Starting phenix.real_space_refine on Wed Mar 20 21:01:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfq_8664/03_2024/5vfq_8664_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfq_8664/03_2024/5vfq_8664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfq_8664/03_2024/5vfq_8664.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfq_8664/03_2024/5vfq_8664.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfq_8664/03_2024/5vfq_8664_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfq_8664/03_2024/5vfq_8664_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 591 5.16 5 C 63874 2.51 5 N 17390 2.21 5 O 19266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 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 "U ARG 140": "NH1" <-> "NH2" Residue "U ARG 159": "NH1" <-> "NH2" Residue "U ARG 194": "NH1" <-> "NH2" Residue "U TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "W ARG 408": "NH1" <-> "NH2" Residue "X TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 85": "NH1" <-> "NH2" Residue "a ARG 196": "NH1" <-> "NH2" Residue "a ARG 226": "NH1" <-> "NH2" Residue "a ARG 247": "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 175": "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 ARG 96": "NH1" <-> "NH2" Residue "l TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "A ARG 428": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "E TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "E ARG 241": "NH1" <-> "NH2" Residue "E ARG 251": "NH1" <-> "NH2" Residue "E ARG 255": "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: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 101134 Number of models: 1 Model: "" Number of chains: 51 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: "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: 3600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3600 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 19, 'TRANS': 427} Chain breaks: 2 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: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3009 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 369} 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: {'CIS': 1, 'PTRANS': 9, 'TRANS': 275} 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: 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: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2893 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'CIS': 2, 'PTRANS': 21, 'TRANS': 356} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2806 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'CIS': 5, 'PTRANS': 17, 'TRANS': 347} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 80 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': 2, 'PTRANS': 17, 'TRANS': 356} 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: "C" 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: 6 residue: pdb=" N GLY Z 30 " occ=0.28 ... (2 atoms not shown) pdb=" O GLY Z 30 " occ=0.28 residue: pdb=" N ILE b 90 " occ=0.94 ... (6 atoms not shown) pdb=" CD1 ILE b 90 " occ=0.94 residue: pdb=" N GLY b 191 " occ=0.48 ... (2 atoms not shown) pdb=" O GLY b 191 " occ=0.48 residue: pdb=" N ILE d 63 " occ=0.81 ... (6 atoms not shown) pdb=" CD1 ILE d 63 " occ=0.81 residue: pdb=" N SER d 70 " occ=0.59 ... (4 atoms not shown) pdb=" OG SER d 70 " occ=0.59 residue: pdb=" N MET d 144 " occ=0.79 ... (6 atoms not shown) pdb=" CE MET d 144 " occ=0.79 Time building chain proxies: 38.52, per 1000 atoms: 0.38 Number of scatterers: 101134 At special positions: 0 Unit cell: (332.25, 205.5, 220.5, 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 591 16.00 P 12 15.00 O 19266 8.00 N 17390 7.00 C 63874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 186 " distance=2.03 Simple disulfide: pdb=" SG CYS U 633 " - pdb=" SG CYS U 659 " distance=2.03 Simple disulfide: pdb=" SG CYS m 41 " - pdb=" SG CYS m 186 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.31 Conformation dependent library (CDL) restraints added in 13.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 401 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 115 " 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 24368 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 477 helices and 78 sheets defined 55.2% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 46.46 Creating SS restraints... Processing helix chain 'G' and resid 22 through 36 removed outlier: 4.332A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA G 31 " --> pdb=" O TYR G 27 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY G 36 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 67 removed outlier: 5.501A pdb=" N VAL G 66 " --> pdb=" O ASP G 62 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR G 67 " --> pdb=" O SER G 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 67' Processing helix chain 'G' and resid 83 through 105 Processing helix chain 'G' and resid 110 through 129 removed outlier: 3.659A pdb=" N LEU G 114 " --> pdb=" O PRO G 110 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ALA G 129 " --> pdb=" O TYR G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 183 Processing helix chain 'G' and resid 190 through 207 removed outlier: 5.409A pdb=" N THR G 194 " --> pdb=" O THR G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 244 removed outlier: 5.509A pdb=" N GLU G 244 " --> pdb=" O VAL G 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 33 removed outlier: 3.745A pdb=" N GLY H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ALA H 33 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 102 removed outlier: 4.058A pdb=" N VAL H 85 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 124 removed outlier: 5.353A pdb=" N SER H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 178 Processing helix chain 'H' and resid 183 through 199 removed outlier: 3.865A pdb=" N SER H 198 " --> pdb=" O THR H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 209 removed outlier: 4.018A pdb=" N ILE H 208 " --> pdb=" O THR H 204 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLU H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 204 through 209' Processing helix chain 'H' and resid 222 through 233 removed outlier: 6.255A pdb=" N ALA H 232 " --> pdb=" O ASP H 228 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE H 233 " --> pdb=" O TYR H 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 31 removed outlier: 4.127A pdb=" N GLU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS I 30 " --> pdb=" O GLU I 26 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 102 removed outlier: 3.636A pdb=" N ALA I 83 " --> pdb=" O ILE I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 124 removed outlier: 6.118A pdb=" N LEU I 110 " --> pdb=" O PRO I 106 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR I 121 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 179 removed outlier: 3.557A pdb=" N ALA I 169 " --> pdb=" O GLY I 165 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ALA I 170 " --> pdb=" O ASN I 166 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA I 171 " --> pdb=" O ASN I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 201 Processing helix chain 'I' and resid 207 through 212 removed outlier: 4.068A pdb=" N VAL I 211 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLU I 212 " --> pdb=" O ALA I 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 207 through 212' Processing helix chain 'I' and resid 229 through 250 removed outlier: 4.128A pdb=" N VAL I 233 " --> pdb=" O LYS I 229 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU I 250 " --> pdb=" O LYS I 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 30 removed outlier: 3.802A pdb=" N GLU J 20 " --> pdb=" O LEU J 16 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY J 29 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER J 30 " --> pdb=" O VAL J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 98 removed outlier: 3.803A pdb=" N ALA J 80 " --> pdb=" O LEU J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 121 removed outlier: 3.509A pdb=" N ILE J 107 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER J 121 " --> pdb=" O ARG J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 176 removed outlier: 3.614A pdb=" N VAL J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 198 Processing helix chain 'J' and resid 221 through 240 removed outlier: 3.629A pdb=" N ILE J 225 " --> pdb=" O ASN J 221 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU J 226 " --> pdb=" O PRO J 222 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU J 240 " --> pdb=" O LYS J 236 " (cutoff:3.500A) Processing helix chain 'j' and resid 16 through 30 removed outlier: 4.174A pdb=" N GLU j 20 " --> pdb=" O LEU j 16 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU j 24 " --> pdb=" O GLU j 20 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA j 25 " --> pdb=" O TYR j 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL j 26 " --> pdb=" O ALA j 22 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY j 29 " --> pdb=" O ALA j 25 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER j 30 " --> pdb=" O VAL j 26 " (cutoff:3.500A) Processing helix chain 'j' and resid 76 through 98 removed outlier: 3.898A pdb=" N ALA j 80 " --> pdb=" O LEU j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 103 through 121 removed outlier: 3.900A pdb=" N SER j 121 " --> pdb=" O ARG j 117 " (cutoff:3.500A) Processing helix chain 'j' and resid 164 through 176 removed outlier: 3.693A pdb=" N LYS j 174 " --> pdb=" O GLU j 170 " (cutoff:3.500A) Processing helix chain 'j' and resid 183 through 198 removed outlier: 3.787A pdb=" N VAL j 198 " --> pdb=" O ALA j 194 " (cutoff:3.500A) Processing helix chain 'j' and resid 221 through 240 removed outlier: 3.946A pdb=" N ILE j 225 " --> pdb=" O ASN j 221 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU j 226 " --> pdb=" O PRO j 222 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU j 240 " --> pdb=" O LYS j 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 34 removed outlier: 4.933A pdb=" N TYR K 26 " --> pdb=" O PHE K 22 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLY K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 103 removed outlier: 3.993A pdb=" N ALA K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 123 removed outlier: 4.610A pdb=" N LEU K 119 " --> pdb=" O ALA K 115 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU K 121 " --> pdb=" O SER K 117 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN K 122 " --> pdb=" O ASN K 118 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N PHE K 123 " --> pdb=" O LEU K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 185 Processing helix chain 'K' and resid 190 through 206 removed outlier: 3.690A pdb=" N ILE K 201 " --> pdb=" O SER K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 231 through 241 removed outlier: 6.494A pdb=" N GLU K 235 " --> pdb=" O LYS K 231 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU K 236 " --> pdb=" O GLU K 232 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'k' and resid 21 through 34 removed outlier: 3.725A pdb=" N GLU k 25 " --> pdb=" O LEU k 21 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS k 32 " --> pdb=" O ILE k 28 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU k 33 " --> pdb=" O GLU k 29 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLY k 34 " --> pdb=" O ALA k 30 " (cutoff:3.500A) Processing helix chain 'k' and resid 81 through 103 removed outlier: 4.367A pdb=" N ALA k 85 " --> pdb=" O LEU k 81 " (cutoff:3.500A) Processing helix chain 'k' and resid 108 through 123 removed outlier: 4.882A pdb=" N LEU k 119 " --> pdb=" O ALA k 115 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU k 121 " --> pdb=" O SER k 117 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLN k 122 " --> pdb=" O ASN k 118 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N PHE k 123 " --> pdb=" O LEU k 119 " (cutoff:3.500A) Processing helix chain 'k' and resid 173 through 185 removed outlier: 3.712A pdb=" N VAL k 184 " --> pdb=" O SER k 180 " (cutoff:3.500A) Processing helix chain 'k' and resid 190 through 206 removed outlier: 3.752A pdb=" N ILE k 201 " --> pdb=" O SER k 197 " (cutoff:3.500A) Processing helix chain 'k' and resid 231 through 241 removed outlier: 6.573A pdb=" N GLU k 235 " --> pdb=" O LYS k 231 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU k 236 " --> pdb=" O GLU k 232 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE k 241 " --> pdb=" O VAL k 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 32 removed outlier: 3.887A pdb=" N GLU L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN L 31 " --> pdb=" O GLU L 27 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 99 removed outlier: 3.695A pdb=" N ALA L 81 " --> pdb=" O LEU L 77 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER L 95 " --> pdb=" O GLU L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 121 removed outlier: 3.682A pdb=" N LEU L 108 " --> pdb=" O PRO L 104 " (cutoff:3.500A) removed outlier: 4.229A 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 165 through 180 removed outlier: 5.047A pdb=" N SER L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLU L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N MET L 180 " --> pdb=" O MET L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 200 removed outlier: 5.175A pdb=" N GLU L 197 " --> pdb=" O ARG L 193 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU L 199 " --> pdb=" O LEU L 195 " (cutoff:3.500A) Proline residue: L 200 - end of helix Processing helix chain 'L' and resid 225 through 235 removed outlier: 5.215A pdb=" N VAL L 229 " --> pdb=" O ASP L 225 " (cutoff:3.500A) Proline residue: L 231 - end of helix removed outlier: 3.659A pdb=" N GLU L 234 " --> pdb=" O SER L 230 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLY L 235 " --> pdb=" O PRO L 231 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 9 removed outlier: 4.779A pdb=" N ASN L 8 " --> pdb=" O GLN L 5 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP L 9 " --> pdb=" O TYR L 6 " (cutoff:3.500A) Processing helix chain 'l' and resid 19 through 32 removed outlier: 3.799A pdb=" N GLU l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY l 32 " --> pdb=" O ALA l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 99 removed outlier: 3.965A pdb=" N ALA l 81 " --> pdb=" O LEU l 77 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER l 95 " --> pdb=" O GLU l 91 " (cutoff:3.500A) Processing helix chain 'l' and resid 104 through 121 removed outlier: 3.572A pdb=" N LEU l 108 " --> pdb=" O PRO l 104 " (cutoff:3.500A) removed outlier: 4.365A 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 165 through 180 removed outlier: 5.061A pdb=" N SER l 177 " --> pdb=" O GLU l 173 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLU l 178 " --> pdb=" O ARG l 174 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET l 180 " --> pdb=" O MET l 176 " (cutoff:3.500A) Processing helix chain 'l' and resid 183 through 200 removed outlier: 5.188A pdb=" N GLU l 197 " --> pdb=" O ARG l 193 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU l 199 " --> pdb=" O LEU l 195 " (cutoff:3.500A) Proline residue: l 200 - end of helix Processing helix chain 'l' and resid 225 through 235 removed outlier: 5.285A pdb=" N VAL l 229 " --> pdb=" O ASP l 225 " (cutoff:3.500A) Proline residue: l 231 - end of helix removed outlier: 3.700A pdb=" N GLU l 234 " --> pdb=" O SER l 230 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLY l 235 " --> pdb=" O PRO l 231 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 9 removed outlier: 4.852A pdb=" N ASN l 8 " --> pdb=" O GLN l 5 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP l 9 " --> pdb=" O TYR l 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 34 removed outlier: 3.695A pdb=" N VAL M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU M 31 " --> pdb=" O MET M 27 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN M 32 " --> pdb=" O LYS M 28 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER M 33 " --> pdb=" O ALA M 29 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER M 34 " --> pdb=" O VAL M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 102 Processing helix chain 'M' and resid 107 through 125 removed outlier: 4.220A pdb=" N TYR M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 179 removed outlier: 4.975A pdb=" N GLU M 175 " --> pdb=" O ALA M 171 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU M 177 " --> pdb=" O LYS M 173 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU M 179 " --> pdb=" O GLU M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 202 removed outlier: 3.510A pdb=" N ILE M 189 " --> pdb=" O THR M 185 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL M 200 " --> pdb=" O ILE M 196 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N HIS M 201 " --> pdb=" O ILE M 197 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASP M 202 " --> pdb=" O TYR M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 233 removed outlier: 4.842A pdb=" N ARG M 232 " --> pdb=" O PRO M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 243 removed outlier: 3.843A pdb=" N TYR M 238 " --> pdb=" O GLU M 234 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU M 241 " --> pdb=" O LYS M 237 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU M 243 " --> pdb=" O ALA M 239 " (cutoff:3.500A) Processing helix chain 'm' and resid 20 through 34 removed outlier: 3.594A pdb=" N GLU m 24 " --> pdb=" O VAL m 20 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL m 30 " --> pdb=" O ALA m 26 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU m 31 " --> pdb=" O MET m 27 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN m 32 " --> pdb=" O LYS m 28 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER m 33 " --> pdb=" O ALA m 29 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N SER m 34 " --> pdb=" O VAL m 30 " (cutoff:3.500A) Processing helix chain 'm' and resid 80 through 102 Processing helix chain 'm' and resid 107 through 125 removed outlier: 4.238A pdb=" N TYR m 125 " --> pdb=" O ALA m 121 " (cutoff:3.500A) Processing helix chain 'm' and resid 168 through 179 removed outlier: 3.574A pdb=" N LYS m 173 " --> pdb=" O ARG m 169 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU m 175 " --> pdb=" O ALA m 171 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU m 177 " --> pdb=" O LYS m 173 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS m 178 " --> pdb=" O THR m 174 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU m 179 " --> pdb=" O GLU m 175 " (cutoff:3.500A) Processing helix chain 'm' and resid 185 through 202 removed outlier: 4.332A pdb=" N LYS m 191 " --> pdb=" O ARG m 187 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N HIS m 201 " --> pdb=" O ILE m 197 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASP m 202 " --> pdb=" O TYR m 198 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 233 removed outlier: 4.810A pdb=" N ARG m 232 " --> pdb=" O PRO m 228 " (cutoff:3.500A) Processing helix chain 'm' and resid 234 through 243 removed outlier: 3.797A pdb=" N TYR m 238 " --> pdb=" O GLU m 234 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU m 241 " --> pdb=" O LYS m 237 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU m 243 " --> pdb=" O ALA m 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 71 removed outlier: 3.955A pdb=" N THR N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 91 removed outlier: 3.831A pdb=" N ALA N 79 " --> pdb=" O LEU N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 143 removed outlier: 4.697A pdb=" N ASP N 140 " --> pdb=" O TYR N 136 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ALA N 141 " --> pdb=" O GLY N 137 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR N 143 " --> pdb=" O VAL N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 167 Processing helix chain 'n' and resid 48 through 71 removed outlier: 3.992A pdb=" N THR n 52 " --> pdb=" O SER n 48 " (cutoff:3.500A) Processing helix chain 'n' and resid 75 through 91 removed outlier: 3.899A pdb=" N ALA n 79 " --> pdb=" O LEU n 75 " (cutoff:3.500A) Processing helix chain 'n' and resid 132 through 143 removed outlier: 4.698A pdb=" N ASP n 140 " --> pdb=" O TYR n 136 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA n 141 " --> pdb=" O GLY n 137 " (cutoff:3.500A) Processing helix chain 'n' and resid 148 through 167 Processing helix chain 'O' and resid 48 through 71 Processing helix chain 'O' and resid 75 through 91 removed outlier: 3.656A pdb=" N ALA O 79 " --> pdb=" O ARG O 75 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN O 91 " --> pdb=" O LEU O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 142 removed outlier: 4.019A pdb=" N ALA O 134 " --> pdb=" O GLY O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 166 removed outlier: 4.242A pdb=" N ASP O 166 " --> pdb=" O GLY O 162 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 71 Processing helix chain 'o' and resid 75 through 91 removed outlier: 3.635A pdb=" N ALA o 79 " --> pdb=" O ARG o 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 130 through 142 removed outlier: 4.103A pdb=" N ALA o 134 " --> pdb=" O GLY o 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 147 through 166 removed outlier: 4.274A pdb=" N ASP o 166 " --> pdb=" O GLY o 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 8 removed outlier: 4.961A pdb=" N ASN P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY P 8 " --> pdb=" O MET P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 79 removed outlier: 4.275A pdb=" N GLY P 79 " --> pdb=" O GLU P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 99 removed outlier: 4.082A pdb=" N LYS P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 154 removed outlier: 5.547A pdb=" N MET P 146 " --> pdb=" O CYS P 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 179 removed outlier: 4.735A pdb=" N ALA P 179 " --> pdb=" O VAL P 175 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 8 removed outlier: 4.948A pdb=" N ASN p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY p 8 " --> pdb=" O MET p 4 " (cutoff:3.500A) Processing helix chain 'p' and resid 56 through 79 removed outlier: 4.356A pdb=" N GLY p 79 " --> pdb=" O GLU p 75 " (cutoff:3.500A) Processing helix chain 'p' and resid 83 through 99 removed outlier: 4.020A pdb=" N LYS p 98 " --> pdb=" O LEU p 94 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG p 99 " --> pdb=" O LEU p 95 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 154 removed outlier: 5.422A pdb=" N MET p 146 " --> pdb=" O CYS p 142 " (cutoff:3.500A) Processing helix chain 'p' and resid 159 through 179 removed outlier: 4.664A pdb=" N ALA p 179 " --> pdb=" O VAL p 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 71 removed outlier: 4.549A pdb=" N VAL Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 94 removed outlier: 4.204A pdb=" N ARG Q 93 " --> pdb=" O ALA Q 89 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER Q 94 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 147 removed outlier: 4.550A pdb=" N PHE Q 137 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR Q 147 " --> pdb=" O LEU Q 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 171 removed outlier: 4.162A pdb=" N LYS Q 169 " --> pdb=" O GLU Q 165 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG Q 170 " --> pdb=" O GLU Q 166 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE Q 171 " --> pdb=" O LEU Q 167 " (cutoff:3.500A) Processing helix chain 'q' and resid 49 through 71 removed outlier: 4.604A pdb=" N VAL q 54 " --> pdb=" O ALA q 50 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN q 55 " --> pdb=" O GLY q 51 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 94 removed outlier: 4.494A pdb=" N ARG q 93 " --> pdb=" O ALA q 89 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N SER q 94 " --> pdb=" O ASP q 90 " (cutoff:3.500A) Processing helix chain 'q' and resid 133 through 147 removed outlier: 4.354A pdb=" N PHE q 137 " --> pdb=" O GLY q 133 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR q 146 " --> pdb=" O ILE q 142 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR q 147 " --> pdb=" O LEU q 143 " (cutoff:3.500A) Processing helix chain 'q' and resid 152 through 171 removed outlier: 4.173A pdb=" N LYS q 169 " --> pdb=" O GLU q 165 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG q 170 " --> pdb=" O GLU q 166 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE q 171 " --> pdb=" O LEU q 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 71 removed outlier: 4.198A pdb=" N CYS R 52 " --> pdb=" O GLY R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 91 removed outlier: 3.542A pdb=" N ALA R 79 " --> pdb=" O SER R 75 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 143 removed outlier: 3.759A pdb=" N ALA R 135 " --> pdb=" O GLY R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 167 Processing helix chain 'R' and resid 191 through 200 Processing helix chain 'r' and resid 48 through 71 removed outlier: 4.143A pdb=" N CYS r 52 " --> pdb=" O GLY r 48 " (cutoff:3.500A) Processing helix chain 'r' and resid 75 through 91 removed outlier: 3.574A pdb=" N ALA r 79 " --> pdb=" O SER r 75 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TYR r 90 " --> pdb=" O MET r 86 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS r 91 " --> pdb=" O VAL r 87 " (cutoff:3.500A) Processing helix chain 'r' and resid 131 through 143 removed outlier: 3.849A pdb=" N ALA r 135 " --> pdb=" O GLY r 131 " (cutoff:3.500A) Processing helix chain 'r' and resid 148 through 167 Processing helix chain 'r' and resid 191 through 200 Processing helix chain 'S' and resid 57 through 79 Processing helix chain 'S' and resid 84 through 100 removed outlier: 3.784A pdb=" N ILE S 88 " --> pdb=" O THR S 84 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG S 100 " --> pdb=" O LEU S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 141 through 153 Proline residue: S 147 - end of helix Processing helix chain 'S' and resid 167 through 186 removed outlier: 3.907A pdb=" N ARG S 185 " --> pdb=" O SER S 181 " (cutoff:3.500A) Processing helix chain 's' and resid 57 through 79 Processing helix chain 's' and resid 84 through 100 removed outlier: 3.936A pdb=" N ILE s 88 " --> pdb=" O THR s 84 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG s 100 " --> pdb=" O LEU s 96 " (cutoff:3.500A) Processing helix chain 's' and resid 141 through 153 Proline residue: s 147 - end of helix Processing helix chain 's' and resid 167 through 186 removed outlier: 3.924A pdb=" N ARG s 185 " --> pdb=" O SER s 181 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 78 removed outlier: 3.738A pdb=" N GLY T 78 " --> pdb=" O GLU T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 103 removed outlier: 3.910A pdb=" N LYS T 102 " --> pdb=" O SER T 98 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET T 103 " --> pdb=" O ARG T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 157 removed outlier: 4.435A pdb=" N TYR T 144 " --> pdb=" O GLY T 140 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLN T 147 " --> pdb=" O ALA T 143 " (cutoff:3.500A) Proline residue: T 148 - end of helix Processing helix chain 'T' and resid 161 through 180 Processing helix chain 'T' and resid 209 through 215 removed outlier: 4.530A pdb=" N HIS T 213 " --> pdb=" O TRP T 209 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N MET T 214 " --> pdb=" O ASP T 210 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ILE T 215 " --> pdb=" O ILE T 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 209 through 215' Processing helix chain 't' and resid 56 through 78 removed outlier: 3.840A pdb=" N GLY t 78 " --> pdb=" O GLU t 74 " (cutoff:3.500A) Processing helix chain 't' and resid 84 through 103 removed outlier: 3.616A pdb=" N LYS t 102 " --> pdb=" O SER t 98 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET t 103 " --> pdb=" O ARG t 99 " (cutoff:3.500A) Processing helix chain 't' and resid 140 through 157 removed outlier: 4.486A pdb=" N TYR t 144 " --> pdb=" O GLY t 140 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLN t 147 " --> pdb=" O ALA t 143 " (cutoff:3.500A) Proline residue: t 148 - end of helix Processing helix chain 't' and resid 161 through 180 Processing helix chain 't' and resid 209 through 215 removed outlier: 4.324A pdb=" N HIS t 213 " --> pdb=" O TRP t 209 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N MET t 214 " --> pdb=" O ASP t 210 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE t 215 " --> pdb=" O ILE t 211 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 209 through 215' Processing helix chain 'U' and resid 7 through 14 removed outlier: 4.872A pdb=" N LEU U 11 " --> pdb=" O GLY U 7 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU U 14 " --> pdb=" O SER U 10 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 31 removed outlier: 5.031A pdb=" N PHE U 22 " --> pdb=" O GLN U 18 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 42 removed outlier: 4.122A pdb=" N ILE U 38 " --> pdb=" O PHE U 34 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER U 39 " --> pdb=" O TRP U 35 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU U 40 " --> pdb=" O ALA U 36 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER U 41 " --> pdb=" O GLU U 37 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 51 Processing helix chain 'U' and resid 56 through 72 Processing helix chain 'U' and resid 73 through 84 removed outlier: 3.739A pdb=" N SER U 77 " --> pdb=" O ALA U 73 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 91 removed outlier: 4.075A pdb=" N ASN U 91 " --> pdb=" O LEU U 87 " (cutoff:3.500A) Processing helix chain 'U' and resid 95 through 119 removed outlier: 4.205A pdb=" N ILE U 100 " --> pdb=" O TYR U 96 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU U 118 " --> pdb=" O GLU U 114 " (cutoff:3.500A) Proline residue: U 119 - end of helix Processing helix chain 'U' and resid 127 through 145 removed outlier: 3.619A pdb=" N GLU U 131 " --> pdb=" O ASP U 127 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL U 134 " --> pdb=" O LEU U 130 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG U 140 " --> pdb=" O LYS U 136 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 158 removed outlier: 4.075A pdb=" N ILE U 153 " --> pdb=" O GLN U 149 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG U 158 " --> pdb=" O ALA U 154 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 169 removed outlier: 3.763A pdb=" N PHE U 163 " --> pdb=" O ARG U 159 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE U 167 " --> pdb=" O PHE U 163 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU U 168 " --> pdb=" O GLU U 164 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU U 169 " --> pdb=" O LYS U 165 " (cutoff:3.500A) Processing helix chain 'U' and resid 173 through 188 removed outlier: 5.290A pdb=" N LEU U 177 " --> pdb=" O VAL U 173 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ALA U 178 " --> pdb=" O PRO U 174 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU U 181 " --> pdb=" O LEU U 177 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LYS U 182 " --> pdb=" O ALA U 178 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU U 187 " --> pdb=" O LEU U 183 " (cutoff:3.500A) Processing helix chain 'U' and resid 191 through 208 removed outlier: 5.112A pdb=" N LYS U 196 " --> pdb=" O GLN U 192 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE U 204 " --> pdb=" O VAL U 200 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 223 removed outlier: 5.238A pdb=" N VAL U 216 " --> pdb=" O ASP U 212 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE U 221 " --> pdb=" O CYS U 217 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 240 removed outlier: 4.273A pdb=" N ASP U 240 " --> pdb=" O LEU U 236 " (cutoff:3.500A) Processing helix chain 'U' and resid 243 through 255 removed outlier: 4.643A pdb=" N GLN U 247 " --> pdb=" O LEU U 243 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE U 248 " --> pdb=" O MET U 244 " (cutoff:3.500A) Processing helix chain 'U' and resid 257 through 269 removed outlier: 3.675A pdb=" N LEU U 261 " --> pdb=" O SER U 257 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N SER U 262 " --> pdb=" O GLN U 258 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN U 267 " --> pdb=" O SER U 263 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ARG U 269 " --> pdb=" O ILE U 265 " (cutoff:3.500A) Processing helix chain 'U' and resid 320 through 331 removed outlier: 4.448A pdb=" N LEU U 329 " --> pdb=" O MET U 325 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER U 330 " --> pdb=" O ILE U 326 " (cutoff:3.500A) Processing helix chain 'U' and resid 332 through 346 removed outlier: 3.691A pdb=" N ASN U 346 " --> pdb=" O LEU U 342 " (cutoff:3.500A) Processing helix chain 'U' and resid 349 through 360 removed outlier: 4.275A pdb=" N LEU U 353 " --> pdb=" O ASP U 349 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ALA U 359 " --> pdb=" O ASN U 355 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL U 360 " --> pdb=" O THR U 356 " (cutoff:3.500A) Processing helix chain 'U' and resid 364 through 378 removed outlier: 3.592A pdb=" N MET U 376 " --> pdb=" O ALA U 372 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 388 removed outlier: 5.350A pdb=" N ARG U 387 " --> pdb=" O ASP U 383 " (cutoff:3.500A) Processing helix chain 'U' and resid 389 through 395 removed outlier: 5.090A pdb=" N LEU U 393 " --> pdb=" O ASN U 389 " (cutoff:3.500A) Processing helix chain 'U' and resid 397 through 413 removed outlier: 5.649A pdb=" N LYS U 401 " --> pdb=" O THR U 397 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N PHE U 402 " --> pdb=" O ASN U 398 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU U 408 " --> pdb=" O ALA U 404 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) Processing helix chain 'U' and resid 416 through 425 removed outlier: 4.591A pdb=" N LEU U 420 " --> pdb=" O GLU U 416 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLN U 421 " --> pdb=" O LYS U 417 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR U 425 " --> pdb=" O GLN U 421 " (cutoff:3.500A) Processing helix chain 'U' and resid 427 through 432 removed outlier: 4.023A pdb=" N THR U 431 " --> pdb=" O LEU U 427 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N SER U 432 " --> pdb=" O PRO U 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 427 through 432' Processing helix chain 'U' and resid 435 through 451 removed outlier: 3.862A pdb=" N LEU U 443 " --> pdb=" O GLU U 439 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 468 removed outlier: 4.880A pdb=" N ASP U 459 " --> pdb=" O GLY U 455 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR U 460 " --> pdb=" O ASP U 456 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN U 467 " --> pdb=" O ASN U 463 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA U 468 " --> pdb=" O GLN U 464 " (cutoff:3.500A) Processing helix chain 'U' and resid 471 through 486 removed outlier: 3.864A pdb=" N HIS U 475 " --> pdb=" O ASP U 471 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY U 476 " --> pdb=" O ILE U 472 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU U 479 " --> pdb=" O HIS U 475 " (cutoff:3.500A) Processing helix chain 'U' and resid 490 through 503 removed outlier: 3.607A pdb=" N TYR U 494 " --> pdb=" O ARG U 490 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR U 499 " --> pdb=" O ASP U 495 " (cutoff:3.500A) Processing helix chain 'U' and resid 505 through 521 removed outlier: 4.688A pdb=" N GLY U 509 " --> pdb=" O ASP U 505 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU U 510 " --> pdb=" O ALA U 506 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ALA U 511 " --> pdb=" O VAL U 507 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 539 removed outlier: 5.301A pdb=" N ILE U 529 " --> pdb=" O ASN U 525 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN U 537 " --> pdb=" O VAL U 533 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLU U 538 " --> pdb=" O GLY U 534 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR U 539 " --> pdb=" O TYR U 535 " (cutoff:3.500A) Processing helix chain 'U' and resid 541 through 557 removed outlier: 4.212A pdb=" N LEU U 545 " --> pdb=" O HIS U 541 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N MET U 556 " --> pdb=" O ILE U 552 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TYR U 557 " --> pdb=" O ALA U 553 " (cutoff:3.500A) Processing helix chain 'U' and resid 563 through 573 removed outlier: 4.499A pdb=" N ASP U 573 " --> pdb=" O SER U 569 " (cutoff:3.500A) Processing helix chain 'U' and resid 575 through 591 removed outlier: 3.532A pdb=" N TYR U 590 " --> pdb=" O VAL U 586 " (cutoff:3.500A) Processing helix chain 'U' and resid 595 through 608 removed outlier: 3.727A pdb=" N ILE U 599 " --> pdb=" O ASN U 595 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG U 601 " --> pdb=" O LYS U 597 " (cutoff:3.500A) Processing helix chain 'U' and resid 611 through 627 removed outlier: 3.615A pdb=" N ARG U 615 " --> pdb=" O ASN U 611 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU U 622 " --> pdb=" O ALA U 618 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) Processing helix chain 'U' and resid 632 through 643 removed outlier: 3.519A pdb=" N VAL U 636 " --> pdb=" O GLN U 632 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU U 640 " --> pdb=" O VAL U 636 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU U 642 " --> pdb=" O SER U 638 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER U 643 " --> pdb=" O LEU U 639 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 660 removed outlier: 3.587A pdb=" N ARG U 649 " --> pdb=" O ASN U 645 " (cutoff:3.500A) Processing helix chain 'U' and resid 665 through 677 removed outlier: 6.442A pdb=" N ILE U 669 " --> pdb=" O ASN U 665 " (cutoff:3.500A) Proline residue: U 674 - end of helix Processing helix chain 'U' and resid 680 through 699 removed outlier: 5.483A pdb=" N GLN U 697 " --> pdb=" O LEU U 693 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLN U 698 " --> pdb=" O ILE U 694 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N THR U 699 " --> pdb=" O MET U 695 " (cutoff:3.500A) Processing helix chain 'U' and resid 704 through 718 removed outlier: 4.554A pdb=" N GLN U 708 " --> pdb=" O PRO U 704 " (cutoff:3.500A) Processing helix chain 'U' and resid 723 through 743 removed outlier: 4.730A pdb=" N GLY U 729 " --> pdb=" O MET U 725 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ALA U 730 " --> pdb=" O ALA U 726 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE U 731 " --> pdb=" O LYS U 727 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU U 732 " --> pdb=" O PHE U 728 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLY U 740 " --> pdb=" O ILE U 736 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLY U 741 " --> pdb=" O LEU U 737 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N HIS U 742 " --> pdb=" O ASP U 738 " (cutoff:3.500A) Processing helix chain 'U' and resid 756 through 769 removed outlier: 5.375A pdb=" N VAL U 763 " --> pdb=" O SER U 759 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLN U 768 " --> pdb=" O LEU U 764 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N PHE U 769 " --> pdb=" O VAL U 765 " (cutoff:3.500A) Processing helix chain 'U' and resid 772 through 783 removed outlier: 4.698A pdb=" N SER U 776 " --> pdb=" O TRP U 772 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N HIS U 777 " --> pdb=" O PHE U 773 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N PHE U 778 " --> pdb=" O PRO U 774 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU U 779 " --> pdb=" O LEU U 775 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N SER U 780 " --> pdb=" O SER U 776 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU U 781 " --> pdb=" O HIS U 777 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA U 782 " --> pdb=" O PHE U 778 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR U 783 " --> pdb=" O LEU U 779 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 772 through 783' Processing helix chain 'U' and resid 807 through 813 removed outlier: 5.320A pdb=" N TYR U 813 " --> pdb=" O SER U 809 " (cutoff:3.500A) Processing helix chain 'U' and resid 885 through 892 removed outlier: 4.030A pdb=" N LEU U 889 " --> pdb=" O MET U 885 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LYS U 890 " --> pdb=" O PRO U 886 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N VAL U 891 " --> pdb=" O ALA U 887 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU U 892 " --> pdb=" O GLN U 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 885 through 892' Processing helix chain 'V' and resid 27 through 54 removed outlier: 4.523A pdb=" N ALA V 31 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Proline residue: V 32 - end of helix removed outlier: 4.145A pdb=" N MET V 37 " --> pdb=" O GLN V 33 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU V 40 " --> pdb=" O GLU V 36 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY V 53 " --> pdb=" O GLY V 49 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LYS V 54 " --> pdb=" O GLU V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 61 removed outlier: 6.918A pdb=" N ALA V 59 " --> pdb=" O THR V 55 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ALA V 60 " --> pdb=" O ALA V 56 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU V 61 " --> pdb=" O ALA V 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 55 through 61' Processing helix chain 'V' and resid 67 through 76 Processing helix chain 'V' and resid 88 through 95 removed outlier: 3.530A pdb=" N ARG V 92 " --> pdb=" O GLY V 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE V 93 " --> pdb=" O LYS V 89 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL V 94 " --> pdb=" O GLU V 90 " (cutoff:3.500A) Processing helix chain 'V' and resid 103 through 115 removed outlier: 4.794A pdb=" N LYS V 115 " --> pdb=" O TYR V 111 " (cutoff:3.500A) Processing helix chain 'V' and resid 133 through 138 Proline residue: V 138 - end of helix Processing helix chain 'V' and resid 147 through 158 removed outlier: 3.510A pdb=" N THR V 151 " --> pdb=" O PHE V 147 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY V 152 " --> pdb=" O ARG V 148 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS V 153 " --> pdb=" O PRO V 149 " (cutoff:3.500A) Proline residue: V 158 - end of helix Processing helix chain 'V' and resid 160 through 166 removed outlier: 4.151A pdb=" N GLU V 164 " --> pdb=" O LEU V 160 " (cutoff:3.500A) Processing helix chain 'V' and resid 169 through 192 removed outlier: 5.604A pdb=" N ILE V 173 " --> pdb=" O LEU V 169 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE V 174 " --> pdb=" O LEU V 170 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ASP V 190 " --> pdb=" O LYS V 186 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU V 191 " --> pdb=" O ILE V 187 " (cutoff:3.500A) Processing helix chain 'V' and resid 197 through 202 removed outlier: 5.632A pdb=" N ARG V 201 " --> pdb=" O THR V 197 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ALA V 202 " --> pdb=" O GLN V 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 197 through 202' Processing helix chain 'V' and resid 203 through 222 removed outlier: 3.793A pdb=" N LYS V 209 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE V 220 " --> pdb=" O ARG V 216 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU V 221 " --> pdb=" O VAL V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 224 through 241 removed outlier: 5.299A pdb=" N ARG V 228 " --> pdb=" O LEU V 224 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER V 229 " --> pdb=" O ASP V 225 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU V 240 " --> pdb=" O ARG V 236 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ARG V 241 " --> pdb=" O THR V 237 " (cutoff:3.500A) Processing helix chain 'V' and resid 245 through 259 removed outlier: 4.437A pdb=" N THR V 249 " --> pdb=" O ASP V 245 " (cutoff:3.500A) Processing helix chain 'V' and resid 264 through 273 removed outlier: 3.763A pdb=" N GLU V 268 " --> pdb=" O TYR V 264 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 300 removed outlier: 6.531A pdb=" N TRP V 285 " --> pdb=" O ASN V 281 " (cutoff:3.500A) Processing helix chain 'V' and resid 302 through 317 removed outlier: 4.198A pdb=" N ARG V 307 " --> pdb=" O SER V 303 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA V 316 " --> pdb=" O ALA V 312 " (cutoff:3.500A) Proline residue: V 317 - end of helix Processing helix chain 'V' and resid 323 through 340 removed outlier: 3.893A pdb=" N LEU V 331 " --> pdb=" O THR V 327 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL V 335 " --> pdb=" O LEU V 331 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU V 336 " --> pdb=" O LEU V 332 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY V 340 " --> pdb=" O GLU V 336 " (cutoff:3.500A) Processing helix chain 'V' and resid 350 through 358 removed outlier: 3.708A pdb=" N LYS V 354 " --> pdb=" O GLN V 350 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ARG V 355 " --> pdb=" O PRO V 351 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N SER V 356 " --> pdb=" O SER V 352 " (cutoff:3.500A) Processing helix chain 'V' and resid 359 through 370 removed outlier: 3.915A pdb=" N GLY V 370 " --> pdb=" O ALA V 366 " (cutoff:3.500A) Processing helix chain 'V' and resid 371 through 381 Processing helix chain 'V' and resid 383 through 390 removed outlier: 4.115A pdb=" N GLN V 387 " --> pdb=" O GLY V 383 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA V 388 " --> pdb=" O GLU V 384 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP V 389 " --> pdb=" O LYS V 385 " (cutoff:3.500A) Processing helix chain 'V' and resid 391 through 414 removed outlier: 4.427A pdb=" N ILE V 395 " --> pdb=" O THR V 391 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE V 396 " --> pdb=" O TYR V 392 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG V 397 " --> pdb=" O THR V 393 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ARG V 399 " --> pdb=" O ILE V 395 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N HIS V 400 " --> pdb=" O ILE V 396 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 427 removed outlier: 5.038A pdb=" N GLN V 424 " --> pdb=" O ALA V 420 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU V 426 " --> pdb=" O ILE V 422 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLN V 427 " --> pdb=" O ALA V 423 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 443 Processing helix chain 'V' and resid 469 through 497 removed outlier: 5.161A pdb=" N GLN V 473 " --> pdb=" O THR V 469 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N HIS V 477 " --> pdb=" O GLN V 473 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLN V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) Proline residue: V 497 - end of helix Processing helix chain 'W' and resid 1 through 19 removed outlier: 4.573A pdb=" N GLY W 5 " --> pdb=" O MET W 1 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N SER W 6 " --> pdb=" O ALA W 2 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL W 14 " --> pdb=" O ASP W 10 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LYS W 15 " --> pdb=" O GLY W 11 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N MET W 16 " --> pdb=" O ARG W 12 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLU W 17 " --> pdb=" O ILE W 13 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL W 18 " --> pdb=" O VAL W 14 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP W 19 " --> pdb=" O LYS W 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 21 through 36 removed outlier: 4.415A pdb=" N ASP W 25 " --> pdb=" O SER W 21 " (cutoff:3.500A) Proline residue: W 29 - end of helix Processing helix chain 'W' and resid 40 through 60 removed outlier: 6.316A pdb=" N ILE W 44 " --> pdb=" O LEU W 40 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLU W 45 " --> pdb=" O GLN W 41 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET W 60 " --> pdb=" O THR W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 87 removed outlier: 5.364A pdb=" N ASN W 86 " --> pdb=" O LEU W 82 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE W 87 " --> pdb=" O LEU W 83 " (cutoff:3.500A) Processing helix chain 'W' and resid 94 through 112 removed outlier: 4.430A pdb=" N LYS W 98 " --> pdb=" O ARG W 94 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN W 99 " --> pdb=" O SER W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 135 removed outlier: 3.781A pdb=" N ARG W 129 " --> pdb=" O ILE W 125 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS W 135 " --> pdb=" O VAL W 131 " (cutoff:3.500A) Processing helix chain 'W' and resid 139 through 156 removed outlier: 4.523A pdb=" N GLN W 155 " --> pdb=" O THR W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 173 removed outlier: 3.849A pdb=" N GLN W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN W 170 " --> pdb=" O LEU W 166 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL W 171 " --> pdb=" O GLN W 167 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLU W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR W 173 " --> pdb=" O LEU W 169 " (cutoff:3.500A) Processing helix chain 'W' and resid 179 through 197 removed outlier: 4.459A pdb=" N VAL W 183 " --> pdb=" O LYS W 179 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLU W 188 " --> pdb=" O GLU W 184 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN W 189 " --> pdb=" O PHE W 185 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET W 190 " --> pdb=" O ILE W 186 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA W 195 " --> pdb=" O ARG W 191 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS W 197 " --> pdb=" O CYS W 193 " (cutoff:3.500A) Processing helix chain 'W' and resid 198 through 212 removed outlier: 5.935A pdb=" N THR W 202 " --> pdb=" O ASP W 198 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR W 211 " --> pdb=" O LYS W 207 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS W 212 " --> pdb=" O LYS W 208 " (cutoff:3.500A) Processing helix chain 'W' and resid 221 through 235 removed outlier: 3.607A pdb=" N TYR W 226 " --> pdb=" O LEU W 222 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASN W 228 " --> pdb=" O LEU W 224 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU W 229 " --> pdb=" O LYS W 225 " (cutoff:3.500A) Processing helix chain 'W' and resid 240 through 258 removed outlier: 4.477A pdb=" N CYS W 244 " --> pdb=" O TYR W 240 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS W 245 " --> pdb=" O LEU W 241 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TYR W 251 " --> pdb=" O TYR W 247 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP W 252 " --> pdb=" O ARG W 248 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N THR W 253 " --> pdb=" O ALA W 249 " (cutoff:3.500A) Proline residue: W 254 - end of helix removed outlier: 3.922A pdb=" N GLN W 257 " --> pdb=" O THR W 253 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA W 258 " --> pdb=" O PRO W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 261 through 278 removed outlier: 4.764A pdb=" N TYR W 273 " --> pdb=" O SER W 269 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL W 274 " --> pdb=" O VAL W 270 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ILE W 275 " --> pdb=" O VAL W 271 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU W 276 " --> pdb=" O LEU W 272 " (cutoff:3.500A) Proline residue: W 278 - end of helix Processing helix chain 'W' and resid 280 through 293 removed outlier: 4.498A pdb=" N HIS W 288 " --> pdb=" O SER W 284 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER W 291 " --> pdb=" O VAL W 287 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLY W 292 " --> pdb=" O HIS W 288 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ASP W 293 " --> pdb=" O ARG W 289 " (cutoff:3.500A) Processing helix chain 'W' and resid 294 through 300 removed outlier: 4.772A pdb=" N GLU W 298 " --> pdb=" O LYS W 294 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE W 299 " --> pdb=" O LYS W 295 " (cutoff:3.500A) Proline residue: W 300 - end of helix No H-bonds generated for 'chain 'W' and resid 294 through 300' Processing helix chain 'W' and resid 301 through 310 removed outlier: 3.893A pdb=" N PHE W 309 " --> pdb=" O LEU W 305 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR W 310 " --> pdb=" O LEU W 306 " (cutoff:3.500A) Processing helix chain 'W' and resid 316 through 330 removed outlier: 3.878A pdb=" N LEU W 320 " --> pdb=" O ARG W 316 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU W 327 " --> pdb=" O ASP W 323 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU W 328 " --> pdb=" O TYR W 324 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG W 329 " --> pdb=" O GLY W 325 " (cutoff:3.500A) Processing helix chain 'W' and resid 334 through 341 Processing helix chain 'W' and resid 345 through 370 removed outlier: 4.101A pdb=" N LYS W 368 " --> pdb=" O ARG W 364 " (cutoff:3.500A) Processing helix chain 'W' and resid 374 through 383 removed outlier: 3.560A pdb=" N MET W 378 " --> pdb=" O THR W 374 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASP W 383 " --> pdb=" O ALA W 379 " (cutoff:3.500A) Processing helix chain 'W' and resid 387 through 400 removed outlier: 4.680A pdb=" N ALA W 391 " --> pdb=" O ASP W 387 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU W 396 " --> pdb=" O PHE W 392 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS W 400 " --> pdb=" O LEU W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 423 through 431 removed outlier: 4.296A pdb=" N ASP W 427 " --> pdb=" O ASN W 423 " (cutoff:3.500A) Processing helix chain 'W' and resid 433 through 455 removed outlier: 3.622A pdb=" N THR W 442 " --> pdb=" O LEU W 438 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR W 443 " --> pdb=" O VAL W 439 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA W 447 " --> pdb=" O THR W 443 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU W 455 " --> pdb=" O MET W 451 " (cutoff:3.500A) Processing helix chain 'X' and resid 43 through 60 removed outlier: 3.675A pdb=" N GLN X 48 " --> pdb=" O GLN X 44 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER X 49 " --> pdb=" O VAL X 45 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU X 51 " --> pdb=" O GLU X 47 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 81 removed outlier: 4.001A pdb=" N ARG X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Proline residue: X 75 - end of helix removed outlier: 3.837A pdb=" N ASN X 78 " --> pdb=" O ARG X 74 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N SER X 81 " --> pdb=" O LEU X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 101 removed outlier: 5.483A pdb=" N ALA X 86 " --> pdb=" O LYS X 82 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ARG X 87 " --> pdb=" O ALA X 83 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU X 95 " --> pdb=" O SER X 91 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N MET X 99 " --> pdb=" O LEU X 95 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU X 100 " --> pdb=" O PHE X 96 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA X 101 " --> pdb=" O LEU X 97 " (cutoff:3.500A) Processing helix chain 'X' and resid 102 through 121 removed outlier: 4.320A pdb=" N VAL X 107 " --> pdb=" O THR X 103 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU X 108 " --> pdb=" O GLY X 104 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 141 removed outlier: 3.699A pdb=" N GLN X 127 " --> pdb=" O THR X 123 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA X 128 " --> pdb=" O PHE X 124 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU X 129 " --> pdb=" O LEU X 125 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR X 140 " --> pdb=" O LEU X 136 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 157 removed outlier: 5.068A pdb=" N LEU X 147 " --> pdb=" O TYR X 143 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN X 152 " --> pdb=" O HIS X 148 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG X 155 " --> pdb=" O SER X 151 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU X 156 " --> pdb=" O GLN X 152 " (cutoff:3.500A) Processing helix chain 'X' and resid 162 through 181 removed outlier: 3.921A pdb=" N LEU X 166 " --> pdb=" O ASP X 162 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL X 167 " --> pdb=" O LYS X 163 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL X 169 " --> pdb=" O LEU X 165 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU X 172 " --> pdb=" O GLU X 168 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 199 removed outlier: 3.861A pdb=" N ASN X 198 " --> pdb=" O ARG X 194 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ALA X 199 " --> pdb=" O THR X 195 " (cutoff:3.500A) Processing helix chain 'X' and resid 205 through 222 removed outlier: 4.428A pdb=" N THR X 209 " --> pdb=" O LYS X 205 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU X 222 " --> pdb=" O HIS X 218 " (cutoff:3.500A) Processing helix chain 'X' and resid 224 through 240 removed outlier: 4.487A pdb=" N ALA X 228 " --> pdb=" O ASP X 224 " (cutoff:3.500A) Processing helix chain 'X' and resid 244 through 262 removed outlier: 4.323A pdb=" N THR X 249 " --> pdb=" O PRO X 245 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU X 251 " --> pdb=" O ALA X 247 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS X 252 " --> pdb=" O ILE X 248 " (cutoff:3.500A) Processing helix chain 'X' and resid 263 through 273 Processing helix chain 'X' and resid 274 through 280 Processing helix chain 'X' and resid 281 through 297 removed outlier: 3.772A pdb=" N GLU X 285 " --> pdb=" O GLY X 281 " (cutoff:3.500A) Processing helix chain 'X' and resid 298 through 310 removed outlier: 3.880A pdb=" N TYR X 309 " --> pdb=" O ALA X 305 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG X 310 " --> pdb=" O LEU X 306 " (cutoff:3.500A) Processing helix chain 'X' and resid 311 through 317 removed outlier: 4.726A pdb=" N ASP X 315 " --> pdb=" O ALA X 311 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASP X 316 " --> pdb=" O GLU X 312 " (cutoff:3.500A) Proline residue: X 317 - end of helix No H-bonds generated for 'chain 'X' and resid 311 through 317' Processing helix chain 'X' and resid 318 through 342 removed outlier: 4.419A pdb=" N HIS X 322 " --> pdb=" O ILE X 318 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLU X 332 " --> pdb=" O ASP X 328 " (cutoff:3.500A) Proline residue: X 341 - end of helix Processing helix chain 'X' and resid 362 through 371 removed outlier: 7.051A pdb=" N SER X 366 " --> pdb=" O GLU X 362 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN X 367 " --> pdb=" O ARG X 363 " (cutoff:3.500A) Processing helix chain 'X' and resid 393 through 422 removed outlier: 4.159A pdb=" N TYR X 397 " --> pdb=" O VAL X 393 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN X 405 " --> pdb=" O LEU X 401 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER X 408 " --> pdb=" O ILE X 404 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR X 415 " --> pdb=" O VAL X 411 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN X 416 " --> pdb=" O ASP X 412 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU X 421 " --> pdb=" O LYS X 417 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR X 422 " --> pdb=" O ALA X 418 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 29 removed outlier: 3.680A pdb=" N LEU Y 28 " --> pdb=" O PHE Y 24 " (cutoff:3.500A) Proline residue: Y 29 - end of helix Processing helix chain 'Y' and resid 34 through 47 removed outlier: 4.753A pdb=" N GLU Y 40 " --> pdb=" O ALA Y 36 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG Y 46 " --> pdb=" O MET Y 42 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP Y 47 " --> pdb=" O ALA Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 49 through 60 removed outlier: 4.675A pdb=" N TYR Y 53 " --> pdb=" O ASN Y 49 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA Y 56 " --> pdb=" O PRO Y 52 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N CYS Y 58 " --> pdb=" O TYR Y 54 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS Y 59 " --> pdb=" O GLU Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 68 through 95 removed outlier: 4.053A pdb=" N MET Y 73 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLU Y 89 " --> pdb=" O ASP Y 85 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU Y 92 " --> pdb=" O LEU Y 88 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS Y 93 " --> pdb=" O GLU Y 89 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN Y 94 " --> pdb=" O ASP Y 90 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LEU Y 95 " --> pdb=" O ALA Y 91 " (cutoff:3.500A) Processing helix chain 'Y' and resid 98 through 115 removed outlier: 4.306A pdb=" N LYS Y 107 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) Processing helix chain 'Y' and resid 116 through 130 removed outlier: 4.491A pdb=" N ALA Y 120 " --> pdb=" O ASP Y 116 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG Y 125 " --> pdb=" O LEU Y 121 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LYS Y 126 " --> pdb=" O THR Y 122 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASP Y 129 " --> pdb=" O ARG Y 125 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS Y 130 " --> pdb=" O LYS Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 152 removed outlier: 4.187A pdb=" N ILE Y 140 " --> pdb=" O HIS Y 136 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE Y 147 " --> pdb=" O TYR Y 143 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET Y 152 " --> pdb=" O GLY Y 148 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 168 removed outlier: 5.491A pdb=" N ILE Y 157 " --> pdb=" O ASP Y 153 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N THR Y 161 " --> pdb=" O ILE Y 157 " (cutoff:3.500A) Processing helix chain 'Y' and resid 173 through 192 removed outlier: 5.615A pdb=" N ARG Y 177 " --> pdb=" O ASP Y 173 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU Y 180 " --> pdb=" O ARG Y 176 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS Y 181 " --> pdb=" O ARG Y 177 " (cutoff:3.500A) Processing helix chain 'Y' and resid 195 through 202 Processing helix chain 'Y' and resid 215 through 231 removed outlier: 5.192A pdb=" N ILE Y 229 " --> pdb=" O TYR Y 225 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU Y 231 " --> pdb=" O SER Y 227 " (cutoff:3.500A) Processing helix chain 'Y' and resid 232 through 240 Processing helix chain 'Y' and resid 243 through 254 removed outlier: 3.998A pdb=" N GLU Y 248 " --> pdb=" O ALA Y 244 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL Y 249 " --> pdb=" O GLU Y 245 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU Y 253 " --> pdb=" O VAL Y 249 " (cutoff:3.500A) Proline residue: Y 254 - end of helix Processing helix chain 'Y' and resid 255 through 266 Processing helix chain 'Y' and resid 268 through 286 removed outlier: 4.264A pdb=" N PHE Y 272 " --> pdb=" O TYR Y 268 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLN Y 273 " --> pdb=" O SER Y 269 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS Y 284 " --> pdb=" O GLN Y 280 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP Y 285 " --> pdb=" O GLU Y 281 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N TRP Y 286 " --> pdb=" O MET Y 282 " (cutoff:3.500A) Processing helix chain 'Y' and resid 291 through 312 removed outlier: 4.265A pdb=" N VAL Y 296 " --> pdb=" O TYR Y 292 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG Y 297 " --> pdb=" O ARG Y 293 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN Y 306 " --> pdb=" O HIS Y 302 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N TYR Y 311 " --> pdb=" O LEU Y 307 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ARG Y 312 " --> pdb=" O LEU Y 308 " (cutoff:3.500A) Processing helix chain 'Y' and resid 315 through 324 Processing helix chain 'Y' and resid 327 through 341 Processing helix chain 'Y' and resid 362 through 389 removed outlier: 5.503A pdb=" N TYR Y 366 " --> pdb=" O LYS Y 362 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR Y 369 " --> pdb=" O GLN Y 365 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE Y 370 " --> pdb=" O TYR Y 366 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU Y 375 " --> pdb=" O LYS Y 371 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU Y 377 " --> pdb=" O GLY Y 373 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE Y 387 " --> pdb=" O LEU Y 383 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASN Y 388 " --> pdb=" O SER Y 384 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N MET Y 389 " --> pdb=" O ARG Y 385 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 30 removed outlier: 4.404A pdb=" N LEU Z 16 " --> pdb=" O HIS Z 12 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N HIS Z 22 " --> pdb=" O SER Z 18 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS Z 28 " --> pdb=" O ASN Z 24 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL Z 29 " --> pdb=" O ARG Z 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 86 removed outlier: 4.391A pdb=" N MET Z 78 " --> pdb=" O TYR Z 74 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR Z 79 " --> pdb=" O LEU Z 75 " (cutoff:3.500A) Processing helix chain 'Z' and resid 102 through 116 removed outlier: 4.648A pdb=" N ILE Z 106 " --> pdb=" O HIS Z 102 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA Z 107 " --> pdb=" O LYS Z 103 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG Z 114 " --> pdb=" O GLU Z 110 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR Z 115 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) Processing helix chain 'Z' and resid 170 through 177 removed outlier: 4.065A pdb=" N HIS Z 174 " --> pdb=" O VAL Z 170 " (cutoff:3.500A) Processing helix chain 'Z' and resid 186 through 217 removed outlier: 4.824A pdb=" N ARG Z 190 " --> pdb=" O THR Z 186 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR Z 192 " --> pdb=" O SER Z 188 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER Z 203 " --> pdb=" O LYS Z 199 " (cutoff:3.500A) Processing helix chain 'Z' and resid 225 through 236 removed outlier: 3.654A pdb=" N VAL Z 233 " --> pdb=" O GLN Z 229 " (cutoff:3.500A) Processing helix chain 'Z' and resid 247 through 287 removed outlier: 4.509A pdb=" N LEU Z 251 " --> pdb=" O LYS Z 247 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL Z 258 " --> pdb=" O ASN Z 254 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL Z 259 " --> pdb=" O ASP Z 255 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE Z 276 " --> pdb=" O LEU Z 272 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN Z 277 " --> pdb=" O HIS Z 273 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 12 Processing helix chain 'a' and resid 17 through 32 removed outlier: 4.975A pdb=" N VAL a 21 " --> pdb=" O GLY a 17 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TRP a 22 " --> pdb=" O GLN a 18 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG a 24 " --> pdb=" O ALA a 20 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N THR a 30 " --> pdb=" O GLU a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 47 removed outlier: 4.294A pdb=" N LEU a 37 " --> pdb=" O LEU a 33 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU a 42 " --> pdb=" O THR a 38 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 66 removed outlier: 4.558A pdb=" N GLY a 55 " --> pdb=" O ALA a 51 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU a 56 " --> pdb=" O GLN a 52 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TYR a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 71 through 84 removed outlier: 4.518A pdb=" N SER a 75 " --> pdb=" O VAL a 71 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU a 76 " --> pdb=" O ASN a 72 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU a 81 " --> pdb=" O VAL a 77 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N HIS a 82 " --> pdb=" O GLU a 78 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL a 84 " --> pdb=" O ILE a 80 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 105 removed outlier: 4.402A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU a 102 " --> pdb=" O GLU a 98 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LYS a 103 " --> pdb=" O LYS a 99 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL a 104 " --> pdb=" O THR a 100 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LYS a 105 " --> pdb=" O ARG a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 109 through 126 removed outlier: 4.615A pdb=" N LEU a 113 " --> pdb=" O GLU a 109 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU a 123 " --> pdb=" O GLY a 119 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ASN a 124 " --> pdb=" O ALA a 120 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ILE a 125 " --> pdb=" O LEU a 121 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY a 126 " --> pdb=" O LYS a 122 " (cutoff:3.500A) Processing helix chain 'a' and resid 129 through 143 removed outlier: 5.003A pdb=" N GLU a 133 " --> pdb=" O GLN a 129 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR a 134 " --> pdb=" O VAL a 130 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU a 139 " --> pdb=" O ILE a 135 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN a 143 " --> pdb=" O GLU a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 150 through 167 removed outlier: 4.327A pdb=" N ARG a 154 " --> pdb=" O SER a 150 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR a 165 " --> pdb=" O LYS a 161 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE a 166 " --> pdb=" O TYR a 162 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLY a 167 " --> pdb=" O TYR a 163 " (cutoff:3.500A) Processing helix chain 'a' and resid 170 through 182 removed outlier: 4.195A pdb=" N LYS a 174 " --> pdb=" O ALA a 170 " (cutoff:3.500A) Processing helix chain 'a' and resid 191 through 207 removed outlier: 4.786A pdb=" N GLU a 195 " --> pdb=" O SER a 191 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG a 196 " --> pdb=" O GLU a 192 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU a 206 " --> pdb=" O LEU a 202 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLY a 207 " --> pdb=" O ALA a 203 " (cutoff:3.500A) Processing helix chain 'a' and resid 214 through 220 removed outlier: 4.285A pdb=" N HIS a 219 " --> pdb=" O GLU a 215 " (cutoff:3.500A) Proline residue: a 220 - end of helix Processing helix chain 'a' and resid 221 through 230 removed outlier: 3.865A pdb=" N LEU a 225 " --> pdb=" O VAL a 221 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR a 228 " --> pdb=" O SER a 224 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP a 229 " --> pdb=" O LEU a 225 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ARG a 230 " --> pdb=" O ARG a 226 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 241 removed outlier: 4.587A pdb=" N ASN a 241 " --> pdb=" O LEU a 237 " (cutoff:3.500A) Processing helix chain 'a' and resid 246 through 258 removed outlier: 3.909A pdb=" N THR a 250 " --> pdb=" O GLU a 246 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU a 251 " --> pdb=" O ARG a 247 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLN a 258 " --> pdb=" O ALA a 254 " (cutoff:3.500A) Processing helix chain 'a' and resid 260 through 283 removed outlier: 4.982A pdb=" N ASN a 264 " --> pdb=" O ASP a 260 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU a 265 " --> pdb=" O LEU a 261 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ALA a 266 " --> pdb=" O ALA a 262 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLN a 267 " --> pdb=" O ALA a 263 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU a 268 " --> pdb=" O ASN a 264 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU a 269 " --> pdb=" O GLU a 265 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU a 277 " --> pdb=" O GLN a 273 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET a 278 " --> pdb=" O LEU a 274 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 301 removed outlier: 4.747A pdb=" N LYS a 301 " --> pdb=" O ALA a 297 " (cutoff:3.500A) Processing helix chain 'a' and resid 306 through 318 removed outlier: 3.705A pdb=" N LEU a 310 " --> pdb=" O GLU a 306 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY a 318 " --> pdb=" O ALA a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 372 removed outlier: 4.723A pdb=" N PHE a 355 " --> pdb=" O ASP a 351 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 44 Processing helix chain 'b' and resid 67 through 76 removed outlier: 3.991A pdb=" N ILE b 71 " --> pdb=" O ASP b 67 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N HIS b 76 " --> pdb=" O LEU b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 100 removed outlier: 4.177A pdb=" N GLY b 89 " --> pdb=" O THR b 85 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE b 90 " --> pdb=" O PHE b 86 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA b 93 " --> pdb=" O GLY b 89 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG b 100 " --> pdb=" O ALA b 96 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 135 removed outlier: 3.564A pdb=" N LEU b 124 " --> pdb=" O ASN b 120 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU b 127 " --> pdb=" O ASP b 123 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 162 removed outlier: 3.504A pdb=" N ASN b 161 " --> pdb=" O VAL b 157 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLY b 162 " --> pdb=" O ASN b 158 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 190 removed outlier: 4.293A pdb=" N LEU b 183 " --> pdb=" O LEU b 179 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE b 184 " --> pdb=" O ALA b 180 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N SER b 186 " --> pdb=" O ALA b 182 " (cutoff:3.500A) Proline residue: b 187 - end of helix removed outlier: 3.778A pdb=" N ALA b 190 " --> pdb=" O SER b 186 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 18 removed outlier: 5.333A pdb=" N ARG b 17 " --> pdb=" O GLU b 14 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASN b 18 " --> pdb=" O TYR b 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 34 through 49 removed outlier: 4.267A pdb=" N VAL c 49 " --> pdb=" O GLY c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 83 through 101 removed outlier: 4.340A pdb=" N VAL c 87 " --> pdb=" O SER c 83 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASP c 88 " --> pdb=" O VAL c 84 " (cutoff:3.500A) Proline residue: c 89 - end of helix removed outlier: 4.465A pdb=" N GLN c 101 " --> pdb=" O ASP c 97 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 137 removed outlier: 3.968A pdb=" N ILE c 127 " --> pdb=" O SER c 123 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLN c 131 " --> pdb=" O ILE c 127 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER c 132 " --> pdb=" O ASN c 128 " (cutoff:3.500A) Processing helix chain 'c' and resid 177 through 187 removed outlier: 4.165A pdb=" N LEU c 181 " --> pdb=" O THR c 177 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS c 186 " --> pdb=" O GLY c 182 " (cutoff:3.500A) Proline residue: c 187 - end of helix Processing helix chain 'c' and resid 190 through 197 removed outlier: 6.490A pdb=" N HIS c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) Processing helix chain 'c' and resid 210 through 224 removed outlier: 3.672A pdb=" N MET c 216 " --> pdb=" O LEU c 212 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER c 224 " --> pdb=" O LEU c 220 " (cutoff:3.500A) Processing helix chain 'c' and resid 229 through 234 removed outlier: 5.933A pdb=" N ASP c 233 " --> pdb=" O LEU c 229 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TYR c 234 " --> pdb=" O THR c 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 229 through 234' Processing helix chain 'c' and resid 246 through 271 removed outlier: 4.954A pdb=" N GLU c 260 " --> pdb=" O ASN c 256 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU c 262 " --> pdb=" O ALA c 258 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR c 266 " --> pdb=" O GLU c 262 " (cutoff:3.500A) Proline residue: c 267 - end of helix removed outlier: 4.248A pdb=" N LEU c 270 " --> pdb=" O THR c 266 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA c 271 " --> pdb=" O PRO c 267 " (cutoff:3.500A) Processing helix chain 'c' and resid 287 through 308 removed outlier: 4.545A pdb=" N LEU c 291 " --> pdb=" O HIS c 287 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU c 304 " --> pdb=" O LEU c 300 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP c 305 " --> pdb=" O ALA c 301 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N THR c 306 " --> pdb=" O ALA c 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 34 removed outlier: 4.263A pdb=" N LEU d 33 " --> pdb=" O VAL d 29 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN d 34 " --> pdb=" O LEU d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 66 removed outlier: 4.376A pdb=" N LYS d 45 " --> pdb=" O THR d 41 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU d 48 " --> pdb=" O THR d 44 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS d 66 " --> pdb=" O SER d 62 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 84 removed outlier: 3.576A pdb=" N ASP d 84 " --> pdb=" O CYS d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 110 removed outlier: 4.680A pdb=" N HIS d 96 " --> pdb=" O SER d 92 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLN d 97 " --> pdb=" O ALA d 93 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN d 110 " --> pdb=" O LEU d 106 " (cutoff:3.500A) Processing helix chain 'd' and resid 111 through 123 removed outlier: 3.648A pdb=" N LEU d 122 " --> pdb=" O GLU d 118 " (cutoff:3.500A) Proline residue: d 123 - end of helix Processing helix chain 'd' and resid 130 through 146 Proline residue: d 136 - end of helix removed outlier: 3.505A pdb=" N GLY d 146 " --> pdb=" O TYR d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 159 removed outlier: 4.589A pdb=" N PHE d 152 " --> pdb=" O TYR d 148 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASN d 157 " --> pdb=" O LEU d 153 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE d 158 " --> pdb=" O ALA d 154 " (cutoff:3.500A) Proline residue: d 159 - end of helix Processing helix chain 'd' and resid 163 through 174 removed outlier: 3.660A pdb=" N ILE d 169 " --> pdb=" O PHE d 165 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 182 Processing helix chain 'd' and resid 203 through 212 Processing helix chain 'd' and resid 236 through 257 removed outlier: 4.442A pdb=" N THR d 240 " --> pdb=" O THR d 236 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU d 241 " --> pdb=" O ILE d 237 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 53 removed outlier: 4.548A pdb=" N ASP e 46 " --> pdb=" O ASN e 42 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASN e 47 " --> pdb=" O TRP e 43 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL e 48 " --> pdb=" O ASP e 44 " (cutoff:3.500A) Processing helix chain 'e' and resid 58 through 70 removed outlier: 6.230A pdb=" N LYS e 62 " --> pdb=" O ALA e 58 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N HIS e 63 " --> pdb=" O GLU e 59 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TYR e 65 " --> pdb=" O GLU e 61 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N MET e 67 " --> pdb=" O HIS e 63 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLU e 68 " --> pdb=" O GLY e 64 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR e 69 " --> pdb=" O TYR e 65 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER e 70 " --> pdb=" O LYS e 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 36 removed outlier: 4.354A pdb=" N GLU g 26 " --> pdb=" O LEU g 22 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LYS g 30 " --> pdb=" O GLU g 26 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE g 32 " --> pdb=" O ALA g 28 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASN g 33 " --> pdb=" O PHE g 29 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN g 34 " --> pdb=" O LYS g 30 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLY g 35 " --> pdb=" O ALA g 31 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY g 36 " --> pdb=" O ILE g 32 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 67 removed outlier: 5.543A pdb=" N VAL g 66 " --> pdb=" O ASP g 62 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR g 67 " --> pdb=" O SER g 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 62 through 67' Processing helix chain 'g' and resid 83 through 105 Processing helix chain 'g' and resid 110 through 129 removed outlier: 3.906A pdb=" N ASN g 128 " --> pdb=" O VAL g 124 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ALA g 129 " --> pdb=" O TYR g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 185 removed outlier: 3.996A pdb=" N LYS g 184 " --> pdb=" O GLU g 180 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LYS g 185 " --> pdb=" O LYS g 181 " (cutoff:3.500A) Processing helix chain 'g' and resid 190 through 207 removed outlier: 5.481A pdb=" N THR g 194 " --> pdb=" O THR g 190 " (cutoff:3.500A) Processing helix chain 'g' and resid 231 through 244 removed outlier: 5.468A pdb=" N GLU g 244 " --> pdb=" O VAL g 240 " (cutoff:3.500A) Processing helix chain 'h' and resid 19 through 33 removed outlier: 3.914A pdb=" N GLY h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ALA h 33 " --> pdb=" O VAL h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 102 removed outlier: 4.239A pdb=" N VAL h 85 " --> pdb=" O PRO h 81 " (cutoff:3.500A) Processing helix chain 'h' and resid 106 through 124 Processing helix chain 'h' and resid 166 through 178 removed outlier: 3.504A pdb=" N LYS h 176 " --> pdb=" O THR h 172 " (cutoff:3.500A) Processing helix chain 'h' and resid 183 through 199 removed outlier: 3.860A pdb=" N SER h 198 " --> pdb=" O THR h 194 " (cutoff:3.500A) Processing helix chain 'h' and resid 204 through 209 removed outlier: 4.177A pdb=" N ILE h 208 " --> pdb=" O THR h 204 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLU h 209 " --> pdb=" O GLU h 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 204 through 209' Processing helix chain 'h' and resid 222 through 231 removed outlier: 3.500A pdb=" N ALA h 231 " --> pdb=" O LYS h 227 " (cutoff:3.500A) Processing helix chain 'i' and resid 18 through 31 removed outlier: 4.282A pdb=" N GLU i 22 " --> pdb=" O LEU i 18 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N HIS i 30 " --> pdb=" O GLU i 26 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ALA i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 102 removed outlier: 3.853A pdb=" N LEU i 86 " --> pdb=" O ASP i 82 " (cutoff:3.500A) Processing helix chain 'i' and resid 106 through 124 removed outlier: 5.966A pdb=" N LEU i 110 " --> pdb=" O PRO i 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR i 121 " --> pdb=" O ILE i 117 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE i 124 " --> pdb=" O ALA i 120 " (cutoff:3.500A) Processing helix chain 'i' and resid 166 through 179 removed outlier: 5.084A pdb=" N ALA i 170 " --> pdb=" O ASN i 166 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA i 171 " --> pdb=" O ASN i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 185 through 201 Processing helix chain 'i' and resid 207 through 212 removed outlier: 4.137A pdb=" N VAL i 211 " --> pdb=" O SER i 207 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLU i 212 " --> pdb=" O ALA i 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 207 through 212' Processing helix chain 'i' and resid 229 through 250 removed outlier: 4.238A pdb=" N VAL i 233 " --> pdb=" O LYS i 229 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU i 250 " --> pdb=" O LYS i 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 71 removed outlier: 3.822A pdb=" N GLU A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 removed outlier: 5.484A pdb=" N LEU A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLN A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N SER A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 130 through 135 removed outlier: 4.360A pdb=" N ILE A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLU A 135 " --> pdb=" O PRO A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 130 through 135' Processing helix chain 'A' and resid 158 through 165 removed outlier: 3.710A pdb=" N THR A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N MET A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 158 through 165' Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.066A pdb=" N VAL A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLY A 178 " --> pdb=" O TYR A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 178' Processing helix chain 'A' and resid 180 through 197 removed outlier: 3.729A pdb=" N GLU A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 198 through 205 removed outlier: 4.612A pdb=" N VAL A 202 " --> pdb=" O PRO A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 241 through 247 removed outlier: 4.347A pdb=" N LEU A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLN A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 247' Processing helix chain 'A' and resid 251 through 268 removed outlier: 4.666A pdb=" N ARG A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LYS A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 3.997A pdb=" N ILE A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 307 Processing helix chain 'A' and resid 328 through 333 removed outlier: 4.085A pdb=" N ARG A 333 " --> pdb=" O PRO A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 363 removed outlier: 5.312A pdb=" N ARG A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N SER A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N MET A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N SER A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 5.276A pdb=" N LEU A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 381 through 400 removed outlier: 3.882A pdb=" N ARG A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'B' and resid 65 through 84 removed outlier: 3.842A pdb=" N LYS B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 4.936A pdb=" N SER B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLY B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 176 removed outlier: 4.013A pdb=" N VAL B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N MET B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 175 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 169 through 176' Processing helix chain 'B' and resid 190 through 206 removed outlier: 4.633A pdb=" N GLN B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 4.260A 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 208 through 215 removed outlier: 4.268A pdb=" N GLU B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 removed outlier: 4.487A pdb=" N THR B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 278 removed outlier: 4.337A pdb=" N LEU B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.748A pdb=" N ILE B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' Processing helix chain 'B' and resid 357 through 370 removed outlier: 4.650A pdb=" N LYS B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 removed outlier: 4.124A pdb=" N LEU B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASP B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 410 removed outlier: 3.817A pdb=" N GLY B 403 " --> pdb=" O CYS B 399 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU B 409 " --> pdb=" O MET B 405 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 428 removed outlier: 3.909A pdb=" N PHE B 419 " --> pdb=" O THR B 415 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 removed outlier: 8.213A pdb=" N TYR B 439 " --> pdb=" O PRO B 435 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N LEU B 440 " --> pdb=" O GLU B 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 435 through 440' Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.515A pdb=" N LEU B 143 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 144 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLU B 145 " --> pdb=" O ASP B 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 140 through 145' Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.610A pdb=" N GLU B 254 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU B 255 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE B 256 " --> pdb=" O SER B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 256' Processing helix chain 'C' and resid 24 through 68 removed outlier: 5.401A pdb=" N ILE C 28 " --> pdb=" O TYR C 24 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN C 40 " --> pdb=" O ASN C 36 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN C 41 " --> pdb=" O ASP C 37 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS C 55 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLN C 64 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 removed outlier: 4.835A pdb=" N THR C 109 " --> pdb=" O ILE C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 removed outlier: 4.436A pdb=" N LEU C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 171 removed outlier: 5.366A 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 179 removed outlier: 3.954A pdb=" N LEU C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 208 removed outlier: 3.530A pdb=" N LEU C 199 " --> pdb=" O GLY C 195 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS C 205 " --> pdb=" O ARG C 201 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR C 207 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 242 removed outlier: 4.776A pdb=" N VAL C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 281 removed outlier: 5.340A pdb=" N MET C 273 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LEU C 274 " --> pdb=" O GLN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 312 removed outlier: 4.148A pdb=" N ASP C 312 " --> pdb=" O PRO C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 337 removed outlier: 4.829A pdb=" N LYS C 335 " --> pdb=" O ILE C 331 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET C 336 " --> pdb=" O HIS C 332 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ASN C 337 " --> pdb=" O SER C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 4.690A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) Proline residue: C 352 - end of helix Processing helix chain 'C' and resid 355 through 374 removed outlier: 6.581A pdb=" N VAL C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS C 363 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU C 373 " --> pdb=" O TYR C 369 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG C 374 " --> pdb=" O ALA C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 391 removed outlier: 3.876A pdb=" N PHE C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N MET C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 81 removed outlier: 4.037A pdb=" N TYR D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN D 48 " --> pdb=" O TYR D 44 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE D 61 " --> pdb=" O GLN D 57 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 removed outlier: 4.967A pdb=" N LEU D 124 " --> pdb=" O ASP D 120 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LYS D 125 " --> pdb=" O ARG D 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 120 through 125' Processing helix chain 'D' and resid 170 through 181 removed outlier: 4.024A pdb=" N GLN D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 removed outlier: 4.542A pdb=" N THR D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 195 Processing helix chain 'D' and resid 211 through 223 Processing helix chain 'D' and resid 241 through 258 removed outlier: 4.010A pdb=" N ARG D 245 " --> pdb=" O GLY D 241 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 299 removed outlier: 4.533A pdb=" N GLY D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N PHE D 299 " --> pdb=" O GLN D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 318 removed outlier: 4.960A pdb=" N LEU D 317 " --> pdb=" O ARG D 313 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ASP D 318 " --> pdb=" O ALA D 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 313 through 318' Processing helix chain 'D' and resid 338 through 352 removed outlier: 6.174A pdb=" N ARG D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR D 349 " --> pdb=" O PHE D 345 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LYS D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 367 Proline residue: D 367 - end of helix Processing helix chain 'D' and resid 371 through 390 removed outlier: 4.197A pdb=" N GLU D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 406 removed outlier: 3.819A pdb=" N GLU D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 53 removed outlier: 4.081A pdb=" N LYS E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER E 52 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL E 53 " --> pdb=" O ALA E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 removed outlier: 5.103A pdb=" N LYS E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 125 removed outlier: 4.182A pdb=" N TYR E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU E 125 " --> pdb=" O ASN E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 156 removed outlier: 4.506A pdb=" N ARG E 143 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU E 151 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Proline residue: E 152 - end of helix Proline residue: E 156 - end of helix Processing helix chain 'E' and resid 180 through 192 removed outlier: 6.122A pdb=" N ALA E 184 " --> pdb=" O LYS E 180 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ARG E 185 " --> pdb=" O THR E 181 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ALA E 186 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL E 187 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ALA E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 205 removed outlier: 4.663A pdb=" N VAL E 204 " --> pdb=" O SER E 200 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASP E 205 " --> pdb=" O SER E 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 200 through 205' Processing helix chain 'E' and resid 208 through 224 removed outlier: 4.971A pdb=" N ALA E 212 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR E 221 " --> pdb=" O GLU E 217 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASP E 224 " --> pdb=" O ASN E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 265 removed outlier: 4.734A pdb=" N GLN E 254 " --> pdb=" O ASP E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 292 removed outlier: 3.579A pdb=" N ARG E 291 " --> pdb=" O PRO E 287 " (cutoff:3.500A) Proline residue: E 292 - end of helix Processing helix chain 'E' and resid 305 through 318 removed outlier: 5.942A pdb=" N ARG E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLY E 318 " --> pdb=" O LYS E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 334 Processing helix chain 'E' and resid 339 through 358 removed outlier: 4.752A pdb=" N ALA E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 381 removed outlier: 3.833A pdb=" N LYS E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU E 380 " --> pdb=" O ASP E 376 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLU E 381 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 84 removed outlier: 4.386A pdb=" N LEU F 48 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET F 55 " --> pdb=" O GLU F 51 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU F 60 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP F 71 " --> pdb=" O GLN F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 146 removed outlier: 3.628A pdb=" N LEU F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LYS F 146 " --> pdb=" O ALA F 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 141 through 146' Processing helix chain 'F' and resid 169 through 177 removed outlier: 3.682A pdb=" N MET F 175 " --> pdb=" O ARG F 171 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL F 177 " --> pdb=" O LYS F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 removed outlier: 3.662A pdb=" N ILE F 188 " --> pdb=" O GLN F 184 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLY F 189 " --> pdb=" O TYR F 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 184 through 189' Processing helix chain 'F' and resid 191 through 208 removed outlier: 4.757A 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 209 through 216 removed outlier: 3.904A pdb=" N LEU F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 244 removed outlier: 4.933A pdb=" N LEU F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA F 237 " --> pdb=" O LYS F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 258 removed outlier: 3.984A pdb=" N LEU F 256 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLN F 258 " --> pdb=" O PRO F 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 252 through 258' Processing helix chain 'F' and resid 262 through 279 removed outlier: 4.039A pdb=" N LYS F 266 " --> pdb=" O GLY F 262 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA F 279 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 293 removed outlier: 3.885A pdb=" N ILE F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR F 293 " --> pdb=" O ASP F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 318 removed outlier: 4.899A pdb=" N GLN F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 344 removed outlier: 4.301A pdb=" N LEU F 343 " --> pdb=" O ASP F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 374 removed outlier: 6.026A pdb=" N ARG F 362 " --> pdb=" O ASN F 358 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA F 363 " --> pdb=" O GLU F 359 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS F 372 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N MET F 373 " --> pdb=" O HIS F 369 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASN F 374 " --> pdb=" O SER F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 392 through 411 removed outlier: 3.877A pdb=" N ARG F 410 " --> pdb=" O ILE F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 429 removed outlier: 3.561A pdb=" N TYR F 420 " --> pdb=" O THR F 416 " (cutoff:3.500A) Processing helix chain 'f' and resid 19 through 34 removed outlier: 3.545A pdb=" N GLY f 23 " --> pdb=" O ALA f 19 " (cutoff:3.500A) Proline residue: f 28 - end of helix Processing helix chain 'f' and resid 44 through 52 removed outlier: 5.188A pdb=" N LYS f 50 " --> pdb=" O SER f 46 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLN f 51 " --> pdb=" O GLU f 47 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU f 52 " --> pdb=" O GLU f 48 " (cutoff:3.500A) Processing helix chain 'f' and resid 71 through 87 Processing helix chain 'f' and resid 89 through 100 Proline residue: f 93 - end of helix removed outlier: 4.540A pdb=" N LEU f 96 " --> pdb=" O VAL f 92 " (cutoff:3.500A) Processing helix chain 'f' and resid 119 through 126 Processing helix chain 'f' and resid 128 through 145 Processing helix chain 'f' and resid 163 through 181 removed outlier: 3.838A pdb=" N ALA f 167 " --> pdb=" O ALA f 163 " (cutoff:3.500A) Processing helix chain 'f' and resid 183 through 193 removed outlier: 4.814A pdb=" N LEU f 187 " --> pdb=" O PRO f 183 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL f 188 " --> pdb=" O LEU f 184 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL f 192 " --> pdb=" O VAL f 188 " (cutoff:3.500A) Proline residue: f 193 - end of helix Processing helix chain 'f' and resid 207 through 217 Processing helix chain 'f' and resid 220 through 225 removed outlier: 4.711A pdb=" N ASN f 224 " --> pdb=" O ASP f 220 " (cutoff:3.500A) Processing helix chain 'f' and resid 227 through 239 Processing helix chain 'f' and resid 241 through 260 removed outlier: 4.339A pdb=" N ASN f 245 " --> pdb=" O PRO f 241 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER f 246 " --> pdb=" O GLU f 242 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA f 247 " --> pdb=" O PRO f 243 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER f 260 " --> pdb=" O PHE f 256 " (cutoff:3.500A) Processing helix chain 'f' and resid 262 through 273 Processing helix chain 'f' and resid 274 through 289 removed outlier: 4.176A pdb=" N VAL f 278 " --> pdb=" O ASP f 274 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU f 279 " --> pdb=" O MET f 275 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL f 289 " --> pdb=" O CYS f 285 " (cutoff:3.500A) Processing helix chain 'f' and resid 297 through 309 Processing helix chain 'f' and resid 310 through 325 removed outlier: 4.248A pdb=" N TYR f 314 " --> pdb=" O ASP f 310 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU f 315 " --> pdb=" O VAL f 311 " (cutoff:3.500A) Processing helix chain 'f' and resid 328 through 334 Processing helix chain 'f' and resid 336 through 351 removed outlier: 6.054A pdb=" N MET f 340 " --> pdb=" O GLU f 336 " (cutoff:3.500A) Proline residue: f 342 - end of helix Proline residue: f 345 - end of helix removed outlier: 3.710A pdb=" N THR f 351 " --> pdb=" O ASP f 347 " (cutoff:3.500A) Processing helix chain 'f' and resid 355 through 364 Processing helix chain 'f' and resid 367 through 382 removed outlier: 5.524A pdb=" N ASN f 371 " --> pdb=" O SER f 367 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU f 372 " --> pdb=" O ALA f 368 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL f 381 " --> pdb=" O VAL f 377 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ASN f 382 " --> pdb=" O ASN f 378 " (cutoff:3.500A) Processing helix chain 'f' and resid 389 through 394 removed outlier: 3.637A pdb=" N ASP f 393 " --> pdb=" O LYS f 389 " (cutoff:3.500A) Processing helix chain 'f' and resid 396 through 403 removed outlier: 6.740A pdb=" N TYR f 400 " --> pdb=" O ASN f 396 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS f 401 " --> pdb=" O LYS f 397 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN f 402 " --> pdb=" O TRP f 398 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LYS f 403 " --> pdb=" O LEU f 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 396 through 403' Processing helix chain 'f' and resid 404 through 417 removed outlier: 3.685A pdb=" N LEU f 414 " --> pdb=" O ALA f 410 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY f 415 " --> pdb=" O ALA f 411 " (cutoff:3.500A) Processing helix chain 'f' and resid 421 through 433 removed outlier: 3.696A pdb=" N LEU f 426 " --> pdb=" O VAL f 422 " (cutoff:3.500A) removed outlier: 3.577A 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: 4.483A pdb=" N TYR f 432 " --> pdb=" O GLN f 428 " (cutoff:3.500A) Processing helix chain 'f' and resid 437 through 452 removed outlier: 4.212A pdb=" N ASN f 452 " --> pdb=" O CYS f 448 " (cutoff:3.500A) Processing helix chain 'f' and resid 458 through 467 removed outlier: 3.921A pdb=" N ALA f 462 " --> pdb=" O GLU f 458 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU f 465 " --> pdb=" O PRO f 461 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N SER f 467 " --> pdb=" O LEU f 463 " (cutoff:3.500A) Processing helix chain 'f' and resid 472 through 490 removed outlier: 4.281A pdb=" N THR f 476 " --> pdb=" O HIS f 472 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ALA f 490 " --> pdb=" O GLY f 486 " (cutoff:3.500A) Processing helix chain 'f' and resid 494 through 508 removed outlier: 4.468A pdb=" N LEU f 498 " --> pdb=" O ARG f 494 " (cutoff:3.500A) Proline residue: f 503 - end of helix Processing helix chain 'f' and resid 511 through 527 removed outlier: 4.597A pdb=" N ALA f 515 " --> pdb=" O SER f 511 " (cutoff:3.500A) Processing helix chain 'f' and resid 535 through 549 removed outlier: 3.919A pdb=" N THR f 548 " --> pdb=" O GLU f 544 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU f 549 " --> pdb=" O LYS f 545 " (cutoff:3.500A) Processing helix chain 'f' and resid 551 through 568 removed outlier: 4.077A pdb=" N ALA f 555 " --> pdb=" O LYS f 551 " (cutoff:3.500A) Proline residue: f 559 - end of helix removed outlier: 5.232A pdb=" N GLY f 568 " --> pdb=" O LEU f 564 " (cutoff:3.500A) Processing helix chain 'f' and resid 573 through 582 Processing helix chain 'f' and resid 585 through 601 removed outlier: 3.566A pdb=" N SER f 589 " --> pdb=" O GLU f 585 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR f 600 " --> pdb=" O ASP f 596 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA f 601 " --> pdb=" O VAL f 597 " (cutoff:3.500A) Processing helix chain 'f' and resid 605 through 619 removed outlier: 4.155A pdb=" N VAL f 609 " --> pdb=" O ASN f 605 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER f 617 " --> pdb=" O LEU f 613 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU f 618 " --> pdb=" O HIS f 614 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N HIS f 619 " --> pdb=" O ILE f 615 " (cutoff:3.500A) Processing helix chain 'f' and resid 620 through 635 removed outlier: 3.733A pdb=" N GLU f 624 " --> pdb=" O PHE f 620 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS f 625 " --> pdb=" O ASP f 621 " (cutoff:3.500A) removed outlier: 4.970A 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 638 through 643 removed outlier: 4.108A pdb=" N ALA f 642 " --> pdb=" O ASP f 638 " (cutoff:3.500A) Proline residue: f 643 - end of helix No H-bonds generated for 'chain 'f' and resid 638 through 643' Processing helix chain 'f' and resid 645 through 650 removed outlier: 4.985A pdb=" N GLN f 650 " --> pdb=" O MET f 646 " (cutoff:3.500A) Processing helix chain 'f' and resid 651 through 663 removed outlier: 4.259A pdb=" N LEU f 655 " --> pdb=" O GLY f 651 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY f 663 " --> pdb=" O LEU f 659 " (cutoff:3.500A) Processing helix chain 'f' and resid 668 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 683 through 699 Proline residue: f 691 - end of helix removed outlier: 3.792A pdb=" N SER f 698 " --> pdb=" O LEU f 694 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL f 699 " --> pdb=" O ALA f 695 " (cutoff:3.500A) Processing helix chain 'f' and resid 715 through 728 Proline residue: f 719 - end of helix Processing helix chain 'f' and resid 739 through 754 Processing helix chain 'f' and resid 774 through 786 removed outlier: 3.541A pdb=" N LEU f 778 " --> pdb=" O GLY f 774 " (cutoff:3.500A) Proline residue: f 780 - end of helix removed outlier: 5.196A pdb=" N GLN f 786 " --> pdb=" O HIS f 782 " (cutoff:3.500A) Processing helix chain 'f' and resid 790 through 798 removed outlier: 4.017A pdb=" N LEU f 796 " --> pdb=" O ALA f 792 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR f 798 " --> pdb=" O ALA f 794 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 17 removed outlier: 3.680A pdb=" N GLN f 14 " --> pdb=" O VAL f 11 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN f 15 " --> pdb=" O GLN f 12 " (cutoff:3.500A) Proline residue: f 17 - end of helix Processing sheet with id= 1, first strand: chain 'G' and resid 68 through 72 removed outlier: 6.430A pdb=" N HIS G 68 " --> pdb=" O MET G 80 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET G 80 " --> pdb=" O HIS G 68 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY G 77 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N CYS G 137 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.865A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU G 214 " --> pdb=" O LYS G 54 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL G 217 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'H' and resid 65 through 68 removed outlier: 6.800A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER H 133 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU H 134 " --> pdb=" O SER H 149 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY H 138 " --> pdb=" O TYR H 145 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU H 146 " --> pdb=" O TRP H 158 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN H 148 " --> pdb=" O PHE H 156 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'H' and resid 160 through 164 removed outlier: 3.600A pdb=" N GLU H 49 " --> pdb=" O PRO H 34 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL H 210 " --> pdb=" O LEU H 221 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'I' and resid 33 through 36 removed outlier: 5.190A pdb=" N THR I 33 " --> pdb=" O GLU I 48 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'I' and resid 64 through 67 removed outlier: 6.712A pdb=" N LYS I 64 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL I 76 " --> pdb=" O LYS I 64 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA I 73 " --> pdb=" O ILE I 137 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER I 75 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU I 134 " --> pdb=" O SER I 150 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY I 138 " --> pdb=" O GLN I 146 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU I 147 " --> pdb=" O TRP I 159 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN I 155 " --> pdb=" O ASP I 151 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'J' and resid 69 through 75 removed outlier: 4.117A pdb=" N SER J 130 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ALA J 131 " --> pdb=" O THR J 147 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'J' and resid 158 through 162 removed outlier: 3.806A pdb=" N ALA J 32 " --> pdb=" O ILE J 161 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N THR J 31 " --> pdb=" O GLU J 46 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'j' and resid 69 through 75 removed outlier: 4.078A pdb=" N SER j 130 " --> pdb=" O ALA j 74 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ALA j 131 " --> pdb=" O THR j 147 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'j' and resid 158 through 162 removed outlier: 3.712A pdb=" N GLY j 34 " --> pdb=" O ASN j 159 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE j 161 " --> pdb=" O ALA j 32 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA j 32 " --> pdb=" O ILE j 161 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N THR j 31 " --> pdb=" O GLU j 46 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'K' and resid 67 through 70 removed outlier: 3.846A pdb=" N VAL K 68 " --> pdb=" O CYS K 76 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS K 76 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY K 144 " --> pdb=" O GLY K 75 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA K 140 " --> pdb=" O SER K 79 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU K 141 " --> pdb=" O MET K 156 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU K 153 " --> pdb=" O CYS K 165 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'K' and resid 167 through 171 removed outlier: 4.286A pdb=" N ALA K 37 " --> pdb=" O ILE K 170 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N THR K 36 " --> pdb=" O GLU K 51 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'k' and resid 67 through 70 removed outlier: 4.117A pdb=" N VAL k 68 " --> pdb=" O CYS k 76 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS k 76 " --> pdb=" O VAL k 68 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE k 74 " --> pdb=" O ILE k 70 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY k 144 " --> pdb=" O GLY k 75 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA k 140 " --> pdb=" O SER k 79 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU k 141 " --> pdb=" O MET k 156 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU k 153 " --> pdb=" O CYS k 165 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'k' and resid 167 through 171 removed outlier: 4.226A pdb=" N ALA k 37 " --> pdb=" O ILE k 170 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N THR k 36 " --> pdb=" O GLU k 51 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'L' and resid 70 through 76 removed outlier: 3.660A pdb=" N ALA L 75 " --> pdb=" O GLY L 131 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N CYS L 148 " --> pdb=" O ASN L 152 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASN L 152 " --> pdb=" O CYS L 148 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'L' and resid 158 through 162 removed outlier: 4.954A pdb=" N ALA L 34 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ASN L 209 " --> pdb=" O LYS L 50 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'l' and resid 70 through 76 removed outlier: 3.712A pdb=" N ALA l 75 " --> pdb=" O GLY l 131 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N CYS l 148 " --> pdb=" O ASN l 152 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASN l 152 " --> pdb=" O CYS l 148 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'l' and resid 158 through 162 removed outlier: 5.013A pdb=" N ALA l 34 " --> pdb=" O LEU l 49 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASN l 209 " --> pdb=" O LYS l 50 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE l 212 " --> pdb=" O TYR l 224 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'M' and resid 66 through 69 removed outlier: 3.609A pdb=" N MET M 75 " --> pdb=" O PHE M 67 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY M 74 " --> pdb=" O GLY M 138 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY M 138 " --> pdb=" O GLY M 74 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET M 136 " --> pdb=" O ALA M 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE M 135 " --> pdb=" O ILE M 151 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU M 137 " --> pdb=" O TYR M 149 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN M 147 " --> pdb=" O SER M 139 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU M 148 " --> pdb=" O TYR M 160 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR M 158 " --> pdb=" O MET M 150 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'M' and resid 162 through 166 removed outlier: 4.164A pdb=" N THR M 35 " --> pdb=" O GLU M 50 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU M 212 " --> pdb=" O VAL M 49 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'm' and resid 66 through 69 removed outlier: 3.633A pdb=" N MET m 75 " --> pdb=" O PHE m 67 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY m 74 " --> pdb=" O GLY m 138 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY m 138 " --> pdb=" O GLY m 74 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA m 76 " --> pdb=" O MET m 136 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N MET m 136 " --> pdb=" O ALA m 76 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA m 78 " --> pdb=" O SER m 134 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN m 147 " --> pdb=" O SER m 139 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU m 148 " --> pdb=" O TYR m 160 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR m 158 " --> pdb=" O MET m 150 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'm' and resid 162 through 166 removed outlier: 3.786A pdb=" N THR m 35 " --> pdb=" O GLU m 50 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'N' and resid 34 through 37 removed outlier: 6.765A pdb=" N ILE N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ARG N 40 " --> pdb=" O TRP N 103 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA N 101 " --> pdb=" O PHE N 42 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER N 46 " --> pdb=" O GLY N 97 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY N 97 " --> pdb=" O SER N 46 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'N' and resid 125 through 129 removed outlier: 6.157A pdb=" N THR N 2 " --> pdb=" O ASP N 17 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA N 177 " --> pdb=" O LEU N 14 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN N 187 " --> pdb=" O LEU N 176 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'n' and resid 34 through 37 removed outlier: 6.798A pdb=" N ILE n 41 " --> pdb=" O ILE n 37 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ARG n 40 " --> pdb=" O TRP n 103 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER n 46 " --> pdb=" O GLY n 97 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'n' and resid 125 through 129 removed outlier: 6.312A pdb=" N THR n 2 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA n 177 " --> pdb=" O LEU n 14 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'O' and resid 34 through 37 removed outlier: 6.489A pdb=" N ILE O 41 " --> pdb=" O ILE O 37 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ASN O 40 " --> pdb=" O VAL O 103 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL O 103 " --> pdb=" O ASN O 40 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'O' and resid 124 through 128 removed outlier: 4.564A pdb=" N LYS O 182 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'o' and resid 34 through 37 removed outlier: 6.436A pdb=" N ILE o 41 " --> pdb=" O ILE o 37 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ASN o 40 " --> pdb=" O VAL o 103 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL o 103 " --> pdb=" O ASN o 40 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'o' and resid 124 through 128 removed outlier: 4.486A pdb=" N LYS o 182 " --> pdb=" O SER o 179 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 42 through 45 removed outlier: 4.772A pdb=" N LEU P 49 " --> pdb=" O MET P 45 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA P 54 " --> pdb=" O GLU P 106 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 136 through 140 removed outlier: 6.402A pdb=" N ALA P 10 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY P 184 " --> pdb=" O ARG P 26 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL P 185 " --> pdb=" O LEU P 200 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'p' and resid 42 through 45 removed outlier: 4.744A pdb=" N LEU p 49 " --> pdb=" O MET p 45 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA p 54 " --> pdb=" O GLU p 106 " (cutoff:3.500A) Processing sheet with id= 34, 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: 6.695A pdb=" N GLY p 184 " --> pdb=" O ARG p 26 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL p 185 " --> pdb=" O LEU p 200 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Q' and resid 4 through 8 removed outlier: 3.650A pdb=" N VAL Q 13 " --> pdb=" O ILE Q 183 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL Q 15 " --> pdb=" O ARG Q 181 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Q' and resid 41 through 48 removed outlier: 5.797A pdb=" N LYS Q 41 " --> pdb=" O TYR Q 107 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU Q 103 " --> pdb=" O LEU Q 45 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU Q 102 " --> pdb=" O MET Q 118 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU Q 115 " --> pdb=" O ALA Q 127 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP Q 119 " --> pdb=" O ALA Q 123 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA Q 123 " --> pdb=" O ASP Q 119 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'q' and resid 4 through 8 removed outlier: 3.511A pdb=" N VAL q 13 " --> pdb=" O ILE q 183 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL q 15 " --> pdb=" O ARG q 181 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'q' and resid 41 through 48 removed outlier: 5.732A pdb=" N LYS q 41 " --> pdb=" O TYR q 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU q 103 " --> pdb=" O LEU q 45 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU q 102 " --> pdb=" O MET q 118 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU q 104 " --> pdb=" O TYR q 116 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU q 115 " --> pdb=" O ALA q 127 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP q 119 " --> pdb=" O ALA q 123 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA q 123 " --> pdb=" O ASP q 119 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'R' and resid 34 through 37 removed outlier: 6.215A pdb=" N LEU R 41 " --> pdb=" O ILE R 37 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR R 44 " --> pdb=" O MET R 100 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N MET R 100 " --> pdb=" O THR R 44 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ALA R 46 " --> pdb=" O GLY R 98 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP R 115 " --> pdb=" O ASN R 119 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN R 119 " --> pdb=" O ASP R 115 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'R' and resid 125 through 129 removed outlier: 6.349A pdb=" N THR R 2 " --> pdb=" O ASP R 17 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ALA R 173 " --> pdb=" O SER R 18 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU R 176 " --> pdb=" O VAL R 187 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY R 183 " --> pdb=" O ARG R 180 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'r' and resid 34 through 37 removed outlier: 6.138A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N MET r 100 " --> pdb=" O THR r 44 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ALA r 46 " --> pdb=" O GLY r 98 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP r 115 " --> pdb=" O ASN r 119 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN r 119 " --> pdb=" O ASP r 115 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'r' and resid 125 through 129 removed outlier: 7.130A pdb=" N THR r 2 " --> pdb=" O ASP r 17 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP r 17 " --> pdb=" O THR r 2 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA r 15 " --> pdb=" O LEU r 4 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ALA r 173 " --> pdb=" O SER r 18 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU r 176 " --> pdb=" O VAL r 187 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY r 183 " --> pdb=" O ARG r 180 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'S' and resid 43 through 46 removed outlier: 6.590A pdb=" N THR S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS S 49 " --> pdb=" O LEU S 113 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'S' and resid 135 through 139 removed outlier: 3.521A pdb=" N LYS S 136 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR S 11 " --> pdb=" O ASP S 26 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP S 26 " --> pdb=" O THR S 11 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR S 27 " --> pdb=" O ALA S 192 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA S 192 " --> pdb=" O THR S 27 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY S 202 " --> pdb=" O THR S 199 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 's' and resid 43 through 46 removed outlier: 6.502A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS s 49 " --> pdb=" O LEU s 113 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 's' and resid 135 through 139 removed outlier: 3.577A pdb=" N LYS s 136 " --> pdb=" O ALA s 14 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N THR s 11 " --> pdb=" O ASP s 26 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP s 26 " --> pdb=" O THR s 11 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR s 27 " --> pdb=" O ALA s 192 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ALA s 192 " --> pdb=" O THR s 27 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY s 202 " --> pdb=" O THR s 199 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'T' and resid 42 through 45 removed outlier: 3.656A pdb=" N VAL T 45 " --> pdb=" O THR T 49 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N THR T 49 " --> pdb=" O VAL T 45 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N SER T 48 " --> pdb=" O TYR T 115 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR T 109 " --> pdb=" O SER T 54 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR T 132 " --> pdb=" O TYR T 124 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL T 130 " --> pdb=" O ASP T 126 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'T' and resid 136 through 139 removed outlier: 4.328A pdb=" N VAL T 11 " --> pdb=" O THR T 139 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL T 6 " --> pdb=" O SER T 29 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER T 29 " --> pdb=" O VAL T 6 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLY T 8 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU T 27 " --> pdb=" O GLY T 8 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N SER T 10 " --> pdb=" O ASP T 25 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASP T 25 " --> pdb=" O SER T 10 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE T 189 " --> pdb=" O GLU T 200 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY T 196 " --> pdb=" O THR T 193 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 't' and resid 42 through 45 removed outlier: 4.797A pdb=" N THR t 49 " --> pdb=" O VAL t 45 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N SER t 48 " --> pdb=" O TYR t 115 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR t 109 " --> pdb=" O SER t 54 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL t 130 " --> pdb=" O ASP t 126 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 't' and resid 136 through 139 removed outlier: 4.429A pdb=" N VAL t 11 " --> pdb=" O THR t 139 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL t 6 " --> pdb=" O SER t 29 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER t 29 " --> pdb=" O VAL t 6 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLY t 8 " --> pdb=" O LEU t 27 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU t 27 " --> pdb=" O GLY t 8 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N SER t 10 " --> pdb=" O ASP t 25 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ASP t 25 " --> pdb=" O SER t 10 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE t 189 " --> pdb=" O GLU t 200 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY t 196 " --> pdb=" O THR t 193 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'U' and resid 801 through 805 No H-bonds generated for sheet with id= 51 Processing sheet with id= 52, first strand: chain 'U' and resid 899 through 902 removed outlier: 6.846A pdb=" N ARG U 899 " --> pdb=" O THR U 917 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR U 917 " --> pdb=" O ARG U 899 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN U 901 " --> pdb=" O LYS U 915 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'W' and resid 404 through 408 removed outlier: 3.742A pdb=" N ASP W 407 " --> pdb=" O ILE W 412 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE W 412 " --> pdb=" O ASP W 407 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'Z' and resid 8 through 11 Processing sheet with id= 55, first strand: chain 'Z' and resid 52 through 55 removed outlier: 4.389A pdb=" N ASN Z 52 " --> pdb=" O LEU Z 40 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER Z 119 " --> pdb=" O SER Z 140 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER Z 140 " --> pdb=" O SER Z 119 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LEU Z 121 " --> pdb=" O TYR Z 138 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE Z 123 " --> pdb=" O GLU Z 136 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA Z 137 " --> pdb=" O VAL Z 158 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'b' and resid 63 through 66 removed outlier: 3.717A pdb=" N ASN b 48 " --> pdb=" O GLU b 4 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE b 110 " --> pdb=" O MET b 7 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL b 171 " --> pdb=" O ILE b 140 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL b 173 " --> pdb=" O ASN b 142 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLY b 144 " --> pdb=" O VAL b 173 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'c' and resid 65 through 69 removed outlier: 5.973A pdb=" N GLU c 29 " --> pdb=" O SER c 202 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE c 33 " --> pdb=" O ASN c 206 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL c 156 " --> pdb=" O ASP c 146 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP c 146 " --> pdb=" O VAL c 156 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'g' and resid 69 through 72 removed outlier: 6.712A pdb=" N ILE g 76 " --> pdb=" O ILE g 72 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N CYS g 137 " --> pdb=" O THR g 81 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL g 151 " --> pdb=" O PHE g 163 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TYR g 159 " --> pdb=" O ASP g 155 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'g' and resid 165 through 169 removed outlier: 3.511A pdb=" N ALA g 168 " --> pdb=" O SER g 39 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N THR g 38 " --> pdb=" O GLN g 53 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN g 53 " --> pdb=" O THR g 38 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU g 214 " --> pdb=" O LYS g 54 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL g 217 " --> pdb=" O LEU g 230 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'h' and resid 65 through 68 removed outlier: 6.557A pdb=" N ILE h 72 " --> pdb=" O ILE h 68 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL h 75 " --> pdb=" O LEU h 135 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER h 133 " --> pdb=" O SER h 77 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU h 134 " --> pdb=" O SER h 149 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY h 138 " --> pdb=" O TYR h 145 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU h 146 " --> pdb=" O TRP h 158 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN h 148 " --> pdb=" O PHE h 156 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP h 150 " --> pdb=" O ALA h 154 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA h 154 " --> pdb=" O ASP h 150 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'h' and resid 160 through 164 Processing sheet with id= 62, first strand: chain 'i' and resid 33 through 36 removed outlier: 5.245A pdb=" N THR i 33 " --> pdb=" O GLU i 48 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'i' and resid 64 through 67 removed outlier: 6.726A pdb=" N LYS i 64 " --> pdb=" O VAL i 76 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL i 76 " --> pdb=" O LYS i 64 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER i 75 " --> pdb=" O LEU i 135 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU i 134 " --> pdb=" O SER i 150 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY i 138 " --> pdb=" O GLN i 146 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU i 147 " --> pdb=" O TRP i 159 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASN i 155 " --> pdb=" O ASP i 151 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'A' and resid 120 through 124 removed outlier: 6.945A pdb=" N ILE A 112 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL A 140 " --> pdb=" O THR A 99 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'A' and resid 210 through 216 removed outlier: 5.619A pdb=" N LYS A 210 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY A 216 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 316 " --> pdb=" O CYS A 270 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 272 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A 320 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N CYS A 236 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP A 275 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'B' and resid 107 through 111 No H-bonds generated for sheet with id= 66 Processing sheet with id= 67, first strand: chain 'B' and resid 119 through 125 removed outlier: 6.809A pdb=" N ASN B 119 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 123 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N HIS B 131 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR B 125 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N SER B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'B' and resid 245 through 250 removed outlier: 3.641A pdb=" N PHE B 283 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 328 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA B 330 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY B 226 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'C' and resid 71 through 77 removed outlier: 3.632A pdb=" N TYR C 72 " --> pdb=" O LEU C 116 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG C 113 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS C 125 " --> pdb=" O ALA C 115 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'C' and resid 84 through 88 Processing sheet with id= 71, first strand: chain 'C' and resid 209 through 214 removed outlier: 4.384A pdb=" N ASP C 249 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 186 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY C 190 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 315 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'D' and resid 87 through 90 removed outlier: 4.055A pdb=" N VAL D 130 " --> pdb=" O GLY D 90 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'D' and resid 226 through 231 removed outlier: 3.562A pdb=" N PHE D 263 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS D 306 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE D 308 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA D 310 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL D 202 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET D 309 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR D 311 " --> pdb=" O MET D 204 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLY D 206 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG D 329 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 331 " --> pdb=" O LEU D 203 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.608A pdb=" N TYR E 79 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL E 71 " --> pdb=" O TYR E 79 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE E 70 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU E 59 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR E 96 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG E 97 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'E' and resid 169 through 173 removed outlier: 4.760A pdb=" N CYS E 170 " --> pdb=" O MET E 275 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS E 228 " --> pdb=" O ARG E 272 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASN E 194 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE E 229 " --> pdb=" O ASN E 194 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU E 196 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N PHE E 231 " --> pdb=" O LEU E 196 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'F' and resid 89 through 94 removed outlier: 4.928A pdb=" N LEU F 89 " --> pdb=" O GLY F 152 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY F 152 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N SER F 91 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F 150 " --> pdb=" O SER F 91 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL F 93 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY F 152 " --> pdb=" O LEU F 161 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU F 159 " --> pdb=" O ASN F 154 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'F' and resid 121 through 126 removed outlier: 3.956A pdb=" N GLN F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'F' and resid 246 through 251 removed outlier: 4.267A pdb=" N THR F 247 " --> pdb=" O PRO F 280 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER F 281 " --> pdb=" O GLN F 325 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY F 227 " --> pdb=" O THR F 332 " (cutoff:3.500A) 5127 hydrogen bonds defined for protein. 15321 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: 49.86 Time building geometry restraints manager: 33.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 34030 1.35 - 1.50: 27837 1.50 - 1.65: 40007 1.65 - 1.80: 679 1.80 - 1.95: 301 Bond restraints: 102854 Sorted by residual: 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 LEU V 132 " pdb=" N PRO V 133 " ideal model delta sigma weight residual 1.333 1.371 -0.038 7.80e-03 1.64e+04 2.40e+01 bond pdb=" O2A AGS A 501 " pdb=" PA AGS A 501 " ideal model delta sigma weight residual 1.531 1.454 0.077 1.60e-02 3.91e+03 2.32e+01 bond pdb=" C ALA Y 289 " pdb=" N PRO Y 290 " ideal model delta sigma weight residual 1.334 1.373 -0.039 8.40e-03 1.42e+04 2.16e+01 bond pdb=" CA ALA J 6 " pdb=" CB ALA J 6 " ideal model delta sigma weight residual 1.526 1.585 -0.059 1.44e-02 4.82e+03 1.69e+01 ... (remaining 102849 not shown) Histogram of bond angle deviations from ideal: 95.65 - 105.45: 2074 105.45 - 115.25: 63002 115.25 - 125.04: 72345 125.04 - 134.84: 1682 134.84 - 144.64: 16 Bond angle restraints: 139119 Sorted by residual: angle pdb=" N ALA f 488 " pdb=" CA ALA f 488 " pdb=" C ALA f 488 " ideal model delta sigma weight residual 111.36 122.90 -11.54 1.09e+00 8.42e-01 1.12e+02 angle pdb=" C LEU K 21 " pdb=" N PHE K 22 " pdb=" CA PHE K 22 " ideal model delta sigma weight residual 121.70 140.42 -18.72 1.80e+00 3.09e-01 1.08e+02 angle pdb=" N VAL X 393 " pdb=" CA VAL X 393 " pdb=" C VAL X 393 " ideal model delta sigma weight residual 113.20 103.88 9.32 9.60e-01 1.09e+00 9.43e+01 angle pdb=" C SER J 2 " pdb=" N TYR J 3 " pdb=" CA TYR J 3 " ideal model delta sigma weight residual 121.54 138.98 -17.44 1.91e+00 2.74e-01 8.34e+01 angle pdb=" C TYR K 8 " pdb=" N ASP K 9 " pdb=" CA ASP K 9 " ideal model delta sigma weight residual 121.54 138.33 -16.79 1.91e+00 2.74e-01 7.73e+01 ... (remaining 139114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.04: 61112 28.04 - 56.08: 1353 56.08 - 84.13: 126 84.13 - 112.17: 3 112.17 - 140.21: 5 Dihedral angle restraints: 62599 sinusoidal: 24747 harmonic: 37852 Sorted by residual: dihedral pdb=" CA GLY o 200 " pdb=" C GLY o 200 " pdb=" N ARG o 201 " pdb=" CA ARG o 201 " ideal model delta harmonic sigma weight residual 180.00 51.68 128.32 0 5.00e+00 4.00e-02 6.59e+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 61.29 118.71 0 5.00e+00 4.00e-02 5.64e+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 -68.31 -111.69 0 5.00e+00 4.00e-02 4.99e+02 ... (remaining 62596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 15346 0.151 - 0.302: 478 0.302 - 0.454: 30 0.454 - 0.605: 10 0.605 - 0.756: 3 Chirality restraints: 15867 Sorted by residual: chirality pdb=" PB AGS C 501 " pdb=" O2B AGS C 501 " pdb=" O3A AGS C 501 " pdb=" O3B AGS C 501 " both_signs ideal model delta sigma weight residual True 3.18 2.43 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" PB AGS F 501 " pdb=" O2B AGS F 501 " pdb=" O3A AGS F 501 " pdb=" O3B AGS F 501 " both_signs ideal model delta sigma weight residual True 3.18 2.45 0.73 2.00e-01 2.50e+01 1.34e+01 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 0.66 2.00e-01 2.50e+01 1.10e+01 ... (remaining 15864 not shown) Planarity restraints: 17980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA a 286 " -0.034 2.00e-02 2.50e+03 6.83e-02 4.67e+01 pdb=" C ALA a 286 " 0.118 2.00e-02 2.50e+03 pdb=" O ALA a 286 " -0.044 2.00e-02 2.50e+03 pdb=" N ASN a 287 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 303 " 0.106 5.00e-02 4.00e+02 1.62e-01 4.22e+01 pdb=" N PRO E 304 " -0.281 5.00e-02 4.00e+02 pdb=" CA PRO E 304 " 0.096 5.00e-02 4.00e+02 pdb=" CD PRO E 304 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP j 4 " -0.032 2.00e-02 2.50e+03 6.48e-02 4.20e+01 pdb=" C ASP j 4 " 0.112 2.00e-02 2.50e+03 pdb=" O ASP j 4 " -0.040 2.00e-02 2.50e+03 pdb=" N ARG j 5 " -0.040 2.00e-02 2.50e+03 ... (remaining 17977 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 1203 2.59 - 3.17: 84976 3.17 - 3.75: 162075 3.75 - 4.32: 218262 4.32 - 4.90: 345457 Nonbonded interactions: 811973 Sorted by model distance: nonbonded pdb=" O SER c 114 " pdb="ZN ZN c 401 " model vdw 2.018 2.230 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 2.062 3.440 nonbonded pdb=" O ALA f 753 " pdb=" CE LYS f 754 " model vdw 2.078 3.440 ... (remaining 811968 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: 12.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 38.880 Check model and map are aligned: 1.110 Set scattering table: 0.680 Process input model: 264.690 Find NCS groups from input model: 6.120 Set up NCS constraints: 0.690 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 327.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 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 : 0.008 0.145 102854 Z= 0.492 Angle : 1.306 28.336 139119 Z= 0.712 Chirality : 0.069 0.756 15867 Planarity : 0.009 0.162 17980 Dihedral : 11.880 140.212 38222 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.57 % Allowed : 9.97 % Favored : 89.46 % Rotamer: Outliers : 0.81 % Allowed : 4.34 % Favored : 94.85 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 2.01 % Twisted General : 0.42 % 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: -4.38 (0.06), residues: 12904 helix: -2.58 (0.05), residues: 5770 sheet: -1.95 (0.12), residues: 1673 loop : -3.52 (0.07), residues: 5461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.005 TRP M 215 HIS 0.023 0.003 HIS f 301 PHE 0.044 0.004 PHE r 8 TYR 0.053 0.004 TYR F 437 ARG 0.040 0.002 ARG Q 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2668 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 2581 time to evaluate : 8.761 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: G 61 LEU cc_start: 0.8091 (tt) cc_final: 0.7341 (tt) REVERT: G 132 ARG cc_start: 0.6364 (ttp-170) cc_final: 0.6001 (ttp80) REVERT: G 215 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8092 (mt) REVERT: H 93 LEU cc_start: 0.9125 (tt) cc_final: 0.8914 (pp) REVERT: H 165 LYS cc_start: 0.8502 (mttm) cc_final: 0.8196 (pttm) REVERT: I 23 TYR cc_start: 0.8762 (m-10) cc_final: 0.8555 (m-10) REVERT: I 86 LEU cc_start: 0.9212 (mt) cc_final: 0.8962 (mm) REVERT: I 121 TYR cc_start: 0.8866 (m-10) cc_final: 0.8664 (m-80) REVERT: I 155 ASN cc_start: 0.7914 (t0) cc_final: 0.7446 (m110) REVERT: I 175 LEU cc_start: 0.9134 (mt) cc_final: 0.8854 (mt) REVERT: J 17 PHE cc_start: 0.7670 (m-80) cc_final: 0.6995 (m-10) REVERT: J 21 TYR cc_start: 0.8226 (m-10) cc_final: 0.7818 (m-10) REVERT: J 24 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7107 (mm-30) REVERT: J 71 MET cc_start: 0.8687 (mmp) cc_final: 0.8173 (mmp) REVERT: J 115 LYS cc_start: 0.8601 (tttt) cc_final: 0.8222 (tptm) REVERT: K 32 LYS cc_start: 0.9082 (tptp) cc_final: 0.8723 (tppt) REVERT: K 52 LYS cc_start: 0.7017 (mttp) cc_final: 0.6727 (mmtm) REVERT: K 84 ASP cc_start: 0.7278 (m-30) cc_final: 0.6859 (p0) REVERT: K 99 HIS cc_start: 0.8446 (t-90) cc_final: 0.8072 (t-90) REVERT: K 107 MET cc_start: 0.6904 (ttm) cc_final: 0.5879 (ttm) REVERT: K 189 MET cc_start: 0.7936 (mmm) cc_final: 0.7239 (tpt) REVERT: K 228 MET cc_start: 0.3743 (mpp) cc_final: 0.3381 (ppp) REVERT: L 6 TYR cc_start: 0.5876 (p90) cc_final: 0.5452 (m-80) REVERT: L 26 MET cc_start: 0.8783 (mmt) cc_final: 0.8419 (mmt) REVERT: L 27 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8587 (mm-30) REVERT: L 63 ILE cc_start: 0.9169 (mt) cc_final: 0.8886 (tt) REVERT: M 24 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8560 (mp0) REVERT: M 129 ARG cc_start: 0.7635 (ptt-90) cc_final: 0.7206 (ptm-80) REVERT: M 130 PRO cc_start: 0.8976 (Cg_exo) cc_final: 0.8151 (Cg_endo) REVERT: M 136 MET cc_start: 0.7795 (mmm) cc_final: 0.6466 (mmm) REVERT: M 158 TYR cc_start: 0.8721 (p90) cc_final: 0.7098 (p90) REVERT: N 33 LYS cc_start: 0.6874 (mmmt) cc_final: 0.6544 (ttmm) REVERT: N 57 ASP cc_start: 0.8536 (m-30) cc_final: 0.8206 (m-30) REVERT: N 98 ILE cc_start: 0.9320 (mm) cc_final: 0.9018 (tp) REVERT: N 123 GLN cc_start: 0.8309 (mt0) cc_final: 0.8087 (mt0) REVERT: O 184 ASP cc_start: 0.8913 (m-30) cc_final: 0.8667 (p0) REVERT: P 50 TYR cc_start: 0.8255 (m-10) cc_final: 0.7812 (m-80) REVERT: P 58 THR cc_start: 0.8718 (m) cc_final: 0.8489 (m) REVERT: P 69 PHE cc_start: 0.8171 (t80) cc_final: 0.7911 (t80) REVERT: P 85 TYR cc_start: 0.7104 (m-80) cc_final: 0.6752 (m-80) REVERT: P 146 MET cc_start: 0.8032 (mtm) cc_final: 0.6949 (ptt) REVERT: Q 45 LEU cc_start: 0.8122 (mt) cc_final: 0.7353 (mt) REVERT: Q 69 MET cc_start: 0.8054 (mmm) cc_final: 0.7433 (tpp) REVERT: Q 82 ASN cc_start: 0.8708 (t0) cc_final: 0.8306 (t0) REVERT: Q 102 LEU cc_start: 0.8817 (mt) cc_final: 0.8130 (mt) REVERT: Q 118 MET cc_start: 0.8884 (mmp) cc_final: 0.8499 (mmp) REVERT: Q 189 HIS cc_start: 0.6862 (m-70) cc_final: 0.6376 (m-70) REVERT: R 35 ILE cc_start: 0.9271 (mt) cc_final: 0.8325 (mm) REVERT: R 45 MET cc_start: 0.8916 (ttm) cc_final: 0.8644 (ttp) REVERT: R 56 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8715 (pt0) REVERT: R 90 TYR cc_start: 0.9251 (m-80) cc_final: 0.8930 (m-10) REVERT: R 115 ASP cc_start: 0.8867 (m-30) cc_final: 0.8585 (m-30) REVERT: R 190 ASP cc_start: 0.7665 (m-30) cc_final: 0.7335 (t0) REVERT: S 61 CYS cc_start: 0.8928 (m) cc_final: 0.7775 (m) REVERT: T 5 MET cc_start: 0.8776 (mmt) cc_final: 0.8389 (mmp) REVERT: T 57 TYR cc_start: 0.8369 (t80) cc_final: 0.7372 (t80) REVERT: T 60 PHE cc_start: 0.8502 (t80) cc_final: 0.8185 (t80) REVERT: T 65 GLN cc_start: 0.8812 (tt0) cc_final: 0.8482 (tm-30) REVERT: T 127 MET cc_start: 0.7830 (ttp) cc_final: 0.7607 (tmm) REVERT: T 188 GLN cc_start: 0.8242 (pt0) cc_final: 0.7291 (pp30) REVERT: T 189 ILE cc_start: 0.8977 (mt) cc_final: 0.8230 (mt) REVERT: T 203 LEU cc_start: 0.8974 (mt) cc_final: 0.8720 (mp) REVERT: T 211 ILE cc_start: 0.8843 (pt) cc_final: 0.8563 (mt) REVERT: U 25 HIS cc_start: 0.5880 (t-170) cc_final: 0.5633 (t-90) REVERT: U 188 MET cc_start: 0.8339 (tpp) cc_final: 0.8048 (tpp) REVERT: U 235 LYS cc_start: 0.7299 (mttt) cc_final: 0.7083 (pttt) REVERT: U 244 MET cc_start: 0.4904 (ptp) cc_final: 0.4418 (mmm) REVERT: U 564 ASP cc_start: 0.6783 (m-30) cc_final: 0.6090 (t70) REVERT: U 575 ASP cc_start: 0.6924 (t0) cc_final: 0.6692 (t0) REVERT: U 586 VAL cc_start: 0.8234 (p) cc_final: 0.8021 (p) REVERT: U 650 TYR cc_start: 0.7349 (t80) cc_final: 0.6793 (t80) REVERT: U 695 MET cc_start: 0.7669 (mtm) cc_final: 0.7333 (ptt) REVERT: U 720 LYS cc_start: 0.6234 (tttt) cc_final: 0.5837 (ttpp) REVERT: U 751 ARG cc_start: 0.5721 (ttt90) cc_final: 0.4443 (ptt90) REVERT: U 779 LEU cc_start: 0.7963 (tp) cc_final: 0.7645 (tt) REVERT: U 905 PRO cc_start: 0.7524 (Cg_exo) cc_final: 0.7064 (Cg_endo) REVERT: V 149 PRO cc_start: 0.6751 (Cg_exo) cc_final: 0.5692 (Cg_endo) REVERT: V 174 PHE cc_start: 0.7979 (m-10) cc_final: 0.7759 (m-80) REVERT: V 181 TYR cc_start: 0.6868 (m-80) cc_final: 0.6530 (m-10) REVERT: V 313 LEU cc_start: 0.8543 (tp) cc_final: 0.8289 (tt) REVERT: V 457 TYR cc_start: 0.7892 (m-80) cc_final: 0.7131 (m-80) REVERT: V 488 ASN cc_start: 0.8533 (m-40) cc_final: 0.8284 (m-40) REVERT: W 56 THR cc_start: 0.7255 (p) cc_final: 0.7013 (p) REVERT: W 88 MET cc_start: 0.3537 (mtm) cc_final: 0.3125 (mmt) REVERT: W 425 LEU cc_start: 0.8264 (tt) cc_final: 0.8034 (mt) REVERT: W 428 TRP cc_start: 0.7192 (m100) cc_final: 0.6937 (t-100) REVERT: X 65 GLU cc_start: 0.8787 (mp0) cc_final: 0.8498 (tm-30) REVERT: X 127 GLN cc_start: 0.4694 (mt0) cc_final: 0.4398 (mm110) REVERT: X 160 MET cc_start: 0.5973 (mmt) cc_final: 0.5710 (ptm) REVERT: X 232 PHE cc_start: 0.7487 (m-80) cc_final: 0.7087 (m-10) REVERT: X 282 ARG cc_start: 0.8470 (mmm-85) cc_final: 0.8242 (mmm-85) REVERT: X 302 PHE cc_start: 0.8595 (t80) cc_final: 0.8391 (t80) REVERT: X 405 GLN cc_start: 0.8847 (mt0) cc_final: 0.8109 (mm110) REVERT: X 415 TYR cc_start: 0.9249 (m-80) cc_final: 0.8937 (m-80) REVERT: Y 117 LYS cc_start: 0.8529 (pttm) cc_final: 0.8296 (tptt) REVERT: Y 137 ARG cc_start: 0.7141 (mtt90) cc_final: 0.6512 (mpt180) REVERT: Y 211 TYR cc_start: 0.6436 (p90) cc_final: 0.5574 (m-10) REVERT: Y 299 MET cc_start: 0.8926 (mmm) cc_final: 0.8574 (mmm) REVERT: Y 333 GLU cc_start: 0.8763 (tt0) cc_final: 0.8433 (tp30) REVERT: Y 346 LYS cc_start: 0.7820 (mmtt) cc_final: 0.7486 (tmmt) REVERT: Y 351 ASN cc_start: 0.6184 (m110) cc_final: 0.5960 (t0) REVERT: Y 364 TRP cc_start: 0.8176 (t-100) cc_final: 0.7617 (m-90) REVERT: Y 389 MET cc_start: 0.5176 (mtt) cc_final: 0.3238 (mmp) REVERT: Z 73 ASP cc_start: 0.7977 (t0) cc_final: 0.7109 (p0) REVERT: Z 84 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8062 (tppt) REVERT: Z 114 ARG cc_start: 0.8151 (ptt180) cc_final: 0.7472 (ptt90) REVERT: Z 257 MET cc_start: 0.8626 (tpt) cc_final: 0.8369 (mmm) REVERT: a 44 PHE cc_start: 0.4179 (m-10) cc_final: 0.3929 (m-80) REVERT: a 127 ASP cc_start: 0.6880 (m-30) cc_final: 0.6084 (t0) REVERT: a 138 VAL cc_start: 0.5583 (t) cc_final: 0.5293 (t) REVERT: a 141 MET cc_start: 0.8706 (mmm) cc_final: 0.8424 (mmm) REVERT: a 234 ILE cc_start: 0.3081 (OUTLIER) cc_final: 0.1787 (mp) REVERT: b 70 ARG cc_start: 0.7676 (ttm170) cc_final: 0.7470 (ptm160) REVERT: b 74 LYS cc_start: 0.7020 (mmtm) cc_final: 0.6340 (tptp) REVERT: b 90 ILE cc_start: 0.4400 (mp) cc_final: 0.3378 (mm) REVERT: b 181 ASP cc_start: 0.7871 (m-30) cc_final: 0.7413 (p0) REVERT: c 56 LEU cc_start: 0.7398 (mt) cc_final: 0.7067 (mt) REVERT: c 62 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.8060 (p) REVERT: c 71 ASP cc_start: 0.7741 (t0) cc_final: 0.7522 (t0) REVERT: c 98 MET cc_start: 0.6725 (mtt) cc_final: 0.6404 (mtt) REVERT: c 104 ARG cc_start: 0.8389 (ttp-170) cc_final: 0.8119 (ttp80) REVERT: c 111 TRP cc_start: 0.6957 (p-90) cc_final: 0.6576 (p-90) REVERT: c 121 TRP cc_start: 0.6853 (p-90) cc_final: 0.6604 (p-90) REVERT: c 209 LYS cc_start: 0.6404 (mmmm) cc_final: 0.4834 (tmtt) REVERT: c 229 LEU cc_start: 0.8956 (tt) cc_final: 0.8744 (tp) REVERT: c 232 GLN cc_start: 0.8901 (mt0) cc_final: 0.8652 (mp10) REVERT: c 248 MET cc_start: 0.8807 (ptm) cc_final: 0.8590 (ptm) REVERT: c 266 THR cc_start: 0.8887 (p) cc_final: 0.8515 (t) REVERT: c 292 MET cc_start: 0.8755 (mmm) cc_final: 0.8553 (mtp) REVERT: d 68 ILE cc_start: 0.7767 (mm) cc_final: 0.7366 (mt) REVERT: d 95 MET cc_start: 0.1832 (ttp) cc_final: 0.0477 (mtm) REVERT: d 125 LYS cc_start: 0.7444 (mmtt) cc_final: 0.7071 (ttpt) REVERT: d 233 GLU cc_start: 0.6747 (mp0) cc_final: 0.6130 (tp30) REVERT: e 49 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7921 (pt0) REVERT: g 113 MET cc_start: 0.8544 (mmp) cc_final: 0.8253 (mmt) REVERT: g 120 ASP cc_start: 0.8318 (m-30) cc_final: 0.8064 (m-30) REVERT: g 128 ASN cc_start: 0.6845 (t0) cc_final: 0.6524 (t0) REVERT: g 216 GLU cc_start: 0.6689 (mp0) cc_final: 0.6475 (mp0) REVERT: h 58 ASP cc_start: 0.7964 (t0) cc_final: 0.7736 (t70) REVERT: h 92 LYS cc_start: 0.8866 (mtpt) cc_final: 0.8171 (mtmm) REVERT: h 150 ASP cc_start: 0.7479 (p0) cc_final: 0.6762 (m-30) REVERT: i 56 LEU cc_start: 0.6653 (mt) cc_final: 0.5932 (mt) REVERT: i 103 GLU cc_start: 0.7768 (tt0) cc_final: 0.7300 (mp0) REVERT: j 24 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8192 (tt0) REVERT: j 30 SER cc_start: 0.7979 (m) cc_final: 0.7585 (t) REVERT: j 43 LEU cc_start: 0.8369 (pp) cc_final: 0.8102 (pp) REVERT: j 67 ASP cc_start: 0.7783 (m-30) cc_final: 0.7583 (t0) REVERT: j 108 THR cc_start: 0.9033 (p) cc_final: 0.8659 (t) REVERT: j 115 LYS cc_start: 0.8725 (ttmt) cc_final: 0.8372 (tttt) REVERT: j 159 ASN cc_start: 0.8357 (t0) cc_final: 0.7974 (t0) REVERT: k 59 MET cc_start: 0.8545 (ttt) cc_final: 0.8208 (ttm) REVERT: l 26 MET cc_start: 0.7793 (mmt) cc_final: 0.7480 (tmm) REVERT: l 88 MET cc_start: 0.9341 (tpp) cc_final: 0.9087 (tpp) REVERT: l 159 MET cc_start: 0.7015 (mmm) cc_final: 0.6143 (tpt) REVERT: l 176 MET cc_start: 0.8817 (ptm) cc_final: 0.8399 (ptm) REVERT: m 35 THR cc_start: 0.8243 (m) cc_final: 0.8000 (p) REVERT: m 47 PHE cc_start: 0.8300 (m-10) cc_final: 0.7908 (m-80) REVERT: m 50 GLU cc_start: 0.7574 (tt0) cc_final: 0.6026 (tm-30) REVERT: m 130 PRO cc_start: 0.8670 (Cg_exo) cc_final: 0.8439 (Cg_endo) REVERT: m 170 GLN cc_start: 0.8014 (mt0) cc_final: 0.7646 (tm-30) REVERT: m 181 MET cc_start: 0.7849 (ptp) cc_final: 0.7595 (ptp) REVERT: n 81 SER cc_start: 0.9581 (m) cc_final: 0.9361 (p) REVERT: n 154 GLN cc_start: 0.8292 (tp-100) cc_final: 0.8067 (tp-100) REVERT: o 26 VAL cc_start: 0.8209 (t) cc_final: 0.7312 (p) REVERT: o 54 MET cc_start: 0.9007 (mmm) cc_final: 0.8676 (tmm) REVERT: o 68 LEU cc_start: 0.8851 (tp) cc_final: 0.8620 (tp) REVERT: o 127 MET cc_start: 0.8032 (mmm) cc_final: 0.7763 (ttm) REVERT: o 135 MET cc_start: 0.8923 (tpp) cc_final: 0.8441 (tpp) REVERT: p 17 LYS cc_start: 0.6594 (tptt) cc_final: 0.6254 (mtpp) REVERT: p 25 ASP cc_start: 0.7654 (p0) cc_final: 0.6886 (m-30) REVERT: p 34 MET cc_start: 0.7256 (ptm) cc_final: 0.6866 (tmm) REVERT: p 135 ASP cc_start: 0.8706 (p0) cc_final: 0.8014 (p0) REVERT: p 194 LYS cc_start: 0.8245 (ptmt) cc_final: 0.7685 (ptmm) REVERT: q 28 MET cc_start: 0.8999 (mtm) cc_final: 0.8536 (mtm) REVERT: q 139 THR cc_start: 0.7812 (p) cc_final: 0.7510 (p) REVERT: r 32 LYS cc_start: 0.9138 (mtpt) cc_final: 0.8759 (mtmm) REVERT: r 45 MET cc_start: 0.8005 (ttm) cc_final: 0.7627 (mtp) REVERT: r 56 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8239 (mt-10) REVERT: r 72 GLU cc_start: 0.8355 (tt0) cc_final: 0.7904 (tp30) REVERT: r 90 TYR cc_start: 0.9317 (m-80) cc_final: 0.9107 (m-10) REVERT: r 91 LYS cc_start: 0.9117 (tttp) cc_final: 0.8774 (ttpp) REVERT: r 139 MET cc_start: 0.7910 (ttp) cc_final: 0.7682 (tmm) REVERT: s 8 ASN cc_start: 0.8855 (m110) cc_final: 0.8571 (m110) REVERT: s 13 LEU cc_start: 0.8108 (tp) cc_final: 0.7578 (mp) REVERT: s 57 PHE cc_start: 0.8958 (t80) cc_final: 0.8625 (t80) REVERT: s 83 MET cc_start: 0.7564 (mtp) cc_final: 0.7009 (mtm) REVERT: s 174 LEU cc_start: 0.9501 (mt) cc_final: 0.9287 (tt) REVERT: s 179 PHE cc_start: 0.8648 (m-80) cc_final: 0.7528 (m-80) REVERT: s 184 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7746 (mm-30) REVERT: t 22 ILE cc_start: 0.9021 (mt) cc_final: 0.8490 (pt) REVERT: t 25 ASP cc_start: 0.8026 (p0) cc_final: 0.7525 (p0) REVERT: t 50 MET cc_start: 0.7522 (ttp) cc_final: 0.7132 (ttp) REVERT: t 59 ASP cc_start: 0.8927 (m-30) cc_final: 0.8659 (m-30) REVERT: t 126 ASP cc_start: 0.9208 (t0) cc_final: 0.8676 (t70) REVERT: t 173 MET cc_start: 0.8711 (mmm) cc_final: 0.8401 (mmt) REVERT: A 101 ILE cc_start: 0.6486 (mt) cc_final: 0.5685 (mt) REVERT: A 113 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6798 (tt) REVERT: A 258 ARG cc_start: 0.7932 (mpt-90) cc_final: 0.7105 (tmm-80) REVERT: A 260 LEU cc_start: 0.8353 (mp) cc_final: 0.8148 (mt) REVERT: A 268 LYS cc_start: 0.4045 (pptt) cc_final: 0.3616 (tppt) REVERT: B 107 MET cc_start: 0.7471 (mtm) cc_final: 0.7261 (mtm) REVERT: B 184 TYR cc_start: 0.7352 (m-10) cc_final: 0.6707 (m-10) REVERT: B 328 ILE cc_start: 0.8825 (mt) cc_final: 0.8505 (mt) REVERT: B 439 TYR cc_start: 0.5166 (m-80) cc_final: 0.4428 (m-10) REVERT: C 138 MET cc_start: 0.6500 (ttt) cc_final: 0.5970 (tmm) REVERT: C 159 LYS cc_start: 0.7399 (mtpt) cc_final: 0.7129 (mmtm) REVERT: C 222 LYS cc_start: 0.5495 (OUTLIER) cc_final: 0.5010 (mttp) REVERT: C 273 MET cc_start: 0.7190 (ttp) cc_final: 0.6986 (mtp) REVERT: D 64 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8127 (mm-30) REVERT: D 70 LYS cc_start: 0.9465 (mttt) cc_final: 0.9058 (mtmm) REVERT: D 85 ILE cc_start: 0.7307 (mm) cc_final: 0.7107 (mm) REVERT: D 351 LYS cc_start: 0.8736 (tppt) cc_final: 0.8267 (pttm) REVERT: D 409 LYS cc_start: 0.5616 (tppt) cc_final: 0.5241 (tmtt) REVERT: E 93 LYS cc_start: 0.9237 (mttt) cc_final: 0.9004 (mmmt) REVERT: E 133 SER cc_start: 0.6454 (p) cc_final: 0.6196 (m) REVERT: E 155 ASN cc_start: 0.8631 (t0) cc_final: 0.8247 (m110) REVERT: E 216 ARG cc_start: 0.8552 (mpt-90) cc_final: 0.8281 (mmp-170) REVERT: E 236 ASP cc_start: 0.5576 (m-30) cc_final: 0.5245 (t0) REVERT: E 259 GLU cc_start: 0.5536 (mm-30) cc_final: 0.4488 (pt0) REVERT: E 277 MET cc_start: 0.7108 (mpm) cc_final: 0.6896 (mmp) REVERT: F 172 VAL cc_start: 0.6371 (t) cc_final: 0.6121 (t) REVERT: F 380 ASN cc_start: 0.7677 (t0) cc_final: 0.7333 (t0) REVERT: f 88 SER cc_start: -0.2664 (OUTLIER) cc_final: -0.2989 (m) REVERT: f 248 LEU cc_start: 0.6043 (tt) cc_final: 0.5517 (tp) REVERT: f 297 MET cc_start: 0.0612 (mtm) cc_final: 0.0186 (mpp) REVERT: f 551 LYS cc_start: 0.4589 (tptp) cc_final: 0.4368 (mtmm) REVERT: f 560 LEU cc_start: 0.7929 (mm) cc_final: 0.7052 (mt) REVERT: f 678 LEU cc_start: 0.7438 (mm) cc_final: 0.7087 (mt) outliers start: 87 outliers final: 14 residues processed: 2660 average time/residue: 1.0538 time to fit residues: 4731.9287 Evaluate side-chains 1227 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1207 time to evaluate : 8.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1285 random chunks: chunk 1085 optimal weight: 6.9990 chunk 973 optimal weight: 7.9990 chunk 540 optimal weight: 9.9990 chunk 332 optimal weight: 6.9990 chunk 656 optimal weight: 10.0000 chunk 520 optimal weight: 20.0000 chunk 1007 optimal weight: 0.9990 chunk 389 optimal weight: 6.9990 chunk 612 optimal weight: 6.9990 chunk 749 optimal weight: 10.0000 chunk 1166 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 123 GLN ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 GLN H 112 GLN H 189 HIS ** I 20 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** ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 23 GLN ** K 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 225 ASN L 16 GLN L 20 HIS L 53 GLN M 101 ASN ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 GLN O 62 ASN ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 160 ASN S 163 HIS T 65 GLN U 18 GLN ** U 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 595 ASN ** U 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 193 GLN ** V 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 319 HIS ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 41 GLN W 430 GLN ** W 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 148 HIS ** X 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 329 ASN ** X 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 136 HIS Y 357 ASN Z 102 HIS ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN ** a 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 34 ASN ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 172 HIS ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 194 HIS ** c 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 GLN ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN ** i 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 102 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** k 118 ASN ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 110 HIS ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 HIS n 154 GLN o 62 ASN p 33 GLN p 93 ASN q 101 ASN ** q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 85 ASN t 89 HIS ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN B 277 HIS ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 ASN E 63 GLN E 262 ASN ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN F 428 GLN f 224 ASN f 452 ASN f 540 GLN ** f 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 102854 Z= 0.292 Angle : 0.853 16.393 139119 Z= 0.446 Chirality : 0.048 0.294 15867 Planarity : 0.006 0.139 17980 Dihedral : 8.061 137.461 14262 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.79 % Favored : 90.00 % Rotamer: Outliers : 0.23 % Allowed : 4.12 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 1.34 % Twisted General : 0.30 % 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: -3.19 (0.07), residues: 12904 helix: -1.35 (0.06), residues: 5824 sheet: -1.44 (0.12), residues: 1674 loop : -3.19 (0.07), residues: 5406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP f 420 HIS 0.016 0.002 HIS C 377 PHE 0.032 0.002 PHE V 496 TYR 0.030 0.002 TYR C 148 ARG 0.016 0.001 ARG c 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1563 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1538 time to evaluate : 8.792 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: G 175 SER cc_start: 0.8698 (t) cc_final: 0.8385 (m) REVERT: H 165 LYS cc_start: 0.8472 (mttm) cc_final: 0.8176 (pttm) REVERT: J 21 TYR cc_start: 0.8391 (m-10) cc_final: 0.8106 (m-10) REVERT: J 24 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7022 (mm-30) REVERT: J 71 MET cc_start: 0.8610 (mmp) cc_final: 0.8392 (mmt) REVERT: K 29 GLU cc_start: 0.8430 (tt0) cc_final: 0.8165 (mm-30) REVERT: K 32 LYS cc_start: 0.8970 (tptp) cc_final: 0.8567 (tppt) REVERT: K 59 MET cc_start: 0.5128 (ttt) cc_final: 0.4874 (ttt) REVERT: K 228 MET cc_start: 0.3981 (mpp) cc_final: 0.3626 (ppp) REVERT: L 6 TYR cc_start: 0.6142 (p90) cc_final: 0.5740 (m-80) REVERT: L 26 MET cc_start: 0.8979 (mmt) cc_final: 0.8487 (mmt) REVERT: L 27 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8658 (mm-30) REVERT: L 63 ILE cc_start: 0.9231 (mt) cc_final: 0.8984 (tt) REVERT: L 88 MET cc_start: 0.9040 (mtp) cc_final: 0.8798 (ptm) REVERT: L 96 ARG cc_start: 0.8717 (mmm160) cc_final: 0.8433 (mmm160) REVERT: L 173 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8091 (mm-30) REVERT: N 87 CYS cc_start: 0.9231 (t) cc_final: 0.9016 (t) REVERT: N 95 MET cc_start: 0.8293 (mmt) cc_final: 0.8076 (mmp) REVERT: N 123 GLN cc_start: 0.8550 (mt0) cc_final: 0.8123 (mt0) REVERT: O 173 ILE cc_start: 0.8467 (mt) cc_final: 0.8253 (mt) REVERT: P 50 TYR cc_start: 0.8155 (m-10) cc_final: 0.7563 (m-80) REVERT: P 70 ARG cc_start: 0.8652 (mtp180) cc_final: 0.8262 (mtp180) REVERT: P 146 MET cc_start: 0.8091 (mtm) cc_final: 0.7205 (ptt) REVERT: P 171 MET cc_start: 0.8320 (mmm) cc_final: 0.8106 (mmm) REVERT: Q 69 MET cc_start: 0.8190 (mmm) cc_final: 0.7569 (tpp) REVERT: Q 102 LEU cc_start: 0.8704 (mt) cc_final: 0.8282 (tp) REVERT: Q 189 HIS cc_start: 0.6787 (m-70) cc_final: 0.6422 (m-70) REVERT: R 56 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8585 (pp20) REVERT: R 100 MET cc_start: 0.8614 (mtm) cc_final: 0.8106 (mtm) REVERT: R 175 ASN cc_start: 0.8945 (m110) cc_final: 0.8708 (m110) REVERT: S 68 ILE cc_start: 0.8568 (tp) cc_final: 0.8349 (tp) REVERT: S 206 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7251 (tm-30) REVERT: T 5 MET cc_start: 0.8710 (mmt) cc_final: 0.8498 (mmt) REVERT: T 43 MET cc_start: 0.7082 (tmm) cc_final: 0.6810 (tmm) REVERT: T 57 TYR cc_start: 0.8038 (t80) cc_final: 0.7444 (t80) REVERT: T 60 PHE cc_start: 0.8747 (t80) cc_final: 0.8485 (t80) REVERT: T 65 GLN cc_start: 0.8758 (tt0) cc_final: 0.8525 (tm-30) REVERT: T 72 ILE cc_start: 0.8697 (mm) cc_final: 0.8292 (mm) REVERT: T 76 LEU cc_start: 0.8225 (mt) cc_final: 0.7590 (mt) REVERT: T 127 MET cc_start: 0.7897 (ttp) cc_final: 0.7557 (ppp) REVERT: U 244 MET cc_start: 0.4677 (ptp) cc_final: 0.4170 (mmm) REVERT: U 340 GLN cc_start: 0.7746 (tp-100) cc_final: 0.7478 (tm-30) REVERT: U 564 ASP cc_start: 0.6910 (m-30) cc_final: 0.6285 (t70) REVERT: U 575 ASP cc_start: 0.7190 (t0) cc_final: 0.6904 (t0) REVERT: U 695 MET cc_start: 0.7664 (mtm) cc_final: 0.7355 (ptt) REVERT: U 720 LYS cc_start: 0.5907 (tttt) cc_final: 0.5651 (ttpp) REVERT: U 751 ARG cc_start: 0.5944 (ttt90) cc_final: 0.4800 (ptt90) REVERT: U 892 LEU cc_start: 0.4336 (OUTLIER) cc_final: 0.4100 (mt) REVERT: U 905 PRO cc_start: 0.7557 (Cg_exo) cc_final: 0.7036 (Cg_endo) REVERT: V 76 LYS cc_start: 0.5796 (tttt) cc_final: 0.5521 (tmtt) REVERT: V 160 LEU cc_start: 0.7853 (mt) cc_final: 0.7448 (tp) REVERT: V 181 TYR cc_start: 0.6925 (m-80) cc_final: 0.6665 (m-10) REVERT: V 200 ARG cc_start: 0.5111 (mmm160) cc_final: 0.4211 (mpp-170) REVERT: V 300 LEU cc_start: 0.7312 (tt) cc_final: 0.6810 (mp) REVERT: V 488 ASN cc_start: 0.8560 (m-40) cc_final: 0.8352 (m-40) REVERT: V 496 PHE cc_start: 0.8122 (m-80) cc_final: 0.7790 (t80) REVERT: W 127 THR cc_start: 0.6868 (t) cc_final: 0.6431 (t) REVERT: W 425 LEU cc_start: 0.8456 (tt) cc_final: 0.8169 (mt) REVERT: X 65 GLU cc_start: 0.8826 (mp0) cc_final: 0.8591 (tp30) REVERT: X 127 GLN cc_start: 0.4796 (mt0) cc_final: 0.4425 (mm110) REVERT: X 130 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6356 (mm-30) REVERT: X 160 MET cc_start: 0.6056 (mmt) cc_final: 0.5776 (ptm) REVERT: X 388 PHE cc_start: 0.6193 (p90) cc_final: 0.5893 (p90) REVERT: X 405 GLN cc_start: 0.8959 (mt0) cc_final: 0.8149 (mm110) REVERT: X 415 TYR cc_start: 0.9292 (m-80) cc_final: 0.8973 (m-80) REVERT: Y 42 MET cc_start: 0.7308 (mmm) cc_final: 0.6926 (mtp) REVERT: Y 79 ASP cc_start: 0.6971 (t0) cc_final: 0.6621 (t0) REVERT: Y 137 ARG cc_start: 0.7119 (mtt90) cc_final: 0.6900 (mtt90) REVERT: Y 211 TYR cc_start: 0.6424 (p90) cc_final: 0.5574 (m-10) REVERT: Y 362 LYS cc_start: 0.7306 (mtmm) cc_final: 0.6659 (ttpt) REVERT: Y 389 MET cc_start: 0.4848 (mtt) cc_final: 0.3330 (mmp) REVERT: Z 33 LYS cc_start: 0.5542 (pptt) cc_final: 0.5291 (mmmm) REVERT: Z 64 ASP cc_start: 0.7451 (t70) cc_final: 0.6731 (p0) REVERT: Z 73 ASP cc_start: 0.7720 (t0) cc_final: 0.7069 (p0) REVERT: Z 84 LYS cc_start: 0.8256 (ttpt) cc_final: 0.7928 (tppt) REVERT: Z 114 ARG cc_start: 0.8158 (ptt180) cc_final: 0.7449 (ptt90) REVERT: Z 256 GLN cc_start: 0.7778 (mm110) cc_final: 0.7095 (mt0) REVERT: Z 257 MET cc_start: 0.8628 (tpt) cc_final: 0.8335 (mmm) REVERT: a 46 GLN cc_start: 0.7356 (tp-100) cc_final: 0.6958 (tm-30) REVERT: a 127 ASP cc_start: 0.7001 (m-30) cc_final: 0.6162 (t0) REVERT: a 141 MET cc_start: 0.8559 (mmm) cc_final: 0.8276 (mmm) REVERT: a 161 LYS cc_start: 0.7842 (mmmt) cc_final: 0.7573 (mttp) REVERT: a 179 PHE cc_start: 0.8263 (t80) cc_final: 0.8012 (t80) REVERT: a 278 MET cc_start: 0.3415 (ttp) cc_final: 0.3035 (tmm) REVERT: b 1 MET cc_start: 0.2050 (tpp) cc_final: 0.1257 (ttp) REVERT: b 107 MET cc_start: 0.5512 (mmp) cc_final: 0.4143 (mtm) REVERT: b 181 ASP cc_start: 0.7892 (m-30) cc_final: 0.7486 (p0) REVERT: c 57 MET cc_start: 0.8443 (mmp) cc_final: 0.7528 (mmm) REVERT: c 98 MET cc_start: 0.6744 (mtt) cc_final: 0.6397 (mtm) REVERT: c 104 ARG cc_start: 0.8458 (ttp-170) cc_final: 0.8060 (ttp80) REVERT: c 111 TRP cc_start: 0.7016 (p-90) cc_final: 0.6779 (p-90) REVERT: c 209 LYS cc_start: 0.6058 (mmmm) cc_final: 0.4671 (tmtt) REVERT: c 232 GLN cc_start: 0.8739 (mt0) cc_final: 0.8388 (mp10) REVERT: c 292 MET cc_start: 0.8666 (mmm) cc_final: 0.8435 (mtp) REVERT: d 125 LYS cc_start: 0.7405 (mmtt) cc_final: 0.7071 (ttpt) REVERT: d 215 TRP cc_start: 0.4688 (m-90) cc_final: 0.4476 (m100) REVERT: d 233 GLU cc_start: 0.6611 (mp0) cc_final: 0.6041 (tp30) REVERT: d 241 GLU cc_start: 0.7253 (tp30) cc_final: 0.6918 (tp30) REVERT: e 5 LYS cc_start: 0.4913 (pptt) cc_final: 0.4030 (pptt) REVERT: e 49 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7844 (pt0) REVERT: g 120 ASP cc_start: 0.8502 (m-30) cc_final: 0.8274 (m-30) REVERT: h 92 LYS cc_start: 0.8897 (mtpt) cc_final: 0.8161 (mtmm) REVERT: h 158 TRP cc_start: 0.6176 (m100) cc_final: 0.5530 (m100) REVERT: h 221 LEU cc_start: 0.7945 (tp) cc_final: 0.7631 (tp) REVERT: i 103 GLU cc_start: 0.7783 (tt0) cc_final: 0.7375 (mp0) REVERT: j 30 SER cc_start: 0.7983 (m) cc_final: 0.7720 (t) REVERT: j 67 ASP cc_start: 0.7834 (m-30) cc_final: 0.7609 (t0) REVERT: j 71 MET cc_start: 0.8594 (tpp) cc_final: 0.8353 (tpt) REVERT: k 78 MET cc_start: 0.7973 (ptp) cc_final: 0.7726 (ptp) REVERT: k 107 MET cc_start: 0.7021 (ttt) cc_final: 0.6363 (ttt) REVERT: k 225 ASN cc_start: 0.7290 (p0) cc_final: 0.6944 (p0) REVERT: l 26 MET cc_start: 0.7869 (mmt) cc_final: 0.7593 (tmm) REVERT: l 50 LYS cc_start: 0.8216 (mttt) cc_final: 0.7816 (mtmt) REVERT: l 176 MET cc_start: 0.8691 (ptm) cc_final: 0.8284 (ptp) REVERT: m 27 MET cc_start: 0.8101 (tpp) cc_final: 0.7853 (tpp) REVERT: m 47 PHE cc_start: 0.8144 (m-10) cc_final: 0.7841 (m-80) REVERT: m 50 GLU cc_start: 0.7470 (tt0) cc_final: 0.6573 (tm-30) REVERT: m 130 PRO cc_start: 0.8619 (Cg_exo) cc_final: 0.8363 (Cg_endo) REVERT: m 170 GLN cc_start: 0.8113 (mt0) cc_final: 0.7749 (tm-30) REVERT: m 181 MET cc_start: 0.7633 (ptp) cc_final: 0.7320 (ptp) REVERT: n 57 ASP cc_start: 0.8688 (t70) cc_final: 0.8434 (t0) REVERT: n 81 SER cc_start: 0.9538 (m) cc_final: 0.9333 (p) REVERT: n 89 ARG cc_start: 0.9056 (ttm110) cc_final: 0.8814 (ttm-80) REVERT: o 26 VAL cc_start: 0.8354 (t) cc_final: 0.7360 (p) REVERT: o 54 MET cc_start: 0.9093 (mmm) cc_final: 0.8691 (tmm) REVERT: o 127 MET cc_start: 0.7934 (mmm) cc_final: 0.7604 (ttm) REVERT: p 12 MET cc_start: 0.8358 (ttm) cc_final: 0.7747 (tmm) REVERT: p 80 ARG cc_start: 0.8272 (ptt180) cc_final: 0.7892 (ptp-110) REVERT: p 135 ASP cc_start: 0.8581 (p0) cc_final: 0.7864 (p0) REVERT: p 146 MET cc_start: 0.8652 (mtm) cc_final: 0.8363 (tpt) REVERT: q 28 MET cc_start: 0.9033 (mtm) cc_final: 0.8522 (mtp) REVERT: q 173 LEU cc_start: 0.9059 (tp) cc_final: 0.8725 (tp) REVERT: r 32 LYS cc_start: 0.9143 (mtpt) cc_final: 0.8939 (mttp) REVERT: r 45 MET cc_start: 0.8268 (ttm) cc_final: 0.8052 (ttm) REVERT: r 56 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8676 (mt-10) REVERT: r 139 MET cc_start: 0.7845 (ttp) cc_final: 0.7526 (tmm) REVERT: s 8 ASN cc_start: 0.8890 (m110) cc_final: 0.8578 (m110) REVERT: s 13 LEU cc_start: 0.8395 (tp) cc_final: 0.8004 (mp) REVERT: s 57 PHE cc_start: 0.8751 (t80) cc_final: 0.8015 (t80) REVERT: s 174 LEU cc_start: 0.9510 (mt) cc_final: 0.9230 (tt) REVERT: s 179 PHE cc_start: 0.8580 (m-80) cc_final: 0.7732 (m-10) REVERT: t 59 ASP cc_start: 0.8984 (m-30) cc_final: 0.8685 (m-30) REVERT: t 103 MET cc_start: 0.8919 (mmp) cc_final: 0.8706 (mmp) REVERT: t 110 MET cc_start: 0.8648 (mtm) cc_final: 0.8358 (mtt) REVERT: t 126 ASP cc_start: 0.9203 (t0) cc_final: 0.8928 (t70) REVERT: t 173 MET cc_start: 0.8807 (mmm) cc_final: 0.8482 (mmt) REVERT: t 188 GLN cc_start: 0.7929 (pt0) cc_final: 0.7357 (pt0) REVERT: A 164 MET cc_start: 0.6322 (ptm) cc_final: 0.6069 (ptp) REVERT: A 258 ARG cc_start: 0.7932 (mpt-90) cc_final: 0.7206 (tmm-80) REVERT: B 309 MET cc_start: 0.7559 (tmm) cc_final: 0.7123 (tmm) REVERT: B 319 PHE cc_start: 0.6789 (m-10) cc_final: 0.6491 (m-80) REVERT: B 328 ILE cc_start: 0.8754 (mt) cc_final: 0.8315 (mt) REVERT: C 50 ASN cc_start: 0.7972 (t0) cc_final: 0.7568 (t0) REVERT: C 158 ILE cc_start: 0.9008 (pt) cc_final: 0.8781 (tt) REVERT: C 159 LYS cc_start: 0.7555 (mtpt) cc_final: 0.7350 (mptt) REVERT: C 233 GLU cc_start: 0.8832 (tp30) cc_final: 0.8378 (tp30) REVERT: C 271 ARG cc_start: 0.6200 (ttp-170) cc_final: 0.5995 (ptt-90) REVERT: D 64 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7675 (tt0) REVERT: D 70 LYS cc_start: 0.9478 (mttt) cc_final: 0.9277 (mtmm) REVERT: D 196 ILE cc_start: 0.7262 (mt) cc_final: 0.7014 (mm) REVERT: D 345 PHE cc_start: 0.7649 (m-10) cc_final: 0.7418 (m-80) REVERT: D 351 LYS cc_start: 0.8708 (tppt) cc_final: 0.8207 (pttm) REVERT: D 384 MET cc_start: 0.6725 (mmm) cc_final: 0.6416 (mmt) REVERT: E 122 MET cc_start: 0.3999 (mtp) cc_final: 0.3548 (ptp) REVERT: E 133 SER cc_start: 0.6407 (p) cc_final: 0.6151 (m) REVERT: E 216 ARG cc_start: 0.8512 (mpt-90) cc_final: 0.8258 (mmp-170) REVERT: E 259 GLU cc_start: 0.5060 (mm-30) cc_final: 0.4643 (pt0) REVERT: F 172 VAL cc_start: 0.6273 (t) cc_final: 0.5817 (t) REVERT: F 175 MET cc_start: 0.6285 (mtt) cc_final: 0.5722 (mtt) REVERT: F 380 ASN cc_start: 0.7552 (t0) cc_final: 0.7100 (t0) REVERT: f 248 LEU cc_start: 0.5979 (tt) cc_final: 0.4873 (tt) REVERT: f 560 LEU cc_start: 0.7892 (mm) cc_final: 0.7502 (mt) outliers start: 25 outliers final: 9 residues processed: 1559 average time/residue: 0.9130 time to fit residues: 2434.5629 Evaluate side-chains 1004 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 994 time to evaluate : 8.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1285 random chunks: chunk 648 optimal weight: 30.0000 chunk 362 optimal weight: 20.0000 chunk 971 optimal weight: 20.0000 chunk 794 optimal weight: 0.0770 chunk 321 optimal weight: 6.9990 chunk 1169 optimal weight: 40.0000 chunk 1262 optimal weight: 6.9990 chunk 1041 optimal weight: 0.0010 chunk 1159 optimal weight: 2.9990 chunk 398 optimal weight: 0.0870 chunk 937 optimal weight: 10.0000 overall best weight: 2.0326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS I 20 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** J 15 HIS J 85 ASN ** J 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 HIS ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 101 ASN ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 165 ASN P 173 ASN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 188 GLN U 18 GLN ** U 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 365 GLN V 400 HIS ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 235 GLN ** W 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 264 ASN ** a 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 345 GLN b 12 ASN ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 HIS d 77 GLN d 96 HIS d 109 GLN d 116 HIS ** h 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 102 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** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 221 GLN l 121 GLN ** m 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 28 ASN ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 HIS ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN F 83 ASN f 180 GLN f 790 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 102854 Z= 0.208 Angle : 0.759 16.749 139119 Z= 0.392 Chirality : 0.047 0.395 15867 Planarity : 0.006 0.128 17980 Dihedral : 7.563 138.376 14262 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.40 % Favored : 90.42 % Rotamer: Outliers : 0.11 % Allowed : 4.33 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.67 % Twisted General : 0.22 % 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: -2.60 (0.07), residues: 12904 helix: -0.82 (0.06), residues: 5912 sheet: -1.04 (0.13), residues: 1646 loop : -3.00 (0.08), residues: 5346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP f 420 HIS 0.020 0.001 HIS C 205 PHE 0.043 0.002 PHE U 138 TYR 0.034 0.002 TYR C 148 ARG 0.015 0.001 ARG i 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1458 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1446 time to evaluate : 8.941 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: G 83 MET cc_start: 0.8411 (mpp) cc_final: 0.8067 (mpp) REVERT: G 171 LYS cc_start: 0.8618 (mmpt) cc_final: 0.8210 (tttm) REVERT: G 175 SER cc_start: 0.8736 (t) cc_final: 0.8473 (m) REVERT: H 165 LYS cc_start: 0.8471 (mttm) cc_final: 0.8217 (pttm) REVERT: J 17 PHE cc_start: 0.7467 (m-80) cc_final: 0.6654 (m-10) REVERT: J 21 TYR cc_start: 0.8603 (m-10) cc_final: 0.7941 (m-10) REVERT: J 24 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7141 (mm-30) REVERT: J 215 GLN cc_start: 0.8074 (mp10) cc_final: 0.7835 (mp10) REVERT: K 9 ASP cc_start: 0.6131 (m-30) cc_final: 0.5031 (t70) REVERT: K 29 GLU cc_start: 0.8383 (tt0) cc_final: 0.8149 (mm-30) REVERT: L 6 TYR cc_start: 0.6191 (p90) cc_final: 0.5795 (m-80) REVERT: L 26 MET cc_start: 0.8965 (mmt) cc_final: 0.8670 (mmt) REVERT: L 88 MET cc_start: 0.9169 (mtp) cc_final: 0.8969 (ptm) REVERT: L 94 ASP cc_start: 0.8697 (m-30) cc_final: 0.8384 (t0) REVERT: N 3 ILE cc_start: 0.7589 (pt) cc_final: 0.6260 (pt) REVERT: N 87 CYS cc_start: 0.9197 (t) cc_final: 0.8974 (t) REVERT: N 123 GLN cc_start: 0.8506 (mt0) cc_final: 0.8136 (mt0) REVERT: O 137 VAL cc_start: 0.8642 (t) cc_final: 0.7866 (t) REVERT: O 157 GLU cc_start: 0.9524 (tm-30) cc_final: 0.9187 (tm-30) REVERT: O 201 ARG cc_start: 0.7073 (tmt170) cc_final: 0.6330 (ptm-80) REVERT: P 50 TYR cc_start: 0.7997 (m-10) cc_final: 0.7533 (m-80) REVERT: P 70 ARG cc_start: 0.8756 (mtp180) cc_final: 0.8219 (ptm160) REVERT: P 117 PHE cc_start: 0.7784 (p90) cc_final: 0.7459 (p90) REVERT: P 169 GLN cc_start: 0.7029 (mm-40) cc_final: 0.6797 (tp40) REVERT: P 173 ASN cc_start: 0.8614 (m-40) cc_final: 0.8155 (m-40) REVERT: Q 45 LEU cc_start: 0.7936 (mt) cc_final: 0.7664 (mt) REVERT: Q 69 MET cc_start: 0.8187 (mmm) cc_final: 0.7600 (tpp) REVERT: Q 118 MET cc_start: 0.8858 (mmp) cc_final: 0.8571 (mmp) REVERT: Q 189 HIS cc_start: 0.6801 (m-70) cc_final: 0.6485 (m-70) REVERT: R 93 MET cc_start: 0.8290 (tpp) cc_final: 0.8066 (tpp) REVERT: R 175 ASN cc_start: 0.8916 (m110) cc_final: 0.8685 (m110) REVERT: S 54 CYS cc_start: 0.8269 (p) cc_final: 0.7282 (p) REVERT: S 61 CYS cc_start: 0.8674 (m) cc_final: 0.7531 (m) REVERT: S 206 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7406 (tm-30) REVERT: T 5 MET cc_start: 0.8767 (mmt) cc_final: 0.8550 (mmt) REVERT: T 26 MET cc_start: 0.7204 (ttm) cc_final: 0.6948 (ttm) REVERT: T 42 ILE cc_start: 0.9246 (mt) cc_final: 0.9026 (mp) REVERT: T 43 MET cc_start: 0.6993 (tmm) cc_final: 0.6362 (tmm) REVERT: T 50 MET cc_start: 0.8288 (ttm) cc_final: 0.7843 (tmm) REVERT: T 57 TYR cc_start: 0.7908 (t80) cc_final: 0.7478 (t80) REVERT: T 127 MET cc_start: 0.7833 (ttp) cc_final: 0.7407 (ppp) REVERT: U 244 MET cc_start: 0.4923 (ptp) cc_final: 0.4538 (mmm) REVERT: U 266 GLN cc_start: 0.7860 (tp-100) cc_final: 0.7469 (pt0) REVERT: U 340 GLN cc_start: 0.7718 (tp-100) cc_final: 0.7391 (tm-30) REVERT: U 564 ASP cc_start: 0.6851 (m-30) cc_final: 0.6302 (t70) REVERT: U 575 ASP cc_start: 0.7098 (t0) cc_final: 0.6798 (t70) REVERT: U 695 MET cc_start: 0.7596 (mtm) cc_final: 0.7324 (ptt) REVERT: U 751 ARG cc_start: 0.5910 (ttt90) cc_final: 0.4673 (ptt90) REVERT: U 905 PRO cc_start: 0.7643 (Cg_exo) cc_final: 0.7224 (Cg_endo) REVERT: V 76 LYS cc_start: 0.5811 (tttt) cc_final: 0.5454 (tmtt) REVERT: V 136 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6591 (mm-30) REVERT: V 160 LEU cc_start: 0.7869 (mt) cc_final: 0.7403 (tp) REVERT: V 181 TYR cc_start: 0.6880 (m-80) cc_final: 0.6476 (m-80) REVERT: V 488 ASN cc_start: 0.8499 (m-40) cc_final: 0.8267 (m-40) REVERT: V 496 PHE cc_start: 0.8117 (m-80) cc_final: 0.7853 (t80) REVERT: W 54 THR cc_start: 0.6602 (p) cc_final: 0.6387 (p) REVERT: W 74 CYS cc_start: 0.8507 (m) cc_final: 0.8251 (t) REVERT: W 220 GLU cc_start: 0.7508 (mp0) cc_final: 0.7239 (mp0) REVERT: W 307 LYS cc_start: 0.8428 (ttpp) cc_final: 0.7990 (mmtt) REVERT: W 425 LEU cc_start: 0.8363 (tt) cc_final: 0.8140 (mt) REVERT: X 65 GLU cc_start: 0.8799 (mp0) cc_final: 0.8576 (tp30) REVERT: X 127 GLN cc_start: 0.4824 (mt0) cc_final: 0.4457 (mm110) REVERT: X 130 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6472 (mm-30) REVERT: X 160 MET cc_start: 0.6059 (mmt) cc_final: 0.5807 (ptm) REVERT: X 388 PHE cc_start: 0.6208 (p90) cc_final: 0.5944 (p90) REVERT: X 405 GLN cc_start: 0.8932 (mt0) cc_final: 0.8095 (mm110) REVERT: X 415 TYR cc_start: 0.9262 (m-80) cc_final: 0.8957 (m-80) REVERT: Y 42 MET cc_start: 0.7435 (mmm) cc_final: 0.7095 (mtp) REVERT: Y 211 TYR cc_start: 0.6246 (p90) cc_final: 0.5571 (m-10) REVERT: Y 214 MET cc_start: 0.7028 (ptm) cc_final: 0.6827 (ptp) REVERT: Y 299 MET cc_start: 0.8733 (mmm) cc_final: 0.8444 (mmm) REVERT: Y 362 LYS cc_start: 0.7303 (mtmm) cc_final: 0.6791 (mmmt) REVERT: Y 389 MET cc_start: 0.4965 (mtt) cc_final: 0.3593 (mmp) REVERT: Z 64 ASP cc_start: 0.7549 (t70) cc_final: 0.6785 (p0) REVERT: Z 73 ASP cc_start: 0.7783 (t0) cc_final: 0.7066 (p0) REVERT: Z 84 LYS cc_start: 0.8259 (ttpt) cc_final: 0.8015 (tppt) REVERT: Z 114 ARG cc_start: 0.8218 (ptt180) cc_final: 0.7460 (ptt90) REVERT: Z 256 GLN cc_start: 0.7725 (mm110) cc_final: 0.6968 (mt0) REVERT: Z 257 MET cc_start: 0.8694 (tpt) cc_final: 0.8399 (mmm) REVERT: a 46 GLN cc_start: 0.7357 (tp-100) cc_final: 0.7007 (tm-30) REVERT: a 127 ASP cc_start: 0.6937 (m-30) cc_final: 0.6068 (t0) REVERT: a 161 LYS cc_start: 0.7826 (mmmt) cc_final: 0.7513 (mttp) REVERT: a 179 PHE cc_start: 0.8148 (t80) cc_final: 0.7853 (t80) REVERT: a 278 MET cc_start: 0.3621 (ttp) cc_final: 0.3252 (tmm) REVERT: b 1 MET cc_start: 0.2451 (tpp) cc_final: 0.1383 (ttp) REVERT: b 107 MET cc_start: 0.5454 (mmp) cc_final: 0.3964 (mtm) REVERT: b 181 ASP cc_start: 0.7838 (m-30) cc_final: 0.7455 (p0) REVERT: c 57 MET cc_start: 0.8411 (mmp) cc_final: 0.7566 (mmm) REVERT: c 98 MET cc_start: 0.6772 (mtt) cc_final: 0.6329 (mtm) REVERT: c 104 ARG cc_start: 0.8442 (ttp-170) cc_final: 0.8044 (ttp80) REVERT: c 111 TRP cc_start: 0.6564 (p-90) cc_final: 0.6329 (p-90) REVERT: c 209 LYS cc_start: 0.5969 (mmmm) cc_final: 0.4314 (tmtt) REVERT: c 213 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8052 (pm20) REVERT: c 232 GLN cc_start: 0.8726 (mt0) cc_final: 0.8319 (mp10) REVERT: c 266 THR cc_start: 0.8644 (p) cc_final: 0.8438 (t) REVERT: d 46 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7751 (mm-40) REVERT: d 95 MET cc_start: -0.2236 (mtt) cc_final: -0.2605 (mtt) REVERT: d 125 LYS cc_start: 0.7246 (mmtt) cc_final: 0.6853 (ttpt) REVERT: d 233 GLU cc_start: 0.6855 (mp0) cc_final: 0.6101 (tp30) REVERT: d 241 GLU cc_start: 0.7173 (tp30) cc_final: 0.6863 (tp30) REVERT: e 5 LYS cc_start: 0.4600 (pptt) cc_final: 0.3995 (pptt) REVERT: e 49 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7829 (pt0) REVERT: g 80 MET cc_start: 0.8162 (mmm) cc_final: 0.7439 (mmm) REVERT: h 92 LYS cc_start: 0.8867 (mtpt) cc_final: 0.8120 (mtmm) REVERT: h 221 LEU cc_start: 0.7900 (tp) cc_final: 0.7564 (tp) REVERT: i 65 ILE cc_start: 0.9066 (pt) cc_final: 0.8639 (tp) REVERT: i 103 GLU cc_start: 0.7798 (tt0) cc_final: 0.7445 (mp0) REVERT: i 172 VAL cc_start: 0.9031 (p) cc_final: 0.8795 (p) REVERT: i 227 VAL cc_start: 0.7574 (t) cc_final: 0.7145 (t) REVERT: k 59 MET cc_start: 0.7831 (ttm) cc_final: 0.7314 (ttm) REVERT: k 107 MET cc_start: 0.6920 (ttt) cc_final: 0.6333 (ttt) REVERT: k 191 LEU cc_start: 0.8246 (tp) cc_final: 0.7916 (pt) REVERT: k 206 MET cc_start: 0.8002 (ptm) cc_final: 0.7670 (ttt) REVERT: k 225 ASN cc_start: 0.7134 (p0) cc_final: 0.6760 (p0) REVERT: l 26 MET cc_start: 0.7799 (mmt) cc_final: 0.7542 (tmm) REVERT: l 50 LYS cc_start: 0.8210 (mttt) cc_final: 0.7824 (mtmt) REVERT: l 176 MET cc_start: 0.8616 (ptm) cc_final: 0.8257 (ptp) REVERT: l 179 PHE cc_start: 0.7778 (m-10) cc_final: 0.7565 (m-10) REVERT: m 27 MET cc_start: 0.8102 (tpp) cc_final: 0.7863 (tpp) REVERT: m 47 PHE cc_start: 0.8031 (m-10) cc_final: 0.7805 (m-80) REVERT: m 50 GLU cc_start: 0.7428 (tt0) cc_final: 0.6861 (tt0) REVERT: m 130 PRO cc_start: 0.8502 (Cg_exo) cc_final: 0.8261 (Cg_endo) REVERT: m 156 VAL cc_start: 0.8468 (t) cc_final: 0.7901 (t) REVERT: m 170 GLN cc_start: 0.8067 (mt0) cc_final: 0.7730 (tm-30) REVERT: m 214 SER cc_start: 0.6863 (t) cc_final: 0.6026 (t) REVERT: n 57 ASP cc_start: 0.8669 (t70) cc_final: 0.8452 (t0) REVERT: n 81 SER cc_start: 0.9460 (m) cc_final: 0.9259 (p) REVERT: n 86 MET cc_start: 0.8501 (ttm) cc_final: 0.8278 (ttm) REVERT: n 93 ASP cc_start: 0.8019 (p0) cc_final: 0.7681 (t0) REVERT: n 116 MET cc_start: 0.8172 (mtt) cc_final: 0.7800 (mtm) REVERT: n 164 MET cc_start: 0.8576 (mtm) cc_final: 0.7973 (mtt) REVERT: o 26 VAL cc_start: 0.8378 (t) cc_final: 0.7290 (p) REVERT: o 54 MET cc_start: 0.9116 (mmm) cc_final: 0.8672 (tmm) REVERT: o 82 MET cc_start: 0.8754 (mtm) cc_final: 0.8477 (mtm) REVERT: o 127 MET cc_start: 0.7786 (mmm) cc_final: 0.7556 (ttm) REVERT: p 12 MET cc_start: 0.8344 (ttm) cc_final: 0.8098 (tmm) REVERT: p 80 ARG cc_start: 0.8287 (ptt180) cc_final: 0.7954 (ptp-110) REVERT: p 129 CYS cc_start: 0.8132 (t) cc_final: 0.7860 (t) REVERT: p 135 ASP cc_start: 0.8627 (p0) cc_final: 0.7966 (p0) REVERT: p 193 ASP cc_start: 0.8024 (m-30) cc_final: 0.7297 (m-30) REVERT: p 204 MET cc_start: 0.7573 (mmm) cc_final: 0.7372 (mmm) REVERT: q 173 LEU cc_start: 0.9028 (tp) cc_final: 0.8711 (tp) REVERT: r 45 MET cc_start: 0.8181 (ttm) cc_final: 0.7800 (ttt) REVERT: r 90 TYR cc_start: 0.9107 (m-80) cc_final: 0.8892 (m-10) REVERT: r 139 MET cc_start: 0.7762 (ttp) cc_final: 0.7521 (tmm) REVERT: s 8 ASN cc_start: 0.8840 (m110) cc_final: 0.8544 (m110) REVERT: s 13 LEU cc_start: 0.8404 (tp) cc_final: 0.8009 (mp) REVERT: s 57 PHE cc_start: 0.8635 (t80) cc_final: 0.8171 (t80) REVERT: s 74 MET cc_start: 0.8581 (mpp) cc_final: 0.8271 (mpp) REVERT: s 108 ASN cc_start: 0.8529 (m-40) cc_final: 0.8200 (m-40) REVERT: s 174 LEU cc_start: 0.9510 (mt) cc_final: 0.9227 (tt) REVERT: s 179 PHE cc_start: 0.8540 (m-80) cc_final: 0.7585 (m-80) REVERT: t 5 MET cc_start: 0.8296 (tpp) cc_final: 0.8086 (tpp) REVERT: t 22 ILE cc_start: 0.9235 (pt) cc_final: 0.8990 (pt) REVERT: t 103 MET cc_start: 0.9008 (mmp) cc_final: 0.8805 (mmp) REVERT: t 173 MET cc_start: 0.8756 (mmm) cc_final: 0.8402 (mmt) REVERT: A 135 GLU cc_start: 0.7029 (pt0) cc_final: 0.6468 (pm20) REVERT: A 258 ARG cc_start: 0.7950 (mpt-90) cc_final: 0.7172 (tmm-80) REVERT: B 319 PHE cc_start: 0.6776 (m-10) cc_final: 0.6497 (m-80) REVERT: B 328 ILE cc_start: 0.8739 (mt) cc_final: 0.8289 (mt) REVERT: C 43 ARG cc_start: 0.6493 (ttt90) cc_final: 0.6204 (ptm160) REVERT: C 158 ILE cc_start: 0.8995 (pt) cc_final: 0.8776 (tt) REVERT: C 233 GLU cc_start: 0.8830 (tp30) cc_final: 0.8394 (tp30) REVERT: C 237 MET cc_start: 0.7734 (ppp) cc_final: 0.7448 (ppp) REVERT: D 64 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7998 (mm-30) REVERT: D 87 LEU cc_start: 0.7048 (mt) cc_final: 0.6780 (mp) REVERT: D 163 MET cc_start: 0.8513 (ptp) cc_final: 0.7876 (pmm) REVERT: D 183 LEU cc_start: 0.9215 (tp) cc_final: 0.9003 (tp) REVERT: D 196 ILE cc_start: 0.7182 (mt) cc_final: 0.6976 (mm) REVERT: D 345 PHE cc_start: 0.7747 (m-10) cc_final: 0.7526 (m-80) REVERT: D 351 LYS cc_start: 0.8665 (tppt) cc_final: 0.8193 (pttm) REVERT: D 384 MET cc_start: 0.6711 (mmm) cc_final: 0.6286 (mmt) REVERT: E 121 ASN cc_start: 0.6369 (m110) cc_final: 0.6117 (p0) REVERT: E 122 MET cc_start: 0.3890 (mtp) cc_final: 0.3595 (ptp) REVERT: E 133 SER cc_start: 0.6298 (p) cc_final: 0.6021 (m) REVERT: E 155 ASN cc_start: 0.8580 (t0) cc_final: 0.8103 (m110) REVERT: E 216 ARG cc_start: 0.8490 (mpt-90) cc_final: 0.8252 (mmp-170) REVERT: E 259 GLU cc_start: 0.5086 (mm-30) cc_final: 0.4577 (pt0) REVERT: E 275 MET cc_start: 0.4575 (mtt) cc_final: 0.4040 (mtt) REVERT: E 303 LEU cc_start: 0.7025 (mp) cc_final: 0.6786 (mp) REVERT: E 368 MET cc_start: 0.2514 (mmp) cc_final: 0.2253 (mmm) REVERT: F 172 VAL cc_start: 0.6294 (t) cc_final: 0.5878 (t) REVERT: F 175 MET cc_start: 0.6290 (mtt) cc_final: 0.5660 (mtp) REVERT: F 380 ASN cc_start: 0.7525 (t0) cc_final: 0.7018 (t0) REVERT: f 80 ARG cc_start: 0.4118 (ptt90) cc_final: 0.3629 (ptt90) REVERT: f 248 LEU cc_start: 0.5856 (tt) cc_final: 0.4970 (tt) REVERT: f 560 LEU cc_start: 0.8284 (mm) cc_final: 0.7416 (mt) outliers start: 12 outliers final: 5 residues processed: 1456 average time/residue: 0.8945 time to fit residues: 2241.1335 Evaluate side-chains 1005 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1000 time to evaluate : 8.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1285 random chunks: chunk 1155 optimal weight: 30.0000 chunk 878 optimal weight: 7.9990 chunk 606 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 557 optimal weight: 6.9990 chunk 784 optimal weight: 1.9990 chunk 1173 optimal weight: 4.9990 chunk 1242 optimal weight: 20.0000 chunk 612 optimal weight: 20.0000 chunk 1111 optimal weight: 2.9990 chunk 334 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 GLN I 240 HIS ** J 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 101 ASN ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN S 163 HIS U 18 GLN ** U 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 GLN V 109 ASN ** V 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 99 GLN W 218 ASN ** W 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 HIS ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 HIS d 77 GLN d 96 HIS d 109 GLN h 71 HIS ** h 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 102 GLN i 109 GLN ** i 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 114 GLN k 152 GLN ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 HIS ** n 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 187 GLN ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN B 241 ASN C 36 ASN ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN F 436 GLN ** f 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 102854 Z= 0.256 Angle : 0.775 15.384 139119 Z= 0.399 Chirality : 0.047 0.345 15867 Planarity : 0.006 0.121 17980 Dihedral : 7.406 140.729 14262 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.03 % Favored : 89.82 % Rotamer: Outliers : 0.06 % Allowed : 3.72 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.67 % Twisted General : 0.18 % 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: -2.31 (0.07), residues: 12904 helix: -0.56 (0.07), residues: 5912 sheet: -0.89 (0.13), residues: 1637 loop : -2.88 (0.08), residues: 5355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP f 420 HIS 0.020 0.001 HIS f 301 PHE 0.033 0.002 PHE Z 69 TYR 0.029 0.002 TYR C 148 ARG 0.018 0.001 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1271 time to evaluate : 8.739 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: G 83 MET cc_start: 0.8476 (mpp) cc_final: 0.8000 (mpp) REVERT: G 175 SER cc_start: 0.8823 (t) cc_final: 0.8538 (m) REVERT: H 165 LYS cc_start: 0.8672 (mttm) cc_final: 0.8199 (ptmm) REVERT: J 17 PHE cc_start: 0.7377 (m-80) cc_final: 0.6402 (m-10) REVERT: J 21 TYR cc_start: 0.8715 (m-10) cc_final: 0.7964 (m-80) REVERT: J 24 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7192 (mm-30) REVERT: J 127 PHE cc_start: 0.7704 (m-10) cc_final: 0.7417 (m-10) REVERT: K 78 MET cc_start: 0.6082 (ptm) cc_final: 0.5862 (tmm) REVERT: L 5 GLN cc_start: 0.8121 (pm20) cc_final: 0.7716 (pp30) REVERT: L 6 TYR cc_start: 0.6353 (p90) cc_final: 0.5679 (p90) REVERT: L 26 MET cc_start: 0.9013 (mmt) cc_final: 0.8523 (mmt) REVERT: L 27 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8819 (mm-30) REVERT: L 63 ILE cc_start: 0.9284 (mt) cc_final: 0.9049 (tt) REVERT: L 88 MET cc_start: 0.9229 (mtp) cc_final: 0.8984 (ptm) REVERT: M 181 MET cc_start: 0.6752 (ptp) cc_final: 0.5959 (ptp) REVERT: N 87 CYS cc_start: 0.9249 (t) cc_final: 0.9037 (t) REVERT: N 123 GLN cc_start: 0.8630 (mt0) cc_final: 0.8193 (mt0) REVERT: O 63 LEU cc_start: 0.9195 (mm) cc_final: 0.8809 (tp) REVERT: O 201 ARG cc_start: 0.6928 (tmt170) cc_final: 0.6403 (ptm-80) REVERT: P 50 TYR cc_start: 0.8036 (m-10) cc_final: 0.7804 (m-80) REVERT: P 117 PHE cc_start: 0.7901 (p90) cc_final: 0.7586 (p90) REVERT: P 151 GLU cc_start: 0.8471 (tp30) cc_final: 0.8153 (tp30) REVERT: Q 69 MET cc_start: 0.8408 (mmm) cc_final: 0.7718 (tpp) REVERT: Q 189 HIS cc_start: 0.6762 (m-70) cc_final: 0.6443 (m-70) REVERT: R 56 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8657 (pp20) REVERT: R 93 MET cc_start: 0.8316 (tpp) cc_final: 0.8028 (tpp) REVERT: R 175 ASN cc_start: 0.8966 (m110) cc_final: 0.8704 (m110) REVERT: R 197 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7981 (mm-30) REVERT: S 54 CYS cc_start: 0.8230 (p) cc_final: 0.7179 (p) REVERT: S 61 CYS cc_start: 0.8666 (m) cc_final: 0.7472 (m) REVERT: T 5 MET cc_start: 0.8840 (mmt) cc_final: 0.8497 (mmt) REVERT: T 26 MET cc_start: 0.7216 (ttm) cc_final: 0.6813 (ttm) REVERT: T 43 MET cc_start: 0.6950 (tmm) cc_final: 0.6448 (tmm) REVERT: T 127 MET cc_start: 0.7799 (ttp) cc_final: 0.7487 (ppp) REVERT: U 196 LYS cc_start: 0.8728 (mttt) cc_final: 0.8510 (mtmm) REVERT: U 244 MET cc_start: 0.4988 (ptp) cc_final: 0.4404 (mmm) REVERT: U 266 GLN cc_start: 0.7911 (tp-100) cc_final: 0.7536 (pt0) REVERT: U 340 GLN cc_start: 0.7814 (tp-100) cc_final: 0.7473 (tm-30) REVERT: U 564 ASP cc_start: 0.7360 (m-30) cc_final: 0.7089 (t70) REVERT: U 695 MET cc_start: 0.7674 (mtm) cc_final: 0.7385 (ptt) REVERT: U 725 MET cc_start: 0.6934 (mpp) cc_final: 0.6677 (mpp) REVERT: U 751 ARG cc_start: 0.6052 (ttt90) cc_final: 0.4766 (ptt-90) REVERT: U 905 PRO cc_start: 0.7673 (Cg_exo) cc_final: 0.7286 (Cg_endo) REVERT: V 76 LYS cc_start: 0.5803 (tttt) cc_final: 0.5596 (tmtt) REVERT: V 112 VAL cc_start: 0.5775 (t) cc_final: 0.5559 (t) REVERT: V 200 ARG cc_start: 0.5007 (mmm160) cc_final: 0.3781 (mtm180) REVERT: V 488 ASN cc_start: 0.8445 (m-40) cc_final: 0.8223 (m-40) REVERT: V 496 PHE cc_start: 0.8162 (m-80) cc_final: 0.7864 (t80) REVERT: W 74 CYS cc_start: 0.8417 (m) cc_final: 0.8165 (t) REVERT: W 307 LYS cc_start: 0.8494 (ttpp) cc_final: 0.8072 (mmtt) REVERT: W 315 MET cc_start: 0.1741 (pmm) cc_final: 0.1272 (ttt) REVERT: X 130 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6476 (mm-30) REVERT: X 160 MET cc_start: 0.6124 (mmt) cc_final: 0.5883 (tmm) REVERT: X 388 PHE cc_start: 0.6318 (p90) cc_final: 0.6074 (p90) REVERT: X 405 GLN cc_start: 0.8964 (mt0) cc_final: 0.8070 (mm110) REVERT: X 415 TYR cc_start: 0.9246 (m-80) cc_final: 0.8943 (m-80) REVERT: Y 42 MET cc_start: 0.7433 (mmm) cc_final: 0.7090 (mtp) REVERT: Y 211 TYR cc_start: 0.6299 (p90) cc_final: 0.5649 (m-10) REVERT: Y 214 MET cc_start: 0.7064 (ptm) cc_final: 0.6848 (ptp) REVERT: Y 362 LYS cc_start: 0.7523 (mtmm) cc_final: 0.7192 (mtmt) REVERT: Y 389 MET cc_start: 0.4948 (mtt) cc_final: 0.3586 (mmp) REVERT: Z 64 ASP cc_start: 0.7643 (t70) cc_final: 0.6864 (p0) REVERT: Z 73 ASP cc_start: 0.7671 (t0) cc_final: 0.7022 (p0) REVERT: Z 84 LYS cc_start: 0.8295 (ttpt) cc_final: 0.8066 (tppt) REVERT: Z 114 ARG cc_start: 0.8272 (ptt180) cc_final: 0.7505 (ptt90) REVERT: Z 256 GLN cc_start: 0.7941 (mm110) cc_final: 0.7701 (pt0) REVERT: Z 257 MET cc_start: 0.8630 (tpt) cc_final: 0.8390 (mmm) REVERT: Z 262 LEU cc_start: 0.8746 (mt) cc_final: 0.8502 (mt) REVERT: a 46 GLN cc_start: 0.7366 (tp-100) cc_final: 0.7061 (tm-30) REVERT: a 127 ASP cc_start: 0.6978 (m-30) cc_final: 0.6059 (t0) REVERT: a 161 LYS cc_start: 0.7873 (mmmt) cc_final: 0.7580 (mptt) REVERT: a 179 PHE cc_start: 0.8162 (t80) cc_final: 0.7863 (t80) REVERT: a 278 MET cc_start: 0.3495 (ttp) cc_final: 0.3193 (tmm) REVERT: b 1 MET cc_start: 0.2442 (tpp) cc_final: 0.1141 (ttp) REVERT: b 107 MET cc_start: 0.5440 (mmp) cc_final: 0.3906 (mtm) REVERT: b 181 ASP cc_start: 0.7789 (m-30) cc_final: 0.7392 (p0) REVERT: c 57 MET cc_start: 0.8482 (mmp) cc_final: 0.7678 (mmm) REVERT: c 98 MET cc_start: 0.6856 (mtt) cc_final: 0.6423 (mtm) REVERT: c 104 ARG cc_start: 0.8505 (ttp-170) cc_final: 0.8080 (ttp80) REVERT: c 232 GLN cc_start: 0.8834 (mt0) cc_final: 0.8292 (mp10) REVERT: d 95 MET cc_start: -0.2195 (mtt) cc_final: -0.2536 (mtt) REVERT: d 125 LYS cc_start: 0.7231 (mmtt) cc_final: 0.6814 (ttpt) REVERT: d 215 TRP cc_start: 0.3454 (m100) cc_final: 0.2786 (m-10) REVERT: d 233 GLU cc_start: 0.6859 (mp0) cc_final: 0.6045 (tp30) REVERT: d 241 GLU cc_start: 0.7218 (tp30) cc_final: 0.6941 (tp30) REVERT: e 5 LYS cc_start: 0.4765 (pptt) cc_final: 0.4203 (pptt) REVERT: h 58 ASP cc_start: 0.8150 (t0) cc_final: 0.7943 (t70) REVERT: h 92 LYS cc_start: 0.8893 (mtpt) cc_final: 0.8189 (mtmm) REVERT: h 158 TRP cc_start: 0.6759 (m100) cc_final: 0.6447 (m100) REVERT: h 221 LEU cc_start: 0.7876 (tp) cc_final: 0.7615 (tp) REVERT: i 103 GLU cc_start: 0.7854 (tt0) cc_final: 0.7456 (mp0) REVERT: k 59 MET cc_start: 0.7914 (ttm) cc_final: 0.7381 (ttm) REVERT: k 191 LEU cc_start: 0.8275 (tp) cc_final: 0.7909 (pt) REVERT: k 206 MET cc_start: 0.8021 (ptm) cc_final: 0.7732 (ttt) REVERT: l 26 MET cc_start: 0.7833 (mmt) cc_final: 0.7579 (tmm) REVERT: l 50 LYS cc_start: 0.8419 (mttt) cc_final: 0.8168 (mtmt) REVERT: l 176 MET cc_start: 0.8545 (ptm) cc_final: 0.8191 (ptp) REVERT: l 179 PHE cc_start: 0.7729 (m-10) cc_final: 0.7481 (m-10) REVERT: m 50 GLU cc_start: 0.7311 (tt0) cc_final: 0.6696 (tt0) REVERT: m 130 PRO cc_start: 0.8467 (Cg_exo) cc_final: 0.8256 (Cg_endo) REVERT: m 156 VAL cc_start: 0.8738 (t) cc_final: 0.8309 (t) REVERT: m 170 GLN cc_start: 0.8065 (mt0) cc_final: 0.7725 (tm-30) REVERT: m 214 SER cc_start: 0.7153 (t) cc_final: 0.6418 (t) REVERT: n 57 ASP cc_start: 0.8689 (t70) cc_final: 0.8371 (t0) REVERT: n 81 SER cc_start: 0.9436 (m) cc_final: 0.9212 (p) REVERT: n 86 MET cc_start: 0.8463 (ttm) cc_final: 0.8213 (ttm) REVERT: n 95 MET cc_start: 0.7666 (tpp) cc_final: 0.7319 (tpt) REVERT: n 116 MET cc_start: 0.8067 (mtt) cc_final: 0.7513 (mtm) REVERT: n 164 MET cc_start: 0.8640 (mtm) cc_final: 0.7989 (mtt) REVERT: o 26 VAL cc_start: 0.8416 (t) cc_final: 0.7342 (p) REVERT: o 54 MET cc_start: 0.9172 (mmm) cc_final: 0.8681 (tmm) REVERT: o 82 MET cc_start: 0.8801 (mtm) cc_final: 0.8528 (mtm) REVERT: o 127 MET cc_start: 0.7859 (mmm) cc_final: 0.7279 (mtt) REVERT: p 129 CYS cc_start: 0.8366 (t) cc_final: 0.8099 (t) REVERT: p 135 ASP cc_start: 0.8645 (p0) cc_final: 0.8000 (p0) REVERT: p 144 GLU cc_start: 0.8489 (pm20) cc_final: 0.8271 (pm20) REVERT: p 146 MET cc_start: 0.8986 (mpp) cc_final: 0.8602 (mpp) REVERT: p 204 MET cc_start: 0.7740 (mmm) cc_final: 0.7402 (mmm) REVERT: q 28 MET cc_start: 0.9063 (mtm) cc_final: 0.8788 (mtm) REVERT: q 35 MET cc_start: 0.8475 (mtt) cc_final: 0.8036 (ppp) REVERT: q 38 MET cc_start: 0.8623 (tpt) cc_final: 0.8422 (tpp) REVERT: q 158 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8634 (mp0) REVERT: q 173 LEU cc_start: 0.8990 (tp) cc_final: 0.8600 (tp) REVERT: r 21 THR cc_start: 0.5532 (p) cc_final: 0.5245 (t) REVERT: r 45 MET cc_start: 0.8156 (ttm) cc_final: 0.7817 (ttt) REVERT: r 90 TYR cc_start: 0.9156 (m-80) cc_final: 0.8707 (m-10) REVERT: r 139 MET cc_start: 0.7784 (ttp) cc_final: 0.7370 (tmm) REVERT: s 8 ASN cc_start: 0.8860 (m110) cc_final: 0.8575 (m110) REVERT: s 13 LEU cc_start: 0.8435 (tp) cc_final: 0.7948 (mp) REVERT: s 57 PHE cc_start: 0.8658 (t80) cc_final: 0.8155 (t80) REVERT: s 74 MET cc_start: 0.8585 (mpp) cc_final: 0.8244 (mpp) REVERT: s 174 LEU cc_start: 0.9522 (mt) cc_final: 0.9212 (tt) REVERT: s 179 PHE cc_start: 0.8575 (m-80) cc_final: 0.7652 (m-80) REVERT: t 22 ILE cc_start: 0.9236 (pt) cc_final: 0.8205 (pt) REVERT: t 26 MET cc_start: 0.5801 (mpp) cc_final: 0.4757 (mpp) REVERT: t 173 MET cc_start: 0.8807 (mmm) cc_final: 0.8467 (mmt) REVERT: t 188 GLN cc_start: 0.8028 (pt0) cc_final: 0.7247 (pt0) REVERT: A 135 GLU cc_start: 0.7016 (pt0) cc_final: 0.6475 (pm20) REVERT: A 258 ARG cc_start: 0.7851 (mpt-90) cc_final: 0.7058 (tmm-80) REVERT: C 43 ARG cc_start: 0.6543 (ttt90) cc_final: 0.6222 (ptm160) REVERT: D 345 PHE cc_start: 0.7805 (m-10) cc_final: 0.7540 (m-80) REVERT: D 351 LYS cc_start: 0.8746 (tppt) cc_final: 0.8260 (pttm) REVERT: D 384 MET cc_start: 0.6669 (mmm) cc_final: 0.6299 (mmt) REVERT: E 121 ASN cc_start: 0.6385 (m110) cc_final: 0.6141 (p0) REVERT: E 122 MET cc_start: 0.3991 (mtp) cc_final: 0.3598 (ptp) REVERT: E 133 SER cc_start: 0.6180 (p) cc_final: 0.5899 (m) REVERT: E 275 MET cc_start: 0.4949 (mtt) cc_final: 0.4524 (mtt) REVERT: F 172 VAL cc_start: 0.6289 (t) cc_final: 0.5827 (t) REVERT: F 175 MET cc_start: 0.6489 (mtt) cc_final: 0.5765 (mtp) REVERT: F 380 ASN cc_start: 0.7651 (t0) cc_final: 0.7119 (t0) REVERT: f 190 GLU cc_start: 0.6715 (pt0) cc_final: 0.6155 (pt0) REVERT: f 248 LEU cc_start: 0.5872 (tt) cc_final: 0.4683 (tt) REVERT: f 560 LEU cc_start: 0.8394 (mm) cc_final: 0.7560 (mt) REVERT: f 788 MET cc_start: 0.5157 (pmm) cc_final: 0.4954 (pmm) outliers start: 6 outliers final: 3 residues processed: 1277 average time/residue: 0.8952 time to fit residues: 1983.0235 Evaluate side-chains 926 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 922 time to evaluate : 8.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1285 random chunks: chunk 1034 optimal weight: 50.0000 chunk 705 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 924 optimal weight: 6.9990 chunk 512 optimal weight: 7.9990 chunk 1059 optimal weight: 8.9990 chunk 858 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 634 optimal weight: 2.9990 chunk 1114 optimal weight: 40.0000 chunk 313 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN H 169 ASN I 30 HIS ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 GLN ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 ASN O 165 ASN P 33 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN S 163 HIS U 18 GLN ** U 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 33 GLN ** V 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 362 ASN ** X 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 48 ASN ** a 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 345 GLN ** a 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 GLN b 161 ASN ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 176 GLN c 183 HIS d 96 HIS d 109 GLN ** h 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 HIS ** 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** k 155 HIS ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 121 GLN ** n 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 187 GLN q 27 GLN ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 38 ASN ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 HIS F 83 ASN F 207 ASN ** f 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 102854 Z= 0.271 Angle : 0.779 20.229 139119 Z= 0.402 Chirality : 0.047 0.461 15867 Planarity : 0.006 0.116 17980 Dihedral : 7.339 140.352 14262 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.14 % Favored : 89.72 % Rotamer: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.67 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.07), residues: 12904 helix: -0.43 (0.07), residues: 5922 sheet: -0.86 (0.13), residues: 1654 loop : -2.85 (0.08), residues: 5328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP f 420 HIS 0.018 0.001 HIS f 301 PHE 0.030 0.002 PHE U 68 TYR 0.033 0.002 TYR U 682 ARG 0.015 0.001 ARG e 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1228 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1222 time to evaluate : 9.051 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: G 83 MET cc_start: 0.8530 (mpp) cc_final: 0.7867 (mpp) REVERT: G 175 SER cc_start: 0.8872 (t) cc_final: 0.8568 (m) REVERT: H 165 LYS cc_start: 0.8594 (mttm) cc_final: 0.8260 (pttm) REVERT: H 203 MET cc_start: 0.7038 (mmm) cc_final: 0.6609 (mpp) REVERT: J 24 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7270 (mm-30) REVERT: K 59 MET cc_start: 0.5009 (ttt) cc_final: 0.4807 (ttt) REVERT: K 78 MET cc_start: 0.6273 (ptm) cc_final: 0.6002 (tmm) REVERT: L 5 GLN cc_start: 0.8191 (pm20) cc_final: 0.7967 (pm20) REVERT: L 6 TYR cc_start: 0.6199 (p90) cc_final: 0.5675 (p90) REVERT: L 26 MET cc_start: 0.9066 (mmt) cc_final: 0.8698 (mmt) REVERT: M 181 MET cc_start: 0.6916 (ptp) cc_final: 0.6112 (ptp) REVERT: N 123 GLN cc_start: 0.8758 (mt0) cc_final: 0.8316 (mt0) REVERT: O 44 CYS cc_start: 0.8978 (m) cc_final: 0.8752 (m) REVERT: O 201 ARG cc_start: 0.6979 (tmt170) cc_final: 0.6381 (ptm-80) REVERT: P 50 TYR cc_start: 0.8023 (m-10) cc_final: 0.7804 (m-80) REVERT: P 151 GLU cc_start: 0.8526 (tp30) cc_final: 0.8257 (tp30) REVERT: Q 38 MET cc_start: 0.9100 (tpt) cc_final: 0.8209 (tpp) REVERT: Q 69 MET cc_start: 0.8535 (mmm) cc_final: 0.7850 (tpp) REVERT: Q 189 HIS cc_start: 0.6653 (m-70) cc_final: 0.6341 (m-70) REVERT: R 56 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8613 (pp20) REVERT: R 93 MET cc_start: 0.8293 (tpp) cc_final: 0.8016 (tpp) REVERT: R 175 ASN cc_start: 0.8964 (m110) cc_final: 0.8647 (m110) REVERT: R 197 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8092 (mm-30) REVERT: S 54 CYS cc_start: 0.8221 (p) cc_final: 0.7185 (p) REVERT: S 61 CYS cc_start: 0.8685 (m) cc_final: 0.7352 (m) REVERT: T 5 MET cc_start: 0.8869 (mmt) cc_final: 0.8498 (mmt) REVERT: T 26 MET cc_start: 0.7283 (ttm) cc_final: 0.6665 (ttm) REVERT: T 43 MET cc_start: 0.6803 (tmm) cc_final: 0.6505 (tmm) REVERT: T 127 MET cc_start: 0.7744 (ttp) cc_final: 0.7477 (ppp) REVERT: U 196 LYS cc_start: 0.8741 (mttt) cc_final: 0.8513 (mtmm) REVERT: U 244 MET cc_start: 0.5071 (ptp) cc_final: 0.4371 (mmm) REVERT: U 266 GLN cc_start: 0.7920 (tp-100) cc_final: 0.7536 (pt0) REVERT: U 340 GLN cc_start: 0.7891 (tp-100) cc_final: 0.7534 (tm-30) REVERT: U 564 ASP cc_start: 0.7347 (m-30) cc_final: 0.6936 (t70) REVERT: U 695 MET cc_start: 0.7772 (mtm) cc_final: 0.7474 (ptt) REVERT: U 725 MET cc_start: 0.7022 (mpp) cc_final: 0.6616 (mpp) REVERT: U 751 ARG cc_start: 0.6208 (ttt90) cc_final: 0.4905 (ptt-90) REVERT: U 905 PRO cc_start: 0.7699 (Cg_exo) cc_final: 0.7313 (Cg_endo) REVERT: V 136 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6932 (mm-30) REVERT: V 177 ASN cc_start: 0.7218 (m-40) cc_final: 0.6687 (m110) REVERT: V 181 TYR cc_start: 0.6977 (m-80) cc_final: 0.6642 (m-80) REVERT: V 200 ARG cc_start: 0.4849 (mmm160) cc_final: 0.3565 (mtm180) REVERT: V 496 PHE cc_start: 0.8161 (m-80) cc_final: 0.7928 (t80) REVERT: W 74 CYS cc_start: 0.8445 (m) cc_final: 0.8165 (t) REVERT: W 220 GLU cc_start: 0.7969 (tp30) cc_final: 0.7342 (mp0) REVERT: W 307 LYS cc_start: 0.8504 (ttpp) cc_final: 0.8042 (mmtt) REVERT: W 315 MET cc_start: 0.1593 (pmm) cc_final: 0.1264 (ttm) REVERT: W 405 LYS cc_start: 0.9069 (ttmt) cc_final: 0.8825 (tttm) REVERT: W 419 LYS cc_start: 0.3800 (mptt) cc_final: 0.3579 (mmtm) REVERT: W 436 MET cc_start: 0.9382 (ttm) cc_final: 0.9134 (tpp) REVERT: X 66 LEU cc_start: -0.1188 (tp) cc_final: -0.1671 (tp) REVERT: X 130 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6641 (mm-30) REVERT: X 160 MET cc_start: 0.6222 (mmt) cc_final: 0.5873 (tmm) REVERT: X 415 TYR cc_start: 0.9247 (m-80) cc_final: 0.8900 (m-80) REVERT: Y 42 MET cc_start: 0.7226 (mmm) cc_final: 0.6880 (mtp) REVERT: Y 211 TYR cc_start: 0.6390 (p90) cc_final: 0.5701 (m-10) REVERT: Y 214 MET cc_start: 0.6964 (ptm) cc_final: 0.6730 (ptp) REVERT: Y 389 MET cc_start: 0.4970 (mtt) cc_final: 0.3726 (mmp) REVERT: Z 64 ASP cc_start: 0.7874 (t70) cc_final: 0.7060 (p0) REVERT: Z 73 ASP cc_start: 0.7665 (t0) cc_final: 0.6971 (p0) REVERT: Z 84 LYS cc_start: 0.8282 (ttpt) cc_final: 0.8045 (tppt) REVERT: Z 114 ARG cc_start: 0.8284 (ptt180) cc_final: 0.7527 (ptt90) REVERT: a 46 GLN cc_start: 0.7369 (tp-100) cc_final: 0.7075 (tm-30) REVERT: a 161 LYS cc_start: 0.7799 (mmmt) cc_final: 0.7401 (mptt) REVERT: a 179 PHE cc_start: 0.8144 (t80) cc_final: 0.7846 (t80) REVERT: b 1 MET cc_start: 0.2604 (tpp) cc_final: 0.1396 (ttp) REVERT: b 181 ASP cc_start: 0.7835 (m-30) cc_final: 0.7419 (p0) REVERT: c 57 MET cc_start: 0.8513 (mmp) cc_final: 0.7653 (mmm) REVERT: c 95 MET cc_start: 0.8281 (tpt) cc_final: 0.8073 (tpp) REVERT: c 98 MET cc_start: 0.6676 (mtt) cc_final: 0.6325 (mtm) REVERT: c 104 ARG cc_start: 0.8551 (ttp-170) cc_final: 0.8071 (ttp80) REVERT: c 232 GLN cc_start: 0.8910 (mt0) cc_final: 0.8233 (mp10) REVERT: c 248 MET cc_start: 0.8574 (ptm) cc_final: 0.7720 (ptm) REVERT: d 95 MET cc_start: -0.1830 (mtt) cc_final: -0.2114 (mtt) REVERT: d 125 LYS cc_start: 0.7107 (mmtt) cc_final: 0.6692 (ttpt) REVERT: d 215 TRP cc_start: 0.3667 (m100) cc_final: 0.3453 (m-90) REVERT: d 233 GLU cc_start: 0.6857 (mp0) cc_final: 0.6033 (tp30) REVERT: d 241 GLU cc_start: 0.7268 (tp30) cc_final: 0.6985 (tp30) REVERT: e 5 LYS cc_start: 0.4748 (pptt) cc_final: 0.4050 (pptt) REVERT: h 58 ASP cc_start: 0.8267 (t0) cc_final: 0.8056 (t70) REVERT: h 92 LYS cc_start: 0.8950 (mtpt) cc_final: 0.8208 (mtmm) REVERT: h 158 TRP cc_start: 0.6623 (m100) cc_final: 0.6322 (m100) REVERT: h 221 LEU cc_start: 0.7816 (tp) cc_final: 0.7576 (tp) REVERT: i 103 GLU cc_start: 0.7844 (tt0) cc_final: 0.7461 (mp0) REVERT: i 227 VAL cc_start: 0.7627 (t) cc_final: 0.7162 (p) REVERT: k 59 MET cc_start: 0.7879 (ttm) cc_final: 0.7374 (ttm) REVERT: k 189 MET cc_start: 0.8524 (mmp) cc_final: 0.7752 (mmm) REVERT: k 206 MET cc_start: 0.8043 (ptm) cc_final: 0.7813 (ttt) REVERT: l 26 MET cc_start: 0.7880 (mmt) cc_final: 0.7600 (tmm) REVERT: l 50 LYS cc_start: 0.8571 (mttt) cc_final: 0.8305 (mtmt) REVERT: l 176 MET cc_start: 0.8468 (ptm) cc_final: 0.8125 (ptp) REVERT: l 179 PHE cc_start: 0.7698 (m-10) cc_final: 0.7456 (m-10) REVERT: m 50 GLU cc_start: 0.7328 (tt0) cc_final: 0.6445 (tm-30) REVERT: m 156 VAL cc_start: 0.8820 (t) cc_final: 0.8381 (t) REVERT: m 170 GLN cc_start: 0.8054 (mt0) cc_final: 0.7717 (tm-30) REVERT: n 81 SER cc_start: 0.9362 (m) cc_final: 0.9095 (p) REVERT: n 95 MET cc_start: 0.7708 (tpp) cc_final: 0.7315 (tpp) REVERT: n 116 MET cc_start: 0.8031 (mtt) cc_final: 0.7595 (mtm) REVERT: o 26 VAL cc_start: 0.8480 (t) cc_final: 0.7382 (p) REVERT: o 54 MET cc_start: 0.9196 (mmm) cc_final: 0.8731 (tmm) REVERT: o 82 MET cc_start: 0.8818 (mtm) cc_final: 0.8535 (mtm) REVERT: o 86 MET cc_start: 0.9043 (ttm) cc_final: 0.8786 (ttp) REVERT: o 127 MET cc_start: 0.7895 (mmm) cc_final: 0.7165 (mtt) REVERT: o 149 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8056 (tm-30) REVERT: p 34 MET cc_start: 0.8158 (ppp) cc_final: 0.7667 (ppp) REVERT: p 88 MET cc_start: 0.9160 (mmm) cc_final: 0.8896 (mmm) REVERT: p 135 ASP cc_start: 0.8700 (p0) cc_final: 0.8070 (p0) REVERT: p 158 MET cc_start: 0.8154 (tpp) cc_final: 0.7834 (tpp) REVERT: p 204 MET cc_start: 0.7783 (mmm) cc_final: 0.7482 (mmm) REVERT: q 28 MET cc_start: 0.9014 (mtm) cc_final: 0.8766 (mtm) REVERT: q 35 MET cc_start: 0.8518 (mtt) cc_final: 0.8174 (ppp) REVERT: q 118 MET cc_start: 0.8483 (mmt) cc_final: 0.8172 (mmt) REVERT: q 173 LEU cc_start: 0.9068 (tp) cc_final: 0.8636 (tp) REVERT: r 21 THR cc_start: 0.5586 (p) cc_final: 0.5243 (t) REVERT: r 45 MET cc_start: 0.8123 (ttm) cc_final: 0.7912 (ttm) REVERT: r 90 TYR cc_start: 0.9174 (m-80) cc_final: 0.8657 (m-10) REVERT: r 97 MET cc_start: 0.7152 (tmm) cc_final: 0.6867 (tmm) REVERT: r 139 MET cc_start: 0.7803 (ttp) cc_final: 0.7438 (tmm) REVERT: r 175 ASN cc_start: 0.9326 (m-40) cc_final: 0.9079 (t0) REVERT: s 8 ASN cc_start: 0.8866 (m110) cc_final: 0.8561 (m110) REVERT: s 13 LEU cc_start: 0.8508 (tp) cc_final: 0.8039 (mp) REVERT: s 57 PHE cc_start: 0.8642 (t80) cc_final: 0.8080 (t80) REVERT: s 74 MET cc_start: 0.8527 (mpp) cc_final: 0.8251 (mpp) REVERT: s 174 LEU cc_start: 0.9531 (mt) cc_final: 0.9225 (tt) REVERT: s 179 PHE cc_start: 0.8130 (m-80) cc_final: 0.7729 (m-80) REVERT: t 26 MET cc_start: 0.6126 (mpp) cc_final: 0.5798 (mpp) REVERT: t 43 MET cc_start: 0.7865 (tmm) cc_final: 0.7307 (tmm) REVERT: t 173 MET cc_start: 0.8828 (mmm) cc_final: 0.8615 (mmm) REVERT: A 258 ARG cc_start: 0.7841 (mpt-90) cc_final: 0.7068 (tmm-80) REVERT: A 268 LYS cc_start: 0.3849 (pptt) cc_final: 0.3126 (tppt) REVERT: A 362 MET cc_start: 0.7742 (mmm) cc_final: 0.7520 (mmm) REVERT: B 288 ASP cc_start: 0.6211 (p0) cc_final: 0.5879 (p0) REVERT: D 122 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6817 (mm-30) REVERT: D 351 LYS cc_start: 0.8821 (tppt) cc_final: 0.8298 (pttm) REVERT: D 384 MET cc_start: 0.6704 (mmm) cc_final: 0.6331 (mmt) REVERT: E 93 LYS cc_start: 0.9224 (mttt) cc_final: 0.8981 (mmmt) REVERT: E 121 ASN cc_start: 0.6257 (m110) cc_final: 0.6013 (p0) REVERT: E 122 MET cc_start: 0.3861 (mtp) cc_final: 0.3502 (ptp) REVERT: E 133 SER cc_start: 0.6264 (p) cc_final: 0.6020 (m) REVERT: E 218 MET cc_start: 0.7231 (mtm) cc_final: 0.6862 (mtm) REVERT: E 275 MET cc_start: 0.5058 (mtt) cc_final: 0.4800 (mtt) REVERT: E 305 ASN cc_start: 0.7299 (t0) cc_final: 0.6569 (p0) REVERT: F 172 VAL cc_start: 0.6323 (t) cc_final: 0.5900 (t) REVERT: F 175 MET cc_start: 0.6589 (mtt) cc_final: 0.5824 (mtp) REVERT: F 380 ASN cc_start: 0.7686 (t0) cc_final: 0.7108 (t0) REVERT: f 80 ARG cc_start: 0.4116 (ptt90) cc_final: 0.3458 (ptt90) REVERT: f 248 LEU cc_start: 0.5886 (tt) cc_final: 0.4798 (tt) REVERT: f 626 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7050 (mm-30) outliers start: 6 outliers final: 3 residues processed: 1228 average time/residue: 0.9431 time to fit residues: 2022.9237 Evaluate side-chains 895 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 892 time to evaluate : 8.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1285 random chunks: chunk 417 optimal weight: 20.0000 chunk 1118 optimal weight: 1.9990 chunk 245 optimal weight: 9.9990 chunk 729 optimal weight: 10.0000 chunk 306 optimal weight: 20.0000 chunk 1243 optimal weight: 4.9990 chunk 1032 optimal weight: 40.0000 chunk 575 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 411 optimal weight: 20.0000 chunk 652 optimal weight: 0.0170 overall best weight: 1.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 ASN H 189 HIS ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82 ASN Q 87 ASN Q 193 ASN S 163 HIS T 81 HIS U 18 GLN ** U 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 595 ASN ** U 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 GLN ** V 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 362 ASN ** X 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 334 ASN ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 13 ASN a 23 HIS ** a 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 183 HIS ** c 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 96 HIS d 109 GLN h 148 GLN i 30 HIS i 109 GLN ** i 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 149 GLN ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 121 GLN ** n 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 187 GLN ** q 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 82 ASN ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 HIS ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 HIS ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 213 GLN f 473 ASN ** f 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 102854 Z= 0.187 Angle : 0.735 16.636 139119 Z= 0.373 Chirality : 0.046 0.387 15867 Planarity : 0.005 0.113 17980 Dihedral : 7.078 142.613 14262 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.25 % Favored : 90.62 % Rotamer: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.67 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.07), residues: 12904 helix: -0.15 (0.07), residues: 5897 sheet: -0.66 (0.13), residues: 1630 loop : -2.73 (0.08), residues: 5377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP f 420 HIS 0.014 0.001 HIS f 301 PHE 0.038 0.002 PHE D 345 TYR 0.025 0.001 TYR f 232 ARG 0.028 0.001 ARG f 785 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1276 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1269 time to evaluate : 8.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 MET cc_start: 0.8666 (mpp) cc_final: 0.8145 (mpp) REVERT: G 175 SER cc_start: 0.8797 (t) cc_final: 0.8527 (m) REVERT: H 165 LYS cc_start: 0.8604 (mttm) cc_final: 0.8138 (pttm) REVERT: I 11 ILE cc_start: 0.7456 (mp) cc_final: 0.7091 (mp) REVERT: J 24 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7203 (mm-30) REVERT: K 118 ASN cc_start: 0.8968 (m110) cc_final: 0.8452 (m110) REVERT: L 5 GLN cc_start: 0.8185 (pm20) cc_final: 0.7741 (pp30) REVERT: L 26 MET cc_start: 0.9034 (mmt) cc_final: 0.8676 (mmt) REVERT: L 63 ILE cc_start: 0.9286 (mt) cc_final: 0.9056 (tt) REVERT: L 94 ASP cc_start: 0.8505 (m-30) cc_final: 0.8120 (m-30) REVERT: M 181 MET cc_start: 0.6930 (ptp) cc_final: 0.6101 (ptp) REVERT: N 43 CYS cc_start: 0.8716 (p) cc_final: 0.8386 (p) REVERT: N 123 GLN cc_start: 0.8726 (mt0) cc_final: 0.8317 (mt0) REVERT: O 17 ASP cc_start: 0.6289 (p0) cc_final: 0.6014 (p0) REVERT: O 44 CYS cc_start: 0.8951 (m) cc_final: 0.8717 (m) REVERT: O 137 VAL cc_start: 0.8678 (t) cc_final: 0.8019 (t) REVERT: O 157 GLU cc_start: 0.9484 (tm-30) cc_final: 0.9229 (tm-30) REVERT: O 201 ARG cc_start: 0.6956 (tmt170) cc_final: 0.6303 (ptm-80) REVERT: P 34 MET cc_start: 0.8323 (tmm) cc_final: 0.8086 (tmm) REVERT: P 147 TYR cc_start: 0.8482 (m-80) cc_final: 0.8247 (m-80) REVERT: P 149 MET cc_start: 0.8942 (mmp) cc_final: 0.8667 (mmp) REVERT: P 173 ASN cc_start: 0.8125 (m-40) cc_final: 0.7884 (m110) REVERT: Q 69 MET cc_start: 0.8426 (mmm) cc_final: 0.7703 (tpp) REVERT: Q 189 HIS cc_start: 0.6643 (m-70) cc_final: 0.6322 (m-70) REVERT: R 35 ILE cc_start: 0.9056 (mm) cc_final: 0.8856 (mm) REVERT: R 56 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8561 (pp20) REVERT: R 93 MET cc_start: 0.8247 (tpp) cc_final: 0.7927 (tpp) REVERT: R 175 ASN cc_start: 0.8952 (m110) cc_final: 0.8661 (m110) REVERT: R 197 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7992 (mm-30) REVERT: S 54 CYS cc_start: 0.8140 (p) cc_final: 0.7142 (p) REVERT: S 61 CYS cc_start: 0.8630 (m) cc_final: 0.7285 (m) REVERT: S 146 GLN cc_start: 0.9009 (mm110) cc_final: 0.8345 (mm-40) REVERT: S 174 LEU cc_start: 0.9240 (tt) cc_final: 0.9020 (tp) REVERT: T 5 MET cc_start: 0.8923 (mmt) cc_final: 0.8516 (mmt) REVERT: T 26 MET cc_start: 0.7303 (ttm) cc_final: 0.6628 (ttm) REVERT: T 43 MET cc_start: 0.6785 (tmm) cc_final: 0.6464 (tmm) REVERT: T 127 MET cc_start: 0.7708 (ttp) cc_final: 0.7445 (ppp) REVERT: U 188 MET cc_start: 0.7515 (ttt) cc_final: 0.7158 (tmm) REVERT: U 244 MET cc_start: 0.5077 (ptp) cc_final: 0.4372 (mmm) REVERT: U 266 GLN cc_start: 0.7764 (tp-100) cc_final: 0.7504 (pt0) REVERT: U 564 ASP cc_start: 0.7317 (m-30) cc_final: 0.6920 (t70) REVERT: U 695 MET cc_start: 0.7700 (mtm) cc_final: 0.7474 (ptt) REVERT: U 725 MET cc_start: 0.6955 (mpp) cc_final: 0.6509 (mpp) REVERT: U 751 ARG cc_start: 0.6191 (ttt90) cc_final: 0.4863 (ptt90) REVERT: U 905 PRO cc_start: 0.7689 (Cg_exo) cc_final: 0.7304 (Cg_endo) REVERT: V 136 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6757 (mm-30) REVERT: V 160 LEU cc_start: 0.7861 (mt) cc_final: 0.7566 (tp) REVERT: V 177 ASN cc_start: 0.7048 (m-40) cc_final: 0.6520 (m-40) REVERT: V 181 TYR cc_start: 0.6943 (m-80) cc_final: 0.6625 (m-80) REVERT: V 200 ARG cc_start: 0.4611 (mmm160) cc_final: 0.3276 (mtm180) REVERT: W 56 THR cc_start: 0.7256 (p) cc_final: 0.6888 (p) REVERT: W 74 CYS cc_start: 0.8409 (m) cc_final: 0.8149 (t) REVERT: W 220 GLU cc_start: 0.8059 (tp30) cc_final: 0.7363 (mp0) REVERT: W 307 LYS cc_start: 0.8494 (ttpp) cc_final: 0.8033 (mmtt) REVERT: W 315 MET cc_start: 0.1188 (pmm) cc_final: 0.0912 (ttm) REVERT: W 419 LYS cc_start: 0.3969 (mptt) cc_final: 0.3687 (mmtm) REVERT: W 436 MET cc_start: 0.9368 (ttm) cc_final: 0.9115 (tpp) REVERT: X 130 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6643 (mm-30) REVERT: X 160 MET cc_start: 0.6220 (mmt) cc_final: 0.5886 (tmm) REVERT: X 397 TYR cc_start: 0.8270 (m-80) cc_final: 0.8029 (m-10) REVERT: X 415 TYR cc_start: 0.9249 (m-80) cc_final: 0.8912 (m-80) REVERT: Y 42 MET cc_start: 0.7395 (mmm) cc_final: 0.7067 (mtp) REVERT: Y 73 MET cc_start: 0.3033 (ttt) cc_final: 0.2800 (ttt) REVERT: Y 211 TYR cc_start: 0.6269 (p90) cc_final: 0.5643 (m-10) REVERT: Y 214 MET cc_start: 0.6976 (ptm) cc_final: 0.6736 (ptp) REVERT: Y 299 MET cc_start: 0.8723 (mmm) cc_final: 0.8346 (mmm) REVERT: Y 389 MET cc_start: 0.4999 (mtt) cc_final: 0.3751 (mmp) REVERT: Z 64 ASP cc_start: 0.7861 (t70) cc_final: 0.7043 (p0) REVERT: Z 73 ASP cc_start: 0.7655 (t0) cc_final: 0.7014 (p0) REVERT: Z 84 LYS cc_start: 0.8275 (ttpt) cc_final: 0.8046 (tppt) REVERT: Z 114 ARG cc_start: 0.8267 (ptt180) cc_final: 0.7421 (ptt90) REVERT: Z 257 MET cc_start: 0.7611 (mmm) cc_final: 0.7364 (mmm) REVERT: a 46 GLN cc_start: 0.7292 (tp-100) cc_final: 0.7018 (tm-30) REVERT: a 161 LYS cc_start: 0.7826 (mmmt) cc_final: 0.7535 (mptt) REVERT: a 179 PHE cc_start: 0.8069 (t80) cc_final: 0.7753 (t80) REVERT: b 1 MET cc_start: 0.2515 (tpp) cc_final: 0.1401 (ttp) REVERT: b 181 ASP cc_start: 0.7874 (m-30) cc_final: 0.7465 (p0) REVERT: c 57 MET cc_start: 0.8436 (mmp) cc_final: 0.7632 (mmm) REVERT: c 95 MET cc_start: 0.8265 (tpt) cc_final: 0.7926 (tpp) REVERT: c 98 MET cc_start: 0.6774 (mtt) cc_final: 0.6263 (mtm) REVERT: c 104 ARG cc_start: 0.8573 (ttp-170) cc_final: 0.8160 (ttp80) REVERT: c 232 GLN cc_start: 0.8829 (mt0) cc_final: 0.8150 (mp10) REVERT: c 248 MET cc_start: 0.8605 (ptm) cc_final: 0.7693 (ptm) REVERT: c 260 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7673 (tp30) REVERT: d 125 LYS cc_start: 0.6994 (mmtt) cc_final: 0.6578 (ttpt) REVERT: d 233 GLU cc_start: 0.6912 (mp0) cc_final: 0.5889 (tp30) REVERT: e 5 LYS cc_start: 0.4670 (pptt) cc_final: 0.3986 (pptt) REVERT: g 80 MET cc_start: 0.7735 (mmm) cc_final: 0.7425 (mmm) REVERT: g 113 MET cc_start: 0.8431 (mmt) cc_final: 0.8002 (mmm) REVERT: h 58 ASP cc_start: 0.8222 (t0) cc_final: 0.7983 (t70) REVERT: h 92 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8138 (mtmm) REVERT: h 95 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8573 (mm110) REVERT: h 158 TRP cc_start: 0.6474 (m100) cc_final: 0.6188 (m100) REVERT: h 221 LEU cc_start: 0.7810 (tp) cc_final: 0.7592 (tp) REVERT: i 103 GLU cc_start: 0.7755 (tt0) cc_final: 0.7427 (mp0) REVERT: k 59 MET cc_start: 0.7818 (ttm) cc_final: 0.7348 (ttm) REVERT: k 189 MET cc_start: 0.8503 (mmp) cc_final: 0.8249 (mmm) REVERT: k 191 LEU cc_start: 0.8180 (tp) cc_final: 0.7965 (pp) REVERT: l 26 MET cc_start: 0.7848 (mmt) cc_final: 0.7565 (tmm) REVERT: l 50 LYS cc_start: 0.8379 (mttt) cc_final: 0.8158 (mtmt) REVERT: l 176 MET cc_start: 0.8451 (ptm) cc_final: 0.8190 (ptp) REVERT: l 179 PHE cc_start: 0.7718 (m-10) cc_final: 0.7490 (m-10) REVERT: m 47 PHE cc_start: 0.7790 (m-80) cc_final: 0.7558 (m-80) REVERT: m 50 GLU cc_start: 0.7253 (tt0) cc_final: 0.6461 (tp30) REVERT: m 156 VAL cc_start: 0.8804 (t) cc_final: 0.8329 (t) REVERT: m 170 GLN cc_start: 0.8019 (mt0) cc_final: 0.7719 (tm-30) REVERT: m 214 SER cc_start: 0.6638 (t) cc_final: 0.6068 (t) REVERT: n 57 ASP cc_start: 0.8575 (t70) cc_final: 0.8307 (t0) REVERT: n 81 SER cc_start: 0.9254 (m) cc_final: 0.8991 (p) REVERT: n 95 MET cc_start: 0.7846 (tpp) cc_final: 0.7314 (mmm) REVERT: n 116 MET cc_start: 0.7945 (mtt) cc_final: 0.7294 (mtm) REVERT: n 164 MET cc_start: 0.8910 (mtp) cc_final: 0.8500 (mtp) REVERT: o 26 VAL cc_start: 0.8428 (t) cc_final: 0.7195 (p) REVERT: o 54 MET cc_start: 0.9161 (mmm) cc_final: 0.8694 (tmm) REVERT: o 82 MET cc_start: 0.8766 (mtm) cc_final: 0.8207 (mtp) REVERT: o 86 MET cc_start: 0.9080 (ttm) cc_final: 0.8838 (ttp) REVERT: o 127 MET cc_start: 0.7760 (mmm) cc_final: 0.6963 (mtt) REVERT: p 88 MET cc_start: 0.9030 (mmm) cc_final: 0.8745 (mmm) REVERT: p 135 ASP cc_start: 0.8659 (p0) cc_final: 0.8037 (p0) REVERT: p 146 MET cc_start: 0.8687 (mpp) cc_final: 0.8409 (mpp) REVERT: p 171 MET cc_start: 0.9276 (tpp) cc_final: 0.9044 (tpp) REVERT: p 204 MET cc_start: 0.7820 (mmm) cc_final: 0.7539 (mmm) REVERT: q 35 MET cc_start: 0.8492 (mtt) cc_final: 0.8144 (ppp) REVERT: q 58 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8328 (tp30) REVERT: q 118 MET cc_start: 0.8356 (mmt) cc_final: 0.8070 (mmt) REVERT: q 173 LEU cc_start: 0.9038 (tp) cc_final: 0.8692 (tp) REVERT: r 21 THR cc_start: 0.5474 (p) cc_final: 0.5178 (t) REVERT: r 45 MET cc_start: 0.8086 (ttm) cc_final: 0.7768 (ttt) REVERT: r 90 TYR cc_start: 0.9141 (m-80) cc_final: 0.8681 (m-10) REVERT: r 139 MET cc_start: 0.7852 (ttp) cc_final: 0.7482 (tmm) REVERT: r 175 ASN cc_start: 0.9320 (m-40) cc_final: 0.9092 (t0) REVERT: s 8 ASN cc_start: 0.8768 (m110) cc_final: 0.8548 (m110) REVERT: s 13 LEU cc_start: 0.8517 (tp) cc_final: 0.8060 (mp) REVERT: s 57 PHE cc_start: 0.8540 (t80) cc_final: 0.7996 (t80) REVERT: s 174 LEU cc_start: 0.9516 (mt) cc_final: 0.9221 (tt) REVERT: s 179 PHE cc_start: 0.8126 (m-80) cc_final: 0.7761 (m-80) REVERT: t 26 MET cc_start: 0.5910 (mpp) cc_final: 0.4773 (mpp) REVERT: t 43 MET cc_start: 0.7993 (tmm) cc_final: 0.7203 (tmm) REVERT: t 50 MET cc_start: 0.7905 (ptm) cc_final: 0.7624 (ppp) REVERT: t 173 MET cc_start: 0.8800 (mmm) cc_final: 0.8441 (mmt) REVERT: t 188 GLN cc_start: 0.7949 (pt0) cc_final: 0.7241 (pt0) REVERT: A 258 ARG cc_start: 0.7896 (mpt-90) cc_final: 0.7277 (tmm-80) REVERT: A 268 LYS cc_start: 0.3902 (pptt) cc_final: 0.3324 (tppt) REVERT: B 288 ASP cc_start: 0.6070 (p0) cc_final: 0.5735 (p0) REVERT: C 273 MET cc_start: 0.8117 (mtp) cc_final: 0.7881 (mtt) REVERT: C 297 ARG cc_start: 0.7392 (mmm160) cc_final: 0.7077 (mtm180) REVERT: D 122 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6817 (mm-30) REVERT: D 183 LEU cc_start: 0.9200 (tp) cc_final: 0.8985 (tp) REVERT: D 189 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7969 (tm-30) REVERT: D 323 ARG cc_start: 0.7701 (ttt180) cc_final: 0.6747 (ttm-80) REVERT: D 328 ASP cc_start: 0.8254 (m-30) cc_final: 0.7144 (p0) REVERT: D 351 LYS cc_start: 0.8773 (tppt) cc_final: 0.8287 (pttm) REVERT: D 384 MET cc_start: 0.6686 (mmm) cc_final: 0.6316 (mmt) REVERT: E 93 LYS cc_start: 0.9216 (mttt) cc_final: 0.8958 (mmmt) REVERT: E 102 MET cc_start: 0.1256 (mtt) cc_final: 0.1049 (mtt) REVERT: E 122 MET cc_start: 0.3776 (mtp) cc_final: 0.3439 (ptp) REVERT: E 133 SER cc_start: 0.6270 (p) cc_final: 0.6026 (m) REVERT: E 155 ASN cc_start: 0.8587 (t0) cc_final: 0.8069 (m110) REVERT: E 218 MET cc_start: 0.7214 (mtm) cc_final: 0.6831 (mtm) REVERT: E 275 MET cc_start: 0.5084 (mtt) cc_final: 0.4814 (mtt) REVERT: E 305 ASN cc_start: 0.7476 (t0) cc_final: 0.6779 (p0) REVERT: F 76 ASN cc_start: 0.7714 (p0) cc_final: 0.7505 (p0) REVERT: F 172 VAL cc_start: 0.6324 (t) cc_final: 0.6100 (t) REVERT: F 175 MET cc_start: 0.6563 (mtt) cc_final: 0.5764 (mtp) REVERT: F 380 ASN cc_start: 0.7634 (t0) cc_final: 0.7054 (t0) REVERT: F 405 MET cc_start: 0.7854 (mtm) cc_final: 0.7399 (mmt) REVERT: f 190 GLU cc_start: 0.6896 (pt0) cc_final: 0.6433 (pt0) REVERT: f 248 LEU cc_start: 0.5953 (tt) cc_final: 0.4872 (tt) outliers start: 7 outliers final: 3 residues processed: 1276 average time/residue: 0.8827 time to fit residues: 1963.9001 Evaluate side-chains 925 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 922 time to evaluate : 8.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1285 random chunks: chunk 1198 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 708 optimal weight: 30.0000 chunk 907 optimal weight: 20.0000 chunk 703 optimal weight: 10.0000 chunk 1046 optimal weight: 5.9990 chunk 694 optimal weight: 20.0000 chunk 1238 optimal weight: 6.9990 chunk 775 optimal weight: 5.9990 chunk 755 optimal weight: 10.0000 chunk 571 optimal weight: 4.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 ASN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 120 HIS ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN Q 193 ASN S 146 GLN S 163 HIS U 18 GLN U 149 GLN ** U 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 GLN V 199 ASN ** V 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 148 HIS ** X 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 334 ASN Y 388 ASN ** Z 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 183 HIS ** c 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 96 HIS d 109 GLN ** i 30 HIS ** 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 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 240 HIS j 116 GLN ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 101 ASN ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 187 GLN o 66 HIS q 65 GLN ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 160 ASN ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 ASN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 ASN ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN E 316 HIS F 316 GLN f 12 GLN ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 102854 Z= 0.297 Angle : 0.803 13.803 139119 Z= 0.415 Chirality : 0.048 0.501 15867 Planarity : 0.006 0.109 17980 Dihedral : 7.153 150.414 14262 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 21.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.47 % Favored : 89.40 % Rotamer: Outliers : 0.05 % Allowed : 2.52 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.67 % 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: -1.97 (0.07), residues: 12904 helix: -0.24 (0.07), residues: 5926 sheet: -0.80 (0.12), residues: 1710 loop : -2.76 (0.08), residues: 5268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP U 392 HIS 0.020 0.002 HIS f 782 PHE 0.026 0.002 PHE f 304 TYR 0.051 0.002 TYR J 118 ARG 0.013 0.001 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1137 time to evaluate : 9.668 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: G 83 MET cc_start: 0.8549 (mpp) cc_final: 0.7714 (mpp) REVERT: G 175 SER cc_start: 0.8886 (t) cc_final: 0.8555 (m) REVERT: H 203 MET cc_start: 0.6787 (mmt) cc_final: 0.6268 (mpp) REVERT: I 11 ILE cc_start: 0.7559 (mp) cc_final: 0.6889 (mp) REVERT: J 24 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7350 (mm-30) REVERT: L 26 MET cc_start: 0.9048 (mmt) cc_final: 0.8677 (mmt) REVERT: L 176 MET cc_start: 0.7944 (ppp) cc_final: 0.7419 (ppp) REVERT: M 136 MET cc_start: 0.7572 (mmp) cc_final: 0.6112 (mmp) REVERT: M 156 VAL cc_start: 0.8990 (t) cc_final: 0.8691 (t) REVERT: N 43 CYS cc_start: 0.8772 (p) cc_final: 0.8463 (p) REVERT: N 123 GLN cc_start: 0.8829 (mt0) cc_final: 0.8418 (mt0) REVERT: O 44 CYS cc_start: 0.9027 (m) cc_final: 0.8792 (m) REVERT: O 146 MET cc_start: 0.8823 (mmt) cc_final: 0.8522 (mmt) REVERT: O 201 ARG cc_start: 0.7040 (tmt170) cc_final: 0.6363 (ptm-80) REVERT: Q 38 MET cc_start: 0.8950 (tpt) cc_final: 0.7980 (tpp) REVERT: Q 65 GLN cc_start: 0.9318 (mm110) cc_final: 0.9100 (mm110) REVERT: Q 189 HIS cc_start: 0.6551 (m-70) cc_final: 0.6289 (m-70) REVERT: R 35 ILE cc_start: 0.9043 (mm) cc_final: 0.8546 (mp) REVERT: R 56 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8785 (pt0) REVERT: R 93 MET cc_start: 0.8308 (tpp) cc_final: 0.8012 (tpp) REVERT: R 100 MET cc_start: 0.8486 (mpp) cc_final: 0.8255 (mpp) REVERT: R 175 ASN cc_start: 0.8958 (m110) cc_final: 0.8643 (m110) REVERT: S 54 CYS cc_start: 0.8227 (p) cc_final: 0.7225 (p) REVERT: S 61 CYS cc_start: 0.8673 (m) cc_final: 0.7279 (m) REVERT: S 144 MET cc_start: 0.9166 (mpp) cc_final: 0.8834 (mpp) REVERT: S 146 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8465 (mm-40) REVERT: T 5 MET cc_start: 0.8852 (mmt) cc_final: 0.8487 (mmt) REVERT: T 26 MET cc_start: 0.7428 (ttm) cc_final: 0.6649 (ttm) REVERT: U 244 MET cc_start: 0.5190 (ptp) cc_final: 0.4452 (mmm) REVERT: U 266 GLN cc_start: 0.7788 (tp-100) cc_final: 0.7505 (pt0) REVERT: U 392 TRP cc_start: 0.6265 (t60) cc_final: 0.6044 (t60) REVERT: U 564 ASP cc_start: 0.7435 (m-30) cc_final: 0.7010 (t70) REVERT: U 695 MET cc_start: 0.7817 (mtm) cc_final: 0.7583 (ptt) REVERT: U 751 ARG cc_start: 0.6467 (ttt90) cc_final: 0.5227 (ptt-90) REVERT: U 905 PRO cc_start: 0.7725 (Cg_exo) cc_final: 0.7330 (Cg_endo) REVERT: V 136 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6862 (mm-30) REVERT: V 181 TYR cc_start: 0.7007 (m-80) cc_final: 0.6618 (m-80) REVERT: V 200 ARG cc_start: 0.4839 (mmm160) cc_final: 0.3271 (mtm180) REVERT: V 212 TYR cc_start: 0.8738 (m-10) cc_final: 0.8369 (m-80) REVERT: W 74 CYS cc_start: 0.8386 (m) cc_final: 0.8102 (t) REVERT: W 220 GLU cc_start: 0.8149 (tp30) cc_final: 0.7466 (mp0) REVERT: W 307 LYS cc_start: 0.8506 (ttpp) cc_final: 0.8029 (mmtt) REVERT: W 315 MET cc_start: 0.1340 (pmm) cc_final: 0.0994 (ttt) REVERT: X 66 LEU cc_start: -0.1405 (tp) cc_final: -0.1720 (tp) REVERT: X 130 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6735 (mm-30) REVERT: X 160 MET cc_start: 0.6239 (mmt) cc_final: 0.5950 (tmm) REVERT: X 415 TYR cc_start: 0.9252 (m-80) cc_final: 0.8899 (m-80) REVERT: Y 42 MET cc_start: 0.7208 (mmm) cc_final: 0.6840 (mtp) REVERT: Y 211 TYR cc_start: 0.6288 (p90) cc_final: 0.5691 (m-10) REVERT: Y 364 TRP cc_start: 0.8056 (t-100) cc_final: 0.7838 (t-100) REVERT: Y 389 MET cc_start: 0.4739 (mtt) cc_final: 0.3545 (mmp) REVERT: Z 64 ASP cc_start: 0.8032 (t70) cc_final: 0.7219 (p0) REVERT: Z 73 ASP cc_start: 0.7669 (t0) cc_final: 0.6982 (p0) REVERT: Z 81 MET cc_start: 0.7978 (mmm) cc_final: 0.7700 (mtt) REVERT: Z 84 LYS cc_start: 0.8255 (ttpt) cc_final: 0.7974 (tppt) REVERT: Z 114 ARG cc_start: 0.8333 (ptt180) cc_final: 0.7524 (ptt90) REVERT: a 46 GLN cc_start: 0.7362 (tp-100) cc_final: 0.7084 (tm-30) REVERT: a 161 LYS cc_start: 0.7661 (mmmt) cc_final: 0.7299 (mptt) REVERT: a 179 PHE cc_start: 0.8080 (t80) cc_final: 0.7760 (t80) REVERT: b 1 MET cc_start: 0.2461 (tpp) cc_final: 0.1350 (ttp) REVERT: b 181 ASP cc_start: 0.7827 (m-30) cc_final: 0.7411 (p0) REVERT: c 57 MET cc_start: 0.8642 (mmp) cc_final: 0.7881 (mmm) REVERT: c 71 ASP cc_start: 0.8163 (t70) cc_final: 0.7894 (t0) REVERT: c 98 MET cc_start: 0.6726 (mtt) cc_final: 0.6387 (mtm) REVERT: c 104 ARG cc_start: 0.8637 (ttp-170) cc_final: 0.8179 (ttp80) REVERT: c 232 GLN cc_start: 0.8831 (mt0) cc_final: 0.7995 (mp10) REVERT: c 248 MET cc_start: 0.8585 (ptm) cc_final: 0.8289 (tmm) REVERT: c 260 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7838 (tp30) REVERT: d 215 TRP cc_start: 0.3847 (m100) cc_final: 0.3137 (m-10) REVERT: d 233 GLU cc_start: 0.6806 (mp0) cc_final: 0.5871 (tp30) REVERT: e 5 LYS cc_start: 0.4821 (pptt) cc_final: 0.4098 (pptt) REVERT: h 58 ASP cc_start: 0.8330 (t0) cc_final: 0.8045 (t70) REVERT: h 92 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8241 (mtmm) REVERT: h 158 TRP cc_start: 0.6642 (m100) cc_final: 0.6012 (m100) REVERT: i 103 GLU cc_start: 0.7830 (tt0) cc_final: 0.7427 (mp0) REVERT: k 59 MET cc_start: 0.7910 (ttm) cc_final: 0.7428 (ttm) REVERT: k 189 MET cc_start: 0.8646 (mmp) cc_final: 0.8238 (mmm) REVERT: k 228 MET cc_start: 0.7114 (mpp) cc_final: 0.6708 (mpp) REVERT: l 26 MET cc_start: 0.7955 (mmt) cc_final: 0.7645 (tmm) REVERT: l 50 LYS cc_start: 0.8622 (mttt) cc_final: 0.8351 (mtmt) REVERT: l 176 MET cc_start: 0.8458 (ptm) cc_final: 0.8132 (ptp) REVERT: l 179 PHE cc_start: 0.7671 (m-10) cc_final: 0.7461 (m-10) REVERT: m 27 MET cc_start: 0.8318 (mmp) cc_final: 0.8056 (mmm) REVERT: m 47 PHE cc_start: 0.8025 (m-80) cc_final: 0.7794 (m-80) REVERT: m 50 GLU cc_start: 0.7307 (tt0) cc_final: 0.6546 (tp30) REVERT: m 156 VAL cc_start: 0.8967 (t) cc_final: 0.8394 (t) REVERT: m 170 GLN cc_start: 0.8059 (mt0) cc_final: 0.7736 (tm-30) REVERT: m 214 SER cc_start: 0.6974 (t) cc_final: 0.6586 (t) REVERT: n 81 SER cc_start: 0.9297 (m) cc_final: 0.8682 (t) REVERT: n 120 MET cc_start: 0.8780 (ppp) cc_final: 0.8007 (ppp) REVERT: o 26 VAL cc_start: 0.8573 (t) cc_final: 0.7483 (p) REVERT: o 54 MET cc_start: 0.9209 (mmm) cc_final: 0.8754 (tmm) REVERT: o 82 MET cc_start: 0.8714 (mtm) cc_final: 0.8370 (mtp) REVERT: o 127 MET cc_start: 0.7938 (mmm) cc_final: 0.7212 (mtt) REVERT: o 149 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7939 (tm-30) REVERT: p 88 MET cc_start: 0.9008 (mmm) cc_final: 0.8805 (mmm) REVERT: p 135 ASP cc_start: 0.8762 (p0) cc_final: 0.8127 (p0) REVERT: p 146 MET cc_start: 0.8718 (mpp) cc_final: 0.8481 (mpp) REVERT: p 204 MET cc_start: 0.7738 (mmm) cc_final: 0.7525 (mmm) REVERT: q 35 MET cc_start: 0.8498 (mtt) cc_final: 0.8238 (ppp) REVERT: q 58 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8406 (tp30) REVERT: q 118 MET cc_start: 0.8301 (mmt) cc_final: 0.8044 (mmt) REVERT: q 173 LEU cc_start: 0.9086 (tp) cc_final: 0.8585 (tp) REVERT: r 45 MET cc_start: 0.8211 (ttm) cc_final: 0.7946 (ttm) REVERT: r 90 TYR cc_start: 0.9177 (m-80) cc_final: 0.8667 (m-10) REVERT: r 97 MET cc_start: 0.7174 (tmm) cc_final: 0.6887 (tmm) REVERT: r 139 MET cc_start: 0.7864 (ttp) cc_final: 0.7346 (tmm) REVERT: r 175 ASN cc_start: 0.9364 (m-40) cc_final: 0.9081 (t0) REVERT: s 8 ASN cc_start: 0.8806 (m110) cc_final: 0.8545 (m110) REVERT: s 13 LEU cc_start: 0.8553 (tp) cc_final: 0.8103 (mp) REVERT: s 57 PHE cc_start: 0.8645 (t80) cc_final: 0.8081 (t80) REVERT: s 74 MET cc_start: 0.9024 (mmt) cc_final: 0.8707 (mmt) REVERT: s 179 PHE cc_start: 0.8264 (m-80) cc_final: 0.7581 (m-80) REVERT: t 22 ILE cc_start: 0.9224 (pt) cc_final: 0.8746 (pt) REVERT: t 26 MET cc_start: 0.6065 (mpp) cc_final: 0.5294 (mpp) REVERT: t 43 MET cc_start: 0.8118 (tmm) cc_final: 0.7310 (tmm) REVERT: t 50 MET cc_start: 0.8022 (ptm) cc_final: 0.7646 (ppp) REVERT: t 173 MET cc_start: 0.8894 (mmm) cc_final: 0.8667 (mmm) REVERT: t 188 GLN cc_start: 0.7936 (pt0) cc_final: 0.7366 (pt0) REVERT: A 258 ARG cc_start: 0.7868 (mpt-90) cc_final: 0.7188 (tmm-80) REVERT: C 297 ARG cc_start: 0.7483 (mmm160) cc_final: 0.7183 (mtm180) REVERT: C 358 GLU cc_start: 0.7446 (pt0) cc_final: 0.6872 (pm20) REVERT: D 153 MET cc_start: 0.6726 (tmm) cc_final: 0.5707 (tpt) REVERT: D 345 PHE cc_start: 0.7806 (m-10) cc_final: 0.7587 (m-10) REVERT: D 351 LYS cc_start: 0.8843 (tppt) cc_final: 0.8310 (pttm) REVERT: D 384 MET cc_start: 0.6586 (mmm) cc_final: 0.6296 (mmt) REVERT: E 121 ASN cc_start: 0.6142 (m110) cc_final: 0.5877 (p0) REVERT: E 133 SER cc_start: 0.6057 (p) cc_final: 0.5801 (m) REVERT: E 305 ASN cc_start: 0.7658 (t0) cc_final: 0.6986 (p0) REVERT: F 172 VAL cc_start: 0.6371 (t) cc_final: 0.6147 (t) REVERT: F 175 MET cc_start: 0.6615 (mtt) cc_final: 0.5884 (mtp) REVERT: F 380 ASN cc_start: 0.7711 (t0) cc_final: 0.7085 (t0) REVERT: f 248 LEU cc_start: 0.5895 (tt) cc_final: 0.4870 (tt) outliers start: 5 outliers final: 3 residues processed: 1141 average time/residue: 0.8759 time to fit residues: 1747.6725 Evaluate side-chains 845 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 842 time to evaluate : 8.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1285 random chunks: chunk 766 optimal weight: 7.9990 chunk 494 optimal weight: 8.9990 chunk 739 optimal weight: 30.0000 chunk 373 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 chunk 787 optimal weight: 6.9990 chunk 843 optimal weight: 20.0000 chunk 612 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 973 optimal weight: 0.2980 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 154 HIS ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82 ASN Q 87 ASN Q 193 ASN S 163 HIS U 18 GLN U 111 GLN ** U 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 48 ASN ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 231 GLN ** a 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 96 HIS d 109 GLN i 30 HIS ** i 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 167 ASN k 97 GLN ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 187 GLN o 66 HIS ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 82 ASN ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN E 316 HIS F 83 ASN f 12 GLN ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 352 HIS f 540 GLN f 782 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 102854 Z= 0.239 Angle : 0.766 16.743 139119 Z= 0.392 Chirality : 0.047 0.488 15867 Planarity : 0.005 0.109 17980 Dihedral : 7.063 152.796 14262 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.97 % Favored : 89.93 % Rotamer: Outliers : 0.05 % Allowed : 1.27 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.67 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.07), residues: 12904 helix: -0.17 (0.07), residues: 5943 sheet: -0.77 (0.12), residues: 1703 loop : -2.72 (0.08), residues: 5258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP U 35 HIS 0.019 0.001 HIS f 301 PHE 0.035 0.002 PHE f 483 TYR 0.046 0.002 TYR X 327 ARG 0.009 0.001 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1141 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1136 time to evaluate : 11.463 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: G 83 MET cc_start: 0.8757 (mpp) cc_final: 0.8071 (mpp) REVERT: G 175 SER cc_start: 0.8885 (t) cc_final: 0.8575 (m) REVERT: I 11 ILE cc_start: 0.7589 (mp) cc_final: 0.6851 (mp) REVERT: J 24 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7300 (mm-30) REVERT: L 26 MET cc_start: 0.9071 (mmt) cc_final: 0.8685 (mmt) REVERT: L 176 MET cc_start: 0.7918 (ppp) cc_final: 0.7319 (ppp) REVERT: M 150 MET cc_start: 0.8302 (mtp) cc_final: 0.7290 (mtm) REVERT: M 160 TYR cc_start: 0.8755 (m-10) cc_final: 0.8455 (m-10) REVERT: N 43 CYS cc_start: 0.8807 (p) cc_final: 0.8503 (p) REVERT: N 123 GLN cc_start: 0.8847 (mt0) cc_final: 0.8455 (mt0) REVERT: O 44 CYS cc_start: 0.9000 (m) cc_final: 0.8742 (m) REVERT: O 137 VAL cc_start: 0.8724 (t) cc_final: 0.8064 (t) REVERT: O 146 MET cc_start: 0.8768 (mmt) cc_final: 0.8437 (mmt) REVERT: O 157 GLU cc_start: 0.9492 (tm-30) cc_final: 0.9194 (tm-30) REVERT: O 201 ARG cc_start: 0.7077 (tmt170) cc_final: 0.6359 (ptm-80) REVERT: Q 189 HIS cc_start: 0.6484 (m-70) cc_final: 0.6258 (m-70) REVERT: R 56 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8632 (pp20) REVERT: R 93 MET cc_start: 0.8296 (tpp) cc_final: 0.8018 (tpp) REVERT: R 175 ASN cc_start: 0.8937 (m110) cc_final: 0.8629 (m110) REVERT: S 54 CYS cc_start: 0.8193 (p) cc_final: 0.7881 (p) REVERT: S 144 MET cc_start: 0.9161 (mpp) cc_final: 0.8851 (mpp) REVERT: S 146 GLN cc_start: 0.8993 (mm-40) cc_final: 0.8370 (mm-40) REVERT: T 5 MET cc_start: 0.8933 (mmt) cc_final: 0.8505 (mmt) REVERT: T 26 MET cc_start: 0.7500 (ttm) cc_final: 0.6694 (ttm) REVERT: U 244 MET cc_start: 0.5177 (ptp) cc_final: 0.4468 (mmm) REVERT: U 266 GLN cc_start: 0.7757 (tp-100) cc_final: 0.7479 (pt0) REVERT: U 564 ASP cc_start: 0.7438 (m-30) cc_final: 0.6969 (t70) REVERT: U 682 TYR cc_start: 0.7005 (p90) cc_final: 0.6786 (p90) REVERT: U 695 MET cc_start: 0.7822 (mtm) cc_final: 0.7560 (ptt) REVERT: U 725 MET cc_start: 0.6542 (mpp) cc_final: 0.6157 (mpp) REVERT: V 136 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6763 (mm-30) REVERT: V 177 ASN cc_start: 0.7293 (m-40) cc_final: 0.6857 (m-40) REVERT: V 181 TYR cc_start: 0.7016 (m-80) cc_final: 0.6624 (m-80) REVERT: V 212 TYR cc_start: 0.8753 (m-10) cc_final: 0.8428 (m-80) REVERT: W 74 CYS cc_start: 0.8406 (m) cc_final: 0.8126 (t) REVERT: W 160 LYS cc_start: 0.7392 (mmtm) cc_final: 0.7052 (tptp) REVERT: W 220 GLU cc_start: 0.8218 (tp30) cc_final: 0.7546 (mp0) REVERT: W 307 LYS cc_start: 0.8524 (ttpp) cc_final: 0.8042 (mmtt) REVERT: W 436 MET cc_start: 0.8997 (tpp) cc_final: 0.8720 (tpp) REVERT: X 73 VAL cc_start: 0.7118 (m) cc_final: 0.6897 (p) REVERT: X 130 GLU cc_start: 0.6985 (mm-30) cc_final: 0.6699 (mm-30) REVERT: X 160 MET cc_start: 0.6249 (mmt) cc_final: 0.5950 (tmm) REVERT: X 415 TYR cc_start: 0.9264 (m-80) cc_final: 0.8885 (m-80) REVERT: Y 42 MET cc_start: 0.7210 (mmm) cc_final: 0.6848 (mtp) REVERT: Y 211 TYR cc_start: 0.6313 (p90) cc_final: 0.5595 (m-10) REVERT: Y 389 MET cc_start: 0.4854 (mtt) cc_final: 0.3723 (mmp) REVERT: Z 40 LEU cc_start: 0.8395 (tp) cc_final: 0.8140 (tp) REVERT: Z 64 ASP cc_start: 0.8106 (t70) cc_final: 0.7313 (p0) REVERT: Z 73 ASP cc_start: 0.7740 (t0) cc_final: 0.7019 (p0) REVERT: Z 81 MET cc_start: 0.8704 (mtt) cc_final: 0.8349 (mtp) REVERT: Z 84 LYS cc_start: 0.8265 (ttpt) cc_final: 0.7965 (tppt) REVERT: Z 114 ARG cc_start: 0.8356 (ptt180) cc_final: 0.7538 (ptt90) REVERT: Z 257 MET cc_start: 0.7393 (mmm) cc_final: 0.7151 (mmm) REVERT: a 46 GLN cc_start: 0.7356 (tp-100) cc_final: 0.7078 (tm-30) REVERT: a 161 LYS cc_start: 0.7629 (mmmt) cc_final: 0.7308 (mptt) REVERT: a 179 PHE cc_start: 0.8050 (t80) cc_final: 0.7732 (t80) REVERT: b 1 MET cc_start: 0.2323 (tpp) cc_final: 0.1201 (ttp) REVERT: b 181 ASP cc_start: 0.7830 (m-30) cc_final: 0.7435 (p0) REVERT: c 57 MET cc_start: 0.8599 (mmp) cc_final: 0.7956 (mmm) REVERT: c 71 ASP cc_start: 0.8088 (t70) cc_final: 0.7829 (t0) REVERT: c 98 MET cc_start: 0.6926 (mtt) cc_final: 0.6502 (mtm) REVERT: c 104 ARG cc_start: 0.8640 (ttp-170) cc_final: 0.8176 (ttp80) REVERT: c 226 MET cc_start: 0.3569 (ppp) cc_final: 0.3326 (ppp) REVERT: c 232 GLN cc_start: 0.8645 (mt0) cc_final: 0.8061 (mp10) REVERT: c 248 MET cc_start: 0.8558 (ptm) cc_final: 0.8263 (tmm) REVERT: d 215 TRP cc_start: 0.3616 (m100) cc_final: 0.3164 (m-10) REVERT: d 233 GLU cc_start: 0.6799 (mp0) cc_final: 0.5781 (tp30) REVERT: e 5 LYS cc_start: 0.5181 (pptt) cc_final: 0.4631 (pptt) REVERT: g 113 MET cc_start: 0.8485 (mmt) cc_final: 0.7959 (mmm) REVERT: h 58 ASP cc_start: 0.8328 (t0) cc_final: 0.8041 (t70) REVERT: h 92 LYS cc_start: 0.8954 (mtpt) cc_final: 0.8207 (mtmm) REVERT: h 158 TRP cc_start: 0.6488 (m100) cc_final: 0.5909 (m100) REVERT: k 59 MET cc_start: 0.7875 (ttm) cc_final: 0.7425 (ttm) REVERT: k 189 MET cc_start: 0.8635 (mmp) cc_final: 0.8204 (mmm) REVERT: k 191 LEU cc_start: 0.8340 (tp) cc_final: 0.8034 (pp) REVERT: k 206 MET cc_start: 0.8033 (ttp) cc_final: 0.7328 (tmm) REVERT: k 225 ASN cc_start: 0.7476 (p0) cc_final: 0.7045 (p0) REVERT: k 228 MET cc_start: 0.7239 (mpp) cc_final: 0.6680 (mpp) REVERT: l 26 MET cc_start: 0.8005 (mmt) cc_final: 0.7679 (tmm) REVERT: l 50 LYS cc_start: 0.8592 (mttt) cc_final: 0.8323 (mtmt) REVERT: l 176 MET cc_start: 0.8451 (ptm) cc_final: 0.8098 (ptp) REVERT: m 27 MET cc_start: 0.8294 (mmp) cc_final: 0.8020 (mmm) REVERT: m 47 PHE cc_start: 0.7905 (m-80) cc_final: 0.7678 (m-80) REVERT: m 50 GLU cc_start: 0.7192 (tt0) cc_final: 0.6465 (tm-30) REVERT: m 156 VAL cc_start: 0.8927 (t) cc_final: 0.8325 (t) REVERT: m 170 GLN cc_start: 0.7958 (mt0) cc_final: 0.7632 (tm-30) REVERT: n 81 SER cc_start: 0.9214 (m) cc_final: 0.8900 (p) REVERT: n 95 MET cc_start: 0.6994 (tpt) cc_final: 0.6577 (tpt) REVERT: n 116 MET cc_start: 0.8022 (mtt) cc_final: 0.7698 (mpp) REVERT: n 120 MET cc_start: 0.8817 (ppp) cc_final: 0.8180 (ppp) REVERT: n 164 MET cc_start: 0.8867 (mtp) cc_final: 0.8644 (mtp) REVERT: o 26 VAL cc_start: 0.8516 (t) cc_final: 0.7283 (p) REVERT: o 54 MET cc_start: 0.9211 (mmm) cc_final: 0.8736 (tmm) REVERT: o 82 MET cc_start: 0.8709 (mtm) cc_final: 0.8378 (mtp) REVERT: o 127 MET cc_start: 0.7914 (mmm) cc_final: 0.7210 (mtt) REVERT: o 149 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8030 (tm-30) REVERT: p 88 MET cc_start: 0.9154 (tpt) cc_final: 0.8774 (mmm) REVERT: p 135 ASP cc_start: 0.8790 (p0) cc_final: 0.8158 (p0) REVERT: p 144 GLU cc_start: 0.8508 (pm20) cc_final: 0.8276 (pm20) REVERT: p 204 MET cc_start: 0.7727 (mmm) cc_final: 0.7521 (mmm) REVERT: q 28 MET cc_start: 0.9089 (mtm) cc_final: 0.8736 (ptp) REVERT: q 35 MET cc_start: 0.8490 (mtt) cc_final: 0.8213 (ppp) REVERT: q 58 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8448 (tp30) REVERT: q 118 MET cc_start: 0.8238 (mmt) cc_final: 0.8022 (mmt) REVERT: q 173 LEU cc_start: 0.9043 (tp) cc_final: 0.8528 (tp) REVERT: r 37 ILE cc_start: 0.8157 (mm) cc_final: 0.7889 (mm) REVERT: r 45 MET cc_start: 0.8159 (ttm) cc_final: 0.7937 (ttm) REVERT: r 90 TYR cc_start: 0.9153 (m-80) cc_final: 0.8645 (m-10) REVERT: r 97 MET cc_start: 0.7051 (tmm) cc_final: 0.6762 (tmm) REVERT: r 139 MET cc_start: 0.7877 (ttp) cc_final: 0.7330 (tmm) REVERT: r 175 ASN cc_start: 0.9365 (m-40) cc_final: 0.9113 (t0) REVERT: s 8 ASN cc_start: 0.8840 (m110) cc_final: 0.8638 (m110) REVERT: s 13 LEU cc_start: 0.8593 (tp) cc_final: 0.8163 (mp) REVERT: s 57 PHE cc_start: 0.8595 (t80) cc_final: 0.8022 (t80) REVERT: s 74 MET cc_start: 0.9046 (mmt) cc_final: 0.8579 (mmt) REVERT: s 179 PHE cc_start: 0.8337 (m-80) cc_final: 0.7582 (m-80) REVERT: t 22 ILE cc_start: 0.9228 (pt) cc_final: 0.8716 (pt) REVERT: t 26 MET cc_start: 0.5974 (mpp) cc_final: 0.5105 (mpp) REVERT: t 43 MET cc_start: 0.8081 (tmm) cc_final: 0.7222 (tmm) REVERT: t 50 MET cc_start: 0.8045 (ptm) cc_final: 0.7616 (ppp) REVERT: t 173 MET cc_start: 0.8903 (mmm) cc_final: 0.8676 (mmm) REVERT: t 188 GLN cc_start: 0.7849 (pt0) cc_final: 0.7345 (pt0) REVERT: A 258 ARG cc_start: 0.7821 (mpt-90) cc_final: 0.7070 (tmm-80) REVERT: C 138 MET cc_start: 0.5640 (tmm) cc_final: 0.5053 (mtt) REVERT: C 297 ARG cc_start: 0.7424 (mmm160) cc_final: 0.7184 (mtm180) REVERT: D 60 TYR cc_start: 0.8253 (t80) cc_final: 0.8025 (t80) REVERT: D 153 MET cc_start: 0.6667 (tmm) cc_final: 0.5563 (tpt) REVERT: D 189 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8024 (tm-30) REVERT: D 309 MET cc_start: 0.8409 (mtp) cc_final: 0.7961 (mmm) REVERT: D 328 ASP cc_start: 0.8270 (m-30) cc_final: 0.7169 (p0) REVERT: D 351 LYS cc_start: 0.8871 (tppt) cc_final: 0.8337 (pttm) REVERT: D 384 MET cc_start: 0.6616 (mmm) cc_final: 0.6395 (mmt) REVERT: E 121 ASN cc_start: 0.6105 (m110) cc_final: 0.5846 (p0) REVERT: E 133 SER cc_start: 0.6056 (p) cc_final: 0.5818 (m) REVERT: E 155 ASN cc_start: 0.8542 (t0) cc_final: 0.7943 (m110) REVERT: E 275 MET cc_start: 0.4637 (mtt) cc_final: 0.4341 (mtt) REVERT: E 305 ASN cc_start: 0.7605 (t0) cc_final: 0.6921 (p0) REVERT: E 352 MET cc_start: 0.6713 (mpp) cc_final: 0.6472 (mpp) REVERT: F 172 VAL cc_start: 0.6298 (t) cc_final: 0.6076 (t) REVERT: F 175 MET cc_start: 0.6565 (mtt) cc_final: 0.5767 (mtp) REVERT: F 380 ASN cc_start: 0.7668 (t0) cc_final: 0.7066 (t0) REVERT: F 405 MET cc_start: 0.7754 (mtm) cc_final: 0.7262 (mmt) REVERT: f 190 GLU cc_start: 0.6720 (pt0) cc_final: 0.6325 (pt0) REVERT: f 248 LEU cc_start: 0.5842 (tt) cc_final: 0.4791 (tt) outliers start: 5 outliers final: 3 residues processed: 1141 average time/residue: 0.8791 time to fit residues: 1758.2478 Evaluate side-chains 854 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 851 time to evaluate : 9.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1285 random chunks: chunk 1126 optimal weight: 0.0670 chunk 1186 optimal weight: 10.0000 chunk 1082 optimal weight: 3.9990 chunk 1154 optimal weight: 8.9990 chunk 694 optimal weight: 10.0000 chunk 502 optimal weight: 20.0000 chunk 906 optimal weight: 20.0000 chunk 354 optimal weight: 6.9990 chunk 1042 optimal weight: 20.0000 chunk 1091 optimal weight: 5.9990 chunk 1150 optimal weight: 20.0000 overall best weight: 5.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 ASN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 214 ASN L 8 ASN ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82 ASN Q 87 ASN S 163 HIS U 18 GLN ** U 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 155 GLN X 148 HIS ** X 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 363 ASN Z 72 HIS ** a 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 101 GLN b 161 ASN ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 HIS ** c 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 GLN i 30 HIS ** i 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 68 ASN ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 187 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 82 ASN ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 HIS F 83 ASN ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 782 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 102854 Z= 0.248 Angle : 0.779 16.098 139119 Z= 0.398 Chirality : 0.048 0.460 15867 Planarity : 0.005 0.109 17980 Dihedral : 7.042 155.989 14262 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.30 % Favored : 89.58 % Rotamer: Outliers : 0.04 % Allowed : 1.02 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.67 % 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: -1.86 (0.07), residues: 12904 helix: -0.16 (0.07), residues: 5956 sheet: -0.76 (0.12), residues: 1722 loop : -2.69 (0.08), residues: 5226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP U 35 HIS 0.020 0.001 HIS f 301 PHE 0.029 0.002 PHE f 483 TYR 0.039 0.002 TYR H 101 ARG 0.021 0.001 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1100 time to evaluate : 8.919 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: G 83 MET cc_start: 0.8725 (mpp) cc_final: 0.7894 (mpp) REVERT: G 175 SER cc_start: 0.8930 (t) cc_final: 0.8608 (m) REVERT: I 11 ILE cc_start: 0.7688 (mp) cc_final: 0.6955 (mp) REVERT: J 24 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7311 (mm-30) REVERT: L 26 MET cc_start: 0.9090 (mmt) cc_final: 0.8684 (mmt) REVERT: M 150 MET cc_start: 0.8320 (mtp) cc_final: 0.7424 (mtp) REVERT: M 160 TYR cc_start: 0.8734 (m-10) cc_final: 0.8461 (m-10) REVERT: N 43 CYS cc_start: 0.8822 (p) cc_final: 0.8522 (p) REVERT: N 123 GLN cc_start: 0.8860 (mt0) cc_final: 0.8477 (mt0) REVERT: O 17 ASP cc_start: 0.6712 (p0) cc_final: 0.6336 (p0) REVERT: O 44 CYS cc_start: 0.8930 (m) cc_final: 0.8645 (m) REVERT: O 201 ARG cc_start: 0.7078 (tmt170) cc_final: 0.6376 (ptm-80) REVERT: P 149 MET cc_start: 0.9005 (mmp) cc_final: 0.8665 (mmt) REVERT: Q 38 MET cc_start: 0.8903 (tpp) cc_final: 0.7988 (tpp) REVERT: R 56 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8734 (pt0) REVERT: R 90 TYR cc_start: 0.8967 (m-80) cc_final: 0.8765 (m-10) REVERT: R 93 MET cc_start: 0.8292 (tpp) cc_final: 0.7991 (tpp) REVERT: R 100 MET cc_start: 0.8532 (mpp) cc_final: 0.8324 (mpp) REVERT: R 175 ASN cc_start: 0.8923 (m110) cc_final: 0.8622 (m110) REVERT: S 54 CYS cc_start: 0.8177 (p) cc_final: 0.7897 (p) REVERT: S 144 MET cc_start: 0.9191 (mpp) cc_final: 0.8889 (mpp) REVERT: S 146 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8344 (mm-40) REVERT: T 5 MET cc_start: 0.8914 (mmt) cc_final: 0.8516 (mmt) REVERT: T 26 MET cc_start: 0.7495 (ttm) cc_final: 0.6683 (ttm) REVERT: T 70 MET cc_start: 0.8815 (tpp) cc_final: 0.8508 (tpp) REVERT: U 244 MET cc_start: 0.5093 (ptp) cc_final: 0.4330 (mmm) REVERT: U 266 GLN cc_start: 0.7722 (tp-100) cc_final: 0.7480 (pt0) REVERT: U 564 ASP cc_start: 0.7406 (m-30) cc_final: 0.6807 (t70) REVERT: U 682 TYR cc_start: 0.7002 (p90) cc_final: 0.6667 (p90) REVERT: U 695 MET cc_start: 0.7865 (mtm) cc_final: 0.7605 (ptt) REVERT: U 770 TRP cc_start: 0.4801 (m-10) cc_final: 0.4558 (m-10) REVERT: V 136 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6761 (mm-30) REVERT: V 177 ASN cc_start: 0.7324 (m-40) cc_final: 0.6873 (m-40) REVERT: V 181 TYR cc_start: 0.7039 (m-80) cc_final: 0.6643 (m-80) REVERT: V 212 TYR cc_start: 0.8752 (m-10) cc_final: 0.8444 (m-80) REVERT: W 74 CYS cc_start: 0.8424 (m) cc_final: 0.8128 (t) REVERT: W 160 LYS cc_start: 0.7423 (mmtm) cc_final: 0.7092 (tptp) REVERT: W 220 GLU cc_start: 0.8215 (tp30) cc_final: 0.7558 (mp0) REVERT: W 307 LYS cc_start: 0.8568 (ttpp) cc_final: 0.8077 (mmtt) REVERT: W 436 MET cc_start: 0.8987 (tpp) cc_final: 0.8701 (tpp) REVERT: X 66 LEU cc_start: -0.0020 (tp) cc_final: -0.0366 (tp) REVERT: X 73 VAL cc_start: 0.7031 (m) cc_final: 0.6829 (p) REVERT: X 130 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6633 (mm-30) REVERT: X 160 MET cc_start: 0.6314 (mmt) cc_final: 0.6033 (tmm) REVERT: X 415 TYR cc_start: 0.9255 (m-80) cc_final: 0.8811 (m-80) REVERT: Y 42 MET cc_start: 0.7115 (mmm) cc_final: 0.6725 (mtp) REVERT: Y 211 TYR cc_start: 0.6349 (p90) cc_final: 0.5675 (m-10) REVERT: Y 389 MET cc_start: 0.4781 (mtt) cc_final: 0.3696 (mmp) REVERT: Z 40 LEU cc_start: 0.8431 (tp) cc_final: 0.8156 (tp) REVERT: Z 73 ASP cc_start: 0.7790 (t0) cc_final: 0.7151 (p0) REVERT: Z 84 LYS cc_start: 0.8264 (ttpt) cc_final: 0.7977 (tppt) REVERT: Z 114 ARG cc_start: 0.8347 (ptt180) cc_final: 0.7551 (ptt90) REVERT: Z 257 MET cc_start: 0.7382 (mmm) cc_final: 0.7127 (mmm) REVERT: a 46 GLN cc_start: 0.7347 (tp-100) cc_final: 0.7095 (pp30) REVERT: a 161 LYS cc_start: 0.7606 (mmmt) cc_final: 0.7267 (mptt) REVERT: a 179 PHE cc_start: 0.8025 (t80) cc_final: 0.7714 (t80) REVERT: a 349 MET cc_start: 0.7505 (ttp) cc_final: 0.7048 (tmm) REVERT: b 1 MET cc_start: 0.2321 (tpp) cc_final: 0.1190 (ttp) REVERT: b 181 ASP cc_start: 0.7766 (m-30) cc_final: 0.7357 (p0) REVERT: c 57 MET cc_start: 0.8685 (mmp) cc_final: 0.7905 (mmm) REVERT: c 71 ASP cc_start: 0.7999 (t70) cc_final: 0.7719 (t0) REVERT: c 104 ARG cc_start: 0.8663 (ttp-170) cc_final: 0.8114 (ttp80) REVERT: c 221 HIS cc_start: 0.7000 (t70) cc_final: 0.6590 (t-170) REVERT: c 226 MET cc_start: 0.3507 (ppp) cc_final: 0.3300 (ppp) REVERT: c 232 GLN cc_start: 0.8670 (mt0) cc_final: 0.8013 (mp10) REVERT: c 248 MET cc_start: 0.8569 (ptm) cc_final: 0.8268 (tmm) REVERT: d 215 TRP cc_start: 0.3711 (m100) cc_final: 0.3233 (m-10) REVERT: d 233 GLU cc_start: 0.6751 (mp0) cc_final: 0.5721 (tp30) REVERT: e 5 LYS cc_start: 0.5209 (pptt) cc_final: 0.4694 (pptt) REVERT: e 60 LEU cc_start: 0.7223 (tp) cc_final: 0.6961 (tp) REVERT: h 58 ASP cc_start: 0.8345 (t0) cc_final: 0.8028 (t70) REVERT: h 92 LYS cc_start: 0.8963 (mtpt) cc_final: 0.8215 (mtmm) REVERT: h 158 TRP cc_start: 0.6523 (m100) cc_final: 0.5950 (m100) REVERT: j 86 ARG cc_start: 0.9080 (mmm-85) cc_final: 0.8850 (mmm-85) REVERT: k 59 MET cc_start: 0.7873 (ttm) cc_final: 0.7449 (ttm) REVERT: k 107 MET cc_start: 0.6874 (ttt) cc_final: 0.6534 (ptm) REVERT: k 189 MET cc_start: 0.8664 (mmp) cc_final: 0.8148 (mmm) REVERT: k 191 LEU cc_start: 0.8466 (tp) cc_final: 0.8080 (pp) REVERT: k 206 MET cc_start: 0.7963 (ttp) cc_final: 0.7262 (tmm) REVERT: k 225 ASN cc_start: 0.7463 (p0) cc_final: 0.6967 (p0) REVERT: k 228 MET cc_start: 0.7311 (mpp) cc_final: 0.6699 (mpp) REVERT: l 26 MET cc_start: 0.8001 (mmt) cc_final: 0.7695 (tmm) REVERT: l 50 LYS cc_start: 0.8621 (mttt) cc_final: 0.8321 (mtmt) REVERT: l 176 MET cc_start: 0.8445 (ptm) cc_final: 0.8202 (ptp) REVERT: m 27 MET cc_start: 0.8321 (mmp) cc_final: 0.8039 (mmm) REVERT: m 50 GLU cc_start: 0.7195 (tt0) cc_final: 0.6493 (tm-30) REVERT: m 156 VAL cc_start: 0.8924 (t) cc_final: 0.8316 (t) REVERT: m 170 GLN cc_start: 0.7942 (mt0) cc_final: 0.7627 (tm-30) REVERT: m 214 SER cc_start: 0.7406 (t) cc_final: 0.6976 (t) REVERT: n 81 SER cc_start: 0.9207 (m) cc_final: 0.8882 (p) REVERT: n 95 MET cc_start: 0.6971 (tpt) cc_final: 0.6499 (tpt) REVERT: n 116 MET cc_start: 0.8035 (mtt) cc_final: 0.7752 (mpp) REVERT: n 120 MET cc_start: 0.8851 (ppp) cc_final: 0.8194 (ppp) REVERT: n 164 MET cc_start: 0.8847 (mtp) cc_final: 0.8632 (mtp) REVERT: o 26 VAL cc_start: 0.8569 (t) cc_final: 0.7346 (p) REVERT: o 54 MET cc_start: 0.9152 (mmm) cc_final: 0.8824 (tmm) REVERT: o 82 MET cc_start: 0.8787 (mtm) cc_final: 0.8494 (mtp) REVERT: o 127 MET cc_start: 0.7921 (mmm) cc_final: 0.7289 (mtt) REVERT: o 146 MET cc_start: 0.8368 (tpt) cc_final: 0.8121 (tpp) REVERT: o 149 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7817 (tm-30) REVERT: p 34 MET cc_start: 0.8175 (ppp) cc_final: 0.7924 (ppp) REVERT: p 88 MET cc_start: 0.9049 (tpt) cc_final: 0.8659 (mmm) REVERT: p 135 ASP cc_start: 0.8834 (p0) cc_final: 0.8209 (p0) REVERT: p 144 GLU cc_start: 0.8498 (pm20) cc_final: 0.8256 (pm20) REVERT: q 28 MET cc_start: 0.9062 (mtm) cc_final: 0.8554 (pmm) REVERT: q 35 MET cc_start: 0.8497 (mtt) cc_final: 0.8228 (ppp) REVERT: q 58 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8478 (tp30) REVERT: q 173 LEU cc_start: 0.9057 (tp) cc_final: 0.8557 (tp) REVERT: r 45 MET cc_start: 0.8142 (ttm) cc_final: 0.7600 (mtp) REVERT: r 90 TYR cc_start: 0.9167 (m-80) cc_final: 0.8647 (m-10) REVERT: r 97 MET cc_start: 0.7021 (tmm) cc_final: 0.6785 (tmm) REVERT: r 139 MET cc_start: 0.7833 (ttp) cc_final: 0.7281 (tmm) REVERT: r 175 ASN cc_start: 0.9364 (m-40) cc_final: 0.9117 (t0) REVERT: s 8 ASN cc_start: 0.8847 (m110) cc_final: 0.8642 (m110) REVERT: s 13 LEU cc_start: 0.8609 (tp) cc_final: 0.8259 (mp) REVERT: s 57 PHE cc_start: 0.8572 (t80) cc_final: 0.8022 (t80) REVERT: s 74 MET cc_start: 0.9060 (mmt) cc_final: 0.8617 (mmt) REVERT: t 22 ILE cc_start: 0.9244 (pt) cc_final: 0.8661 (pt) REVERT: t 26 MET cc_start: 0.5986 (mpp) cc_final: 0.5055 (mpp) REVERT: t 43 MET cc_start: 0.8100 (tmm) cc_final: 0.7307 (tmm) REVERT: t 50 MET cc_start: 0.7970 (ptm) cc_final: 0.7673 (ppp) REVERT: t 173 MET cc_start: 0.8928 (mmm) cc_final: 0.8694 (mmm) REVERT: t 188 GLN cc_start: 0.7914 (pt0) cc_final: 0.7393 (pt0) REVERT: A 258 ARG cc_start: 0.7872 (mpt-90) cc_final: 0.7066 (tmm-80) REVERT: B 288 ASP cc_start: 0.6170 (p0) cc_final: 0.5740 (p0) REVERT: C 138 MET cc_start: 0.5722 (tmm) cc_final: 0.5087 (mtt) REVERT: C 297 ARG cc_start: 0.7488 (mmm160) cc_final: 0.7270 (mtm180) REVERT: D 60 TYR cc_start: 0.8257 (t80) cc_final: 0.8026 (t80) REVERT: D 153 MET cc_start: 0.6625 (tmm) cc_final: 0.5532 (tpt) REVERT: D 189 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8022 (tm-30) REVERT: D 261 ILE cc_start: 0.9164 (mm) cc_final: 0.8868 (pt) REVERT: D 309 MET cc_start: 0.8405 (mtp) cc_final: 0.7985 (mmm) REVERT: D 328 ASP cc_start: 0.8247 (m-30) cc_final: 0.7188 (p0) REVERT: D 351 LYS cc_start: 0.8919 (tppt) cc_final: 0.8378 (pttm) REVERT: E 69 PHE cc_start: 0.8335 (m-80) cc_final: 0.8082 (m-10) REVERT: E 133 SER cc_start: 0.5894 (p) cc_final: 0.5631 (m) REVERT: E 155 ASN cc_start: 0.8546 (t0) cc_final: 0.7926 (m110) REVERT: E 305 ASN cc_start: 0.7673 (t0) cc_final: 0.7015 (p0) REVERT: E 352 MET cc_start: 0.6733 (mpp) cc_final: 0.6493 (mpp) REVERT: F 172 VAL cc_start: 0.6312 (t) cc_final: 0.6098 (t) REVERT: F 175 MET cc_start: 0.6539 (mtt) cc_final: 0.5771 (mtp) REVERT: F 380 ASN cc_start: 0.7734 (t0) cc_final: 0.7117 (t0) REVERT: F 405 MET cc_start: 0.7732 (mtm) cc_final: 0.7238 (mmt) REVERT: f 190 GLU cc_start: 0.6750 (pt0) cc_final: 0.6354 (pt0) REVERT: f 248 LEU cc_start: 0.5798 (tt) cc_final: 0.4716 (tt) outliers start: 4 outliers final: 3 residues processed: 1104 average time/residue: 0.8931 time to fit residues: 1734.4038 Evaluate side-chains 843 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 840 time to evaluate : 9.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1285 random chunks: chunk 757 optimal weight: 5.9990 chunk 1220 optimal weight: 0.0040 chunk 744 optimal weight: 10.0000 chunk 578 optimal weight: 9.9990 chunk 848 optimal weight: 8.9990 chunk 1280 optimal weight: 7.9990 chunk 1178 optimal weight: 9.9990 chunk 1019 optimal weight: 0.0270 chunk 105 optimal weight: 8.9990 chunk 787 optimal weight: 5.9990 chunk 625 optimal weight: 1.9990 overall best weight: 2.8056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 ASN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 23 GLN L 8 ASN ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 GLN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82 ASN Q 87 ASN U 18 GLN ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 880 ASN U 888 GLN ** V 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 362 ASN X 144 GLN X 148 HIS ** X 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 72 HIS ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 HIS ** c 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 GLN g 224 ASN i 30 HIS ** i 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 116 GLN ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 187 GLN o 172 ASN q 65 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 82 ASN ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 HIS f 782 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.5842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 102854 Z= 0.201 Angle : 0.754 17.324 139119 Z= 0.383 Chirality : 0.047 0.443 15867 Planarity : 0.005 0.109 17980 Dihedral : 6.888 156.697 14262 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.39 % Favored : 90.50 % Rotamer: Outliers : 0.06 % Allowed : 0.40 % Favored : 99.54 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.67 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.07), residues: 12904 helix: -0.02 (0.07), residues: 5938 sheet: -0.72 (0.12), residues: 1728 loop : -2.61 (0.08), residues: 5238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP U 35 HIS 0.019 0.001 HIS f 301 PHE 0.043 0.002 PHE D 345 TYR 0.029 0.002 TYR H 101 ARG 0.014 0.000 ARG E 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25808 Ramachandran restraints generated. 12904 Oldfield, 0 Emsley, 12904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1119 time to evaluate : 8.867 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: G 83 MET cc_start: 0.8800 (mpp) cc_final: 0.8057 (mpp) REVERT: G 155 ASP cc_start: 0.8734 (m-30) cc_final: 0.8342 (m-30) REVERT: G 175 SER cc_start: 0.8933 (t) cc_final: 0.8641 (m) REVERT: H 203 MET cc_start: 0.6503 (mmt) cc_final: 0.6234 (mmp) REVERT: I 11 ILE cc_start: 0.7735 (mp) cc_final: 0.7005 (mp) REVERT: J 24 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7272 (mm-30) REVERT: L 26 MET cc_start: 0.9045 (mmt) cc_final: 0.8641 (mmt) REVERT: L 94 ASP cc_start: 0.8456 (m-30) cc_final: 0.8097 (m-30) REVERT: L 176 MET cc_start: 0.7631 (ppp) cc_final: 0.7334 (ppp) REVERT: M 150 MET cc_start: 0.8310 (mtp) cc_final: 0.7088 (mtm) REVERT: M 160 TYR cc_start: 0.8604 (m-10) cc_final: 0.8401 (m-10) REVERT: N 43 CYS cc_start: 0.8701 (p) cc_final: 0.8458 (p) REVERT: N 123 GLN cc_start: 0.8815 (mt0) cc_final: 0.8444 (mt0) REVERT: N 152 CYS cc_start: 0.8783 (m) cc_final: 0.8380 (m) REVERT: O 17 ASP cc_start: 0.6677 (p0) cc_final: 0.6300 (p0) REVERT: O 44 CYS cc_start: 0.8901 (m) cc_final: 0.8612 (m) REVERT: O 137 VAL cc_start: 0.8721 (t) cc_final: 0.8031 (t) REVERT: O 157 GLU cc_start: 0.9482 (tm-30) cc_final: 0.9202 (tm-30) REVERT: O 201 ARG cc_start: 0.7044 (tmt170) cc_final: 0.6326 (ptm-80) REVERT: P 129 CYS cc_start: 0.6973 (t) cc_final: 0.6766 (t) REVERT: P 149 MET cc_start: 0.9073 (mmp) cc_final: 0.8583 (mmp) REVERT: Q 189 HIS cc_start: 0.7102 (m-70) cc_final: 0.6728 (m-70) REVERT: R 45 MET cc_start: 0.9031 (ttm) cc_final: 0.8431 (mtm) REVERT: R 56 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8682 (pt0) REVERT: R 90 TYR cc_start: 0.8957 (m-80) cc_final: 0.8704 (m-10) REVERT: R 93 MET cc_start: 0.8277 (tpp) cc_final: 0.7951 (tpp) REVERT: R 175 ASN cc_start: 0.8913 (m110) cc_final: 0.8627 (m110) REVERT: S 54 CYS cc_start: 0.8133 (p) cc_final: 0.7856 (p) REVERT: S 146 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8266 (mm-40) REVERT: S 149 LEU cc_start: 0.9280 (mt) cc_final: 0.9040 (mt) REVERT: S 155 PHE cc_start: 0.7466 (m-10) cc_final: 0.7066 (t80) REVERT: T 5 MET cc_start: 0.8985 (mmt) cc_final: 0.8519 (mmt) REVERT: T 26 MET cc_start: 0.7559 (ttm) cc_final: 0.6758 (ttm) REVERT: U 244 MET cc_start: 0.5213 (ptp) cc_final: 0.4570 (mmm) REVERT: U 564 ASP cc_start: 0.7401 (m-30) cc_final: 0.6830 (t70) REVERT: U 695 MET cc_start: 0.7825 (mtm) cc_final: 0.7535 (ptt) REVERT: U 725 MET cc_start: 0.6568 (mpp) cc_final: 0.6137 (mpp) REVERT: U 880 ASN cc_start: 0.6432 (OUTLIER) cc_final: 0.5578 (t0) REVERT: V 136 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6480 (mm-30) REVERT: V 177 ASN cc_start: 0.7318 (m-40) cc_final: 0.6857 (m-40) REVERT: V 181 TYR cc_start: 0.6996 (m-80) cc_final: 0.6601 (m-80) REVERT: V 212 TYR cc_start: 0.8691 (m-10) cc_final: 0.8455 (m-80) REVERT: W 74 CYS cc_start: 0.8414 (m) cc_final: 0.8119 (t) REVERT: W 160 LYS cc_start: 0.7558 (mmtm) cc_final: 0.7230 (tptp) REVERT: W 220 GLU cc_start: 0.8232 (tp30) cc_final: 0.7577 (mp0) REVERT: W 307 LYS cc_start: 0.8563 (ttpp) cc_final: 0.8077 (mmtt) REVERT: W 436 MET cc_start: 0.8972 (tpp) cc_final: 0.8586 (tpp) REVERT: X 130 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6674 (mm-30) REVERT: X 160 MET cc_start: 0.6335 (mmt) cc_final: 0.6054 (tmm) REVERT: X 397 TYR cc_start: 0.8320 (m-80) cc_final: 0.8120 (m-10) REVERT: X 415 TYR cc_start: 0.9244 (m-80) cc_final: 0.8805 (m-80) REVERT: Y 42 MET cc_start: 0.7220 (mmm) cc_final: 0.6858 (mtp) REVERT: Y 211 TYR cc_start: 0.6289 (p90) cc_final: 0.5620 (m-10) REVERT: Y 389 MET cc_start: 0.4848 (mtt) cc_final: 0.4016 (mmt) REVERT: Z 40 LEU cc_start: 0.8415 (tp) cc_final: 0.8143 (tp) REVERT: Z 73 ASP cc_start: 0.7623 (t0) cc_final: 0.7010 (p0) REVERT: Z 84 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7792 (tppt) REVERT: Z 114 ARG cc_start: 0.8318 (ptt180) cc_final: 0.7498 (ptt90) REVERT: Z 257 MET cc_start: 0.8572 (tpt) cc_final: 0.8235 (tpt) REVERT: a 46 GLN cc_start: 0.7260 (tp-100) cc_final: 0.6992 (tm-30) REVERT: a 138 VAL cc_start: 0.4750 (t) cc_final: 0.4410 (t) REVERT: a 161 LYS cc_start: 0.7600 (mmmt) cc_final: 0.7251 (mptt) REVERT: a 179 PHE cc_start: 0.7961 (t80) cc_final: 0.7655 (t80) REVERT: b 1 MET cc_start: 0.2299 (tpp) cc_final: 0.1096 (ttp) REVERT: b 181 ASP cc_start: 0.7782 (m-30) cc_final: 0.7380 (p0) REVERT: c 57 MET cc_start: 0.8614 (mmp) cc_final: 0.7830 (mmm) REVERT: c 71 ASP cc_start: 0.7933 (t70) cc_final: 0.7664 (t0) REVERT: c 98 MET cc_start: 0.6038 (mtm) cc_final: 0.5274 (mtm) REVERT: c 104 ARG cc_start: 0.8668 (ttp-170) cc_final: 0.8209 (ttp80) REVERT: c 221 HIS cc_start: 0.7214 (t-90) cc_final: 0.6910 (t-170) REVERT: c 226 MET cc_start: 0.3467 (ppp) cc_final: 0.3256 (ppp) REVERT: c 232 GLN cc_start: 0.8648 (mt0) cc_final: 0.7965 (mp10) REVERT: c 248 MET cc_start: 0.8550 (ptm) cc_final: 0.8239 (tmm) REVERT: d 96 HIS cc_start: 0.5598 (m-70) cc_final: 0.5386 (m-70) REVERT: d 144 MET cc_start: 0.5224 (ptt) cc_final: 0.5010 (ptt) REVERT: d 215 TRP cc_start: 0.3768 (m100) cc_final: 0.3284 (m-10) REVERT: d 233 GLU cc_start: 0.6857 (mp0) cc_final: 0.5650 (tp30) REVERT: e 5 LYS cc_start: 0.5227 (pptt) cc_final: 0.4746 (pptt) REVERT: e 43 TRP cc_start: 0.4917 (t60) cc_final: 0.3204 (m-90) REVERT: g 113 MET cc_start: 0.8517 (mmt) cc_final: 0.7933 (mmm) REVERT: h 58 ASP cc_start: 0.8338 (t0) cc_final: 0.8019 (t70) REVERT: h 147 PHE cc_start: 0.7762 (m-80) cc_final: 0.7499 (m-10) REVERT: h 158 TRP cc_start: 0.6469 (m100) cc_final: 0.5924 (m100) REVERT: i 103 GLU cc_start: 0.7780 (tt0) cc_final: 0.7505 (mp0) REVERT: k 59 MET cc_start: 0.7809 (ttm) cc_final: 0.7391 (ttm) REVERT: k 107 MET cc_start: 0.6848 (ttt) cc_final: 0.6579 (ptm) REVERT: k 156 MET cc_start: 0.8590 (tpt) cc_final: 0.7863 (tpp) REVERT: k 191 LEU cc_start: 0.8434 (tp) cc_final: 0.8082 (pp) REVERT: k 206 MET cc_start: 0.7976 (ttp) cc_final: 0.7250 (tmm) REVERT: k 225 ASN cc_start: 0.7343 (p0) cc_final: 0.6898 (p0) REVERT: k 228 MET cc_start: 0.7402 (mpp) cc_final: 0.6665 (mpp) REVERT: l 26 MET cc_start: 0.7957 (mmt) cc_final: 0.7654 (tmm) REVERT: l 50 LYS cc_start: 0.8495 (mttt) cc_final: 0.8227 (mtmt) REVERT: l 176 MET cc_start: 0.8496 (ptm) cc_final: 0.7551 (ptp) REVERT: m 27 MET cc_start: 0.8356 (mmp) cc_final: 0.8075 (mmm) REVERT: m 50 GLU cc_start: 0.7143 (tt0) cc_final: 0.6508 (tm-30) REVERT: m 170 GLN cc_start: 0.7888 (mt0) cc_final: 0.7612 (tm-30) REVERT: m 214 SER cc_start: 0.7206 (t) cc_final: 0.6749 (t) REVERT: n 57 ASP cc_start: 0.8581 (t70) cc_final: 0.8319 (t0) REVERT: n 81 SER cc_start: 0.9116 (m) cc_final: 0.8806 (p) REVERT: n 95 MET cc_start: 0.6837 (tpt) cc_final: 0.6472 (tpt) REVERT: n 116 MET cc_start: 0.7973 (mtt) cc_final: 0.7703 (mpp) REVERT: n 120 MET cc_start: 0.8878 (ppp) cc_final: 0.8236 (ppp) REVERT: o 26 VAL cc_start: 0.8556 (t) cc_final: 0.7299 (p) REVERT: o 54 MET cc_start: 0.9139 (mmm) cc_final: 0.8763 (tmm) REVERT: o 82 MET cc_start: 0.8728 (mtm) cc_final: 0.8416 (mtp) REVERT: o 127 MET cc_start: 0.7915 (mmm) cc_final: 0.7315 (mtt) REVERT: o 146 MET cc_start: 0.8369 (tpt) cc_final: 0.8051 (tpp) REVERT: o 149 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7812 (tm-30) REVERT: p 34 MET cc_start: 0.8190 (ppp) cc_final: 0.7856 (ppp) REVERT: p 88 MET cc_start: 0.8967 (tpt) cc_final: 0.8545 (mmm) REVERT: p 135 ASP cc_start: 0.8859 (p0) cc_final: 0.8275 (p0) REVERT: q 28 MET cc_start: 0.8987 (mtm) cc_final: 0.8540 (pmm) REVERT: q 35 MET cc_start: 0.8522 (mtt) cc_final: 0.8153 (ppp) REVERT: q 58 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8539 (tp30) REVERT: q 173 LEU cc_start: 0.9005 (tp) cc_final: 0.8697 (tp) REVERT: r 45 MET cc_start: 0.8060 (ttm) cc_final: 0.7629 (mtp) REVERT: r 56 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8755 (mt-10) REVERT: r 90 TYR cc_start: 0.9137 (m-80) cc_final: 0.8649 (m-10) REVERT: r 100 MET cc_start: 0.8046 (mmm) cc_final: 0.7659 (mmm) REVERT: r 139 MET cc_start: 0.7846 (ttp) cc_final: 0.7326 (tmm) REVERT: r 175 ASN cc_start: 0.9351 (m-40) cc_final: 0.9124 (t0) REVERT: s 57 PHE cc_start: 0.8484 (t80) cc_final: 0.7948 (t80) REVERT: s 74 MET cc_start: 0.9068 (mmt) cc_final: 0.8684 (mmt) REVERT: s 193 LEU cc_start: 0.8285 (tp) cc_final: 0.7576 (mt) REVERT: t 22 ILE cc_start: 0.9253 (pt) cc_final: 0.8672 (pt) REVERT: t 26 MET cc_start: 0.5993 (mpp) cc_final: 0.5668 (mpp) REVERT: t 43 MET cc_start: 0.8079 (tmm) cc_final: 0.7304 (tmm) REVERT: t 50 MET cc_start: 0.8011 (ptm) cc_final: 0.7631 (ppp) REVERT: t 173 MET cc_start: 0.8903 (mmm) cc_final: 0.8655 (mmm) REVERT: A 258 ARG cc_start: 0.7856 (mpt-90) cc_final: 0.7056 (tmm-80) REVERT: C 43 ARG cc_start: 0.6754 (ttt90) cc_final: 0.6307 (ptm160) REVERT: C 138 MET cc_start: 0.5796 (tmm) cc_final: 0.5193 (mtt) REVERT: D 60 TYR cc_start: 0.8269 (t80) cc_final: 0.8053 (t80) REVERT: D 153 MET cc_start: 0.6490 (tmm) cc_final: 0.5338 (tpt) REVERT: D 189 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7964 (tm-30) REVERT: D 261 ILE cc_start: 0.9134 (mm) cc_final: 0.8824 (pt) REVERT: D 309 MET cc_start: 0.8412 (mtp) cc_final: 0.8031 (mmm) REVERT: D 328 ASP cc_start: 0.8383 (m-30) cc_final: 0.7346 (p0) REVERT: D 351 LYS cc_start: 0.8901 (tppt) cc_final: 0.8384 (pttm) REVERT: E 133 SER cc_start: 0.5897 (p) cc_final: 0.5633 (m) REVERT: E 155 ASN cc_start: 0.8521 (t0) cc_final: 0.7877 (m110) REVERT: E 305 ASN cc_start: 0.7546 (t0) cc_final: 0.6818 (p0) REVERT: E 352 MET cc_start: 0.6746 (mpp) cc_final: 0.6537 (mpp) REVERT: F 85 THR cc_start: 0.2816 (p) cc_final: 0.2417 (t) REVERT: F 172 VAL cc_start: 0.6306 (t) cc_final: 0.6087 (t) REVERT: F 175 MET cc_start: 0.6502 (mtt) cc_final: 0.5472 (mtp) REVERT: F 380 ASN cc_start: 0.7706 (t0) cc_final: 0.7068 (t0) REVERT: F 405 MET cc_start: 0.7678 (mtm) cc_final: 0.7215 (mmt) REVERT: f 190 GLU cc_start: 0.6568 (pt0) cc_final: 0.6194 (pt0) REVERT: f 248 LEU cc_start: 0.5934 (tt) cc_final: 0.4910 (tt) REVERT: f 512 MET cc_start: 0.2182 (tpt) cc_final: 0.1926 (tpt) outliers start: 6 outliers final: 3 residues processed: 1124 average time/residue: 0.8859 time to fit residues: 1750.8950 Evaluate side-chains 867 residues out of total 11125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 863 time to evaluate : 8.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.679 > 50: distance: 49 - 71: 21.903 distance: 58 - 78: 4.183 distance: 67 - 71: 22.758 distance: 71 - 72: 35.523 distance: 72 - 73: 13.281 distance: 72 - 75: 27.024 distance: 73 - 74: 11.315 distance: 73 - 78: 29.386 distance: 75 - 76: 41.899 distance: 75 - 77: 32.133 distance: 78 - 79: 30.371 distance: 79 - 80: 30.348 distance: 80 - 81: 17.029 distance: 80 - 82: 9.182 distance: 82 - 83: 23.583 distance: 83 - 84: 21.533 distance: 83 - 86: 15.384 distance: 84 - 85: 37.649 distance: 84 - 93: 50.844 distance: 86 - 87: 25.716 distance: 87 - 88: 11.986 distance: 88 - 89: 8.715 distance: 89 - 90: 15.201 distance: 90 - 91: 3.914 distance: 90 - 92: 11.202 distance: 93 - 94: 9.798 distance: 94 - 95: 30.042 distance: 94 - 97: 19.537 distance: 95 - 96: 7.572 distance: 95 - 101: 7.370 distance: 97 - 98: 20.703 distance: 98 - 99: 25.108 distance: 98 - 100: 25.539 distance: 101 - 102: 5.279 distance: 101 - 107: 21.074 distance: 102 - 103: 24.942 distance: 102 - 105: 23.727 distance: 103 - 104: 22.472 distance: 103 - 108: 15.811 distance: 105 - 106: 45.587 distance: 106 - 107: 13.562 distance: 108 - 109: 36.430 distance: 109 - 110: 21.246 distance: 109 - 112: 27.225 distance: 110 - 111: 28.255 distance: 110 - 119: 8.579 distance: 112 - 113: 33.708 distance: 113 - 114: 41.533 distance: 114 - 115: 21.940 distance: 115 - 116: 35.654 distance: 116 - 117: 7.889 distance: 116 - 118: 21.022 distance: 119 - 120: 9.078 distance: 120 - 121: 13.544 distance: 120 - 123: 14.359 distance: 121 - 122: 6.896 distance: 121 - 126: 38.401 distance: 122 - 145: 22.608 distance: 123 - 124: 16.092 distance: 123 - 125: 3.833 distance: 126 - 127: 34.588 distance: 127 - 128: 11.165 distance: 127 - 130: 8.922 distance: 128 - 129: 9.545 distance: 128 - 133: 16.721 distance: 129 - 152: 28.229 distance: 130 - 131: 15.157 distance: 130 - 132: 33.439 distance: 133 - 134: 7.084 distance: 134 - 135: 25.196 distance: 134 - 137: 20.972 distance: 135 - 136: 16.393 distance: 135 - 140: 9.300 distance: 136 - 158: 30.334 distance: 137 - 138: 27.938 distance: 137 - 139: 17.277 distance: 140 - 141: 16.769 distance: 141 - 142: 34.736 distance: 141 - 144: 16.877 distance: 142 - 143: 28.863 distance: 142 - 145: 17.291 distance: 143 - 164: 22.235