp) outliers start: 13 outliers final: 7 residues processed: 157 average time/residue: 0.1875 time to fit residues: 39.1531 Evaluate side-chains 110 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 0.657 Evaluate side-chains 142 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4625 (mmt) cc_final: 0.3731 (ttt) REVERT: B 63 LYS cc_start: 0.6345 (tttt) cc_final: 0.5694 (tttt) REVERT: B 64 PHE cc_start: 0.7882 (t80) cc_final: 0.7655 (t80) REVERT: B 118 LYS cc_start: 0.9098 (tptt) cc_final: 0.8859 (tptp) REVERT: B 217 GLU cc_start: 0.8903 (pp20) cc_final: 0.8507 (pp20) REVERT: B 245 GLN cc_start: 0.8099 (mt0) cc_final: 0.7333 (mp-120) REVERT: B 454 ASP cc_start: 0.6153 (m-30) cc_final: 0.5803 (t0) REVERT: B 464 ASP cc_start: 0.8063 (t0) cc_final: 0.7372 (m-30) REVERT: B 468 LEU cc_start: 0.8746 (mt) cc_final: 0.8065 (mp) REVERT: B 478 ARG cc_start: 0.8862 (ttp80) cc_final: 0.7698 (ptm160) REVERT: B 495 GLN cc_start: 0.7759 (mm-40) cc_final: 0.7496 (mp10) REVERT: B 1676 MET cc_start: 0.9290 (tpp) cc_final: 0.8467 (mpp) REVERT: B 1693 ARG cc_start: 0.8928 (tpp80) cc_final: 0.8689 (tpp80) REVERT: B 1725 LYS cc_start: 0.7927 (mmtp) cc_final: 0.7099 (mptt) REVERT: B 1783 LEU cc_start: 0.9592 (tp) cc_final: 0.8923 (tp) REVERT: B 1784 MET cc_start: 0.8610 (tmm) cc_final: 0.8396 (tmm) REVERT: B 1822 MET cc_start: 0.8791 (ptp) cc_final: 0.8502 (pmm) REVERT: B 1827 LEU cc_start: 0.9437 (tp) cc_final: 0.9043 (tt) REVERT: B 1926 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6574 (pm20) outliers start: 17 outliers final: 7 residues processed: 139 average time/residue: 0.2230 time to fit residues: 42.7315 Evaluate side-chains 96 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.798 Evaluate side-chains 20 residues out of total 64 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 17 time to evaluate : 0.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1500 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7467 (tm-30) outliers start: 3 outliers final: 1 residues processed: 20 average time/residue: 0.1208 time to fit residues: 2.5968 Evaluate side-chains 13 residues out of total 64 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 0.0980 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 0.0050 chunk 10 optimal weight: 9.9990 chunk 16 optimal weight: 0.0870 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.0170 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 overall best weight: 0.1410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 783 HIS A 821 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN B 102 HIS B 110 GLN B 273 HIS B 348 GLN B 350 GLN B 354 ASN B 418 ASN B 430 HIS B1892 ASN ** B1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1939 HIS Total number of N/Q/H flips: 11 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 63528 Z= 0.188 Angle : 0.874 11.879 87111 Z= 0.441 Chirality : 0.043 0.291 10881 Planarity : 0.006 0.120 11748 Dihedral : 7.557 56.114 10176 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 1.81 % Allowed : 20.53 % Favored : 77.66 % Rotamer: Outliers : 0.15 % Allowed : 6.16 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 4.71 % Twisted General : 1.08 % 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: -5.51 (0.09), residues: 5802 helix: -3.04 (0.08), residues: 2124 sheet: -3.05 (0.26), residues: 273 loop : -4.37 (0.09), residues: 3405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 289 HIS 0.005 0.001 HIS G 102 PHE 0.025 0.002 PHE F 28 TYR 0.021 0.002 TYR F1702 ARG 0.006 0.001 ARG D 852 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11600 Ramachandran restraints generated. 5800 Oldfield, 0 Emsley, 5800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11600 Ramachandran restraints generated. 5800 Oldfield, 0 Emsley, 5800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 712 LYS cc_start: 0.8006 (tttt) cc_final: 0.7793 (tttt) REVERT: A 765 LEU cc_start: 0.8836 (mt) cc_final: 0.8623 (mt) REVERT: A 794 ILE cc_start: 0.9290 (tt) cc_final: 0.9056 (tt) REVERT: A 797 THR cc_start: 0.9387 (m) cc_final: 0.9082 (m) REVERT: A 799 ILE cc_start: 0.8928 (mt) cc_final: 0.8182 (mp) REVERT: A 801 ARG cc_start: 0.7548 (mtm180) cc_final: 0.5406 (mmt180) REVERT: A 838 MET cc_start: 0.8223 (mtp) cc_final: 0.8016 (mtt) REVERT: A 841 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7189 (tp30) REVERT: A 846 LEU cc_start: 0.8931 (mt) cc_final: 0.8589 (mp) REVERT: A 871 TRP cc_start: 0.8715 (t-100) cc_final: 0.8286 (t-100) REVERT: A 891 MET cc_start: 0.8888 (mtm) cc_final: 0.8174 (ptp) REVERT: A 923 MET cc_start: 0.4132 (mtm) cc_final: 0.3929 (ttp) REVERT: A 932 PHE cc_start: 0.8366 (m-80) cc_final: 0.7897 (m-80) REVERT: A 1024 PHE cc_start: 0.8332 (p90) cc_final: 0.8051 (p90) REVERT: A 1090 LYS cc_start: 0.6555 (mttm) cc_final: 0.5905 (pttp) REVERT: A 1270 VAL cc_start: 0.8123 (t) cc_final: 0.7269 (t) REVERT: A 1280 ILE cc_start: 0.9036 (tp) cc_final: 0.8823 (tp) REVERT: A 1283 MET cc_start: 0.8901 (mpp) cc_final: 0.8659 (mpp) REVERT: A 1357 GLU cc_start: 0.8179 (tp30) cc_final: 0.7855 (tp30) REVERT: A 1360 ARG cc_start: 0.6736 (mpt180) cc_final: 0.6322 (mmt90) REVERT: A 1400 ILE cc_start: 0.7968 (mp) cc_final: 0.7747 (pt) outliers start: 2 outliers final: 1 residues processed: 165 average time/residue: 0.1672 time to fit residues: 38.4522 Evaluate side-chains 121 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 0.654 Evaluate side-chains 128 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4818 (mmt) cc_final: 0.3835 (ttt) REVERT: B 118 LYS cc_start: 0.9029 (tptt) cc_final: 0.8788 (tmtt) REVERT: B 216 LEU cc_start: 0.9333 (mt) cc_final: 0.9078 (mp) REVERT: B 230 TYR cc_start: 0.8292 (m-10) cc_final: 0.8071 (m-10) REVERT: B 245 GLN cc_start: 0.8442 (mt0) cc_final: 0.7454 (mp10) REVERT: B 493 THR cc_start: 0.8810 (p) cc_final: 0.8562 (p) REVERT: B 518 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7982 (tmm-80) REVERT: B 1676 MET cc_start: 0.9289 (tpp) cc_final: 0.8911 (mmm) REVERT: B 1725 LYS cc_start: 0.7290 (mmtp) cc_final: 0.6485 (pttt) REVERT: B 1753 LYS cc_start: 0.7933 (mmtm) cc_final: 0.7467 (mmtm) REVERT: B 1783 LEU cc_start: 0.9288 (tp) cc_final: 0.8876 (tp) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2250 time to fit residues: 39.7325 Evaluate side-chains 92 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.798 Evaluate side-chains 23 residues out of total 64 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.058 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0896 time to fit residues: 2.2523 Evaluate side-chains 15 residues out of total 64 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 0.2980 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1442 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 430 HIS B 440 ASN B 451 ASN ** B1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1692 ASN ** B1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1495 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 63528 Z= 0.189 Angle : 0.906 14.235 87111 Z= 0.446 Chirality : 0.046 0.524 10881 Planarity : 0.008 0.350 11748 Dihedral : 7.330 56.313 10176 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 1.71 % Allowed : 23.47 % Favored : 74.82 % Rotamer: Outliers : 0.44 % Allowed : 6.01 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 3.53 % Twisted General : 0.86 % 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: -5.10 (0.09), residues: 5802 helix: -2.45 (0.09), residues: 2139 sheet: -2.98 (0.26), residues: 324 loop : -4.31 (0.09), residues: 3339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 289 HIS 0.034 0.003 HIS B 500 PHE 0.060 0.003 PHE B 292 TYR 0.038 0.002 TYR G 266 ARG 0.057 0.002 ARG F 518 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11600 Ramachandran restraints generated. 5800 Oldfield, 0 Emsley, 5800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11600 Ramachandran restraints generated. 5800 Oldfield, 0 Emsley, 5800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 765 LEU cc_start: 0.8900 (mt) cc_final: 0.8649 (mt) REVERT: A 785 ASP cc_start: 0.8597 (p0) cc_final: 0.8307 (p0) REVERT: A 797 THR cc_start: 0.9445 (m) cc_final: 0.9044 (m) REVERT: A 799 ILE cc_start: 0.9030 (mt) cc_final: 0.8361 (mp) REVERT: A 801 ARG cc_start: 0.7876 (mtm180) cc_final: 0.5335 (mmt-90) REVERT: A 808 LYS cc_start: 0.7287 (mttp) cc_final: 0.7038 (mmtm) REVERT: A 841 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7376 (tp30) REVERT: A 871 TRP cc_start: 0.8721 (t-100) cc_final: 0.8469 (t-100) REVERT: A 891 MET cc_start: 0.8894 (mtm) cc_final: 0.8232 (ptp) REVERT: A 930 LEU cc_start: 0.8443 (mp) cc_final: 0.7203 (tt) REVERT: A 932 PHE cc_start: 0.8361 (m-80) cc_final: 0.7901 (m-80) REVERT: A 1090 LYS cc_start: 0.6518 (mttm) cc_final: 0.5894 (pttp) REVERT: A 1121 MET cc_start: 0.8459 (mpp) cc_final: 0.8164 (mpp) REVERT: A 1175 ILE cc_start: 0.4118 (OUTLIER) cc_final: 0.3836 (tt) REVERT: A 1270 VAL cc_start: 0.8069 (t) cc_final: 0.7586 (p) REVERT: A 1280 ILE cc_start: 0.9068 (tp) cc_final: 0.8832 (tp) REVERT: A 1283 MET cc_start: 0.8921 (mpp) cc_final: 0.8656 (mpp) REVERT: A 1357 GLU cc_start: 0.8025 (tp30) cc_final: 0.7755 (tp30) REVERT: A 1400 ILE cc_start: 0.7980 (mp) cc_final: 0.7753 (pt) REVERT: A 1515 ARG cc_start: 0.7631 (pmt170) cc_final: 0.6547 (ptt180) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.1712 time to fit residues: 35.7969 Evaluate side-chains 110 residues out of total 745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.667 Evaluate side-chains 126 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4714 (mmt) cc_final: 0.3732 (ttp) REVERT: B 63 LYS cc_start: 0.7286 (tttt) cc_final: 0.6921 (tttt) REVERT: B 67 TYR cc_start: 0.6171 (m-80) cc_final: 0.5955 (m-80) REVERT: B 118 LYS cc_start: 0.9026 (tptt) cc_final: 0.8761 (tmtt) REVERT: B 174 ARG cc_start: 0.8807 (tpp80) cc_final: 0.8547 (tpp80) REVERT: B 216 LEU cc_start: 0.9273 (mt) cc_final: 0.9027 (mp) REVERT: B 230 TYR cc_start: 0.8183 (m-10) cc_final: 0.7944 (m-10) REVERT: B 241 ILE cc_start: 0.9462 (mm) cc_final: 0.9113 (mm) REVERT: B 245 GLN cc_start: 0.8063 (mt0) cc_final: 0.7333 (mp10) REVERT: B 256 LEU cc_start: 0.8588 (mm) cc_final: 0.8349 (mm) REVERT: B 421 LEU cc_start: 0.9183 (tp) cc_final: 0.8917 (mt) REVERT: B 1692 ASN cc_start: 0.8873 (m110) cc_final: 0.8376 (m-40) REVERT: B 1700 ASP cc_start: 0.7826 (m-30) cc_final: 0.7576 (m-30) REVERT: B 1725 LYS cc_start: 0.7337 (mmtp) cc_final: 0.6529 (pptt) REVERT: B 1783 LEU cc_start: 0.9325 (tp) cc_final: 0.8894 (tp) REVERT: B 1811 GLU cc_start: 0.7930 (pm20) cc_final: 0.7596 (tp30) REVERT: B 1827 LEU cc_start: 0.9359 (tt) cc_final: 0.8992 (mt) outliers start: 5 outliers final: 1 residues processed: 123 average time/residue: 0.2327 time to fit residues: 39.3010 Evaluate side-chains 94 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.808 Evaluate side-chains 21 residues out of total 64 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.058 Fit side-chains revert: symmetry clash REVERT: C 1506 GLN cc_start: 0.8609 (mp10) cc_final: 0.8170 (mp10) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0958 time to fit residues: 2.2044 Evaluate side-chains 15 residues out of total 64 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7939 > 50: distance: 0 - 1: 40.815 distance: 0 - 3: 30.585 distance: 1 - 2: 47.877 distance: 1 - 6: 37.669 distance: 2 - 25: 41.346 distance: 3 - 4: 24.030 distance: 3 - 5: 14.104 distance: 6 - 7: 52.068 distance: 7 - 8: 41.318 distance: 7 - 10: 9.189 distance: 8 - 9: 44.221 distance: 8 - 13: 33.068 distance: 9 - 34: 52.278 distance: 10 - 11: 40.894 distance: 10 - 12: 57.879 distance: 13 - 14: 18.579 distance: 13 - 19: 29.495 distance: 14 - 15: 32.929 distance: 14 - 17: 33.504 distance: 15 - 16: 12.812 distance: 15 - 20: 12.149 distance: 16 - 42: 29.289 distance: 17 - 18: 22.374 distance: 18 - 19: 39.959 distance: 20 - 21: 15.592 distance: 21 - 22: 14.045 distance: 21 - 24: 18.130 distance: 22 - 23: 10.063 distance: 22 - 25: 12.870 distance: 23 - 49: 18.698 distance: 25 - 26: 16.463 distance: 26 - 27: 9.503 distance: 26 - 29: 15.257 distance: 27 - 28: 3.907 distance: 27 - 34: 27.096 distance: 28 - 53: 26.396 distance: 29 - 30: 10.604 distance: 30 - 31: 9.635 distance: 31 - 32: 3.546 distance: 31 - 33: 3.796 distance: 34 - 35: 14.808 distance: 35 - 36: 20.357 distance: 35 - 38: 16.177 distance: 36 - 37: 32.027 distance: 36 - 42: 39.899 distance: 37 - 62: 31.679 distance: 38 - 39: 20.172 distance: 39 - 40: 4.325 distance: 39 - 41: 6.458 distance: 42 - 43: 31.258 distance: 43 - 44: 34.503 distance: 43 - 46: 16.486 distance: 44 - 45: 27.475 distance: 44 - 49: 27.870 distance: 45 - 73: 22.172 distance: 46 - 47: 17.410 distance: 46 - 48: 29.618 distance: 49 - 50: 26.540 distance: 50 - 51: 11.566 distance: 51 - 52: 59.626 distance: 51 - 53: 30.565 distance: 53 - 54: 29.520 distance: 54 - 55: 35.883 distance: 54 - 57: 17.540 distance: 55 - 56: 9.717 distance: 55 - 62: 32.570 distance: 57 - 58: 38.577 distance: 58 - 59: 54.754 distance: 59 - 60: 13.380 distance: 60 - 61: 28.017 distance: 62 - 63: 15.339 distance: 63 - 64: 21.062 distance: 63 - 66: 12.143 distance: 64 - 65: 38.198 distance: 64 - 73: 24.092 distance: 66 - 67: 13.685 distance: 67 - 68: 3.794 distance: 67 - 69: 3.639 distance: 71 - 72: 3.232 distance: 73 - 74: 7.877 distance: 74 - 75: 8.560 distance: 74 - 77: 6.951 distance: 77 - 78: 3.034