Starting phenix.real_space_refine (version: 1.21rc1) on Wed May 17 05:50:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfr_8665/05_2023/5vfr_8665_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfr_8665/05_2023/5vfr_8665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfr_8665/05_2023/5vfr_8665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfr_8665/05_2023/5vfr_8665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfr_8665/05_2023/5vfr_8665_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfr_8665/05_2023/5vfr_8665_updated.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 12 5.49 5 S 585 5.16 5 C 63101 2.51 5 N 17177 2.21 5 O 19032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "U ARG 140": "NH1" <-> "NH2" Residue "U ARG 159": "NH1" <-> "NH2" Residue "U PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 194": "NH1" <-> "NH2" Residue "V ARG 306": "NH1" <-> "NH2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ARG 355": "NH1" <-> "NH2" Residue "V ARG 397": "NH1" <-> "NH2" Residue "W ARG 8": "NH1" <-> "NH2" Residue "W ARG 12": "NH1" <-> "NH2" Residue "W ARG 55": "NH1" <-> "NH2" Residue "W ARG 182": "NH1" <-> "NH2" Residue "W ARG 357": "NH1" <-> "NH2" Residue "W ARG 364": "NH1" <-> "NH2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 137": "NH1" <-> "NH2" Residue "Y ARG 176": "NH1" <-> "NH2" Residue "Y ARG 177": "NH1" <-> "NH2" Residue "Y ARG 179": "NH1" <-> "NH2" Residue "Y ARG 267": "NH1" <-> "NH2" Residue "Y ARG 297": "NH1" <-> "NH2" Residue "Y ARG 300": "NH1" <-> "NH2" Residue "Y ARG 312": "NH1" <-> "NH2" Residue "Y ARG 342": "NH1" <-> "NH2" Residue "Y ARG 358": "NH1" <-> "NH2" Residue "Z TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 267": "NH1" <-> "NH2" Residue "a PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 196": "NH1" <-> "NH2" Residue "a ARG 226": "NH1" <-> "NH2" Residue "a ARG 270": "NH1" <-> "NH2" Residue "a ARG 284": "NH1" <-> "NH2" Residue "b ARG 70": "NH1" <-> "NH2" Residue "c ARG 68": "NH1" <-> "NH2" Residue "c ARG 104": "NH1" <-> "NH2" Residue "d ARG 52": "NH1" <-> "NH2" Residue "d ARG 65": "NH1" <-> "NH2" Residue "d ARG 111": "NH1" <-> "NH2" Residue "d ARG 175": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 249": "NH1" <-> "NH2" Residue "K ARG 10": "NH1" <-> "NH2" Residue "K ARG 20": "NH1" <-> "NH2" Residue "L TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "L ARG 157": "NH1" <-> "NH2" Residue "L ARG 239": "NH1" <-> "NH2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 187": "NH1" <-> "NH2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "Q ARG 93": "NH1" <-> "NH2" Residue "S ARG 173": "NH1" <-> "NH2" Residue "T ARG 182": "NH1" <-> "NH2" Residue "g ARG 21": "NH1" <-> "NH2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "g ARG 132": "NH1" <-> "NH2" Residue "g PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 4": "NH1" <-> "NH2" Residue "h PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 249": "NH1" <-> "NH2" Residue "k ARG 20": "NH1" <-> "NH2" Residue "l TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 96": "NH1" <-> "NH2" Residue "l ARG 157": "NH1" <-> "NH2" Residue "l ARG 239": "NH1" <-> "NH2" Residue "m ARG 19": "NH1" <-> "NH2" Residue "m ARG 187": "NH1" <-> "NH2" Residue "m ARG 232": "NH1" <-> "NH2" Residue "n ARG 45": "NH1" <-> "NH2" Residue "o ARG 201": "NH1" <-> "NH2" Residue "p ARG 66": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "E ARG 251": "NH1" <-> "NH2" Residue "E ARG 255": "NH1" <-> "NH2" Residue "E ARG 291": "NH1" <-> "NH2" Residue "F ARG 238": "NH1" <-> "NH2" Residue "F ARG 269": "NH1" <-> "NH2" Residue "F ARG 334": "NH1" <-> "NH2" Residue "F ARG 364": "NH1" <-> "NH2" Residue "f PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 388": "OD1" <-> "OD2" Residue "f GLU 641": "OE1" <-> "OE2" Residue "f TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.24s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 99908 Number of models: 1 Model: "" Number of chains: 51 Chain: "U" Number of atoms: 6287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6287 Classifications: {'peptide': 806} Link IDs: {'PTRANS': 26, 'TRANS': 779} Chain breaks: 3 Chain: "V" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3799 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 20, 'TRANS': 451} Chain: "W" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3703 Classifications: {'peptide': 456} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 447} Chain: "X" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1905 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain: "Y" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3115 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 370} Chain: "Z" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "a" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2995 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain: "b" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1458 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain: "c" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2187 Classifications: {'peptide': 278} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 267} Chain breaks: 1 Chain: "d" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2116 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 245} Chain: "e" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 334 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain breaks: 1 Chain: "G" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1820 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 228} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1688 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 216} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "I" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1895 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 3, 'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1704 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'CIS': 4, 'PTRANS': 6, 'TRANS': 228} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "K" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1850 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "M" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1856 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1430 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "O" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1643 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1585 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1570 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1548 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1667 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 207} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1826 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "h" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1708 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "i" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1912 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "j" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1704 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "k" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1722 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "l" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1850 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "m" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1856 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "n" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1430 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "o" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1643 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "p" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1585 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "q" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1570 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "r" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1548 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "s" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1667 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 207} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2672 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2706 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 329} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2859 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3040 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 17, 'TRANS': 359} Chain: "E" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2860 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 18, 'TRANS': 356} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "F" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2859 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'CIS': 3, 'PTRANS': 17, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "f" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5319 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 25, 'TRANS': 663} Chain breaks: 9 Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 11 residue: pdb=" N ALA X 359 " occ=0.98 ... (3 atoms not shown) pdb=" CB ALA X 359 " occ=0.98 residue: pdb=" N GLN X 380 " occ=0.83 ... (7 atoms not shown) pdb=" NE2 GLN X 380 " occ=0.83 residue: pdb=" N GLY Z 30 " occ=0.40 ... (2 atoms not shown) pdb=" O GLY Z 30 " occ=0.40 residue: pdb=" N ILE b 90 " occ=0.79 ... (6 atoms not shown) pdb=" CD1 ILE b 90 " occ=0.79 residue: pdb=" N SER b 115 " occ=0.80 ... (4 atoms not shown) pdb=" OG SER b 115 " occ=0.80 residue: pdb=" N ILE b 140 " occ=0.60 ... (6 atoms not shown) pdb=" CD1 ILE b 140 " occ=0.60 residue: pdb=" N VAL b 173 " occ=0.49 ... (5 atoms not shown) pdb=" CG2 VAL b 173 " occ=0.49 residue: pdb=" N GLY b 191 " occ=0.88 ... (2 atoms not shown) pdb=" O GLY b 191 " occ=0.88 residue: pdb=" N ILE d 63 " occ=0.67 ... (6 atoms not shown) pdb=" CD1 ILE d 63 " occ=0.67 residue: pdb=" N SER d 70 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER d 70 " occ=0.00 residue: pdb=" N MET d 95 " occ=0.99 ... (6 atoms not shown) pdb=" CE MET d 95 " occ=0.99 Time building chain proxies: 38.03, per 1000 atoms: 0.38 Number of scatterers: 99908 At special positions: 0 Unit cell: (333.75, 213, 219.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 585 16.00 P 12 15.00 O 19032 8.00 N 17177 7.00 C 63101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 186 " distance=2.03 Simple disulfide: pdb=" SG CYS m 41 " - pdb=" SG CYS m 186 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 32.36 Conformation dependent library (CDL) restraints added in 11.3 seconds 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 24038 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 454 helices and 84 sheets defined 42.1% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.97 Creating SS restraints... Processing helix chain 'U' and resid 17 through 30 removed outlier: 4.422A pdb=" N PHE U 22 " --> pdb=" O GLN U 18 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA U 29 " --> pdb=" O HIS U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 50 removed outlier: 4.356A pdb=" N ALA U 36 " --> pdb=" O ASP U 33 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE U 38 " --> pdb=" O TRP U 35 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER U 39 " --> pdb=" O ALA U 36 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU U 40 " --> pdb=" O GLU U 37 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL U 42 " --> pdb=" O SER U 39 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP U 43 " --> pdb=" O GLU U 40 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU U 50 " --> pdb=" O VAL U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 71 Processing helix chain 'U' and resid 75 through 82 Processing helix chain 'U' and resid 96 through 116 Processing helix chain 'U' and resid 132 through 143 removed outlier: 4.011A pdb=" N GLN U 139 " --> pdb=" O ASN U 135 " (cutoff:3.500A) Processing helix chain 'U' and resid 148 through 157 removed outlier: 4.180A pdb=" N ALA U 154 " --> pdb=" O ALA U 150 " (cutoff:3.500A) Processing helix chain 'U' and resid 162 through 165 No H-bonds generated for 'chain 'U' and resid 162 through 165' Processing helix chain 'U' and resid 174 through 186 removed outlier: 3.609A pdb=" N TYR U 179 " --> pdb=" O MET U 176 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS U 184 " --> pdb=" O LEU U 181 " (cutoff:3.500A) Processing helix chain 'U' and resid 194 through 205 removed outlier: 4.014A pdb=" N VAL U 202 " --> pdb=" O LEU U 198 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS U 203 " --> pdb=" O ARG U 199 " (cutoff:3.500A) Processing helix chain 'U' and resid 214 through 222 removed outlier: 4.454A pdb=" N ILE U 221 " --> pdb=" O CYS U 217 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 238 Processing helix chain 'U' and resid 246 through 254 Processing helix chain 'U' and resid 258 through 268 Processing helix chain 'U' and resid 321 through 330 removed outlier: 5.184A pdb=" N ILE U 326 " --> pdb=" O THR U 322 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU U 329 " --> pdb=" O MET U 325 " (cutoff:3.500A) Processing helix chain 'U' and resid 332 through 344 Processing helix chain 'U' and resid 350 through 359 removed outlier: 5.533A pdb=" N ALA U 359 " --> pdb=" O ASN U 355 " (cutoff:3.500A) Processing helix chain 'U' and resid 364 through 375 removed outlier: 4.819A pdb=" N VAL U 370 " --> pdb=" O HIS U 366 " (cutoff:3.500A) Processing helix chain 'U' and resid 399 through 410 removed outlier: 5.377A pdb=" N LEU U 408 " --> pdb=" O ALA U 404 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLY U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) Processing helix chain 'U' and resid 417 through 422 removed outlier: 4.251A pdb=" N LEU U 420 " --> pdb=" O LYS U 417 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN U 421 " --> pdb=" O GLU U 418 " (cutoff:3.500A) Processing helix chain 'U' and resid 437 through 449 removed outlier: 4.949A pdb=" N GLY U 442 " --> pdb=" O GLN U 438 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU U 443 " --> pdb=" O GLU U 439 " (cutoff:3.500A) Processing helix chain 'U' and resid 457 through 465 Processing helix chain 'U' and resid 474 through 484 removed outlier: 5.570A pdb=" N LEU U 479 " --> pdb=" O HIS U 475 " (cutoff:3.500A) Processing helix chain 'U' and resid 492 through 503 removed outlier: 4.008A pdb=" N THR U 499 " --> pdb=" O ASP U 495 " (cutoff:3.500A) Processing helix chain 'U' and resid 506 through 519 removed outlier: 4.820A pdb=" N ALA U 511 " --> pdb=" O VAL U 507 " (cutoff:3.500A) Processing helix chain 'U' and resid 528 through 538 removed outlier: 4.394A pdb=" N TYR U 535 " --> pdb=" O ASP U 531 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA U 536 " --> pdb=" O MET U 532 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN U 537 " --> pdb=" O VAL U 533 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU U 538 " --> pdb=" O GLY U 534 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 Processing helix chain 'U' and resid 564 through 572 Processing helix chain 'U' and resid 576 through 589 Processing helix chain 'U' and resid 599 through 607 Processing helix chain 'U' and resid 612 through 625 removed outlier: 3.972A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) Processing helix chain 'U' and resid 631 through 642 removed outlier: 4.704A pdb=" N SER U 635 " --> pdb=" O GLU U 631 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU U 642 " --> pdb=" O SER U 638 " (cutoff:3.500A) Processing helix chain 'U' and resid 646 through 659 Processing helix chain 'U' and resid 667 through 676 Proline residue: U 674 - end of helix Processing helix chain 'U' and resid 681 through 695 Processing helix chain 'U' and resid 706 through 718 removed outlier: 3.986A pdb=" N SER U 714 " --> pdb=" O ARG U 710 " (cutoff:3.500A) Processing helix chain 'U' and resid 730 through 738 Processing helix chain 'U' and resid 757 through 766 Processing helix chain 'U' and resid 773 through 777 Processing helix chain 'U' and resid 888 through 890 No H-bonds generated for 'chain 'U' and resid 888 through 890' Processing helix chain 'V' and resid 29 through 52 removed outlier: 3.615A pdb=" N MET V 37 " --> pdb=" O GLN V 33 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA V 42 " --> pdb=" O LYS V 38 " (cutoff:3.500A) Processing helix chain 'V' and resid 61 through 75 Processing helix chain 'V' and resid 90 through 93 No H-bonds generated for 'chain 'V' and resid 90 through 93' Processing helix chain 'V' and resid 105 through 113 Processing helix chain 'V' and resid 116 through 119 No H-bonds generated for 'chain 'V' and resid 116 through 119' Processing helix chain 'V' and resid 130 through 140 Proline residue: V 133 - end of helix Proline residue: V 138 - end of helix Processing helix chain 'V' and resid 148 through 156 Processing helix chain 'V' and resid 160 through 162 No H-bonds generated for 'chain 'V' and resid 160 through 162' Processing helix chain 'V' and resid 172 through 190 Processing helix chain 'V' and resid 199 through 219 removed outlier: 5.910A pdb=" N ASP V 204 " --> pdb=" O ARG V 201 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL V 206 " --> pdb=" O LEU V 203 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA V 208 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS V 210 " --> pdb=" O ALA V 207 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR V 218 " --> pdb=" O ALA V 215 " (cutoff:3.500A) Processing helix chain 'V' and resid 227 through 237 Processing helix chain 'V' and resid 247 through 260 Processing helix chain 'V' and resid 267 through 271 Processing helix chain 'V' and resid 284 through 299 Processing helix chain 'V' and resid 303 through 314 Processing helix chain 'V' and resid 324 through 332 removed outlier: 4.326A pdb=" N VAL V 328 " --> pdb=" O PHE V 324 " (cutoff:3.500A) Processing helix chain 'V' and resid 334 through 339 Processing helix chain 'V' and resid 346 through 348 No H-bonds generated for 'chain 'V' and resid 346 through 348' Processing helix chain 'V' and resid 354 through 357 No H-bonds generated for 'chain 'V' and resid 354 through 357' Processing helix chain 'V' and resid 360 through 368 Processing helix chain 'V' and resid 372 through 389 removed outlier: 4.033A pdb=" N LEU V 379 " --> pdb=" O PHE V 375 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLU V 384 " --> pdb=" O ASP V 380 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS V 385 " --> pdb=" O GLN V 381 " (cutoff:3.500A) Processing helix chain 'V' and resid 393 through 413 removed outlier: 3.659A pdb=" N ARG V 397 " --> pdb=" O THR V 393 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG V 399 " --> pdb=" O ILE V 395 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N HIS V 400 " --> pdb=" O ILE V 396 " (cutoff:3.500A) Processing helix chain 'V' and resid 419 through 423 Processing helix chain 'V' and resid 431 through 444 Processing helix chain 'V' and resid 470 through 496 removed outlier: 3.543A pdb=" N ALA V 475 " --> pdb=" O GLU V 471 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS V 477 " --> pdb=" O GLN V 473 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE V 496 " --> pdb=" O LYS V 492 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 12 removed outlier: 4.298A pdb=" N ARG W 8 " --> pdb=" O GLY W 4 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 16 No H-bonds generated for 'chain 'W' and resid 14 through 16' Processing helix chain 'W' and resid 22 through 37 Proline residue: W 29 - end of helix Processing helix chain 'W' and resid 43 through 63 Processing helix chain 'W' and resid 70 through 84 Processing helix chain 'W' and resid 95 through 112 removed outlier: 4.234A pdb=" N GLN W 99 " --> pdb=" O SER W 95 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA W 100 " --> pdb=" O GLN W 96 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 133 removed outlier: 4.020A pdb=" N ARG W 129 " --> pdb=" O ILE W 125 " (cutoff:3.500A) Processing helix chain 'W' and resid 139 through 155 removed outlier: 4.662A pdb=" N GLN W 155 " --> pdb=" O THR W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 159 through 167 Processing helix chain 'W' and resid 181 through 186 Processing helix chain 'W' and resid 188 through 194 removed outlier: 3.558A pdb=" N LEU W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 199 through 209 Processing helix chain 'W' and resid 222 through 232 removed outlier: 4.548A pdb=" N ASN W 228 " --> pdb=" O LEU W 224 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU W 229 " --> pdb=" O LYS W 225 " (cutoff:3.500A) Processing helix chain 'W' and resid 246 through 249 No H-bonds generated for 'chain 'W' and resid 246 through 249' Processing helix chain 'W' and resid 262 through 271 Processing helix chain 'W' and resid 283 through 289 removed outlier: 4.921A pdb=" N HIS W 288 " --> pdb=" O SER W 284 " (cutoff:3.500A) Processing helix chain 'W' and resid 300 through 307 Processing helix chain 'W' and resid 317 through 325 Processing helix chain 'W' and resid 335 through 340 Processing helix chain 'W' and resid 347 through 366 Processing helix chain 'W' and resid 376 through 381 Processing helix chain 'W' and resid 387 through 399 Processing helix chain 'W' and resid 425 through 453 removed outlier: 4.155A pdb=" N THR W 442 " --> pdb=" O LEU W 438 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR W 443 " --> pdb=" O VAL W 439 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA W 447 " --> pdb=" O THR W 443 " (cutoff:3.500A) Processing helix chain 'X' and resid 183 through 196 removed outlier: 4.490A pdb=" N THR X 195 " --> pdb=" O THR X 191 " (cutoff:3.500A) Processing helix chain 'X' and resid 206 through 220 removed outlier: 3.651A pdb=" N HIS X 218 " --> pdb=" O SER X 214 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA X 219 " --> pdb=" O GLY X 215 " (cutoff:3.500A) Processing helix chain 'X' and resid 225 through 236 Processing helix chain 'X' and resid 244 through 247 No H-bonds generated for 'chain 'X' and resid 244 through 247' Processing helix chain 'X' and resid 252 through 261 Processing helix chain 'X' and resid 267 through 270 No H-bonds generated for 'chain 'X' and resid 267 through 270' Processing helix chain 'X' and resid 282 through 296 removed outlier: 3.984A pdb=" N CYS X 289 " --> pdb=" O GLU X 285 " (cutoff:3.500A) Processing helix chain 'X' and resid 299 through 302 No H-bonds generated for 'chain 'X' and resid 299 through 302' Processing helix chain 'X' and resid 305 through 308 No H-bonds generated for 'chain 'X' and resid 305 through 308' Processing helix chain 'X' and resid 321 through 338 removed outlier: 4.258A pdb=" N LEU X 326 " --> pdb=" O HIS X 322 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU X 332 " --> pdb=" O ASP X 328 " (cutoff:3.500A) Processing helix chain 'X' and resid 347 through 350 No H-bonds generated for 'chain 'X' and resid 347 through 350' Processing helix chain 'X' and resid 361 through 370 Processing helix chain 'X' and resid 394 through 421 removed outlier: 4.323A pdb=" N ALA X 399 " --> pdb=" O LYS X 395 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR X 415 " --> pdb=" O VAL X 411 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN X 416 " --> pdb=" O ASP X 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 14 through 27 Processing helix chain 'Y' and resid 35 through 45 Processing helix chain 'Y' and resid 51 through 58 removed outlier: 4.404A pdb=" N ALA Y 56 " --> pdb=" O PRO Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 68 through 91 removed outlier: 4.674A pdb=" N MET Y 73 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLU Y 89 " --> pdb=" O ASP Y 85 " (cutoff:3.500A) Processing helix chain 'Y' and resid 99 through 114 removed outlier: 3.895A pdb=" N LYS Y 107 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) Processing helix chain 'Y' and resid 117 through 123 Processing helix chain 'Y' and resid 135 through 150 removed outlier: 4.518A pdb=" N ILE Y 140 " --> pdb=" O HIS Y 136 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE Y 147 " --> pdb=" O TYR Y 143 " (cutoff:3.500A) Processing helix chain 'Y' and resid 155 through 166 removed outlier: 4.155A pdb=" N THR Y 161 " --> pdb=" O ILE Y 157 " (cutoff:3.500A) Processing helix chain 'Y' and resid 176 through 190 Processing helix chain 'Y' and resid 194 through 200 removed outlier: 3.702A pdb=" N ALA Y 198 " --> pdb=" O PHE Y 194 " (cutoff:3.500A) Processing helix chain 'Y' and resid 216 through 230 removed outlier: 3.716A pdb=" N VAL Y 226 " --> pdb=" O TYR Y 222 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ILE Y 229 " --> pdb=" O TYR Y 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 233 through 240 Processing helix chain 'Y' and resid 254 through 263 Processing helix chain 'Y' and resid 269 through 283 Processing helix chain 'Y' and resid 292 through 310 removed outlier: 4.099A pdb=" N VAL Y 296 " --> pdb=" O ARG Y 293 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG Y 297 " --> pdb=" O TYR Y 294 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER Y 305 " --> pdb=" O HIS Y 302 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN Y 306 " --> pdb=" O ALA Y 303 " (cutoff:3.500A) Processing helix chain 'Y' and resid 320 through 323 No H-bonds generated for 'chain 'Y' and resid 320 through 323' Processing helix chain 'Y' and resid 329 through 339 Processing helix chain 'Y' and resid 364 through 383 removed outlier: 4.926A pdb=" N THR Y 369 " --> pdb=" O GLN Y 365 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE Y 370 " --> pdb=" O TYR Y 366 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU Y 375 " --> pdb=" O LYS Y 371 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU Y 377 " --> pdb=" O GLY Y 373 " (cutoff:3.500A) Processing helix chain 'Z' and resid 13 through 29 removed outlier: 3.721A pdb=" N GLY Z 27 " --> pdb=" O PHE Z 23 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS Z 28 " --> pdb=" O ASN Z 24 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 85 Processing helix chain 'Z' and resid 103 through 115 removed outlier: 3.805A pdb=" N ILE Z 106 " --> pdb=" O LYS Z 103 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU Z 111 " --> pdb=" O ILE Z 108 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS Z 113 " --> pdb=" O GLU Z 110 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG Z 114 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) Processing helix chain 'Z' and resid 169 through 175 removed outlier: 4.072A pdb=" N HIS Z 174 " --> pdb=" O VAL Z 170 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 216 removed outlier: 3.578A pdb=" N SER Z 203 " --> pdb=" O LYS Z 199 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL Z 215 " --> pdb=" O TYR Z 211 " (cutoff:3.500A) Processing helix chain 'Z' and resid 220 through 223 removed outlier: 4.319A pdb=" N ASN Z 223 " --> pdb=" O LEU Z 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 220 through 223' Processing helix chain 'Z' and resid 228 through 236 removed outlier: 4.353A pdb=" N VAL Z 233 " --> pdb=" O GLN Z 229 " (cutoff:3.500A) Processing helix chain 'Z' and resid 246 through 288 removed outlier: 4.153A pdb=" N TYR Z 250 " --> pdb=" O VAL Z 246 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL Z 258 " --> pdb=" O ASN Z 254 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL Z 259 " --> pdb=" O ASP Z 255 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN Z 277 " --> pdb=" O HIS Z 273 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 10 Processing helix chain 'a' and resid 19 through 31 removed outlier: 4.916A pdb=" N ARG a 24 " --> pdb=" O ALA a 20 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU a 27 " --> pdb=" O HIS a 23 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR a 29 " --> pdb=" O LEU a 25 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR a 30 " --> pdb=" O GLU a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 35 through 46 Processing helix chain 'a' and resid 53 through 67 removed outlier: 5.942A pdb=" N LEU a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TYR a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 87 removed outlier: 5.163A pdb=" N ARG a 85 " --> pdb=" O LEU a 81 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLN a 86 " --> pdb=" O HIS a 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 103 removed outlier: 4.391A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 120 Processing helix chain 'a' and resid 122 through 124 No H-bonds generated for 'chain 'a' and resid 122 through 124' Processing helix chain 'a' and resid 131 through 141 removed outlier: 3.644A pdb=" N GLU a 139 " --> pdb=" O ILE a 135 " (cutoff:3.500A) Processing helix chain 'a' and resid 150 through 164 Processing helix chain 'a' and resid 171 through 180 Processing helix chain 'a' and resid 190 through 205 Processing helix chain 'a' and resid 216 through 218 No H-bonds generated for 'chain 'a' and resid 216 through 218' Processing helix chain 'a' and resid 220 through 228 removed outlier: 4.240A pdb=" N LEU a 225 " --> pdb=" O VAL a 221 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR a 228 " --> pdb=" O SER a 224 " (cutoff:3.500A) Processing helix chain 'a' and resid 233 through 239 Processing helix chain 'a' and resid 247 through 255 removed outlier: 4.968A pdb=" N ALA a 254 " --> pdb=" O THR a 250 " (cutoff:3.500A) Processing helix chain 'a' and resid 265 through 282 removed outlier: 3.922A pdb=" N GLN a 273 " --> pdb=" O LEU a 269 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET a 278 " --> pdb=" O LEU a 274 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 299 Processing helix chain 'a' and resid 304 through 317 removed outlier: 3.686A pdb=" N VAL a 307 " --> pdb=" O VAL a 304 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLU a 308 " --> pdb=" O ASN a 305 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS a 313 " --> pdb=" O LEU a 310 " (cutoff:3.500A) Processing helix chain 'a' and resid 343 through 370 removed outlier: 5.660A pdb=" N LYS a 350 " --> pdb=" O ILE a 346 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASP a 351 " --> pdb=" O LYS a 347 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ARG a 352 " --> pdb=" O GLY a 348 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE a 355 " --> pdb=" O ASP a 351 " (cutoff:3.500A) Processing helix chain 'a' and resid 372 through 374 No H-bonds generated for 'chain 'a' and resid 372 through 374' Processing helix chain 'b' and resid 26 through 43 Processing helix chain 'b' and resid 69 through 75 Processing helix chain 'b' and resid 86 through 97 removed outlier: 4.359A pdb=" N ILE b 90 " --> pdb=" O PHE b 86 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 133 Processing helix chain 'b' and resid 152 through 158 Processing helix chain 'b' and resid 181 through 189 removed outlier: 3.887A pdb=" N SER b 186 " --> pdb=" O ALA b 182 " (cutoff:3.500A) Proline residue: b 187 - end of helix Processing helix chain 'c' and resid 35 through 46 Processing helix chain 'c' and resid 84 through 86 No H-bonds generated for 'chain 'c' and resid 84 through 86' Processing helix chain 'c' and resid 89 through 101 Processing helix chain 'c' and resid 126 through 134 removed outlier: 5.256A pdb=" N GLN c 131 " --> pdb=" O ILE c 127 " (cutoff:3.500A) Processing helix chain 'c' and resid 165 through 168 removed outlier: 3.827A pdb=" N MET c 168 " --> pdb=" O ALA c 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 165 through 168' Processing helix chain 'c' and resid 180 through 187 Proline residue: c 187 - end of helix Processing helix chain 'c' and resid 191 through 195 Processing helix chain 'c' and resid 211 through 224 removed outlier: 5.063A pdb=" N MET c 216 " --> pdb=" O LEU c 212 " (cutoff:3.500A) Processing helix chain 'c' and resid 247 through 258 Processing helix chain 'c' and resid 260 through 264 Processing helix chain 'c' and resid 267 through 270 No H-bonds generated for 'chain 'c' and resid 267 through 270' Processing helix chain 'c' and resid 289 through 308 removed outlier: 3.828A pdb=" N ASP c 305 " --> pdb=" O ALA c 301 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR c 306 " --> pdb=" O ALA c 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 3 through 6 Processing helix chain 'd' and resid 18 through 32 Processing helix chain 'd' and resid 46 through 64 Processing helix chain 'd' and resid 68 through 81 Processing helix chain 'd' and resid 93 through 109 removed outlier: 4.485A pdb=" N HIS d 96 " --> pdb=" O ALA d 93 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU d 98 " --> pdb=" O MET d 95 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU d 99 " --> pdb=" O HIS d 96 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN d 102 " --> pdb=" O LEU d 99 " (cutoff:3.500A) Processing helix chain 'd' and resid 114 through 121 Processing helix chain 'd' and resid 131 through 143 Proline residue: d 136 - end of helix Processing helix chain 'd' and resid 150 through 155 Processing helix chain 'd' and resid 164 through 180 removed outlier: 3.727A pdb=" N GLU d 177 " --> pdb=" O THR d 173 " (cutoff:3.500A) Processing helix chain 'd' and resid 191 through 197 Processing helix chain 'd' and resid 204 through 210 Processing helix chain 'd' and resid 240 through 253 Processing helix chain 'e' and resid 5 through 7 No H-bonds generated for 'chain 'e' and resid 5 through 7' Processing helix chain 'e' and resid 45 through 50 Processing helix chain 'e' and resid 62 through 65 No H-bonds generated for 'chain 'e' and resid 62 through 65' Processing helix chain 'G' and resid 23 through 30 removed outlier: 5.099A pdb=" N LYS G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 105 Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 172 through 180 Processing helix chain 'G' and resid 192 through 205 Processing helix chain 'G' and resid 232 through 241 Processing helix chain 'H' and resid 20 through 30 Processing helix chain 'H' and resid 80 through 101 removed outlier: 4.039A pdb=" N VAL H 85 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 122 Processing helix chain 'H' and resid 167 through 177 removed outlier: 3.505A pdb=" N LYS H 176 " --> pdb=" O THR H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 196 Processing helix chain 'H' and resid 223 through 229 Processing helix chain 'I' and resid 20 through 28 Processing helix chain 'I' and resid 82 through 101 Processing helix chain 'I' and resid 108 through 123 removed outlier: 3.815A pdb=" N TYR I 121 " --> pdb=" O ILE I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 177 Processing helix chain 'I' and resid 186 through 200 Processing helix chain 'I' and resid 208 through 210 No H-bonds generated for 'chain 'I' and resid 208 through 210' Processing helix chain 'I' and resid 230 through 250 removed outlier: 4.404A pdb=" N GLU I 250 " --> pdb=" O LYS I 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 removed outlier: 3.544A pdb=" N GLU J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 97 Processing helix chain 'J' and resid 104 through 119 Processing helix chain 'J' and resid 138 through 140 No H-bonds generated for 'chain 'J' and resid 138 through 140' Processing helix chain 'J' and resid 165 through 173 Processing helix chain 'J' and resid 184 through 196 Processing helix chain 'J' and resid 224 through 239 Processing helix chain 'K' and resid 24 through 32 removed outlier: 4.023A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 103 Processing helix chain 'K' and resid 109 through 120 removed outlier: 4.601A pdb=" N LEU K 119 " --> pdb=" O ALA K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 184 removed outlier: 3.682A pdb=" N VAL K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 205 Processing helix chain 'K' and resid 234 through 240 Processing helix chain 'L' and resid 20 through 31 removed outlier: 3.695A pdb=" N GLN L 31 " --> pdb=" O GLU L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 98 Processing helix chain 'L' and resid 105 through 120 removed outlier: 4.205A pdb=" N ILE L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) Proline residue: L 119 - end of helix Processing helix chain 'L' and resid 166 through 175 Processing helix chain 'L' and resid 178 through 181 removed outlier: 3.951A pdb=" N GLU L 181 " --> pdb=" O GLU L 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 178 through 181' Processing helix chain 'L' and resid 184 through 195 Processing helix chain 'L' and resid 230 through 233 No H-bonds generated for 'chain 'L' and resid 230 through 233' Processing helix chain 'M' and resid 21 through 27 Processing helix chain 'M' and resid 30 through 32 No H-bonds generated for 'chain 'M' and resid 30 through 32' Processing helix chain 'M' and resid 81 through 102 Processing helix chain 'M' and resid 108 through 124 Processing helix chain 'M' and resid 169 through 176 removed outlier: 3.542A pdb=" N LYS M 173 " --> pdb=" O ARG M 169 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU M 175 " --> pdb=" O ALA M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 199 removed outlier: 4.459A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 239 No H-bonds generated for 'chain 'M' and resid 236 through 239' Processing helix chain 'N' and resid 49 through 70 Processing helix chain 'N' and resid 76 through 89 Processing helix chain 'N' and resid 130 through 142 removed outlier: 4.425A pdb=" N SER N 133 " --> pdb=" O SER N 130 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR N 134 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE N 135 " --> pdb=" O SER N 132 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL N 139 " --> pdb=" O TYR N 136 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP N 140 " --> pdb=" O GLY N 137 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR N 142 " --> pdb=" O VAL N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 166 Processing helix chain 'O' and resid 49 through 70 Processing helix chain 'O' and resid 76 through 89 Processing helix chain 'O' and resid 131 through 141 Processing helix chain 'O' and resid 148 through 164 Processing helix chain 'P' and resid 57 through 77 Processing helix chain 'P' and resid 84 through 98 removed outlier: 4.114A pdb=" N LYS P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 144 through 153 Processing helix chain 'P' and resid 160 through 177 Processing helix chain 'Q' and resid 52 through 70 Processing helix chain 'Q' and resid 77 through 92 Processing helix chain 'Q' and resid 135 through 145 removed outlier: 3.511A pdb=" N ILE Q 142 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 153 through 167 Processing helix chain 'R' and resid 50 through 70 Processing helix chain 'R' and resid 76 through 90 removed outlier: 3.944A pdb=" N GLN R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TYR R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 142 Processing helix chain 'R' and resid 149 through 166 Processing helix chain 'R' and resid 192 through 199 Processing helix chain 'S' and resid 58 through 79 Processing helix chain 'S' and resid 85 through 98 Processing helix chain 'S' and resid 143 through 152 Proline residue: S 147 - end of helix Processing helix chain 'S' and resid 168 through 185 removed outlier: 3.992A pdb=" N ARG S 185 " --> pdb=" O SER S 181 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 77 Processing helix chain 'T' and resid 85 through 102 removed outlier: 3.806A pdb=" N LYS T 102 " --> pdb=" O SER T 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 142 through 145 No H-bonds generated for 'chain 'T' and resid 142 through 145' Processing helix chain 'T' and resid 147 through 156 Processing helix chain 'T' and resid 162 through 179 Processing helix chain 'g' and resid 18 through 20 No H-bonds generated for 'chain 'g' and resid 18 through 20' Processing helix chain 'g' and resid 23 through 28 Processing helix chain 'g' and resid 84 through 105 Processing helix chain 'g' and resid 111 through 127 Processing helix chain 'g' and resid 172 through 182 Processing helix chain 'g' and resid 192 through 205 Processing helix chain 'g' and resid 232 through 241 Processing helix chain 'h' and resid 20 through 30 Processing helix chain 'h' and resid 80 through 101 removed outlier: 4.301A pdb=" N VAL h 85 " --> pdb=" O PRO h 81 " (cutoff:3.500A) Processing helix chain 'h' and resid 107 through 123 Processing helix chain 'h' and resid 167 through 177 removed outlier: 3.551A pdb=" N LYS h 176 " --> pdb=" O THR h 172 " (cutoff:3.500A) Processing helix chain 'h' and resid 184 through 196 Processing helix chain 'h' and resid 223 through 229 Processing helix chain 'i' and resid 20 through 28 Processing helix chain 'i' and resid 80 through 101 removed outlier: 3.757A pdb=" N LEU i 86 " --> pdb=" O ASP i 82 " (cutoff:3.500A) Processing helix chain 'i' and resid 108 through 123 removed outlier: 3.766A pdb=" N TYR i 121 " --> pdb=" O ILE i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 169 through 177 Processing helix chain 'i' and resid 186 through 200 Processing helix chain 'i' and resid 208 through 210 No H-bonds generated for 'chain 'i' and resid 208 through 210' Processing helix chain 'i' and resid 231 through 250 removed outlier: 4.448A pdb=" N GLU i 250 " --> pdb=" O LYS i 246 " (cutoff:3.500A) Processing helix chain 'j' and resid 19 through 27 removed outlier: 3.821A pdb=" N GLU j 24 " --> pdb=" O GLU j 20 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA j 25 " --> pdb=" O TYR j 21 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL j 26 " --> pdb=" O ALA j 22 " (cutoff:3.500A) Processing helix chain 'j' and resid 77 through 97 removed outlier: 3.563A pdb=" N THR j 97 " --> pdb=" O SER j 93 " (cutoff:3.500A) Processing helix chain 'j' and resid 104 through 120 Processing helix chain 'j' and resid 138 through 140 No H-bonds generated for 'chain 'j' and resid 138 through 140' Processing helix chain 'j' and resid 165 through 175 removed outlier: 3.768A pdb=" N LYS j 174 " --> pdb=" O GLU j 170 " (cutoff:3.500A) Processing helix chain 'j' and resid 184 through 196 Processing helix chain 'j' and resid 224 through 239 Processing helix chain 'k' and resid 22 through 33 removed outlier: 4.314A pdb=" N LYS k 32 " --> pdb=" O ILE k 28 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU k 33 " --> pdb=" O GLU k 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 61 through 63 No H-bonds generated for 'chain 'k' and resid 61 through 63' Processing helix chain 'k' and resid 83 through 103 Processing helix chain 'k' and resid 109 through 117 Processing helix chain 'k' and resid 174 through 184 removed outlier: 3.655A pdb=" N VAL k 184 " --> pdb=" O SER k 180 " (cutoff:3.500A) Processing helix chain 'k' and resid 191 through 205 removed outlier: 3.714A pdb=" N ILE k 201 " --> pdb=" O SER k 197 " (cutoff:3.500A) Processing helix chain 'k' and resid 234 through 240 removed outlier: 3.511A pdb=" N ASP k 240 " --> pdb=" O GLU k 236 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 31 Processing helix chain 'l' and resid 79 through 98 removed outlier: 3.624A pdb=" N SER l 95 " --> pdb=" O GLU l 91 " (cutoff:3.500A) Processing helix chain 'l' and resid 105 through 120 removed outlier: 4.280A pdb=" N ILE l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) Proline residue: l 119 - end of helix Processing helix chain 'l' and resid 166 through 175 Processing helix chain 'l' and resid 179 through 181 No H-bonds generated for 'chain 'l' and resid 179 through 181' Processing helix chain 'l' and resid 184 through 195 Processing helix chain 'l' and resid 230 through 233 No H-bonds generated for 'chain 'l' and resid 230 through 233' Processing helix chain 'm' and resid 21 through 27 Processing helix chain 'm' and resid 30 through 32 No H-bonds generated for 'chain 'm' and resid 30 through 32' Processing helix chain 'm' and resid 81 through 102 Processing helix chain 'm' and resid 108 through 124 Processing helix chain 'm' and resid 169 through 176 removed outlier: 3.594A pdb=" N LYS m 173 " --> pdb=" O ARG m 169 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLU m 175 " --> pdb=" O ALA m 171 " (cutoff:3.500A) Processing helix chain 'm' and resid 186 through 199 removed outlier: 4.489A pdb=" N LYS m 191 " --> pdb=" O ARG m 187 " (cutoff:3.500A) Processing helix chain 'm' and resid 236 through 239 No H-bonds generated for 'chain 'm' and resid 236 through 239' Processing helix chain 'n' and resid 49 through 70 Processing helix chain 'n' and resid 76 through 89 Processing helix chain 'n' and resid 133 through 142 removed outlier: 4.569A pdb=" N ASP n 140 " --> pdb=" O TYR n 136 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ALA n 141 " --> pdb=" O GLY n 137 " (cutoff:3.500A) Processing helix chain 'n' and resid 149 through 166 Processing helix chain 'o' and resid 49 through 70 Processing helix chain 'o' and resid 76 through 89 Processing helix chain 'o' and resid 131 through 141 Processing helix chain 'o' and resid 148 through 164 Processing helix chain 'p' and resid 57 through 77 Processing helix chain 'p' and resid 84 through 98 removed outlier: 4.179A pdb=" N LYS p 98 " --> pdb=" O LEU p 94 " (cutoff:3.500A) Processing helix chain 'p' and resid 144 through 153 Processing helix chain 'p' and resid 160 through 177 Processing helix chain 'q' and resid 52 through 70 Processing helix chain 'q' and resid 77 through 92 Processing helix chain 'q' and resid 135 through 145 removed outlier: 4.269A pdb=" N SER q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE q 142 " --> pdb=" O LEU q 138 " (cutoff:3.500A) Processing helix chain 'q' and resid 153 through 167 Processing helix chain 'r' and resid 50 through 70 Processing helix chain 'r' and resid 76 through 90 removed outlier: 3.934A pdb=" N GLN r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR r 90 " --> pdb=" O MET r 86 " (cutoff:3.500A) Processing helix chain 'r' and resid 132 through 142 Processing helix chain 'r' and resid 149 through 166 Processing helix chain 'r' and resid 192 through 199 Processing helix chain 's' and resid 58 through 79 Processing helix chain 's' and resid 85 through 98 Processing helix chain 's' and resid 143 through 152 Proline residue: s 147 - end of helix Processing helix chain 's' and resid 168 through 185 removed outlier: 4.106A pdb=" N ARG s 185 " --> pdb=" O SER s 181 " (cutoff:3.500A) Processing helix chain 't' and resid 57 through 77 Processing helix chain 't' and resid 85 through 102 removed outlier: 3.796A pdb=" N LYS t 102 " --> pdb=" O SER t 98 " (cutoff:3.500A) Processing helix chain 't' and resid 142 through 145 No H-bonds generated for 'chain 't' and resid 142 through 145' Processing helix chain 't' and resid 147 through 156 Processing helix chain 't' and resid 162 through 179 Processing helix chain 'A' and resid 84 through 87 No H-bonds generated for 'chain 'A' and resid 84 through 87' Processing helix chain 'A' and resid 181 through 196 removed outlier: 4.066A pdb=" N GLU A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 222 through 231 removed outlier: 4.175A pdb=" N ALA A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 245 Processing helix chain 'A' and resid 252 through 264 Processing helix chain 'A' and resid 277 through 280 No H-bonds generated for 'chain 'A' and resid 277 through 280' Processing helix chain 'A' and resid 294 through 306 Processing helix chain 'A' and resid 349 through 360 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 382 through 398 Processing helix chain 'A' and resid 406 through 418 removed outlier: 3.516A pdb=" N LYS A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 102 Processing helix chain 'B' and resid 141 through 143 No H-bonds generated for 'chain 'B' and resid 141 through 143' Processing helix chain 'B' and resid 171 through 174 No H-bonds generated for 'chain 'B' and resid 171 through 174' Processing helix chain 'B' and resid 193 through 206 removed outlier: 5.329A pdb=" N LEU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Proline residue: B 204 - end of helix Processing helix chain 'B' and resid 211 through 214 No H-bonds generated for 'chain 'B' and resid 211 through 214' Processing helix chain 'B' and resid 232 through 241 Processing helix chain 'B' and resid 252 through 255 removed outlier: 3.934A pdb=" N LEU B 255 " --> pdb=" O GLY B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 255' Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 301 through 303 No H-bonds generated for 'chain 'B' and resid 301 through 303' Processing helix chain 'B' and resid 305 through 316 Processing helix chain 'B' and resid 339 through 342 No H-bonds generated for 'chain 'B' and resid 339 through 342' Processing helix chain 'B' and resid 358 through 368 removed outlier: 4.605A pdb=" N ARG B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 386 Processing helix chain 'B' and resid 392 through 409 removed outlier: 4.189A pdb=" N GLY B 403 " --> pdb=" O CYS B 399 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU B 409 " --> pdb=" O MET B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 426 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'C' and resid 39 through 67 removed outlier: 3.560A pdb=" N GLU C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLN C 64 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 155 through 170 removed outlier: 4.749A pdb=" N LEU C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 172 through 175 No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 196 through 203 Processing helix chain 'C' and resid 233 through 240 Processing helix chain 'C' and resid 268 through 279 Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 322 through 334 Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 358 through 372 Processing helix chain 'C' and resid 380 through 390 Processing helix chain 'D' and resid 49 through 79 removed outlier: 4.419A pdb=" N PHE D 53 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 186 removed outlier: 4.782A pdb=" N LEU D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Proline residue: D 184 - end of helix Processing helix chain 'D' and resid 190 through 193 No H-bonds generated for 'chain 'D' and resid 190 through 193' Processing helix chain 'D' and resid 214 through 222 Processing helix chain 'D' and resid 242 through 257 Processing helix chain 'D' and resid 282 through 296 Processing helix chain 'D' and resid 341 through 347 Processing helix chain 'D' and resid 361 through 364 No H-bonds generated for 'chain 'D' and resid 361 through 364' Processing helix chain 'D' and resid 374 through 388 Processing helix chain 'D' and resid 397 through 401 Processing helix chain 'E' and resid 17 through 51 removed outlier: 4.490A pdb=" N ARG E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 120 through 123 No H-bonds generated for 'chain 'E' and resid 120 through 123' Processing helix chain 'E' and resid 139 through 149 Processing helix chain 'E' and resid 151 through 154 No H-bonds generated for 'chain 'E' and resid 151 through 154' Processing helix chain 'E' and resid 158 through 162 Processing helix chain 'E' and resid 180 through 190 Processing helix chain 'E' and resid 210 through 224 Processing helix chain 'E' and resid 248 through 263 removed outlier: 3.860A pdb=" N GLU E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 316 Processing helix chain 'E' and resid 328 through 334 Processing helix chain 'E' and resid 340 through 355 Processing helix chain 'E' and resid 365 through 380 removed outlier: 3.539A pdb=" N LYS E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU E 380 " --> pdb=" O ASP E 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 83 removed outlier: 4.291A pdb=" N ASP F 71 " --> pdb=" O GLN F 67 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS F 74 " --> pdb=" O LYS F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 175 Processing helix chain 'F' and resid 192 through 207 removed outlier: 4.675A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) Proline residue: F 205 - end of helix Processing helix chain 'F' and resid 210 through 213 No H-bonds generated for 'chain 'F' and resid 210 through 213' Processing helix chain 'F' and resid 234 through 243 Processing helix chain 'F' and resid 264 through 277 Processing helix chain 'F' and resid 305 through 317 Processing helix chain 'F' and resid 340 through 342 No H-bonds generated for 'chain 'F' and resid 340 through 342' Processing helix chain 'F' and resid 360 through 369 Processing helix chain 'F' and resid 381 through 387 Processing helix chain 'F' and resid 393 through 409 Processing helix chain 'F' and resid 417 through 425 Processing helix chain 'f' and resid 9 through 15 Proline residue: f 13 - end of helix No H-bonds generated for 'chain 'f' and resid 9 through 15' Processing helix chain 'f' and resid 20 through 35 Proline residue: f 28 - end of helix removed outlier: 4.054A pdb=" N ASP f 35 " --> pdb=" O LYS f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 45 through 48 No H-bonds generated for 'chain 'f' and resid 45 through 48' Processing helix chain 'f' and resid 50 through 52 No H-bonds generated for 'chain 'f' and resid 50 through 52' Processing helix chain 'f' and resid 72 through 86 Processing helix chain 'f' and resid 94 through 97 No H-bonds generated for 'chain 'f' and resid 94 through 97' Processing helix chain 'f' and resid 120 through 125 Processing helix chain 'f' and resid 127 through 144 Processing helix chain 'f' and resid 164 through 180 Processing helix chain 'f' and resid 185 through 191 Processing helix chain 'f' and resid 208 through 216 Processing helix chain 'f' and resid 222 through 238 Processing helix chain 'f' and resid 242 through 258 removed outlier: 3.678A pdb=" N SER f 246 " --> pdb=" O PRO f 243 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG f 250 " --> pdb=" O ALA f 247 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS f 251 " --> pdb=" O LEU f 248 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA f 252 " --> pdb=" O LEU f 249 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL f 255 " --> pdb=" O ALA f 252 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE f 256 " --> pdb=" O LEU f 253 " (cutoff:3.500A) Processing helix chain 'f' and resid 262 through 272 removed outlier: 3.632A pdb=" N MET f 271 " --> pdb=" O LEU f 268 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU f 272 " --> pdb=" O ALA f 269 " (cutoff:3.500A) Processing helix chain 'f' and resid 276 through 287 Processing helix chain 'f' and resid 298 through 308 Processing helix chain 'f' and resid 313 through 323 Processing helix chain 'f' and resid 329 through 333 Processing helix chain 'f' and resid 341 through 350 Proline residue: f 345 - end of helix Processing helix chain 'f' and resid 356 through 359 No H-bonds generated for 'chain 'f' and resid 356 through 359' Processing helix chain 'f' and resid 370 through 381 removed outlier: 3.644A pdb=" N VAL f 381 " --> pdb=" O VAL f 377 " (cutoff:3.500A) Processing helix chain 'f' and resid 404 through 411 Processing helix chain 'f' and resid 413 through 416 No H-bonds generated for 'chain 'f' and resid 413 through 416' Processing helix chain 'f' and resid 422 through 432 removed outlier: 3.697A pdb=" N LEU f 426 " --> pdb=" O VAL f 422 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR f 427 " --> pdb=" O ASP f 423 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYS f 431 " --> pdb=" O THR f 427 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR f 432 " --> pdb=" O GLN f 428 " (cutoff:3.500A) Processing helix chain 'f' and resid 438 through 451 Processing helix chain 'f' and resid 459 through 463 Processing helix chain 'f' and resid 473 through 488 removed outlier: 3.576A pdb=" N MET f 477 " --> pdb=" O SER f 474 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY f 480 " --> pdb=" O MET f 477 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER f 481 " --> pdb=" O ARG f 478 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE f 482 " --> pdb=" O LEU f 479 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE f 483 " --> pdb=" O GLY f 480 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY f 484 " --> pdb=" O SER f 481 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU f 485 " --> pdb=" O ILE f 482 " (cutoff:3.500A) Processing helix chain 'f' and resid 496 through 505 Proline residue: f 503 - end of helix Processing helix chain 'f' and resid 512 through 526 Processing helix chain 'f' and resid 536 through 547 Processing helix chain 'f' and resid 554 through 566 Proline residue: f 559 - end of helix Processing helix chain 'f' and resid 574 through 582 Processing helix chain 'f' and resid 586 through 598 Processing helix chain 'f' and resid 606 through 617 removed outlier: 3.512A pdb=" N GLN f 610 " --> pdb=" O LEU f 607 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN f 611 " --> pdb=" O LYS f 608 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE f 615 " --> pdb=" O LEU f 612 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N CYS f 616 " --> pdb=" O LEU f 613 " (cutoff:3.500A) Processing helix chain 'f' and resid 623 through 634 removed outlier: 4.971A pdb=" N LYS f 631 " --> pdb=" O GLU f 627 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LYS f 632 " --> pdb=" O ASP f 628 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLU f 633 " --> pdb=" O LYS f 629 " (cutoff:3.500A) Processing helix chain 'f' and resid 653 through 662 Processing helix chain 'f' and resid 669 through 679 removed outlier: 3.896A pdb=" N HIS f 677 " --> pdb=" O ARG f 673 " (cutoff:3.500A) Processing helix chain 'f' and resid 684 through 696 Proline residue: f 691 - end of helix Processing helix chain 'f' and resid 718 through 727 Processing helix chain 'f' and resid 740 through 753 Processing helix chain 'f' and resid 775 through 777 No H-bonds generated for 'chain 'f' and resid 775 through 777' Processing helix chain 'f' and resid 779 through 786 removed outlier: 5.195A pdb=" N GLN f 786 " --> pdb=" O HIS f 782 " (cutoff:3.500A) Processing helix chain 'f' and resid 791 through 794 No H-bonds generated for 'chain 'f' and resid 791 through 794' Processing helix chain 'f' and resid 797 through 799 No H-bonds generated for 'chain 'f' and resid 797 through 799' Processing sheet with id= A, first strand: chain 'U' and resid 744 through 746 Processing sheet with id= B, first strand: chain 'U' and resid 788 through 790 removed outlier: 7.340A pdb=" N GLY U 910 " --> pdb=" O ILE U 789 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'Z' and resid 120 through 123 removed outlier: 3.860A pdb=" N HIS Z 96 " --> pdb=" O VAL Z 122 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU Z 39 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TRP Z 94 " --> pdb=" O GLY Z 37 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY Z 37 " --> pdb=" O TRP Z 94 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'b' and resid 5 through 8 removed outlier: 7.397A pdb=" N ASN b 137 " --> pdb=" O ILE b 109 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N ALA b 111 " --> pdb=" O ASN b 137 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASP b 139 " --> pdb=" O ALA b 111 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N VAL b 113 " --> pdb=" O ASP b 139 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE b 141 " --> pdb=" O VAL b 113 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'c' and resid 67 through 69 removed outlier: 3.516A pdb=" N VAL c 69 " --> pdb=" O TYR c 32 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN c 206 " --> pdb=" O VAL c 31 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE c 33 " --> pdb=" O ASN c 206 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'c' and resid 142 through 144 removed outlier: 3.532A pdb=" N PHE c 160 " --> pdb=" O ALA c 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'c' and resid 57 through 59 removed outlier: 4.973A pdb=" N GLY c 59 " --> pdb=" O VAL c 108 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL c 108 " --> pdb=" O GLY c 59 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'd' and resid 216 through 218 removed outlier: 4.090A pdb=" N VAL d 216 " --> pdb=" O TYR d 223 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR d 223 " --> pdb=" O VAL d 216 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.763A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 148 through 154 removed outlier: 6.815A pdb=" N CYS G 78 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS G 71 " --> pdb=" O CYS G 78 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 160 through 163 removed outlier: 3.644A pdb=" N THR H 48 " --> pdb=" O GLU H 209 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU H 209 " --> pdb=" O THR H 48 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 72 through 78 removed outlier: 3.722A pdb=" N SER H 133 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY H 138 " --> pdb=" O TYR H 145 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 34 through 36 Processing sheet with id= N, first strand: chain 'I' and resid 134 through 138 removed outlier: 3.866A pdb=" N LEU I 134 " --> pdb=" O SER I 150 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR I 148 " --> pdb=" O TYR I 136 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY I 138 " --> pdb=" O GLN I 146 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'J' and resid 158 through 160 removed outlier: 3.626A pdb=" N GLY J 34 " --> pdb=" O ASN J 159 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 132 through 136 removed outlier: 4.479A pdb=" N LEU J 144 " --> pdb=" O TRP J 156 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'K' and resid 167 through 169 removed outlier: 3.568A pdb=" N VAL K 50 " --> pdb=" O GLU K 216 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU K 216 " --> pdb=" O VAL K 50 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'K' and resid 141 through 147 removed outlier: 4.045A pdb=" N LEU K 141 " --> pdb=" O MET K 156 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 158 through 161 removed outlier: 3.816A pdb=" N ILE L 212 " --> pdb=" O TYR L 224 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 71 through 73 removed outlier: 3.777A pdb=" N ASP L 138 " --> pdb=" O GLY L 141 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY L 141 " --> pdb=" O ASP L 138 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE L 144 " --> pdb=" O CYS L 156 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'M' and resid 162 through 165 removed outlier: 3.717A pdb=" N GLY M 44 " --> pdb=" O CYS M 41 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'M' and resid 49 through 52 Processing sheet with id= W, first strand: chain 'M' and resid 135 through 141 removed outlier: 3.652A pdb=" N PHE M 135 " --> pdb=" O ILE M 151 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE M 151 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN M 147 " --> pdb=" O SER M 139 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'N' and resid 125 through 128 removed outlier: 3.599A pdb=" N ALA N 177 " --> pdb=" O LEU N 14 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE N 174 " --> pdb=" O LEU N 189 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'N' and resid 34 through 36 Processing sheet with id= Z, first strand: chain 'O' and resid 124 through 128 Processing sheet with id= AA, first strand: chain 'O' and resid 34 through 36 removed outlier: 3.614A pdb=" N SER O 118 " --> pdb=" O TYR O 114 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'O' and resid 20 through 22 removed outlier: 6.111A pdb=" N GLU O 22 " --> pdb=" O VAL O 26 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL O 26 " --> pdb=" O GLU O 22 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'P' and resid 136 through 140 removed outlier: 6.465A pdb=" N ALA P 10 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL P 20 " --> pdb=" O ILE P 190 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL P 185 " --> pdb=" O LEU P 200 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'P' and resid 42 through 44 Processing sheet with id= AE, first strand: chain 'Q' and resid 5 through 8 removed outlier: 3.637A pdb=" N VAL Q 13 " --> pdb=" O ILE Q 183 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL Q 15 " --> pdb=" O ARG Q 181 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Q' and resid 43 through 48 removed outlier: 3.731A pdb=" N LEU Q 103 " --> pdb=" O LEU Q 45 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'R' and resid 125 through 129 removed outlier: 3.589A pdb=" N LEU R 176 " --> pdb=" O SER R 188 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER R 188 " --> pdb=" O LEU R 176 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS R 178 " --> pdb=" O ARG R 186 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ARG R 186 " --> pdb=" O HIS R 178 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'R' and resid 41 through 43 Processing sheet with id= AI, first strand: chain 'R' and resid 20 through 22 removed outlier: 3.811A pdb=" N ALA R 20 " --> pdb=" O SER R 28 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER R 28 " --> pdb=" O ALA R 20 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ALA R 22 " --> pdb=" O ILE R 26 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE R 26 " --> pdb=" O ALA R 22 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'S' and resid 135 through 139 removed outlier: 3.849A pdb=" N GLY S 202 " --> pdb=" O THR S 199 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'S' and resid 130 through 133 removed outlier: 3.898A pdb=" N GLN S 131 " --> pdb=" O SER S 123 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL S 121 " --> pdb=" O ASP S 133 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASN S 108 " --> pdb=" O PHE S 124 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR S 50 " --> pdb=" O THR S 47 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE S 52 " --> pdb=" O LYS S 45 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LYS S 45 " --> pdb=" O ILE S 52 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N CYS S 54 " --> pdb=" O CYS S 43 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N CYS S 43 " --> pdb=" O CYS S 54 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'T' and resid 136 through 138 removed outlier: 3.535A pdb=" N GLY T 19 " --> pdb=" O PHE T 16 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY T 196 " --> pdb=" O THR T 193 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'T' and resid 49 through 55 removed outlier: 3.535A pdb=" N THR T 109 " --> pdb=" O SER T 54 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR T 132 " --> pdb=" O TYR T 124 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'g' and resid 165 through 169 removed outlier: 5.739A pdb=" N THR g 38 " --> pdb=" O GLN g 53 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN g 53 " --> pdb=" O THR g 38 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'g' and resid 148 through 154 removed outlier: 3.670A pdb=" N ILE g 139 " --> pdb=" O VAL g 79 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL g 79 " --> pdb=" O ILE g 139 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY g 77 " --> pdb=" O ILE g 141 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N CYS g 78 " --> pdb=" O LYS g 71 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LYS g 71 " --> pdb=" O CYS g 78 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'h' and resid 160 through 163 removed outlier: 3.701A pdb=" N GLU h 209 " --> pdb=" O THR h 48 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'h' and resid 72 through 75 removed outlier: 3.518A pdb=" N VAL h 75 " --> pdb=" O LEU h 135 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY h 138 " --> pdb=" O TYR h 145 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'i' and resid 34 through 36 Processing sheet with id= AS, first strand: chain 'i' and resid 134 through 138 removed outlier: 4.001A pdb=" N LEU i 134 " --> pdb=" O SER i 150 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR i 148 " --> pdb=" O TYR i 136 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY i 138 " --> pdb=" O GLN i 146 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'j' and resid 158 through 161 removed outlier: 3.601A pdb=" N GLY j 34 " --> pdb=" O ASN j 159 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA j 32 " --> pdb=" O ILE j 161 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU j 207 " --> pdb=" O VAL j 45 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'j' and resid 132 through 136 removed outlier: 4.534A pdb=" N LEU j 144 " --> pdb=" O TRP j 156 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'k' and resid 167 through 169 removed outlier: 3.622A pdb=" N VAL k 50 " --> pdb=" O GLU k 216 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU k 216 " --> pdb=" O VAL k 50 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'k' and resid 74 through 77 removed outlier: 3.567A pdb=" N GLY k 144 " --> pdb=" O GLY k 75 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'l' and resid 158 through 161 removed outlier: 3.694A pdb=" N ILE l 212 " --> pdb=" O TYR l 224 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'l' and resid 71 through 73 removed outlier: 3.503A pdb=" N LEU l 133 " --> pdb=" O SER l 73 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP l 138 " --> pdb=" O GLY l 141 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY l 141 " --> pdb=" O ASP l 138 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'm' and resid 162 through 165 removed outlier: 3.674A pdb=" N GLY m 44 " --> pdb=" O CYS m 41 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'm' and resid 49 through 52 removed outlier: 3.793A pdb=" N GLU m 212 " --> pdb=" O VAL m 49 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'm' and resid 135 through 141 removed outlier: 3.529A pdb=" N LEU m 137 " --> pdb=" O TYR m 149 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN m 147 " --> pdb=" O SER m 139 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'n' and resid 125 through 128 removed outlier: 3.860A pdb=" N ALA n 177 " --> pdb=" O LEU n 14 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'n' and resid 34 through 36 removed outlier: 4.222A pdb=" N VAL n 111 " --> pdb=" O GLN n 123 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'n' and resid 20 through 22 removed outlier: 6.296A pdb=" N THR n 22 " --> pdb=" O ILE n 26 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE n 26 " --> pdb=" O THR n 22 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'o' and resid 124 through 128 removed outlier: 3.555A pdb=" N VAL o 125 " --> pdb=" O GLY o 5 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET o 127 " --> pdb=" O ILE o 3 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'o' and resid 34 through 36 removed outlier: 3.540A pdb=" N CYS o 43 " --> pdb=" O HIS o 35 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER o 112 " --> pdb=" O ASP o 120 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP o 120 " --> pdb=" O SER o 112 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR o 114 " --> pdb=" O SER o 118 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER o 118 " --> pdb=" O TYR o 114 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'p' and resid 136 through 140 removed outlier: 6.337A pdb=" N ALA p 10 " --> pdb=" O ASP p 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL p 20 " --> pdb=" O ILE p 190 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL p 185 " --> pdb=" O LEU p 200 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'p' and resid 42 through 44 Processing sheet with id= BJ, first strand: chain 'q' and resid 4 through 8 removed outlier: 3.709A pdb=" N VAL q 13 " --> pdb=" O ILE q 183 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL q 15 " --> pdb=" O ARG q 181 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'q' and resid 42 through 48 removed outlier: 3.775A pdb=" N LEU q 103 " --> pdb=" O LEU q 45 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'r' and resid 125 through 129 removed outlier: 3.539A pdb=" N ALA r 15 " --> pdb=" O LEU r 4 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY r 11 " --> pdb=" O PHE r 8 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER r 188 " --> pdb=" O LEU r 176 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N HIS r 178 " --> pdb=" O ARG r 186 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ARG r 186 " --> pdb=" O HIS r 178 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'r' and resid 41 through 43 removed outlier: 3.527A pdb=" N GLY r 103 " --> pdb=" O GLY r 110 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'r' and resid 20 through 22 removed outlier: 3.732A pdb=" N ALA r 20 " --> pdb=" O SER r 28 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER r 28 " --> pdb=" O ALA r 20 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ALA r 22 " --> pdb=" O ILE r 26 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE r 26 " --> pdb=" O ALA r 22 " (cutoff:3.500A) No H-bonds generated for sheet with id= BN Processing sheet with id= BO, first strand: chain 's' and resid 135 through 139 removed outlier: 3.907A pdb=" N GLY s 202 " --> pdb=" O THR s 199 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 's' and resid 130 through 133 removed outlier: 3.963A pdb=" N GLN s 131 " --> pdb=" O SER s 123 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL s 121 " --> pdb=" O ASP s 133 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASN s 108 " --> pdb=" O PHE s 124 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR s 50 " --> pdb=" O THR s 47 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR s 47 " --> pdb=" O THR s 50 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE s 52 " --> pdb=" O LYS s 45 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LYS s 45 " --> pdb=" O ILE s 52 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N CYS s 54 " --> pdb=" O CYS s 43 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS s 43 " --> pdb=" O CYS s 54 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 's' and resid 29 through 31 removed outlier: 3.722A pdb=" N LEU s 29 " --> pdb=" O THR s 37 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU s 31 " --> pdb=" O ILE s 35 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE s 35 " --> pdb=" O GLU s 31 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 't' and resid 136 through 138 removed outlier: 3.727A pdb=" N GLY t 196 " --> pdb=" O THR t 193 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 't' and resid 49 through 55 removed outlier: 3.576A pdb=" N TYR t 132 " --> pdb=" O TYR t 124 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.359A pdb=" N ASN A 114 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE A 101 " --> pdb=" O ASN A 114 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'A' and resid 270 through 274 removed outlier: 3.758A pdb=" N ILE A 272 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 318 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'B' and resid 107 through 110 removed outlier: 3.726A pdb=" N GLY B 110 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 150 " --> pdb=" O GLY B 110 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN B 153 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 159 " --> pdb=" O ASN B 153 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'B' and resid 349 through 351 removed outlier: 3.602A pdb=" N ARG B 349 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL B 327 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LEU B 224 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET B 329 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR B 246 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE B 283 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU B 248 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ASP B 285 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 250 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'C' and resid 114 through 116 Processing sheet with id= BY, first strand: chain 'D' and resid 129 through 132 removed outlier: 6.781A pdb=" N ILE D 102 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ALA D 95 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR D 100 " --> pdb=" O ALA D 95 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'D' and resid 202 through 204 Processing sheet with id= CA, first strand: chain 'D' and resid 228 through 230 Processing sheet with id= CB, first strand: chain 'E' and resid 78 through 81 removed outlier: 5.899A pdb=" N LYS E 72 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL E 60 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG E 97 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG E 109 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'E' and resid 297 through 300 removed outlier: 3.779A pdb=" N ARG E 297 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR E 173 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N MET E 275 " --> pdb=" O CYS E 170 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N LEU E 172 " --> pdb=" O MET E 275 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N MET E 277 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 278 " --> pdb=" O MET E 232 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP E 233 " --> pdb=" O VAL E 198 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'F' and resid 131 through 134 removed outlier: 3.969A pdb=" N GLU F 95 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LYS F 125 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL F 93 " --> pdb=" O LYS F 125 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP F 149 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU F 162 " --> pdb=" O GLY F 152 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'F' and resid 223 through 226 removed outlier: 6.727A pdb=" N ARG F 350 " --> pdb=" O LEU F 224 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N TYR F 226 " --> pdb=" O ARG F 350 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE F 352 " --> pdb=" O TYR F 226 " (cutoff:3.500A) No H-bonds generated for sheet with id= CE Processing sheet with id= CF, first strand: chain 'F' and resid 247 through 251 removed outlier: 6.412A pdb=" N LYS F 327 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE F 285 " --> pdb=" O LYS F 327 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE F 329 " --> pdb=" O ILE F 285 " (cutoff:3.500A) 4098 hydrogen bonds defined for protein. 11736 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: 40.31 Time building geometry restraints manager: 35.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 33607 1.36 - 1.50: 26469 1.50 - 1.65: 40576 1.65 - 1.80: 617 1.80 - 1.95: 353 Bond restraints: 101622 Sorted by residual: bond pdb=" C ASP c 279 " pdb=" N PRO c 280 " ideal model delta sigma weight residual 1.335 1.422 -0.087 1.28e-02 6.10e+03 4.65e+01 bond pdb=" C PRO D 144 " pdb=" N PRO D 145 " ideal model delta sigma weight residual 1.328 1.393 -0.065 1.25e-02 6.40e+03 2.73e+01 bond pdb=" CA ARG f 494 " pdb=" C ARG f 494 " ideal model delta sigma weight residual 1.523 1.592 -0.069 1.32e-02 5.74e+03 2.71e+01 bond pdb=" C ALA Y 51 " pdb=" N PRO Y 52 " ideal model delta sigma weight residual 1.337 1.379 -0.042 9.80e-03 1.04e+04 1.84e+01 bond pdb=" C PRO X 203 " pdb=" N PRO X 204 " ideal model delta sigma weight residual 1.331 1.364 -0.033 7.90e-03 1.60e+04 1.73e+01 ... (remaining 101617 not shown) Histogram of bond angle deviations from ideal: 95.94 - 105.34: 1995 105.34 - 114.75: 60437 114.75 - 124.16: 72546 124.16 - 133.57: 2382 133.57 - 142.97: 98 Bond angle restraints: 137458 Sorted by residual: angle pdb=" N HIS D 414 " pdb=" CA HIS D 414 " pdb=" C HIS D 414 " ideal model delta sigma weight residual 113.50 126.71 -13.21 1.23e+00 6.61e-01 1.15e+02 angle pdb=" N ALA f 488 " pdb=" CA ALA f 488 " pdb=" C ALA f 488 " ideal model delta sigma weight residual 111.36 122.82 -11.46 1.09e+00 8.42e-01 1.11e+02 angle pdb=" C LEU K 21 " pdb=" N PHE K 22 " pdb=" CA PHE K 22 " ideal model delta sigma weight residual 121.70 139.56 -17.86 1.80e+00 3.09e-01 9.84e+01 angle pdb=" C LEU D 335 " pdb=" N PRO D 336 " pdb=" CA PRO D 336 " ideal model delta sigma weight residual 119.85 129.67 -9.82 1.01e+00 9.80e-01 9.45e+01 angle pdb=" C GLY M 6 " pdb=" N TYR M 7 " pdb=" CA TYR M 7 " ideal model delta sigma weight residual 121.70 138.63 -16.93 1.80e+00 3.09e-01 8.84e+01 ... (remaining 137453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.79: 60917 32.79 - 65.58: 756 65.58 - 98.37: 106 98.37 - 131.15: 4 131.15 - 163.94: 1 Dihedral angle restraints: 61784 sinusoidal: 24435 harmonic: 37349 Sorted by residual: dihedral pdb=" CA GLU D 413 " pdb=" C GLU D 413 " pdb=" N HIS D 414 " pdb=" CA HIS D 414 " ideal model delta harmonic sigma weight residual 180.00 65.66 114.34 0 5.00e+00 4.00e-02 5.23e+02 dihedral pdb=" CA SER C 400 " pdb=" C SER C 400 " pdb=" N ILE C 401 " pdb=" CA ILE C 401 " ideal model delta harmonic sigma weight residual 180.00 67.67 112.33 0 5.00e+00 4.00e-02 5.05e+02 dihedral pdb=" CA ARG J 5 " pdb=" C ARG J 5 " pdb=" N ALA J 6 " pdb=" CA ALA J 6 " ideal model delta harmonic sigma weight residual -180.00 -73.43 -106.57 0 5.00e+00 4.00e-02 4.54e+02 ... (remaining 61781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 14915 0.133 - 0.266: 688 0.266 - 0.399: 47 0.399 - 0.533: 9 0.533 - 0.666: 1 Chirality restraints: 15660 Sorted by residual: chirality pdb=" CA VAL f 365 " pdb=" N VAL f 365 " pdb=" C VAL f 365 " pdb=" CB VAL f 365 " both_signs ideal model delta sigma weight residual False 2.44 1.78 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" PB AGS B 501 " pdb=" O2B AGS B 501 " pdb=" O3A AGS B 501 " pdb=" O3B AGS B 501 " both_signs ideal model delta sigma weight residual True 3.18 -2.65 0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" CB ILE h 105 " pdb=" CA ILE h 105 " pdb=" CG1 ILE h 105 " pdb=" CG2 ILE h 105 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.59e+00 ... (remaining 15657 not shown) Planarity restraints: 17770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP J 184 " 0.028 2.00e-02 2.50e+03 5.52e-02 3.05e+01 pdb=" C ASP J 184 " -0.095 2.00e-02 2.50e+03 pdb=" O ASP J 184 " 0.035 2.00e-02 2.50e+03 pdb=" N ASP J 185 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG f 369 " -0.022 2.00e-02 2.50e+03 4.75e-02 2.25e+01 pdb=" C ARG f 369 " 0.082 2.00e-02 2.50e+03 pdb=" O ARG f 369 " -0.032 2.00e-02 2.50e+03 pdb=" N MET f 370 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 132 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO C 133 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO C 133 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 133 " 0.061 5.00e-02 4.00e+02 ... (remaining 17767 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 1271 2.61 - 3.19: 85933 3.19 - 3.76: 159295 3.76 - 4.33: 215506 4.33 - 4.90: 338618 Nonbonded interactions: 800623 Sorted by model distance: nonbonded pdb=" O SER f 363 " pdb=" N VAL f 365 " model vdw 2.042 2.520 nonbonded pdb=" OD1 ASP f 366 " pdb=" N SER f 367 " model vdw 2.042 2.520 nonbonded pdb=" CD ARG f 494 " pdb=" OD1 ASP f 496 " model vdw 2.061 3.440 nonbonded pdb=" O ALA f 753 " pdb=" CE LYS f 754 " model vdw 2.078 3.440 nonbonded pdb=" O VAL f 311 " pdb=" O ALA f 490 " model vdw 2.087 3.040 ... (remaining 800618 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 'G' selection = (chain 'g' and resid 6 through 244) } ncs_group { reference = chain 'H' selection = (chain 'h' and resid 5 through 234) } ncs_group { reference = chain 'I' selection = (chain 'i' and resid 4 through 251) } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = (chain 'K' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 241)) selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'O' selection = chain 'o' } ncs_group { reference = chain 'P' selection = chain 'p' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'R' selection = chain 'r' } ncs_group { reference = chain 'S' selection = chain 's' } ncs_group { reference = chain 'T' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 10.320 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: 0.100 Extract box with map and model: 40.990 Check model and map are aligned: 1.120 Set scattering table: 0.700 Process input model: 197.250 Find NCS groups from input model: 6.670 Set up NCS constraints: 0.790 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 260.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.087 101622 Z= 0.394 Angle : 1.245 21.174 137458 Z= 0.685 Chirality : 0.066 0.666 15660 Planarity : 0.008 0.113 17770 Dihedral : 11.750 163.944 37740 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.59 % Favored : 89.85 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.19 % Twisted Proline : 1.35 % Twisted General : 0.36 % 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: -4.40 (0.06), residues: 12738 helix: -2.65 (0.05), residues: 5598 sheet: -1.91 (0.12), residues: 1636 loop : -3.46 (0.07), residues: 5504 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2481 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 2402 time to evaluate : 9.315 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash outliers start: 79 outliers final: 10 residues processed: 2469 average time/residue: 0.9545 time to fit residues: 3962.2247 Evaluate side-chains 1044 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1034 time to evaluate : 10.824 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 3 residues processed: 10 average time/residue: 0.8173 time to fit residues: 27.3365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1268 random chunks: chunk 1070 optimal weight: 20.0000 chunk 961 optimal weight: 7.9990 chunk 533 optimal weight: 9.9990 chunk 328 optimal weight: 8.9990 chunk 648 optimal weight: 20.0000 chunk 513 optimal weight: 2.9990 chunk 993 optimal weight: 0.9990 chunk 384 optimal weight: 3.9990 chunk 604 optimal weight: 7.9990 chunk 739 optimal weight: 20.0000 chunk 1151 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 389 ASN U 880 ASN V 110 HIS ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 260 HIS ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 362 ASN W 380 GLN ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 349 HIS Y 344 HIS Y 381 GLN Z 96 HIS Z 174 HIS a 23 HIS a 129 GLN a 305 ASN ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 63 HIS ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN H 148 GLN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 240 HIS J 15 HIS J 116 GLN K 23 GLN ** K 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 HIS L 152 ASN L 190 HIS N 154 GLN P 169 GLN ** Q 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82 ASN Q 101 ASN ** T 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 69 GLN ** g 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 102 GLN ** h 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 207 ASN ** i 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 99 HIS ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 HIS o 66 HIS o 165 ASN p 169 GLN ** q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 101 ASN q 168 GLN r 38 ASN ** t 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 412 GLN E 190 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 ASN F 321 GLN f 14 GLN f 102 HIS f 224 ASN f 329 ASN f 387 GLN f 452 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 101622 Z= 0.246 Angle : 0.815 14.159 137458 Z= 0.425 Chirality : 0.047 0.383 15660 Planarity : 0.006 0.098 17770 Dihedral : 7.825 159.871 14038 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.65 % Favored : 90.12 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.19 % Twisted Proline : 0.67 % Twisted General : 0.24 % 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: -3.21 (0.07), residues: 12738 helix: -1.44 (0.06), residues: 5591 sheet: -1.38 (0.13), residues: 1614 loop : -3.09 (0.07), residues: 5533 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1437 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1412 time to evaluate : 9.242 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 1432 average time/residue: 1.0181 time to fit residues: 2518.8082 Evaluate side-chains 892 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 883 time to evaluate : 9.273 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 3 residues processed: 9 average time/residue: 0.7460 time to fit residues: 25.6705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1268 random chunks: chunk 639 optimal weight: 0.8980 chunk 357 optimal weight: 0.9980 chunk 958 optimal weight: 6.9990 chunk 784 optimal weight: 20.0000 chunk 317 optimal weight: 9.9990 chunk 1153 optimal weight: 1.9990 chunk 1246 optimal weight: 1.9990 chunk 1027 optimal weight: 0.7980 chunk 1143 optimal weight: 20.0000 chunk 393 optimal weight: 0.0770 chunk 925 optimal weight: 20.0000 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 698 GLN V 110 HIS ** V 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 326 GLN ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 184 GLN ** Y 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 129 GLN ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 34 ASN ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 240 HIS ** K 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 HIS ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 GLN L 190 HIS ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN ** T 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 157 GLN h 95 GLN h 109 GLN ** h 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 207 ASN i 95 GLN i 109 GLN ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 28 ASN n 66 HIS p 61 GLN ** q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN ** q 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 352 HIS ** f 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 782 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 101622 Z= 0.190 Angle : 0.743 12.605 137458 Z= 0.381 Chirality : 0.046 0.273 15660 Planarity : 0.005 0.108 17770 Dihedral : 7.280 154.269 14038 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.00 % Favored : 90.82 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.19 % Twisted Proline : 0.45 % Twisted General : 0.16 % 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: -2.62 (0.07), residues: 12738 helix: -0.90 (0.07), residues: 5622 sheet: -1.06 (0.13), residues: 1625 loop : -2.86 (0.08), residues: 5491 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1315 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1300 time to evaluate : 9.249 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 1314 average time/residue: 0.9368 time to fit residues: 2131.5214 Evaluate side-chains 864 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 858 time to evaluate : 9.312 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 6 average time/residue: 0.7258 time to fit residues: 20.7136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1268 random chunks: chunk 1139 optimal weight: 9.9990 chunk 867 optimal weight: 9.9990 chunk 598 optimal weight: 30.0000 chunk 127 optimal weight: 8.9990 chunk 550 optimal weight: 20.0000 chunk 774 optimal weight: 20.0000 chunk 1157 optimal weight: 20.0000 chunk 1225 optimal weight: 20.0000 chunk 604 optimal weight: 5.9990 chunk 1097 optimal weight: 30.0000 chunk 330 optimal weight: 4.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN U 463 ASN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 HIS ** V 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 299 GLN ** W 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 174 HIS ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN a 129 GLN a 152 HIS a 227 ASN ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 HIS ** c 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 GLN I 240 HIS K 23 GLN ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 HIS N 123 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 99 HIS T 61 GLN T 65 GLN ** g 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 88 HIS ** h 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 94 HIS j 116 GLN j 154 HIS ** k 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 152 GLN k 155 HIS ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 HIS o 153 ASN ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 47 ASN ** t 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN f 180 GLN f 224 ASN f 327 ASN f 329 ASN f 364 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 101622 Z= 0.297 Angle : 0.822 13.318 137458 Z= 0.425 Chirality : 0.048 0.301 15660 Planarity : 0.006 0.083 17770 Dihedral : 7.251 147.916 14038 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 24.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.27 % Favored : 89.61 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.19 % Twisted Proline : 0.45 % Twisted General : 0.15 % 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: -2.43 (0.07), residues: 12738 helix: -0.72 (0.07), residues: 5584 sheet: -1.00 (0.13), residues: 1622 loop : -2.76 (0.08), residues: 5532 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1106 time to evaluate : 11.257 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 1114 average time/residue: 0.9220 time to fit residues: 1798.7959 Evaluate side-chains 796 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 790 time to evaluate : 9.152 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 6 average time/residue: 0.7472 time to fit residues: 20.7871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1268 random chunks: chunk 1020 optimal weight: 8.9990 chunk 695 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 912 optimal weight: 8.9990 chunk 505 optimal weight: 20.0000 chunk 1045 optimal weight: 5.9990 chunk 847 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 625 optimal weight: 5.9990 chunk 1100 optimal weight: 30.0000 chunk 309 optimal weight: 0.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: