Starting phenix.real_space_refine on Wed Mar 20 13:15:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfr_8665/03_2024/5vfr_8665_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfr_8665/03_2024/5vfr_8665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfr_8665/03_2024/5vfr_8665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfr_8665/03_2024/5vfr_8665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfr_8665/03_2024/5vfr_8665_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfr_8665/03_2024/5vfr_8665_updated.pdb" } resolution = 4.9 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 12 5.49 5 S 585 5.16 5 C 63101 2.51 5 N 17177 2.21 5 O 19032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "U ARG 140": "NH1" <-> "NH2" Residue "U ARG 159": "NH1" <-> "NH2" Residue "U PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 194": "NH1" <-> "NH2" Residue "V ARG 306": "NH1" <-> "NH2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ARG 355": "NH1" <-> "NH2" Residue "V ARG 397": "NH1" <-> "NH2" Residue "W ARG 8": "NH1" <-> "NH2" Residue "W ARG 12": "NH1" <-> "NH2" Residue "W ARG 55": "NH1" <-> "NH2" Residue "W ARG 182": "NH1" <-> "NH2" Residue "W ARG 357": "NH1" <-> "NH2" Residue "W ARG 364": "NH1" <-> "NH2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 137": "NH1" <-> "NH2" Residue "Y ARG 176": "NH1" <-> "NH2" Residue "Y ARG 177": "NH1" <-> "NH2" Residue "Y ARG 179": "NH1" <-> "NH2" Residue "Y ARG 267": "NH1" <-> "NH2" Residue "Y ARG 297": "NH1" <-> "NH2" Residue "Y ARG 300": "NH1" <-> "NH2" Residue "Y ARG 312": "NH1" <-> "NH2" Residue "Y ARG 342": "NH1" <-> "NH2" Residue "Y ARG 358": "NH1" <-> "NH2" Residue "Z TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 267": "NH1" <-> "NH2" Residue "a PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 196": "NH1" <-> "NH2" Residue "a ARG 226": "NH1" <-> "NH2" Residue "a ARG 270": "NH1" <-> "NH2" Residue "a ARG 284": "NH1" <-> "NH2" Residue "b ARG 70": "NH1" <-> "NH2" Residue "c ARG 68": "NH1" <-> "NH2" Residue "c ARG 104": "NH1" <-> "NH2" Residue "d ARG 52": "NH1" <-> "NH2" Residue "d ARG 65": "NH1" <-> "NH2" Residue "d ARG 111": "NH1" <-> "NH2" Residue "d ARG 175": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 249": "NH1" <-> "NH2" Residue "K ARG 10": "NH1" <-> "NH2" Residue "K ARG 20": "NH1" <-> "NH2" Residue "L TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "L ARG 157": "NH1" <-> "NH2" Residue "L ARG 239": "NH1" <-> "NH2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 187": "NH1" <-> "NH2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "Q ARG 93": "NH1" <-> "NH2" Residue "S ARG 173": "NH1" <-> "NH2" Residue "T ARG 182": "NH1" <-> "NH2" Residue "g ARG 21": "NH1" <-> "NH2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "g ARG 132": "NH1" <-> "NH2" Residue "g PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 4": "NH1" <-> "NH2" Residue "h PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 249": "NH1" <-> "NH2" Residue "k ARG 20": "NH1" <-> "NH2" Residue "l TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 96": "NH1" <-> "NH2" Residue "l ARG 157": "NH1" <-> "NH2" Residue "l ARG 239": "NH1" <-> "NH2" Residue "m ARG 19": "NH1" <-> "NH2" Residue "m ARG 187": "NH1" <-> "NH2" Residue "m ARG 232": "NH1" <-> "NH2" Residue "n ARG 45": "NH1" <-> "NH2" Residue "o ARG 201": "NH1" <-> "NH2" Residue "p ARG 66": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "E ARG 251": "NH1" <-> "NH2" Residue "E ARG 255": "NH1" <-> "NH2" Residue "E ARG 291": "NH1" <-> "NH2" Residue "F ARG 238": "NH1" <-> "NH2" Residue "F ARG 269": "NH1" <-> "NH2" Residue "F ARG 334": "NH1" <-> "NH2" Residue "F ARG 364": "NH1" <-> "NH2" Residue "f PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 388": "OD1" <-> "OD2" Residue "f GLU 641": "OE1" <-> "OE2" Residue "f TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 99908 Number of models: 1 Model: "" Number of chains: 51 Chain: "U" Number of atoms: 6287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6287 Classifications: {'peptide': 806} Link IDs: {'PTRANS': 26, 'TRANS': 779} Chain breaks: 3 Chain: "V" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3799 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 20, 'TRANS': 451} Chain: "W" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3703 Classifications: {'peptide': 456} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 447} Chain: "X" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1905 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain: "Y" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3115 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 370} Chain: "Z" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "a" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2995 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain: "b" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1458 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain: "c" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2187 Classifications: {'peptide': 278} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 267} Chain breaks: 1 Chain: "d" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2116 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 245} Chain: "e" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 334 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain breaks: 1 Chain: "G" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1820 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 228} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1688 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 216} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "I" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1895 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 3, 'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1704 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'CIS': 4, 'PTRANS': 6, 'TRANS': 228} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "K" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1850 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "M" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1856 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1430 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "O" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1643 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1585 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1570 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1548 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1667 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 207} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1826 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "h" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1708 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "i" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1912 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "j" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1704 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "k" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1722 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "l" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1850 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "m" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1856 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "n" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1430 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "o" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1643 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "p" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1585 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "q" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1570 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "r" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1548 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "s" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1667 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 207} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2672 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2706 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 329} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2859 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3040 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 17, 'TRANS': 359} Chain: "E" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2860 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 18, 'TRANS': 356} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "F" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2859 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'CIS': 3, 'PTRANS': 17, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "f" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5319 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 25, 'TRANS': 663} Chain breaks: 9 Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 11 residue: pdb=" N ALA X 359 " occ=0.98 ... (3 atoms not shown) pdb=" CB ALA X 359 " occ=0.98 residue: pdb=" N GLN X 380 " occ=0.83 ... (7 atoms not shown) pdb=" NE2 GLN X 380 " occ=0.83 residue: pdb=" N GLY Z 30 " occ=0.40 ... (2 atoms not shown) pdb=" O GLY Z 30 " occ=0.40 residue: pdb=" N ILE b 90 " occ=0.79 ... (6 atoms not shown) pdb=" CD1 ILE b 90 " occ=0.79 residue: pdb=" N SER b 115 " occ=0.80 ... (4 atoms not shown) pdb=" OG SER b 115 " occ=0.80 residue: pdb=" N ILE b 140 " occ=0.60 ... (6 atoms not shown) pdb=" CD1 ILE b 140 " occ=0.60 residue: pdb=" N VAL b 173 " occ=0.49 ... (5 atoms not shown) pdb=" CG2 VAL b 173 " occ=0.49 residue: pdb=" N GLY b 191 " occ=0.88 ... (2 atoms not shown) pdb=" O GLY b 191 " occ=0.88 residue: pdb=" N ILE d 63 " occ=0.67 ... (6 atoms not shown) pdb=" CD1 ILE d 63 " occ=0.67 residue: pdb=" N SER d 70 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER d 70 " occ=0.00 residue: pdb=" N MET d 95 " occ=0.99 ... (6 atoms not shown) pdb=" CE MET d 95 " occ=0.99 Time building chain proxies: 39.28, per 1000 atoms: 0.39 Number of scatterers: 99908 At special positions: 0 Unit cell: (333.75, 213, 219.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 585 16.00 P 12 15.00 O 19032 8.00 N 17177 7.00 C 63101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 186 " distance=2.03 Simple disulfide: pdb=" SG CYS m 41 " - pdb=" SG CYS m 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 29.68 Conformation dependent library (CDL) restraints added in 14.0 seconds 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 24038 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 454 helices and 84 sheets defined 42.1% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.18 Creating SS restraints... Processing helix chain 'U' and resid 17 through 30 removed outlier: 4.422A pdb=" N PHE U 22 " --> pdb=" O GLN U 18 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA U 29 " --> pdb=" O HIS U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 50 removed outlier: 4.356A pdb=" N ALA U 36 " --> pdb=" O ASP U 33 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE U 38 " --> pdb=" O TRP U 35 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER U 39 " --> pdb=" O ALA U 36 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU U 40 " --> pdb=" O GLU U 37 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL U 42 " --> pdb=" O SER U 39 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP U 43 " --> pdb=" O GLU U 40 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU U 50 " --> pdb=" O VAL U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 71 Processing helix chain 'U' and resid 75 through 82 Processing helix chain 'U' and resid 96 through 116 Processing helix chain 'U' and resid 132 through 143 removed outlier: 4.011A pdb=" N GLN U 139 " --> pdb=" O ASN U 135 " (cutoff:3.500A) Processing helix chain 'U' and resid 148 through 157 removed outlier: 4.180A pdb=" N ALA U 154 " --> pdb=" O ALA U 150 " (cutoff:3.500A) Processing helix chain 'U' and resid 162 through 165 No H-bonds generated for 'chain 'U' and resid 162 through 165' Processing helix chain 'U' and resid 174 through 186 removed outlier: 3.609A pdb=" N TYR U 179 " --> pdb=" O MET U 176 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS U 184 " --> pdb=" O LEU U 181 " (cutoff:3.500A) Processing helix chain 'U' and resid 194 through 205 removed outlier: 4.014A pdb=" N VAL U 202 " --> pdb=" O LEU U 198 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS U 203 " --> pdb=" O ARG U 199 " (cutoff:3.500A) Processing helix chain 'U' and resid 214 through 222 removed outlier: 4.454A pdb=" N ILE U 221 " --> pdb=" O CYS U 217 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 238 Processing helix chain 'U' and resid 246 through 254 Processing helix chain 'U' and resid 258 through 268 Processing helix chain 'U' and resid 321 through 330 removed outlier: 5.184A pdb=" N ILE U 326 " --> pdb=" O THR U 322 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU U 329 " --> pdb=" O MET U 325 " (cutoff:3.500A) Processing helix chain 'U' and resid 332 through 344 Processing helix chain 'U' and resid 350 through 359 removed outlier: 5.533A pdb=" N ALA U 359 " --> pdb=" O ASN U 355 " (cutoff:3.500A) Processing helix chain 'U' and resid 364 through 375 removed outlier: 4.819A pdb=" N VAL U 370 " --> pdb=" O HIS U 366 " (cutoff:3.500A) Processing helix chain 'U' and resid 399 through 410 removed outlier: 5.377A pdb=" N LEU U 408 " --> pdb=" O ALA U 404 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLY U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) Processing helix chain 'U' and resid 417 through 422 removed outlier: 4.251A pdb=" N LEU U 420 " --> pdb=" O LYS U 417 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN U 421 " --> pdb=" O GLU U 418 " (cutoff:3.500A) Processing helix chain 'U' and resid 437 through 449 removed outlier: 4.949A pdb=" N GLY U 442 " --> pdb=" O GLN U 438 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU U 443 " --> pdb=" O GLU U 439 " (cutoff:3.500A) Processing helix chain 'U' and resid 457 through 465 Processing helix chain 'U' and resid 474 through 484 removed outlier: 5.570A pdb=" N LEU U 479 " --> pdb=" O HIS U 475 " (cutoff:3.500A) Processing helix chain 'U' and resid 492 through 503 removed outlier: 4.008A pdb=" N THR U 499 " --> pdb=" O ASP U 495 " (cutoff:3.500A) Processing helix chain 'U' and resid 506 through 519 removed outlier: 4.820A pdb=" N ALA U 511 " --> pdb=" O VAL U 507 " (cutoff:3.500A) Processing helix chain 'U' and resid 528 through 538 removed outlier: 4.394A pdb=" N TYR U 535 " --> pdb=" O ASP U 531 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA U 536 " --> pdb=" O MET U 532 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN U 537 " --> pdb=" O VAL U 533 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU U 538 " --> pdb=" O GLY U 534 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 Processing helix chain 'U' and resid 564 through 572 Processing helix chain 'U' and resid 576 through 589 Processing helix chain 'U' and resid 599 through 607 Processing helix chain 'U' and resid 612 through 625 removed outlier: 3.972A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) Processing helix chain 'U' and resid 631 through 642 removed outlier: 4.704A pdb=" N SER U 635 " --> pdb=" O GLU U 631 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU U 642 " --> pdb=" O SER U 638 " (cutoff:3.500A) Processing helix chain 'U' and resid 646 through 659 Processing helix chain 'U' and resid 667 through 676 Proline residue: U 674 - end of helix Processing helix chain 'U' and resid 681 through 695 Processing helix chain 'U' and resid 706 through 718 removed outlier: 3.986A pdb=" N SER U 714 " --> pdb=" O ARG U 710 " (cutoff:3.500A) Processing helix chain 'U' and resid 730 through 738 Processing helix chain 'U' and resid 757 through 766 Processing helix chain 'U' and resid 773 through 777 Processing helix chain 'U' and resid 888 through 890 No H-bonds generated for 'chain 'U' and resid 888 through 890' Processing helix chain 'V' and resid 29 through 52 removed outlier: 3.615A pdb=" N MET V 37 " --> pdb=" O GLN V 33 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA V 42 " --> pdb=" O LYS V 38 " (cutoff:3.500A) Processing helix chain 'V' and resid 61 through 75 Processing helix chain 'V' and resid 90 through 93 No H-bonds generated for 'chain 'V' and resid 90 through 93' Processing helix chain 'V' and resid 105 through 113 Processing helix chain 'V' and resid 116 through 119 No H-bonds generated for 'chain 'V' and resid 116 through 119' Processing helix chain 'V' and resid 130 through 140 Proline residue: V 133 - end of helix Proline residue: V 138 - end of helix Processing helix chain 'V' and resid 148 through 156 Processing helix chain 'V' and resid 160 through 162 No H-bonds generated for 'chain 'V' and resid 160 through 162' Processing helix chain 'V' and resid 172 through 190 Processing helix chain 'V' and resid 199 through 219 removed outlier: 5.910A pdb=" N ASP V 204 " --> pdb=" O ARG V 201 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL V 206 " --> pdb=" O LEU V 203 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA V 208 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS V 210 " --> pdb=" O ALA V 207 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR V 218 " --> pdb=" O ALA V 215 " (cutoff:3.500A) Processing helix chain 'V' and resid 227 through 237 Processing helix chain 'V' and resid 247 through 260 Processing helix chain 'V' and resid 267 through 271 Processing helix chain 'V' and resid 284 through 299 Processing helix chain 'V' and resid 303 through 314 Processing helix chain 'V' and resid 324 through 332 removed outlier: 4.326A pdb=" N VAL V 328 " --> pdb=" O PHE V 324 " (cutoff:3.500A) Processing helix chain 'V' and resid 334 through 339 Processing helix chain 'V' and resid 346 through 348 No H-bonds generated for 'chain 'V' and resid 346 through 348' Processing helix chain 'V' and resid 354 through 357 No H-bonds generated for 'chain 'V' and resid 354 through 357' Processing helix chain 'V' and resid 360 through 368 Processing helix chain 'V' and resid 372 through 389 removed outlier: 4.033A pdb=" N LEU V 379 " --> pdb=" O PHE V 375 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLU V 384 " --> pdb=" O ASP V 380 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS V 385 " --> pdb=" O GLN V 381 " (cutoff:3.500A) Processing helix chain 'V' and resid 393 through 413 removed outlier: 3.659A pdb=" N ARG V 397 " --> pdb=" O THR V 393 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG V 399 " --> pdb=" O ILE V 395 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N HIS V 400 " --> pdb=" O ILE V 396 " (cutoff:3.500A) Processing helix chain 'V' and resid 419 through 423 Processing helix chain 'V' and resid 431 through 444 Processing helix chain 'V' and resid 470 through 496 removed outlier: 3.543A pdb=" N ALA V 475 " --> pdb=" O GLU V 471 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS V 477 " --> pdb=" O GLN V 473 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE V 496 " --> pdb=" O LYS V 492 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 12 removed outlier: 4.298A pdb=" N ARG W 8 " --> pdb=" O GLY W 4 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 16 No H-bonds generated for 'chain 'W' and resid 14 through 16' Processing helix chain 'W' and resid 22 through 37 Proline residue: W 29 - end of helix Processing helix chain 'W' and resid 43 through 63 Processing helix chain 'W' and resid 70 through 84 Processing helix chain 'W' and resid 95 through 112 removed outlier: 4.234A pdb=" N GLN W 99 " --> pdb=" O SER W 95 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA W 100 " --> pdb=" O GLN W 96 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 133 removed outlier: 4.020A pdb=" N ARG W 129 " --> pdb=" O ILE W 125 " (cutoff:3.500A) Processing helix chain 'W' and resid 139 through 155 removed outlier: 4.662A pdb=" N GLN W 155 " --> pdb=" O THR W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 159 through 167 Processing helix chain 'W' and resid 181 through 186 Processing helix chain 'W' and resid 188 through 194 removed outlier: 3.558A pdb=" N LEU W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 199 through 209 Processing helix chain 'W' and resid 222 through 232 removed outlier: 4.548A pdb=" N ASN W 228 " --> pdb=" O LEU W 224 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU W 229 " --> pdb=" O LYS W 225 " (cutoff:3.500A) Processing helix chain 'W' and resid 246 through 249 No H-bonds generated for 'chain 'W' and resid 246 through 249' Processing helix chain 'W' and resid 262 through 271 Processing helix chain 'W' and resid 283 through 289 removed outlier: 4.921A pdb=" N HIS W 288 " --> pdb=" O SER W 284 " (cutoff:3.500A) Processing helix chain 'W' and resid 300 through 307 Processing helix chain 'W' and resid 317 through 325 Processing helix chain 'W' and resid 335 through 340 Processing helix chain 'W' and resid 347 through 366 Processing helix chain 'W' and resid 376 through 381 Processing helix chain 'W' and resid 387 through 399 Processing helix chain 'W' and resid 425 through 453 removed outlier: 4.155A pdb=" N THR W 442 " --> pdb=" O LEU W 438 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR W 443 " --> pdb=" O VAL W 439 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA W 447 " --> pdb=" O THR W 443 " (cutoff:3.500A) Processing helix chain 'X' and resid 183 through 196 removed outlier: 4.490A pdb=" N THR X 195 " --> pdb=" O THR X 191 " (cutoff:3.500A) Processing helix chain 'X' and resid 206 through 220 removed outlier: 3.651A pdb=" N HIS X 218 " --> pdb=" O SER X 214 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA X 219 " --> pdb=" O GLY X 215 " (cutoff:3.500A) Processing helix chain 'X' and resid 225 through 236 Processing helix chain 'X' and resid 244 through 247 No H-bonds generated for 'chain 'X' and resid 244 through 247' Processing helix chain 'X' and resid 252 through 261 Processing helix chain 'X' and resid 267 through 270 No H-bonds generated for 'chain 'X' and resid 267 through 270' Processing helix chain 'X' and resid 282 through 296 removed outlier: 3.984A pdb=" N CYS X 289 " --> pdb=" O GLU X 285 " (cutoff:3.500A) Processing helix chain 'X' and resid 299 through 302 No H-bonds generated for 'chain 'X' and resid 299 through 302' Processing helix chain 'X' and resid 305 through 308 No H-bonds generated for 'chain 'X' and resid 305 through 308' Processing helix chain 'X' and resid 321 through 338 removed outlier: 4.258A pdb=" N LEU X 326 " --> pdb=" O HIS X 322 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU X 332 " --> pdb=" O ASP X 328 " (cutoff:3.500A) Processing helix chain 'X' and resid 347 through 350 No H-bonds generated for 'chain 'X' and resid 347 through 350' Processing helix chain 'X' and resid 361 through 370 Processing helix chain 'X' and resid 394 through 421 removed outlier: 4.323A pdb=" N ALA X 399 " --> pdb=" O LYS X 395 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR X 415 " --> pdb=" O VAL X 411 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN X 416 " --> pdb=" O ASP X 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 14 through 27 Processing helix chain 'Y' and resid 35 through 45 Processing helix chain 'Y' and resid 51 through 58 removed outlier: 4.404A pdb=" N ALA Y 56 " --> pdb=" O PRO Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 68 through 91 removed outlier: 4.674A pdb=" N MET Y 73 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLU Y 89 " --> pdb=" O ASP Y 85 " (cutoff:3.500A) Processing helix chain 'Y' and resid 99 through 114 removed outlier: 3.895A pdb=" N LYS Y 107 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) Processing helix chain 'Y' and resid 117 through 123 Processing helix chain 'Y' and resid 135 through 150 removed outlier: 4.518A pdb=" N ILE Y 140 " --> pdb=" O HIS Y 136 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE Y 147 " --> pdb=" O TYR Y 143 " (cutoff:3.500A) Processing helix chain 'Y' and resid 155 through 166 removed outlier: 4.155A pdb=" N THR Y 161 " --> pdb=" O ILE Y 157 " (cutoff:3.500A) Processing helix chain 'Y' and resid 176 through 190 Processing helix chain 'Y' and resid 194 through 200 removed outlier: 3.702A pdb=" N ALA Y 198 " --> pdb=" O PHE Y 194 " (cutoff:3.500A) Processing helix chain 'Y' and resid 216 through 230 removed outlier: 3.716A pdb=" N VAL Y 226 " --> pdb=" O TYR Y 222 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ILE Y 229 " --> pdb=" O TYR Y 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 233 through 240 Processing helix chain 'Y' and resid 254 through 263 Processing helix chain 'Y' and resid 269 through 283 Processing helix chain 'Y' and resid 292 through 310 removed outlier: 4.099A pdb=" N VAL Y 296 " --> pdb=" O ARG Y 293 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG Y 297 " --> pdb=" O TYR Y 294 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER Y 305 " --> pdb=" O HIS Y 302 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN Y 306 " --> pdb=" O ALA Y 303 " (cutoff:3.500A) Processing helix chain 'Y' and resid 320 through 323 No H-bonds generated for 'chain 'Y' and resid 320 through 323' Processing helix chain 'Y' and resid 329 through 339 Processing helix chain 'Y' and resid 364 through 383 removed outlier: 4.926A pdb=" N THR Y 369 " --> pdb=" O GLN Y 365 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE Y 370 " --> pdb=" O TYR Y 366 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU Y 375 " --> pdb=" O LYS Y 371 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU Y 377 " --> pdb=" O GLY Y 373 " (cutoff:3.500A) Processing helix chain 'Z' and resid 13 through 29 removed outlier: 3.721A pdb=" N GLY Z 27 " --> pdb=" O PHE Z 23 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS Z 28 " --> pdb=" O ASN Z 24 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 85 Processing helix chain 'Z' and resid 103 through 115 removed outlier: 3.805A pdb=" N ILE Z 106 " --> pdb=" O LYS Z 103 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU Z 111 " --> pdb=" O ILE Z 108 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS Z 113 " --> pdb=" O GLU Z 110 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG Z 114 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) Processing helix chain 'Z' and resid 169 through 175 removed outlier: 4.072A pdb=" N HIS Z 174 " --> pdb=" O VAL Z 170 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 216 removed outlier: 3.578A pdb=" N SER Z 203 " --> pdb=" O LYS Z 199 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL Z 215 " --> pdb=" O TYR Z 211 " (cutoff:3.500A) Processing helix chain 'Z' and resid 220 through 223 removed outlier: 4.319A pdb=" N ASN Z 223 " --> pdb=" O LEU Z 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 220 through 223' Processing helix chain 'Z' and resid 228 through 236 removed outlier: 4.353A pdb=" N VAL Z 233 " --> pdb=" O GLN Z 229 " (cutoff:3.500A) Processing helix chain 'Z' and resid 246 through 288 removed outlier: 4.153A pdb=" N TYR Z 250 " --> pdb=" O VAL Z 246 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL Z 258 " --> pdb=" O ASN Z 254 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL Z 259 " --> pdb=" O ASP Z 255 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN Z 277 " --> pdb=" O HIS Z 273 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 10 Processing helix chain 'a' and resid 19 through 31 removed outlier: 4.916A pdb=" N ARG a 24 " --> pdb=" O ALA a 20 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU a 27 " --> pdb=" O HIS a 23 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR a 29 " --> pdb=" O LEU a 25 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR a 30 " --> pdb=" O GLU a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 35 through 46 Processing helix chain 'a' and resid 53 through 67 removed outlier: 5.942A pdb=" N LEU a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TYR a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 87 removed outlier: 5.163A pdb=" N ARG a 85 " --> pdb=" O LEU a 81 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLN a 86 " --> pdb=" O HIS a 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 103 removed outlier: 4.391A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 120 Processing helix chain 'a' and resid 122 through 124 No H-bonds generated for 'chain 'a' and resid 122 through 124' Processing helix chain 'a' and resid 131 through 141 removed outlier: 3.644A pdb=" N GLU a 139 " --> pdb=" O ILE a 135 " (cutoff:3.500A) Processing helix chain 'a' and resid 150 through 164 Processing helix chain 'a' and resid 171 through 180 Processing helix chain 'a' and resid 190 through 205 Processing helix chain 'a' and resid 216 through 218 No H-bonds generated for 'chain 'a' and resid 216 through 218' Processing helix chain 'a' and resid 220 through 228 removed outlier: 4.240A pdb=" N LEU a 225 " --> pdb=" O VAL a 221 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR a 228 " --> pdb=" O SER a 224 " (cutoff:3.500A) Processing helix chain 'a' and resid 233 through 239 Processing helix chain 'a' and resid 247 through 255 removed outlier: 4.968A pdb=" N ALA a 254 " --> pdb=" O THR a 250 " (cutoff:3.500A) Processing helix chain 'a' and resid 265 through 282 removed outlier: 3.922A pdb=" N GLN a 273 " --> pdb=" O LEU a 269 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET a 278 " --> pdb=" O LEU a 274 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 299 Processing helix chain 'a' and resid 304 through 317 removed outlier: 3.686A pdb=" N VAL a 307 " --> pdb=" O VAL a 304 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLU a 308 " --> pdb=" O ASN a 305 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS a 313 " --> pdb=" O LEU a 310 " (cutoff:3.500A) Processing helix chain 'a' and resid 343 through 370 removed outlier: 5.660A pdb=" N LYS a 350 " --> pdb=" O ILE a 346 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASP a 351 " --> pdb=" O LYS a 347 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ARG a 352 " --> pdb=" O GLY a 348 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE a 355 " --> pdb=" O ASP a 351 " (cutoff:3.500A) Processing helix chain 'a' and resid 372 through 374 No H-bonds generated for 'chain 'a' and resid 372 through 374' Processing helix chain 'b' and resid 26 through 43 Processing helix chain 'b' and resid 69 through 75 Processing helix chain 'b' and resid 86 through 97 removed outlier: 4.359A pdb=" N ILE b 90 " --> pdb=" O PHE b 86 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 133 Processing helix chain 'b' and resid 152 through 158 Processing helix chain 'b' and resid 181 through 189 removed outlier: 3.887A pdb=" N SER b 186 " --> pdb=" O ALA b 182 " (cutoff:3.500A) Proline residue: b 187 - end of helix Processing helix chain 'c' and resid 35 through 46 Processing helix chain 'c' and resid 84 through 86 No H-bonds generated for 'chain 'c' and resid 84 through 86' Processing helix chain 'c' and resid 89 through 101 Processing helix chain 'c' and resid 126 through 134 removed outlier: 5.256A pdb=" N GLN c 131 " --> pdb=" O ILE c 127 " (cutoff:3.500A) Processing helix chain 'c' and resid 165 through 168 removed outlier: 3.827A pdb=" N MET c 168 " --> pdb=" O ALA c 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 165 through 168' Processing helix chain 'c' and resid 180 through 187 Proline residue: c 187 - end of helix Processing helix chain 'c' and resid 191 through 195 Processing helix chain 'c' and resid 211 through 224 removed outlier: 5.063A pdb=" N MET c 216 " --> pdb=" O LEU c 212 " (cutoff:3.500A) Processing helix chain 'c' and resid 247 through 258 Processing helix chain 'c' and resid 260 through 264 Processing helix chain 'c' and resid 267 through 270 No H-bonds generated for 'chain 'c' and resid 267 through 270' Processing helix chain 'c' and resid 289 through 308 removed outlier: 3.828A pdb=" N ASP c 305 " --> pdb=" O ALA c 301 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR c 306 " --> pdb=" O ALA c 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 3 through 6 Processing helix chain 'd' and resid 18 through 32 Processing helix chain 'd' and resid 46 through 64 Processing helix chain 'd' and resid 68 through 81 Processing helix chain 'd' and resid 93 through 109 removed outlier: 4.485A pdb=" N HIS d 96 " --> pdb=" O ALA d 93 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU d 98 " --> pdb=" O MET d 95 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU d 99 " --> pdb=" O HIS d 96 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN d 102 " --> pdb=" O LEU d 99 " (cutoff:3.500A) Processing helix chain 'd' and resid 114 through 121 Processing helix chain 'd' and resid 131 through 143 Proline residue: d 136 - end of helix Processing helix chain 'd' and resid 150 through 155 Processing helix chain 'd' and resid 164 through 180 removed outlier: 3.727A pdb=" N GLU d 177 " --> pdb=" O THR d 173 " (cutoff:3.500A) Processing helix chain 'd' and resid 191 through 197 Processing helix chain 'd' and resid 204 through 210 Processing helix chain 'd' and resid 240 through 253 Processing helix chain 'e' and resid 5 through 7 No H-bonds generated for 'chain 'e' and resid 5 through 7' Processing helix chain 'e' and resid 45 through 50 Processing helix chain 'e' and resid 62 through 65 No H-bonds generated for 'chain 'e' and resid 62 through 65' Processing helix chain 'G' and resid 23 through 30 removed outlier: 5.099A pdb=" N LYS G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 105 Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 172 through 180 Processing helix chain 'G' and resid 192 through 205 Processing helix chain 'G' and resid 232 through 241 Processing helix chain 'H' and resid 20 through 30 Processing helix chain 'H' and resid 80 through 101 removed outlier: 4.039A pdb=" N VAL H 85 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 122 Processing helix chain 'H' and resid 167 through 177 removed outlier: 3.505A pdb=" N LYS H 176 " --> pdb=" O THR H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 196 Processing helix chain 'H' and resid 223 through 229 Processing helix chain 'I' and resid 20 through 28 Processing helix chain 'I' and resid 82 through 101 Processing helix chain 'I' and resid 108 through 123 removed outlier: 3.815A pdb=" N TYR I 121 " --> pdb=" O ILE I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 177 Processing helix chain 'I' and resid 186 through 200 Processing helix chain 'I' and resid 208 through 210 No H-bonds generated for 'chain 'I' and resid 208 through 210' Processing helix chain 'I' and resid 230 through 250 removed outlier: 4.404A pdb=" N GLU I 250 " --> pdb=" O LYS I 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 removed outlier: 3.544A pdb=" N GLU J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 97 Processing helix chain 'J' and resid 104 through 119 Processing helix chain 'J' and resid 138 through 140 No H-bonds generated for 'chain 'J' and resid 138 through 140' Processing helix chain 'J' and resid 165 through 173 Processing helix chain 'J' and resid 184 through 196 Processing helix chain 'J' and resid 224 through 239 Processing helix chain 'K' and resid 24 through 32 removed outlier: 4.023A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 103 Processing helix chain 'K' and resid 109 through 120 removed outlier: 4.601A pdb=" N LEU K 119 " --> pdb=" O ALA K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 184 removed outlier: 3.682A pdb=" N VAL K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 205 Processing helix chain 'K' and resid 234 through 240 Processing helix chain 'L' and resid 20 through 31 removed outlier: 3.695A pdb=" N GLN L 31 " --> pdb=" O GLU L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 98 Processing helix chain 'L' and resid 105 through 120 removed outlier: 4.205A pdb=" N ILE L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) Proline residue: L 119 - end of helix Processing helix chain 'L' and resid 166 through 175 Processing helix chain 'L' and resid 178 through 181 removed outlier: 3.951A pdb=" N GLU L 181 " --> pdb=" O GLU L 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 178 through 181' Processing helix chain 'L' and resid 184 through 195 Processing helix chain 'L' and resid 230 through 233 No H-bonds generated for 'chain 'L' and resid 230 through 233' Processing helix chain 'M' and resid 21 through 27 Processing helix chain 'M' and resid 30 through 32 No H-bonds generated for 'chain 'M' and resid 30 through 32' Processing helix chain 'M' and resid 81 through 102 Processing helix chain 'M' and resid 108 through 124 Processing helix chain 'M' and resid 169 through 176 removed outlier: 3.542A pdb=" N LYS M 173 " --> pdb=" O ARG M 169 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU M 175 " --> pdb=" O ALA M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 199 removed outlier: 4.459A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 239 No H-bonds generated for 'chain 'M' and resid 236 through 239' Processing helix chain 'N' and resid 49 through 70 Processing helix chain 'N' and resid 76 through 89 Processing helix chain 'N' and resid 130 through 142 removed outlier: 4.425A pdb=" N SER N 133 " --> pdb=" O SER N 130 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR N 134 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE N 135 " --> pdb=" O SER N 132 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL N 139 " --> pdb=" O TYR N 136 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP N 140 " --> pdb=" O GLY N 137 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR N 142 " --> pdb=" O VAL N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 166 Processing helix chain 'O' and resid 49 through 70 Processing helix chain 'O' and resid 76 through 89 Processing helix chain 'O' and resid 131 through 141 Processing helix chain 'O' and resid 148 through 164 Processing helix chain 'P' and resid 57 through 77 Processing helix chain 'P' and resid 84 through 98 removed outlier: 4.114A pdb=" N LYS P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 144 through 153 Processing helix chain 'P' and resid 160 through 177 Processing helix chain 'Q' and resid 52 through 70 Processing helix chain 'Q' and resid 77 through 92 Processing helix chain 'Q' and resid 135 through 145 removed outlier: 3.511A pdb=" N ILE Q 142 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 153 through 167 Processing helix chain 'R' and resid 50 through 70 Processing helix chain 'R' and resid 76 through 90 removed outlier: 3.944A pdb=" N GLN R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TYR R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 142 Processing helix chain 'R' and resid 149 through 166 Processing helix chain 'R' and resid 192 through 199 Processing helix chain 'S' and resid 58 through 79 Processing helix chain 'S' and resid 85 through 98 Processing helix chain 'S' and resid 143 through 152 Proline residue: S 147 - end of helix Processing helix chain 'S' and resid 168 through 185 removed outlier: 3.992A pdb=" N ARG S 185 " --> pdb=" O SER S 181 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 77 Processing helix chain 'T' and resid 85 through 102 removed outlier: 3.806A pdb=" N LYS T 102 " --> pdb=" O SER T 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 142 through 145 No H-bonds generated for 'chain 'T' and resid 142 through 145' Processing helix chain 'T' and resid 147 through 156 Processing helix chain 'T' and resid 162 through 179 Processing helix chain 'g' and resid 18 through 20 No H-bonds generated for 'chain 'g' and resid 18 through 20' Processing helix chain 'g' and resid 23 through 28 Processing helix chain 'g' and resid 84 through 105 Processing helix chain 'g' and resid 111 through 127 Processing helix chain 'g' and resid 172 through 182 Processing helix chain 'g' and resid 192 through 205 Processing helix chain 'g' and resid 232 through 241 Processing helix chain 'h' and resid 20 through 30 Processing helix chain 'h' and resid 80 through 101 removed outlier: 4.301A pdb=" N VAL h 85 " --> pdb=" O PRO h 81 " (cutoff:3.500A) Processing helix chain 'h' and resid 107 through 123 Processing helix chain 'h' and resid 167 through 177 removed outlier: 3.551A pdb=" N LYS h 176 " --> pdb=" O THR h 172 " (cutoff:3.500A) Processing helix chain 'h' and resid 184 through 196 Processing helix chain 'h' and resid 223 through 229 Processing helix chain 'i' and resid 20 through 28 Processing helix chain 'i' and resid 80 through 101 removed outlier: 3.757A pdb=" N LEU i 86 " --> pdb=" O ASP i 82 " (cutoff:3.500A) Processing helix chain 'i' and resid 108 through 123 removed outlier: 3.766A pdb=" N TYR i 121 " --> pdb=" O ILE i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 169 through 177 Processing helix chain 'i' and resid 186 through 200 Processing helix chain 'i' and resid 208 through 210 No H-bonds generated for 'chain 'i' and resid 208 through 210' Processing helix chain 'i' and resid 231 through 250 removed outlier: 4.448A pdb=" N GLU i 250 " --> pdb=" O LYS i 246 " (cutoff:3.500A) Processing helix chain 'j' and resid 19 through 27 removed outlier: 3.821A pdb=" N GLU j 24 " --> pdb=" O GLU j 20 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA j 25 " --> pdb=" O TYR j 21 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL j 26 " --> pdb=" O ALA j 22 " (cutoff:3.500A) Processing helix chain 'j' and resid 77 through 97 removed outlier: 3.563A pdb=" N THR j 97 " --> pdb=" O SER j 93 " (cutoff:3.500A) Processing helix chain 'j' and resid 104 through 120 Processing helix chain 'j' and resid 138 through 140 No H-bonds generated for 'chain 'j' and resid 138 through 140' Processing helix chain 'j' and resid 165 through 175 removed outlier: 3.768A pdb=" N LYS j 174 " --> pdb=" O GLU j 170 " (cutoff:3.500A) Processing helix chain 'j' and resid 184 through 196 Processing helix chain 'j' and resid 224 through 239 Processing helix chain 'k' and resid 22 through 33 removed outlier: 4.314A pdb=" N LYS k 32 " --> pdb=" O ILE k 28 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU k 33 " --> pdb=" O GLU k 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 61 through 63 No H-bonds generated for 'chain 'k' and resid 61 through 63' Processing helix chain 'k' and resid 83 through 103 Processing helix chain 'k' and resid 109 through 117 Processing helix chain 'k' and resid 174 through 184 removed outlier: 3.655A pdb=" N VAL k 184 " --> pdb=" O SER k 180 " (cutoff:3.500A) Processing helix chain 'k' and resid 191 through 205 removed outlier: 3.714A pdb=" N ILE k 201 " --> pdb=" O SER k 197 " (cutoff:3.500A) Processing helix chain 'k' and resid 234 through 240 removed outlier: 3.511A pdb=" N ASP k 240 " --> pdb=" O GLU k 236 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 31 Processing helix chain 'l' and resid 79 through 98 removed outlier: 3.624A pdb=" N SER l 95 " --> pdb=" O GLU l 91 " (cutoff:3.500A) Processing helix chain 'l' and resid 105 through 120 removed outlier: 4.280A pdb=" N ILE l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) Proline residue: l 119 - end of helix Processing helix chain 'l' and resid 166 through 175 Processing helix chain 'l' and resid 179 through 181 No H-bonds generated for 'chain 'l' and resid 179 through 181' Processing helix chain 'l' and resid 184 through 195 Processing helix chain 'l' and resid 230 through 233 No H-bonds generated for 'chain 'l' and resid 230 through 233' Processing helix chain 'm' and resid 21 through 27 Processing helix chain 'm' and resid 30 through 32 No H-bonds generated for 'chain 'm' and resid 30 through 32' Processing helix chain 'm' and resid 81 through 102 Processing helix chain 'm' and resid 108 through 124 Processing helix chain 'm' and resid 169 through 176 removed outlier: 3.594A pdb=" N LYS m 173 " --> pdb=" O ARG m 169 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLU m 175 " --> pdb=" O ALA m 171 " (cutoff:3.500A) Processing helix chain 'm' and resid 186 through 199 removed outlier: 4.489A pdb=" N LYS m 191 " --> pdb=" O ARG m 187 " (cutoff:3.500A) Processing helix chain 'm' and resid 236 through 239 No H-bonds generated for 'chain 'm' and resid 236 through 239' Processing helix chain 'n' and resid 49 through 70 Processing helix chain 'n' and resid 76 through 89 Processing helix chain 'n' and resid 133 through 142 removed outlier: 4.569A pdb=" N ASP n 140 " --> pdb=" O TYR n 136 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ALA n 141 " --> pdb=" O GLY n 137 " (cutoff:3.500A) Processing helix chain 'n' and resid 149 through 166 Processing helix chain 'o' and resid 49 through 70 Processing helix chain 'o' and resid 76 through 89 Processing helix chain 'o' and resid 131 through 141 Processing helix chain 'o' and resid 148 through 164 Processing helix chain 'p' and resid 57 through 77 Processing helix chain 'p' and resid 84 through 98 removed outlier: 4.179A pdb=" N LYS p 98 " --> pdb=" O LEU p 94 " (cutoff:3.500A) Processing helix chain 'p' and resid 144 through 153 Processing helix chain 'p' and resid 160 through 177 Processing helix chain 'q' and resid 52 through 70 Processing helix chain 'q' and resid 77 through 92 Processing helix chain 'q' and resid 135 through 145 removed outlier: 4.269A pdb=" N SER q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE q 142 " --> pdb=" O LEU q 138 " (cutoff:3.500A) Processing helix chain 'q' and resid 153 through 167 Processing helix chain 'r' and resid 50 through 70 Processing helix chain 'r' and resid 76 through 90 removed outlier: 3.934A pdb=" N GLN r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR r 90 " --> pdb=" O MET r 86 " (cutoff:3.500A) Processing helix chain 'r' and resid 132 through 142 Processing helix chain 'r' and resid 149 through 166 Processing helix chain 'r' and resid 192 through 199 Processing helix chain 's' and resid 58 through 79 Processing helix chain 's' and resid 85 through 98 Processing helix chain 's' and resid 143 through 152 Proline residue: s 147 - end of helix Processing helix chain 's' and resid 168 through 185 removed outlier: 4.106A pdb=" N ARG s 185 " --> pdb=" O SER s 181 " (cutoff:3.500A) Processing helix chain 't' and resid 57 through 77 Processing helix chain 't' and resid 85 through 102 removed outlier: 3.796A pdb=" N LYS t 102 " --> pdb=" O SER t 98 " (cutoff:3.500A) Processing helix chain 't' and resid 142 through 145 No H-bonds generated for 'chain 't' and resid 142 through 145' Processing helix chain 't' and resid 147 through 156 Processing helix chain 't' and resid 162 through 179 Processing helix chain 'A' and resid 84 through 87 No H-bonds generated for 'chain 'A' and resid 84 through 87' Processing helix chain 'A' and resid 181 through 196 removed outlier: 4.066A pdb=" N GLU A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 222 through 231 removed outlier: 4.175A pdb=" N ALA A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 245 Processing helix chain 'A' and resid 252 through 264 Processing helix chain 'A' and resid 277 through 280 No H-bonds generated for 'chain 'A' and resid 277 through 280' Processing helix chain 'A' and resid 294 through 306 Processing helix chain 'A' and resid 349 through 360 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 382 through 398 Processing helix chain 'A' and resid 406 through 418 removed outlier: 3.516A pdb=" N LYS A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 102 Processing helix chain 'B' and resid 141 through 143 No H-bonds generated for 'chain 'B' and resid 141 through 143' Processing helix chain 'B' and resid 171 through 174 No H-bonds generated for 'chain 'B' and resid 171 through 174' Processing helix chain 'B' and resid 193 through 206 removed outlier: 5.329A pdb=" N LEU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Proline residue: B 204 - end of helix Processing helix chain 'B' and resid 211 through 214 No H-bonds generated for 'chain 'B' and resid 211 through 214' Processing helix chain 'B' and resid 232 through 241 Processing helix chain 'B' and resid 252 through 255 removed outlier: 3.934A pdb=" N LEU B 255 " --> pdb=" O GLY B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 255' Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 301 through 303 No H-bonds generated for 'chain 'B' and resid 301 through 303' Processing helix chain 'B' and resid 305 through 316 Processing helix chain 'B' and resid 339 through 342 No H-bonds generated for 'chain 'B' and resid 339 through 342' Processing helix chain 'B' and resid 358 through 368 removed outlier: 4.605A pdb=" N ARG B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 386 Processing helix chain 'B' and resid 392 through 409 removed outlier: 4.189A pdb=" N GLY B 403 " --> pdb=" O CYS B 399 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU B 409 " --> pdb=" O MET B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 426 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'C' and resid 39 through 67 removed outlier: 3.560A pdb=" N GLU C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLN C 64 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 155 through 170 removed outlier: 4.749A pdb=" N LEU C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 172 through 175 No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 196 through 203 Processing helix chain 'C' and resid 233 through 240 Processing helix chain 'C' and resid 268 through 279 Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 322 through 334 Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 358 through 372 Processing helix chain 'C' and resid 380 through 390 Processing helix chain 'D' and resid 49 through 79 removed outlier: 4.419A pdb=" N PHE D 53 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 186 removed outlier: 4.782A pdb=" N LEU D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Proline residue: D 184 - end of helix Processing helix chain 'D' and resid 190 through 193 No H-bonds generated for 'chain 'D' and resid 190 through 193' Processing helix chain 'D' and resid 214 through 222 Processing helix chain 'D' and resid 242 through 257 Processing helix chain 'D' and resid 282 through 296 Processing helix chain 'D' and resid 341 through 347 Processing helix chain 'D' and resid 361 through 364 No H-bonds generated for 'chain 'D' and resid 361 through 364' Processing helix chain 'D' and resid 374 through 388 Processing helix chain 'D' and resid 397 through 401 Processing helix chain 'E' and resid 17 through 51 removed outlier: 4.490A pdb=" N ARG E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 120 through 123 No H-bonds generated for 'chain 'E' and resid 120 through 123' Processing helix chain 'E' and resid 139 through 149 Processing helix chain 'E' and resid 151 through 154 No H-bonds generated for 'chain 'E' and resid 151 through 154' Processing helix chain 'E' and resid 158 through 162 Processing helix chain 'E' and resid 180 through 190 Processing helix chain 'E' and resid 210 through 224 Processing helix chain 'E' and resid 248 through 263 removed outlier: 3.860A pdb=" N GLU E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 316 Processing helix chain 'E' and resid 328 through 334 Processing helix chain 'E' and resid 340 through 355 Processing helix chain 'E' and resid 365 through 380 removed outlier: 3.539A pdb=" N LYS E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU E 380 " --> pdb=" O ASP E 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 83 removed outlier: 4.291A pdb=" N ASP F 71 " --> pdb=" O GLN F 67 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS F 74 " --> pdb=" O LYS F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 175 Processing helix chain 'F' and resid 192 through 207 removed outlier: 4.675A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) Proline residue: F 205 - end of helix Processing helix chain 'F' and resid 210 through 213 No H-bonds generated for 'chain 'F' and resid 210 through 213' Processing helix chain 'F' and resid 234 through 243 Processing helix chain 'F' and resid 264 through 277 Processing helix chain 'F' and resid 305 through 317 Processing helix chain 'F' and resid 340 through 342 No H-bonds generated for 'chain 'F' and resid 340 through 342' Processing helix chain 'F' and resid 360 through 369 Processing helix chain 'F' and resid 381 through 387 Processing helix chain 'F' and resid 393 through 409 Processing helix chain 'F' and resid 417 through 425 Processing helix chain 'f' and resid 9 through 15 Proline residue: f 13 - end of helix No H-bonds generated for 'chain 'f' and resid 9 through 15' Processing helix chain 'f' and resid 20 through 35 Proline residue: f 28 - end of helix removed outlier: 4.054A pdb=" N ASP f 35 " --> pdb=" O LYS f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 45 through 48 No H-bonds generated for 'chain 'f' and resid 45 through 48' Processing helix chain 'f' and resid 50 through 52 No H-bonds generated for 'chain 'f' and resid 50 through 52' Processing helix chain 'f' and resid 72 through 86 Processing helix chain 'f' and resid 94 through 97 No H-bonds generated for 'chain 'f' and resid 94 through 97' Processing helix chain 'f' and resid 120 through 125 Processing helix chain 'f' and resid 127 through 144 Processing helix chain 'f' and resid 164 through 180 Processing helix chain 'f' and resid 185 through 191 Processing helix chain 'f' and resid 208 through 216 Processing helix chain 'f' and resid 222 through 238 Processing helix chain 'f' and resid 242 through 258 removed outlier: 3.678A pdb=" N SER f 246 " --> pdb=" O PRO f 243 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG f 250 " --> pdb=" O ALA f 247 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS f 251 " --> pdb=" O LEU f 248 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA f 252 " --> pdb=" O LEU f 249 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL f 255 " --> pdb=" O ALA f 252 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE f 256 " --> pdb=" O LEU f 253 " (cutoff:3.500A) Processing helix chain 'f' and resid 262 through 272 removed outlier: 3.632A pdb=" N MET f 271 " --> pdb=" O LEU f 268 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU f 272 " --> pdb=" O ALA f 269 " (cutoff:3.500A) Processing helix chain 'f' and resid 276 through 287 Processing helix chain 'f' and resid 298 through 308 Processing helix chain 'f' and resid 313 through 323 Processing helix chain 'f' and resid 329 through 333 Processing helix chain 'f' and resid 341 through 350 Proline residue: f 345 - end of helix Processing helix chain 'f' and resid 356 through 359 No H-bonds generated for 'chain 'f' and resid 356 through 359' Processing helix chain 'f' and resid 370 through 381 removed outlier: 3.644A pdb=" N VAL f 381 " --> pdb=" O VAL f 377 " (cutoff:3.500A) Processing helix chain 'f' and resid 404 through 411 Processing helix chain 'f' and resid 413 through 416 No H-bonds generated for 'chain 'f' and resid 413 through 416' Processing helix chain 'f' and resid 422 through 432 removed outlier: 3.697A pdb=" N LEU f 426 " --> pdb=" O VAL f 422 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR f 427 " --> pdb=" O ASP f 423 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYS f 431 " --> pdb=" O THR f 427 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR f 432 " --> pdb=" O GLN f 428 " (cutoff:3.500A) Processing helix chain 'f' and resid 438 through 451 Processing helix chain 'f' and resid 459 through 463 Processing helix chain 'f' and resid 473 through 488 removed outlier: 3.576A pdb=" N MET f 477 " --> pdb=" O SER f 474 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY f 480 " --> pdb=" O MET f 477 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER f 481 " --> pdb=" O ARG f 478 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE f 482 " --> pdb=" O LEU f 479 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE f 483 " --> pdb=" O GLY f 480 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY f 484 " --> pdb=" O SER f 481 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU f 485 " --> pdb=" O ILE f 482 " (cutoff:3.500A) Processing helix chain 'f' and resid 496 through 505 Proline residue: f 503 - end of helix Processing helix chain 'f' and resid 512 through 526 Processing helix chain 'f' and resid 536 through 547 Processing helix chain 'f' and resid 554 through 566 Proline residue: f 559 - end of helix Processing helix chain 'f' and resid 574 through 582 Processing helix chain 'f' and resid 586 through 598 Processing helix chain 'f' and resid 606 through 617 removed outlier: 3.512A pdb=" N GLN f 610 " --> pdb=" O LEU f 607 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN f 611 " --> pdb=" O LYS f 608 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE f 615 " --> pdb=" O LEU f 612 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N CYS f 616 " --> pdb=" O LEU f 613 " (cutoff:3.500A) Processing helix chain 'f' and resid 623 through 634 removed outlier: 4.971A pdb=" N LYS f 631 " --> pdb=" O GLU f 627 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LYS f 632 " --> pdb=" O ASP f 628 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLU f 633 " --> pdb=" O LYS f 629 " (cutoff:3.500A) Processing helix chain 'f' and resid 653 through 662 Processing helix chain 'f' and resid 669 through 679 removed outlier: 3.896A pdb=" N HIS f 677 " --> pdb=" O ARG f 673 " (cutoff:3.500A) Processing helix chain 'f' and resid 684 through 696 Proline residue: f 691 - end of helix Processing helix chain 'f' and resid 718 through 727 Processing helix chain 'f' and resid 740 through 753 Processing helix chain 'f' and resid 775 through 777 No H-bonds generated for 'chain 'f' and resid 775 through 777' Processing helix chain 'f' and resid 779 through 786 removed outlier: 5.195A pdb=" N GLN f 786 " --> pdb=" O HIS f 782 " (cutoff:3.500A) Processing helix chain 'f' and resid 791 through 794 No H-bonds generated for 'chain 'f' and resid 791 through 794' Processing helix chain 'f' and resid 797 through 799 No H-bonds generated for 'chain 'f' and resid 797 through 799' Processing sheet with id= A, first strand: chain 'U' and resid 744 through 746 Processing sheet with id= B, first strand: chain 'U' and resid 788 through 790 removed outlier: 7.340A pdb=" N GLY U 910 " --> pdb=" O ILE U 789 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'Z' and resid 120 through 123 removed outlier: 3.860A pdb=" N HIS Z 96 " --> pdb=" O VAL Z 122 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU Z 39 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TRP Z 94 " --> pdb=" O GLY Z 37 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY Z 37 " --> pdb=" O TRP Z 94 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'b' and resid 5 through 8 removed outlier: 7.397A pdb=" N ASN b 137 " --> pdb=" O ILE b 109 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N ALA b 111 " --> pdb=" O ASN b 137 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASP b 139 " --> pdb=" O ALA b 111 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N VAL b 113 " --> pdb=" O ASP b 139 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE b 141 " --> pdb=" O VAL b 113 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'c' and resid 67 through 69 removed outlier: 3.516A pdb=" N VAL c 69 " --> pdb=" O TYR c 32 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN c 206 " --> pdb=" O VAL c 31 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE c 33 " --> pdb=" O ASN c 206 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'c' and resid 142 through 144 removed outlier: 3.532A pdb=" N PHE c 160 " --> pdb=" O ALA c 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'c' and resid 57 through 59 removed outlier: 4.973A pdb=" N GLY c 59 " --> pdb=" O VAL c 108 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL c 108 " --> pdb=" O GLY c 59 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'd' and resid 216 through 218 removed outlier: 4.090A pdb=" N VAL d 216 " --> pdb=" O TYR d 223 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR d 223 " --> pdb=" O VAL d 216 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.763A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 148 through 154 removed outlier: 6.815A pdb=" N CYS G 78 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS G 71 " --> pdb=" O CYS G 78 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 160 through 163 removed outlier: 3.644A pdb=" N THR H 48 " --> pdb=" O GLU H 209 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU H 209 " --> pdb=" O THR H 48 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 72 through 78 removed outlier: 3.722A pdb=" N SER H 133 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY H 138 " --> pdb=" O TYR H 145 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 34 through 36 Processing sheet with id= N, first strand: chain 'I' and resid 134 through 138 removed outlier: 3.866A pdb=" N LEU I 134 " --> pdb=" O SER I 150 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR I 148 " --> pdb=" O TYR I 136 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY I 138 " --> pdb=" O GLN I 146 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'J' and resid 158 through 160 removed outlier: 3.626A pdb=" N GLY J 34 " --> pdb=" O ASN J 159 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 132 through 136 removed outlier: 4.479A pdb=" N LEU J 144 " --> pdb=" O TRP J 156 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'K' and resid 167 through 169 removed outlier: 3.568A pdb=" N VAL K 50 " --> pdb=" O GLU K 216 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU K 216 " --> pdb=" O VAL K 50 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'K' and resid 141 through 147 removed outlier: 4.045A pdb=" N LEU K 141 " --> pdb=" O MET K 156 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 158 through 161 removed outlier: 3.816A pdb=" N ILE L 212 " --> pdb=" O TYR L 224 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 71 through 73 removed outlier: 3.777A pdb=" N ASP L 138 " --> pdb=" O GLY L 141 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY L 141 " --> pdb=" O ASP L 138 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE L 144 " --> pdb=" O CYS L 156 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'M' and resid 162 through 165 removed outlier: 3.717A pdb=" N GLY M 44 " --> pdb=" O CYS M 41 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'M' and resid 49 through 52 Processing sheet with id= W, first strand: chain 'M' and resid 135 through 141 removed outlier: 3.652A pdb=" N PHE M 135 " --> pdb=" O ILE M 151 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE M 151 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN M 147 " --> pdb=" O SER M 139 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'N' and resid 125 through 128 removed outlier: 3.599A pdb=" N ALA N 177 " --> pdb=" O LEU N 14 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE N 174 " --> pdb=" O LEU N 189 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'N' and resid 34 through 36 Processing sheet with id= Z, first strand: chain 'O' and resid 124 through 128 Processing sheet with id= AA, first strand: chain 'O' and resid 34 through 36 removed outlier: 3.614A pdb=" N SER O 118 " --> pdb=" O TYR O 114 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'O' and resid 20 through 22 removed outlier: 6.111A pdb=" N GLU O 22 " --> pdb=" O VAL O 26 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL O 26 " --> pdb=" O GLU O 22 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'P' and resid 136 through 140 removed outlier: 6.465A pdb=" N ALA P 10 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL P 20 " --> pdb=" O ILE P 190 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL P 185 " --> pdb=" O LEU P 200 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'P' and resid 42 through 44 Processing sheet with id= AE, first strand: chain 'Q' and resid 5 through 8 removed outlier: 3.637A pdb=" N VAL Q 13 " --> pdb=" O ILE Q 183 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL Q 15 " --> pdb=" O ARG Q 181 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Q' and resid 43 through 48 removed outlier: 3.731A pdb=" N LEU Q 103 " --> pdb=" O LEU Q 45 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'R' and resid 125 through 129 removed outlier: 3.589A pdb=" N LEU R 176 " --> pdb=" O SER R 188 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER R 188 " --> pdb=" O LEU R 176 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS R 178 " --> pdb=" O ARG R 186 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ARG R 186 " --> pdb=" O HIS R 178 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'R' and resid 41 through 43 Processing sheet with id= AI, first strand: chain 'R' and resid 20 through 22 removed outlier: 3.811A pdb=" N ALA R 20 " --> pdb=" O SER R 28 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER R 28 " --> pdb=" O ALA R 20 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ALA R 22 " --> pdb=" O ILE R 26 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE R 26 " --> pdb=" O ALA R 22 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'S' and resid 135 through 139 removed outlier: 3.849A pdb=" N GLY S 202 " --> pdb=" O THR S 199 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'S' and resid 130 through 133 removed outlier: 3.898A pdb=" N GLN S 131 " --> pdb=" O SER S 123 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL S 121 " --> pdb=" O ASP S 133 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASN S 108 " --> pdb=" O PHE S 124 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR S 50 " --> pdb=" O THR S 47 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE S 52 " --> pdb=" O LYS S 45 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LYS S 45 " --> pdb=" O ILE S 52 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N CYS S 54 " --> pdb=" O CYS S 43 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N CYS S 43 " --> pdb=" O CYS S 54 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'T' and resid 136 through 138 removed outlier: 3.535A pdb=" N GLY T 19 " --> pdb=" O PHE T 16 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY T 196 " --> pdb=" O THR T 193 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'T' and resid 49 through 55 removed outlier: 3.535A pdb=" N THR T 109 " --> pdb=" O SER T 54 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR T 132 " --> pdb=" O TYR T 124 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'g' and resid 165 through 169 removed outlier: 5.739A pdb=" N THR g 38 " --> pdb=" O GLN g 53 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN g 53 " --> pdb=" O THR g 38 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'g' and resid 148 through 154 removed outlier: 3.670A pdb=" N ILE g 139 " --> pdb=" O VAL g 79 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL g 79 " --> pdb=" O ILE g 139 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY g 77 " --> pdb=" O ILE g 141 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N CYS g 78 " --> pdb=" O LYS g 71 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LYS g 71 " --> pdb=" O CYS g 78 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'h' and resid 160 through 163 removed outlier: 3.701A pdb=" N GLU h 209 " --> pdb=" O THR h 48 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'h' and resid 72 through 75 removed outlier: 3.518A pdb=" N VAL h 75 " --> pdb=" O LEU h 135 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY h 138 " --> pdb=" O TYR h 145 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'i' and resid 34 through 36 Processing sheet with id= AS, first strand: chain 'i' and resid 134 through 138 removed outlier: 4.001A pdb=" N LEU i 134 " --> pdb=" O SER i 150 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR i 148 " --> pdb=" O TYR i 136 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY i 138 " --> pdb=" O GLN i 146 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'j' and resid 158 through 161 removed outlier: 3.601A pdb=" N GLY j 34 " --> pdb=" O ASN j 159 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA j 32 " --> pdb=" O ILE j 161 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU j 207 " --> pdb=" O VAL j 45 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'j' and resid 132 through 136 removed outlier: 4.534A pdb=" N LEU j 144 " --> pdb=" O TRP j 156 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'k' and resid 167 through 169 removed outlier: 3.622A pdb=" N VAL k 50 " --> pdb=" O GLU k 216 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU k 216 " --> pdb=" O VAL k 50 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'k' and resid 74 through 77 removed outlier: 3.567A pdb=" N GLY k 144 " --> pdb=" O GLY k 75 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'l' and resid 158 through 161 removed outlier: 3.694A pdb=" N ILE l 212 " --> pdb=" O TYR l 224 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'l' and resid 71 through 73 removed outlier: 3.503A pdb=" N LEU l 133 " --> pdb=" O SER l 73 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP l 138 " --> pdb=" O GLY l 141 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY l 141 " --> pdb=" O ASP l 138 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'm' and resid 162 through 165 removed outlier: 3.674A pdb=" N GLY m 44 " --> pdb=" O CYS m 41 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'm' and resid 49 through 52 removed outlier: 3.793A pdb=" N GLU m 212 " --> pdb=" O VAL m 49 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'm' and resid 135 through 141 removed outlier: 3.529A pdb=" N LEU m 137 " --> pdb=" O TYR m 149 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN m 147 " --> pdb=" O SER m 139 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'n' and resid 125 through 128 removed outlier: 3.860A pdb=" N ALA n 177 " --> pdb=" O LEU n 14 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'n' and resid 34 through 36 removed outlier: 4.222A pdb=" N VAL n 111 " --> pdb=" O GLN n 123 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'n' and resid 20 through 22 removed outlier: 6.296A pdb=" N THR n 22 " --> pdb=" O ILE n 26 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE n 26 " --> pdb=" O THR n 22 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'o' and resid 124 through 128 removed outlier: 3.555A pdb=" N VAL o 125 " --> pdb=" O GLY o 5 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET o 127 " --> pdb=" O ILE o 3 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'o' and resid 34 through 36 removed outlier: 3.540A pdb=" N CYS o 43 " --> pdb=" O HIS o 35 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER o 112 " --> pdb=" O ASP o 120 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP o 120 " --> pdb=" O SER o 112 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR o 114 " --> pdb=" O SER o 118 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER o 118 " --> pdb=" O TYR o 114 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'p' and resid 136 through 140 removed outlier: 6.337A pdb=" N ALA p 10 " --> pdb=" O ASP p 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL p 20 " --> pdb=" O ILE p 190 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL p 185 " --> pdb=" O LEU p 200 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'p' and resid 42 through 44 Processing sheet with id= BJ, first strand: chain 'q' and resid 4 through 8 removed outlier: 3.709A pdb=" N VAL q 13 " --> pdb=" O ILE q 183 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL q 15 " --> pdb=" O ARG q 181 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'q' and resid 42 through 48 removed outlier: 3.775A pdb=" N LEU q 103 " --> pdb=" O LEU q 45 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'r' and resid 125 through 129 removed outlier: 3.539A pdb=" N ALA r 15 " --> pdb=" O LEU r 4 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY r 11 " --> pdb=" O PHE r 8 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER r 188 " --> pdb=" O LEU r 176 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N HIS r 178 " --> pdb=" O ARG r 186 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ARG r 186 " --> pdb=" O HIS r 178 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'r' and resid 41 through 43 removed outlier: 3.527A pdb=" N GLY r 103 " --> pdb=" O GLY r 110 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'r' and resid 20 through 22 removed outlier: 3.732A pdb=" N ALA r 20 " --> pdb=" O SER r 28 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER r 28 " --> pdb=" O ALA r 20 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ALA r 22 " --> pdb=" O ILE r 26 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE r 26 " --> pdb=" O ALA r 22 " (cutoff:3.500A) No H-bonds generated for sheet with id= BN Processing sheet with id= BO, first strand: chain 's' and resid 135 through 139 removed outlier: 3.907A pdb=" N GLY s 202 " --> pdb=" O THR s 199 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 's' and resid 130 through 133 removed outlier: 3.963A pdb=" N GLN s 131 " --> pdb=" O SER s 123 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL s 121 " --> pdb=" O ASP s 133 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASN s 108 " --> pdb=" O PHE s 124 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR s 50 " --> pdb=" O THR s 47 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR s 47 " --> pdb=" O THR s 50 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE s 52 " --> pdb=" O LYS s 45 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LYS s 45 " --> pdb=" O ILE s 52 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N CYS s 54 " --> pdb=" O CYS s 43 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS s 43 " --> pdb=" O CYS s 54 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 's' and resid 29 through 31 removed outlier: 3.722A pdb=" N LEU s 29 " --> pdb=" O THR s 37 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU s 31 " --> pdb=" O ILE s 35 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE s 35 " --> pdb=" O GLU s 31 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 't' and resid 136 through 138 removed outlier: 3.727A pdb=" N GLY t 196 " --> pdb=" O THR t 193 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 't' and resid 49 through 55 removed outlier: 3.576A pdb=" N TYR t 132 " --> pdb=" O TYR t 124 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.359A pdb=" N ASN A 114 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE A 101 " --> pdb=" O ASN A 114 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'A' and resid 270 through 274 removed outlier: 3.758A pdb=" N ILE A 272 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 318 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'B' and resid 107 through 110 removed outlier: 3.726A pdb=" N GLY B 110 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 150 " --> pdb=" O GLY B 110 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN B 153 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 159 " --> pdb=" O ASN B 153 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'B' and resid 349 through 351 removed outlier: 3.602A pdb=" N ARG B 349 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL B 327 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LEU B 224 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET B 329 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR B 246 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE B 283 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU B 248 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ASP B 285 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 250 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'C' and resid 114 through 116 Processing sheet with id= BY, first strand: chain 'D' and resid 129 through 132 removed outlier: 6.781A pdb=" N ILE D 102 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ALA D 95 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR D 100 " --> pdb=" O ALA D 95 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'D' and resid 202 through 204 Processing sheet with id= CA, first strand: chain 'D' and resid 228 through 230 Processing sheet with id= CB, first strand: chain 'E' and resid 78 through 81 removed outlier: 5.899A pdb=" N LYS E 72 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL E 60 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG E 97 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG E 109 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'E' and resid 297 through 300 removed outlier: 3.779A pdb=" N ARG E 297 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR E 173 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N MET E 275 " --> pdb=" O CYS E 170 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N LEU E 172 " --> pdb=" O MET E 275 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N MET E 277 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 278 " --> pdb=" O MET E 232 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP E 233 " --> pdb=" O VAL E 198 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'F' and resid 131 through 134 removed outlier: 3.969A pdb=" N GLU F 95 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LYS F 125 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL F 93 " --> pdb=" O LYS F 125 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP F 149 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU F 162 " --> pdb=" O GLY F 152 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'F' and resid 223 through 226 removed outlier: 6.727A pdb=" N ARG F 350 " --> pdb=" O LEU F 224 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N TYR F 226 " --> pdb=" O ARG F 350 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE F 352 " --> pdb=" O TYR F 226 " (cutoff:3.500A) No H-bonds generated for sheet with id= CE Processing sheet with id= CF, first strand: chain 'F' and resid 247 through 251 removed outlier: 6.412A pdb=" N LYS F 327 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE F 285 " --> pdb=" O LYS F 327 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE F 329 " --> pdb=" O ILE F 285 " (cutoff:3.500A) 4098 hydrogen bonds defined for protein. 11736 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 40.61 Time building geometry restraints manager: 32.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 33607 1.36 - 1.50: 26469 1.50 - 1.65: 40576 1.65 - 1.80: 617 1.80 - 1.95: 353 Bond restraints: 101622 Sorted by residual: bond pdb=" C ASP c 279 " pdb=" N PRO c 280 " ideal model delta sigma weight residual 1.335 1.422 -0.087 1.28e-02 6.10e+03 4.65e+01 bond pdb=" C PRO D 144 " pdb=" N PRO D 145 " ideal model delta sigma weight residual 1.328 1.393 -0.065 1.25e-02 6.40e+03 2.73e+01 bond pdb=" CA ARG f 494 " pdb=" C ARG f 494 " ideal model delta sigma weight residual 1.523 1.592 -0.069 1.32e-02 5.74e+03 2.71e+01 bond pdb=" C ALA Y 51 " pdb=" N PRO Y 52 " ideal model delta sigma weight residual 1.337 1.379 -0.042 9.80e-03 1.04e+04 1.84e+01 bond pdb=" C PRO X 203 " pdb=" N PRO X 204 " ideal model delta sigma weight residual 1.331 1.364 -0.033 7.90e-03 1.60e+04 1.73e+01 ... (remaining 101617 not shown) Histogram of bond angle deviations from ideal: 95.94 - 105.34: 1995 105.34 - 114.75: 60437 114.75 - 124.16: 72546 124.16 - 133.57: 2382 133.57 - 142.97: 98 Bond angle restraints: 137458 Sorted by residual: angle pdb=" N HIS D 414 " pdb=" CA HIS D 414 " pdb=" C HIS D 414 " ideal model delta sigma weight residual 113.50 126.71 -13.21 1.23e+00 6.61e-01 1.15e+02 angle pdb=" N ALA f 488 " pdb=" CA ALA f 488 " pdb=" C ALA f 488 " ideal model delta sigma weight residual 111.36 122.82 -11.46 1.09e+00 8.42e-01 1.11e+02 angle pdb=" C LEU K 21 " pdb=" N PHE K 22 " pdb=" CA PHE K 22 " ideal model delta sigma weight residual 121.70 139.56 -17.86 1.80e+00 3.09e-01 9.84e+01 angle pdb=" C LEU D 335 " pdb=" N PRO D 336 " pdb=" CA PRO D 336 " ideal model delta sigma weight residual 119.85 129.67 -9.82 1.01e+00 9.80e-01 9.45e+01 angle pdb=" C GLY M 6 " pdb=" N TYR M 7 " pdb=" CA TYR M 7 " ideal model delta sigma weight residual 121.70 138.63 -16.93 1.80e+00 3.09e-01 8.84e+01 ... (remaining 137453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.79: 60940 32.79 - 65.58: 777 65.58 - 98.37: 106 98.37 - 131.15: 4 131.15 - 163.94: 1 Dihedral angle restraints: 61828 sinusoidal: 24479 harmonic: 37349 Sorted by residual: dihedral pdb=" CA GLU D 413 " pdb=" C GLU D 413 " pdb=" N HIS D 414 " pdb=" CA HIS D 414 " ideal model delta harmonic sigma weight residual 180.00 65.66 114.34 0 5.00e+00 4.00e-02 5.23e+02 dihedral pdb=" CA SER C 400 " pdb=" C SER C 400 " pdb=" N ILE C 401 " pdb=" CA ILE C 401 " ideal model delta harmonic sigma weight residual 180.00 67.67 112.33 0 5.00e+00 4.00e-02 5.05e+02 dihedral pdb=" CA ARG J 5 " pdb=" C ARG J 5 " pdb=" N ALA J 6 " pdb=" CA ALA J 6 " ideal model delta harmonic sigma weight residual -180.00 -73.43 -106.57 0 5.00e+00 4.00e-02 4.54e+02 ... (remaining 61825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 14915 0.133 - 0.266: 688 0.266 - 0.399: 47 0.399 - 0.533: 9 0.533 - 0.666: 1 Chirality restraints: 15660 Sorted by residual: chirality pdb=" CA VAL f 365 " pdb=" N VAL f 365 " pdb=" C VAL f 365 " pdb=" CB VAL f 365 " both_signs ideal model delta sigma weight residual False 2.44 1.78 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" PB AGS B 501 " pdb=" O2B AGS B 501 " pdb=" O3A AGS B 501 " pdb=" O3B AGS B 501 " both_signs ideal model delta sigma weight residual True 3.18 -2.65 0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" CB ILE h 105 " pdb=" CA ILE h 105 " pdb=" CG1 ILE h 105 " pdb=" CG2 ILE h 105 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.59e+00 ... (remaining 15657 not shown) Planarity restraints: 17770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP J 184 " 0.028 2.00e-02 2.50e+03 5.52e-02 3.05e+01 pdb=" C ASP J 184 " -0.095 2.00e-02 2.50e+03 pdb=" O ASP J 184 " 0.035 2.00e-02 2.50e+03 pdb=" N ASP J 185 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG f 369 " -0.022 2.00e-02 2.50e+03 4.75e-02 2.25e+01 pdb=" C ARG f 369 " 0.082 2.00e-02 2.50e+03 pdb=" O ARG f 369 " -0.032 2.00e-02 2.50e+03 pdb=" N MET f 370 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 132 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO C 133 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO C 133 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 133 " 0.061 5.00e-02 4.00e+02 ... (remaining 17767 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 1271 2.61 - 3.19: 85933 3.19 - 3.76: 159295 3.76 - 4.33: 215506 4.33 - 4.90: 338618 Nonbonded interactions: 800623 Sorted by model distance: nonbonded pdb=" O SER f 363 " pdb=" N VAL f 365 " model vdw 2.042 2.520 nonbonded pdb=" OD1 ASP f 366 " pdb=" N SER f 367 " model vdw 2.042 2.520 nonbonded pdb=" CD ARG f 494 " pdb=" OD1 ASP f 496 " model vdw 2.061 3.440 nonbonded pdb=" O ALA f 753 " pdb=" CE LYS f 754 " model vdw 2.078 3.440 nonbonded pdb=" O VAL f 311 " pdb=" O ALA f 490 " model vdw 2.087 3.040 ... (remaining 800618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'G' selection = (chain 'g' and resid 6 through 244) } ncs_group { reference = chain 'H' selection = (chain 'h' and resid 5 through 234) } ncs_group { reference = chain 'I' selection = (chain 'i' and resid 4 through 251) } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = (chain 'K' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 241)) selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'O' selection = chain 'o' } ncs_group { reference = chain 'P' selection = chain 'p' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'R' selection = chain 'r' } ncs_group { reference = chain 'S' selection = chain 's' } ncs_group { reference = chain 'T' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.630 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: 0.090 Extract box with map and model: 37.470 Check model and map are aligned: 1.280 Set scattering table: 0.690 Process input model: 209.600 Find NCS groups from input model: 6.250 Set up NCS constraints: 0.770 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 266.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 101622 Z= 0.394 Angle : 1.245 21.174 137458 Z= 0.685 Chirality : 0.066 0.666 15660 Planarity : 0.008 0.113 17770 Dihedral : 11.805 163.944 37784 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.59 % Favored : 89.85 % Rotamer: Outliers : 0.74 % Allowed : 3.77 % Favored : 95.48 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.19 % Twisted Proline : 1.35 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.06), residues: 12738 helix: -2.65 (0.05), residues: 5598 sheet: -1.91 (0.12), residues: 1636 loop : -3.46 (0.07), residues: 5504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP i 159 HIS 0.024 0.003 HIS Q 132 PHE 0.056 0.004 PHE U 728 TYR 0.064 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) ************************************************ 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2481 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 2402 time to evaluate : 9.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 168 LEU cc_start: 0.7569 (tp) cc_final: 0.7351 (mt) REVERT: U 362 ASN cc_start: 0.5453 (t0) cc_final: 0.5145 (t0) REVERT: U 650 TYR cc_start: 0.9095 (t80) cc_final: 0.8759 (t80) REVERT: U 672 LEU cc_start: 0.8941 (mt) cc_final: 0.8631 (mt) REVERT: U 675 MET cc_start: 0.7288 (mmm) cc_final: 0.6733 (ptm) REVERT: U 774 PRO cc_start: 0.8474 (Cg_exo) cc_final: 0.7432 (Cg_endo) REVERT: U 793 LYS cc_start: 0.8146 (ttpp) cc_final: 0.7484 (mmtt) REVERT: V 139 MET cc_start: 0.5219 (mmm) cc_final: 0.4813 (ttt) REVERT: W 85 GLU cc_start: 0.3137 (OUTLIER) cc_final: 0.2407 (mm-30) REVERT: W 88 MET cc_start: 0.3048 (mtm) cc_final: 0.2511 (mtp) REVERT: W 94 ARG cc_start: 0.5024 (ttt-90) cc_final: 0.4454 (tpp80) REVERT: W 124 LEU cc_start: 0.7731 (mt) cc_final: 0.7159 (tt) REVERT: W 129 ARG cc_start: 0.7980 (mmt90) cc_final: 0.7772 (tmm-80) REVERT: W 270 VAL cc_start: 0.5482 (p) cc_final: 0.5101 (p) REVERT: W 286 LEU cc_start: 0.7025 (tp) cc_final: 0.6752 (mm) REVERT: W 288 HIS cc_start: 0.7255 (m170) cc_final: 0.6992 (p90) REVERT: W 326 MET cc_start: 0.7806 (mtm) cc_final: 0.7529 (mpp) REVERT: W 366 MET cc_start: 0.8794 (mtt) cc_final: 0.8455 (tpt) REVERT: W 428 TRP cc_start: 0.8192 (m100) cc_final: 0.7341 (t-100) REVERT: X 209 THR cc_start: 0.7560 (m) cc_final: 0.7307 (m) REVERT: X 265 GLU cc_start: 0.6464 (tp30) cc_final: 0.6231 (mt-10) REVERT: X 283 GLN cc_start: 0.8048 (mt0) cc_final: 0.7761 (mp10) REVERT: X 337 ARG cc_start: 0.6880 (mtt180) cc_final: 0.6318 (tpm170) REVERT: X 363 ARG cc_start: 0.8197 (mtm110) cc_final: 0.7844 (ttt180) REVERT: X 407 MET cc_start: 0.8756 (mmt) cc_final: 0.8101 (tmm) REVERT: Y 379 ARG cc_start: 0.9149 (tpp-160) cc_final: 0.8734 (tpt-90) REVERT: Y 384 SER cc_start: 0.8577 (t) cc_final: 0.8358 (p) REVERT: Y 386 VAL cc_start: 0.2767 (t) cc_final: 0.2493 (t) REVERT: Y 389 MET cc_start: 0.0539 (ttm) cc_final: -0.0296 (pmm) REVERT: Z 91 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7444 (tp) REVERT: Z 94 TRP cc_start: 0.7420 (p-90) cc_final: 0.7215 (p-90) REVERT: Z 99 PRO cc_start: 0.7720 (Cg_endo) cc_final: 0.7274 (Cg_exo) REVERT: Z 103 LYS cc_start: 0.8192 (tttt) cc_final: 0.7345 (mmmt) REVERT: Z 194 GLN cc_start: 0.8816 (mt0) cc_final: 0.8418 (tp-100) REVERT: Z 228 TYR cc_start: 0.7860 (p90) cc_final: 0.7569 (p90) REVERT: Z 237 LEU cc_start: 0.1565 (OUTLIER) cc_final: 0.1222 (mt) REVERT: a 295 GLU cc_start: 0.8136 (tm-30) cc_final: 0.6674 (pm20) REVERT: a 339 ARG cc_start: 0.5533 (mmt180) cc_final: 0.4300 (ptt180) REVERT: c 27 THR cc_start: 0.4946 (m) cc_final: 0.4271 (p) REVERT: c 155 VAL cc_start: 0.8421 (m) cc_final: 0.8182 (p) REVERT: c 167 MET cc_start: 0.6312 (mtp) cc_final: 0.5766 (ttm) REVERT: c 175 ARG cc_start: 0.8068 (mmp80) cc_final: 0.7814 (mmm-85) REVERT: c 189 ILE cc_start: 0.7303 (tp) cc_final: 0.6994 (pt) REVERT: c 198 ARG cc_start: 0.8350 (ttp-170) cc_final: 0.7911 (ttp-170) REVERT: c 211 GLU cc_start: 0.8024 (tp30) cc_final: 0.7661 (tp30) REVERT: c 216 MET cc_start: 0.7417 (ptm) cc_final: 0.7031 (ttp) REVERT: c 260 GLU cc_start: 0.9363 (mt-10) cc_final: 0.8940 (pt0) REVERT: c 272 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8427 (mp) REVERT: d 1 MET cc_start: 0.5012 (ttt) cc_final: 0.4052 (tpp) REVERT: d 35 PHE cc_start: 0.3178 (t80) cc_final: 0.2841 (t80) REVERT: d 105 PHE cc_start: 0.8922 (t80) cc_final: 0.8692 (t80) REVERT: d 116 HIS cc_start: 0.6073 (m-70) cc_final: 0.5799 (m-70) REVERT: d 206 MET cc_start: 0.0035 (ptm) cc_final: -0.0191 (ppp) REVERT: e 1 MET cc_start: 0.4753 (mmp) cc_final: 0.4212 (mtp) REVERT: e 3 GLU cc_start: 0.8226 (tt0) cc_final: 0.7613 (mp0) REVERT: e 55 GLN cc_start: 0.8232 (mt0) cc_final: 0.7971 (tp40) REVERT: G 70 PHE cc_start: 0.8333 (m-10) cc_final: 0.7591 (m-10) REVERT: G 120 ASP cc_start: 0.8802 (m-30) cc_final: 0.8595 (t0) REVERT: G 139 ILE cc_start: 0.9170 (mt) cc_final: 0.8939 (mm) REVERT: G 155 ASP cc_start: 0.8540 (m-30) cc_final: 0.8100 (t70) REVERT: H 39 LYS cc_start: 0.7941 (tmtt) cc_final: 0.7550 (ttpt) REVERT: H 113 ARG cc_start: 0.9073 (mtt-85) cc_final: 0.8671 (ttm110) REVERT: H 122 THR cc_start: 0.6770 (p) cc_final: 0.6460 (p) REVERT: H 169 ASN cc_start: 0.8500 (m110) cc_final: 0.8197 (t0) REVERT: I 6 ASP cc_start: 0.5313 (m-30) cc_final: 0.4764 (m-30) REVERT: I 57 ASP cc_start: 0.6141 (m-30) cc_final: 0.5681 (m-30) REVERT: I 75 SER cc_start: 0.8091 (m) cc_final: 0.7710 (p) REVERT: I 136 TYR cc_start: 0.7087 (m-80) cc_final: 0.6769 (m-80) REVERT: J 10 PHE cc_start: 0.7479 (m-10) cc_final: 0.7276 (m-10) REVERT: J 177 THR cc_start: 0.7012 (p) cc_final: 0.6529 (p) REVERT: K 84 ASP cc_start: 0.7326 (m-30) cc_final: 0.6035 (p0) REVERT: K 137 PHE cc_start: 0.8670 (m-10) cc_final: 0.8187 (m-80) REVERT: K 168 ARG cc_start: 0.8659 (tpt170) cc_final: 0.8188 (tpp-160) REVERT: K 215 ILE cc_start: 0.8759 (pp) cc_final: 0.8469 (pp) REVERT: K 229 PHE cc_start: 0.8749 (t80) cc_final: 0.8470 (t80) REVERT: L 36 VAL cc_start: 0.9364 (t) cc_final: 0.8991 (p) REVERT: L 56 LEU cc_start: 0.8362 (pp) cc_final: 0.8109 (mp) REVERT: L 73 SER cc_start: 0.8766 (t) cc_final: 0.8559 (p) REVERT: L 88 MET cc_start: 0.9201 (tpp) cc_final: 0.8804 (tpp) REVERT: L 104 PRO cc_start: 0.7520 (Cg_exo) cc_final: 0.7080 (Cg_endo) REVERT: M 75 MET cc_start: 0.7095 (mtp) cc_final: 0.6644 (mtp) REVERT: M 98 PHE cc_start: 0.8580 (t80) cc_final: 0.8307 (t80) REVERT: M 130 PRO cc_start: 0.9091 (Cg_exo) cc_final: 0.8788 (Cg_endo) REVERT: M 131 PHE cc_start: 0.7302 (m-10) cc_final: 0.6397 (m-80) REVERT: M 140 TYR cc_start: 0.7643 (t80) cc_final: 0.6199 (t80) REVERT: M 177 GLU cc_start: 0.8863 (pt0) cc_final: 0.8306 (pp20) REVERT: M 197 ILE cc_start: 0.7999 (mm) cc_final: 0.7632 (tp) REVERT: N 98 ILE cc_start: 0.8802 (mm) cc_final: 0.8140 (pt) REVERT: N 110 GLN cc_start: 0.8612 (mt0) cc_final: 0.7906 (mt0) REVERT: N 151 GLU cc_start: 0.9384 (mt-10) cc_final: 0.9161 (mt-10) REVERT: O 93 TYR cc_start: 0.8361 (m-10) cc_final: 0.8121 (m-10) REVERT: O 146 MET cc_start: 0.8440 (mtm) cc_final: 0.8179 (mtm) REVERT: O 172 ASN cc_start: 0.7187 (p0) cc_final: 0.6893 (p0) REVERT: O 203 ARG cc_start: 0.5750 (ttm170) cc_final: 0.5479 (tpp-160) REVERT: P 56 LEU cc_start: 0.9292 (tp) cc_final: 0.9020 (mp) REVERT: P 59 ASP cc_start: 0.8699 (m-30) cc_final: 0.8338 (p0) REVERT: P 117 PHE cc_start: 0.7077 (p90) cc_final: 0.6719 (p90) REVERT: P 126 LEU cc_start: 0.9139 (pp) cc_final: 0.8366 (tt) REVERT: P 149 MET cc_start: 0.6042 (mmm) cc_final: 0.5227 (tpp) REVERT: P 161 ASP cc_start: 0.7759 (m-30) cc_final: 0.7169 (p0) REVERT: P 173 ASN cc_start: 0.9008 (m-40) cc_final: 0.8757 (m-40) REVERT: Q 28 MET cc_start: 0.8813 (mtm) cc_final: 0.8531 (mpp) REVERT: Q 31 ASP cc_start: 0.8315 (p0) cc_final: 0.7931 (m-30) REVERT: Q 75 LEU cc_start: 0.8502 (mt) cc_final: 0.7972 (tp) REVERT: Q 82 ASN cc_start: 0.9086 (t0) cc_final: 0.8735 (t0) REVERT: Q 186 ASN cc_start: 0.9036 (m-40) cc_final: 0.8655 (m110) REVERT: R 35 ILE cc_start: 0.9233 (mt) cc_final: 0.8437 (mt) REVERT: R 37 ILE cc_start: 0.8442 (mt) cc_final: 0.7558 (mm) REVERT: R 42 LEU cc_start: 0.9028 (mt) cc_final: 0.8639 (pp) REVERT: R 54 PHE cc_start: 0.8977 (t80) cc_final: 0.8581 (t80) REVERT: R 67 GLU cc_start: 0.8966 (tt0) cc_final: 0.8602 (tt0) REVERT: R 71 LYS cc_start: 0.8911 (mtpp) cc_final: 0.8441 (tppt) REVERT: R 190 ASP cc_start: 0.8081 (m-30) cc_final: 0.7584 (p0) REVERT: R 194 ASP cc_start: 0.8956 (m-30) cc_final: 0.8608 (m-30) REVERT: R 198 LYS cc_start: 0.8670 (tttt) cc_final: 0.8246 (ptpp) REVERT: S 15 ILE cc_start: 0.9543 (mt) cc_final: 0.9306 (pt) REVERT: S 40 SER cc_start: 0.8952 (t) cc_final: 0.8596 (m) REVERT: S 73 LYS cc_start: 0.8947 (mttt) cc_final: 0.8728 (mmtp) REVERT: S 83 MET cc_start: 0.5877 (mtp) cc_final: 0.4965 (mtp) REVERT: S 144 MET cc_start: 0.9210 (mtt) cc_final: 0.8031 (tpp) REVERT: S 145 LEU cc_start: 0.9427 (mt) cc_final: 0.9190 (mm) REVERT: T 5 MET cc_start: 0.8784 (mmt) cc_final: 0.8465 (mmp) REVERT: T 7 THR cc_start: 0.8715 (p) cc_final: 0.8398 (t) REVERT: T 26 MET cc_start: 0.8351 (mtp) cc_final: 0.7636 (mpp) REVERT: T 39 ILE cc_start: 0.8876 (pt) cc_final: 0.8629 (pt) REVERT: T 43 MET cc_start: 0.9170 (ttp) cc_final: 0.8638 (tmm) REVERT: T 106 LEU cc_start: 0.8940 (mt) cc_final: 0.8706 (mt) REVERT: T 133 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7932 (tp30) REVERT: T 160 LEU cc_start: 0.8841 (mt) cc_final: 0.8577 (tp) REVERT: T 168 LEU cc_start: 0.9173 (tt) cc_final: 0.8916 (pp) REVERT: T 179 ARG cc_start: 0.6456 (pmt100) cc_final: 0.5815 (pmt100) REVERT: T 180 ASP cc_start: 0.8692 (t0) cc_final: 0.8125 (t70) REVERT: T 187 PHE cc_start: 0.8853 (p90) cc_final: 0.8110 (p90) REVERT: T 199 ILE cc_start: 0.9432 (mt) cc_final: 0.9095 (tp) REVERT: g 80 MET cc_start: 0.6341 (mmm) cc_final: 0.5883 (mmm) REVERT: g 120 ASP cc_start: 0.8903 (m-30) cc_final: 0.8602 (m-30) REVERT: g 138 MET cc_start: 0.8895 (ttm) cc_final: 0.8668 (tpp) REVERT: h 20 VAL cc_start: 0.8821 (t) cc_final: 0.8460 (p) REVERT: h 69 THR cc_start: 0.9116 (m) cc_final: 0.8840 (p) REVERT: h 92 LYS cc_start: 0.8555 (mtpt) cc_final: 0.7980 (mtmm) REVERT: h 117 VAL cc_start: 0.9149 (t) cc_final: 0.8755 (t) REVERT: h 180 GLU cc_start: 0.6885 (tm-30) cc_final: 0.6273 (pm20) REVERT: i 3 ARG cc_start: 0.4475 (ptt180) cc_final: 0.4134 (ptt180) REVERT: j 70 CYS cc_start: 0.7618 (m) cc_final: 0.6683 (p) REVERT: k 59 MET cc_start: 0.8146 (ttt) cc_final: 0.7894 (ttm) REVERT: k 76 CYS cc_start: 0.4430 (t) cc_final: 0.3100 (t) REVERT: k 103 TYR cc_start: 0.8707 (m-80) cc_final: 0.8216 (m-80) REVERT: k 166 ASP cc_start: 0.8042 (m-30) cc_final: 0.7569 (p0) REVERT: k 204 GLN cc_start: 0.8516 (mt0) cc_final: 0.7732 (tp40) REVERT: l 64 LEU cc_start: 0.9339 (pp) cc_final: 0.9002 (tp) REVERT: l 80 ASP cc_start: 0.8003 (m-30) cc_final: 0.7544 (t0) REVERT: l 88 MET cc_start: 0.8433 (tpp) cc_final: 0.8084 (mmm) REVERT: l 230 SER cc_start: 0.9036 (m) cc_final: 0.8682 (t) REVERT: m 27 MET cc_start: 0.8013 (mtt) cc_final: 0.7792 (mmt) REVERT: m 232 ARG cc_start: 0.8302 (mtp85) cc_final: 0.7843 (mtm-85) REVERT: n 42 PHE cc_start: 0.8219 (m-10) cc_final: 0.7950 (m-80) REVERT: n 51 ASP cc_start: 0.8528 (m-30) cc_final: 0.8045 (p0) REVERT: n 57 ASP cc_start: 0.9065 (m-30) cc_final: 0.8786 (t70) REVERT: n 95 MET cc_start: 0.6721 (mtp) cc_final: 0.6148 (ptp) REVERT: o 54 MET cc_start: 0.9063 (mmm) cc_final: 0.8635 (mmt) REVERT: o 98 LEU cc_start: 0.9196 (mt) cc_final: 0.8963 (mm) REVERT: o 135 MET cc_start: 0.8575 (tpp) cc_final: 0.7809 (tpp) REVERT: o 138 PHE cc_start: 0.9201 (m-10) cc_final: 0.8977 (m-80) REVERT: p 28 PHE cc_start: 0.9117 (t80) cc_final: 0.8679 (t80) REVERT: p 34 MET cc_start: 0.7031 (ptm) cc_final: 0.5448 (ptm) REVERT: p 59 ASP cc_start: 0.8760 (m-30) cc_final: 0.8496 (p0) REVERT: p 72 ASN cc_start: 0.8974 (m110) cc_final: 0.8718 (t0) REVERT: p 76 LEU cc_start: 0.8991 (mt) cc_final: 0.8533 (pp) REVERT: p 94 LEU cc_start: 0.9600 (tt) cc_final: 0.9264 (pp) REVERT: p 104 TYR cc_start: 0.8616 (m-80) cc_final: 0.7810 (m-10) REVERT: p 109 ILE cc_start: 0.9233 (mt) cc_final: 0.9027 (mt) REVERT: p 146 MET cc_start: 0.8220 (mtm) cc_final: 0.7945 (mmt) REVERT: p 149 MET cc_start: 0.8547 (mmm) cc_final: 0.8156 (mmm) REVERT: q 27 GLN cc_start: 0.8553 (tt0) cc_final: 0.7987 (tp40) REVERT: q 58 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8594 (mm-30) REVERT: q 142 ILE cc_start: 0.8915 (mt) cc_final: 0.8648 (tp) REVERT: r 7 LYS cc_start: 0.7671 (pttt) cc_final: 0.7238 (ptmt) REVERT: r 67 GLU cc_start: 0.9298 (tt0) cc_final: 0.8863 (tp30) REVERT: r 91 LYS cc_start: 0.8215 (tttp) cc_final: 0.7996 (tttm) REVERT: r 115 ASP cc_start: 0.8173 (m-30) cc_final: 0.6703 (m-30) REVERT: s 2 PHE cc_start: 0.7657 (t80) cc_final: 0.7351 (t80) REVERT: s 94 THR cc_start: 0.9344 (p) cc_final: 0.9108 (p) REVERT: t 3 ASN cc_start: 0.8892 (m-40) cc_final: 0.7945 (p0) REVERT: t 25 ASP cc_start: 0.7361 (p0) cc_final: 0.7040 (m-30) REVERT: t 59 ASP cc_start: 0.8423 (m-30) cc_final: 0.8098 (m-30) REVERT: t 71 VAL cc_start: 0.9189 (t) cc_final: 0.8791 (p) REVERT: t 73 ASP cc_start: 0.8775 (m-30) cc_final: 0.8504 (t70) REVERT: t 103 MET cc_start: 0.9012 (mmm) cc_final: 0.8710 (mmt) REVERT: t 110 MET cc_start: 0.8939 (mtm) cc_final: 0.8127 (mpp) REVERT: t 126 ASP cc_start: 0.8880 (t0) cc_final: 0.8331 (t0) REVERT: t 180 ASP cc_start: 0.8416 (t0) cc_final: 0.8016 (t0) REVERT: A 263 MET cc_start: 0.7113 (mtm) cc_final: 0.6496 (ptp) REVERT: A 357 ILE cc_start: 0.8692 (mt) cc_final: 0.8106 (mm) REVERT: A 377 CYS cc_start: 0.9161 (m) cc_final: 0.8718 (p) REVERT: A 433 ASN cc_start: 0.4889 (m-40) cc_final: 0.4243 (p0) REVERT: B 184 TYR cc_start: 0.7210 (p90) cc_final: 0.6896 (p90) REVERT: B 272 ARG cc_start: 0.8188 (ttm170) cc_final: 0.7872 (tmt170) REVERT: B 312 LEU cc_start: 0.8925 (tp) cc_final: 0.8713 (tp) REVERT: C 121 TYR cc_start: 0.8644 (m-10) cc_final: 0.8317 (m-80) REVERT: C 127 LEU cc_start: 0.7364 (mt) cc_final: 0.6956 (pp) REVERT: C 150 MET cc_start: 0.8146 (ptp) cc_final: 0.7823 (mmm) REVERT: C 167 LEU cc_start: 0.7672 (tp) cc_final: 0.7385 (tt) REVERT: C 327 ASP cc_start: 0.8963 (m-30) cc_final: 0.8704 (t70) REVERT: C 384 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8096 (pt0) REVERT: D 98 GLN cc_start: 0.6510 (tp-100) cc_final: 0.5982 (mm-40) REVERT: D 122 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8374 (pp20) REVERT: D 124 LEU cc_start: 0.8690 (mm) cc_final: 0.8431 (mt) REVERT: D 187 HIS cc_start: 0.8154 (m-70) cc_final: 0.7831 (m90) REVERT: D 204 MET cc_start: 0.8165 (mtp) cc_final: 0.7887 (mpp) REVERT: D 229 ARG cc_start: 0.8028 (ppt-90) cc_final: 0.7610 (ppt170) REVERT: E 108 MET cc_start: 0.7677 (mmp) cc_final: 0.7342 (mmm) REVERT: E 203 ILE cc_start: 0.7746 (mt) cc_final: 0.7544 (mp) REVERT: E 261 LEU cc_start: 0.8564 (mt) cc_final: 0.8150 (mt) REVERT: E 272 ARG cc_start: 0.8411 (mtt180) cc_final: 0.7901 (ttm110) REVERT: F 88 TYR cc_start: 0.7573 (p90) cc_final: 0.6980 (p90) REVERT: F 89 LEU cc_start: 0.9034 (tp) cc_final: 0.8695 (tt) REVERT: F 134 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8339 (mp) REVERT: F 143 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8666 (mm-30) REVERT: F 310 MET cc_start: 0.7326 (ttp) cc_final: 0.6938 (tmm) REVERT: F 405 MET cc_start: 0.8277 (mtm) cc_final: 0.7769 (mpp) REVERT: f 414 LEU cc_start: 0.5145 (mt) cc_final: 0.4759 (tt) REVERT: f 440 ILE cc_start: 0.4658 (mt) cc_final: 0.4339 (tp) REVERT: f 477 MET cc_start: 0.1347 (ttm) cc_final: 0.0604 (ttp) REVERT: f 641 GLU cc_start: 0.0042 (OUTLIER) cc_final: -0.0529 (mm-30) REVERT: f 788 MET cc_start: -0.0472 (pmt) cc_final: -0.1662 (mpp) outliers start: 79 outliers final: 10 residues processed: 2469 average time/residue: 0.9806 time to fit residues: 4074.2233 Evaluate side-chains 1162 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1146 time to evaluate : 9.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1268 random chunks: chunk 1070 optimal weight: 20.0000 chunk 961 optimal weight: 7.9990 chunk 533 optimal weight: 9.9990 chunk 328 optimal weight: 8.9990 chunk 648 optimal weight: 8.9990 chunk 513 optimal weight: 5.9990 chunk 993 optimal weight: 0.9990 chunk 384 optimal weight: 5.9990 chunk 604 optimal weight: 2.9990 chunk 739 optimal weight: 20.0000 chunk 1151 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 389 ASN U 880 ASN V 110 HIS ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 380 GLN ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 349 HIS Y 71 ASN Y 344 HIS Y 381 GLN Z 96 HIS ** Z 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 23 HIS a 129 GLN a 305 ASN ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 GLN c 199 HIS ** c 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 63 HIS ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN H 148 GLN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 GLN I 240 HIS J 15 HIS J 116 GLN K 23 GLN ** K 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 GLN L 152 ASN L 190 HIS N 154 GLN ** Q 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82 ASN Q 101 ASN ** T 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 69 GLN g 224 ASN ** h 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 207 ASN ** i 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 99 HIS ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 HIS o 66 HIS o 165 ASN p 169 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 101 ASN q 168 GLN r 38 ASN ** t 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 187 HIS D 412 GLN E 190 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 ASN F 321 GLN f 14 GLN f 102 HIS f 224 ASN f 329 ASN f 387 GLN f 452 ASN ** f 782 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 101622 Z= 0.241 Angle : 0.807 14.516 137458 Z= 0.420 Chirality : 0.047 0.387 15660 Planarity : 0.006 0.098 17770 Dihedral : 7.926 151.380 14082 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.58 % Favored : 90.19 % Rotamer: Outliers : 0.25 % Allowed : 4.03 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.19 % Twisted Proline : 0.67 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.07), residues: 12738 helix: -1.36 (0.06), residues: 5566 sheet: -1.33 (0.13), residues: 1580 loop : -3.09 (0.07), residues: 5592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP d 61 HIS 0.015 0.002 HIS f 301 PHE 0.058 0.002 PHE U 728 TYR 0.029 0.002 TYR F 438 ARG 0.014 0.001 ARG Y 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1514 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1488 time to evaluate : 9.462 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: U 8 ILE cc_start: 0.7326 (pt) cc_final: 0.7075 (pt) REVERT: U 19 LEU cc_start: 0.7572 (tp) cc_final: 0.7258 (tp) REVERT: U 362 ASN cc_start: 0.5521 (t0) cc_final: 0.5219 (t0) REVERT: U 650 TYR cc_start: 0.9086 (t80) cc_final: 0.8886 (t80) REVERT: U 728 PHE cc_start: 0.8649 (m-80) cc_final: 0.8317 (m-10) REVERT: U 793 LYS cc_start: 0.8089 (ttpp) cc_final: 0.7530 (mmtt) REVERT: V 36 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7143 (mt-10) REVERT: V 139 MET cc_start: 0.5174 (mmm) cc_final: 0.4844 (ttt) REVERT: V 175 MET cc_start: 0.3562 (mtt) cc_final: 0.3358 (mtt) REVERT: V 241 ARG cc_start: 0.5674 (mpp-170) cc_final: 0.3856 (tpp80) REVERT: V 309 MET cc_start: 0.7275 (ptm) cc_final: 0.7074 (ptm) REVERT: V 336 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8342 (mm-30) REVERT: V 489 MET cc_start: 0.8254 (mmp) cc_final: 0.7967 (mmm) REVERT: W 94 ARG cc_start: 0.5054 (ttt-90) cc_final: 0.4723 (tpm170) REVERT: W 124 LEU cc_start: 0.7630 (mt) cc_final: 0.7136 (tt) REVERT: W 315 MET cc_start: 0.3508 (ptp) cc_final: 0.1118 (mmt) REVERT: W 352 LYS cc_start: 0.8274 (mmtp) cc_final: 0.7978 (tmtt) REVERT: W 377 ARG cc_start: 0.6788 (ttt90) cc_final: 0.5891 (mpt-90) REVERT: W 378 MET cc_start: 0.6714 (tpp) cc_final: 0.6485 (tpp) REVERT: W 428 TRP cc_start: 0.8298 (m100) cc_final: 0.7620 (t-100) REVERT: X 283 GLN cc_start: 0.8081 (mt0) cc_final: 0.7805 (mp10) REVERT: X 337 ARG cc_start: 0.6831 (mtt180) cc_final: 0.6378 (tpm170) REVERT: X 363 ARG cc_start: 0.8245 (mtm110) cc_final: 0.7718 (ttt180) REVERT: X 406 ASN cc_start: 0.8953 (m110) cc_final: 0.8416 (m110) REVERT: X 407 MET cc_start: 0.8657 (mmt) cc_final: 0.8379 (tpp) REVERT: Y 40 GLU cc_start: 0.5479 (mm-30) cc_final: 0.5045 (pt0) REVERT: Y 319 MET cc_start: 0.6868 (mmm) cc_final: 0.6639 (mmm) REVERT: Y 367 GLN cc_start: 0.8953 (tp-100) cc_final: 0.8166 (mt0) REVERT: Y 379 ARG cc_start: 0.9181 (tpp-160) cc_final: 0.8734 (tpt-90) REVERT: Y 384 SER cc_start: 0.8615 (t) cc_final: 0.8376 (p) REVERT: Y 389 MET cc_start: 0.0605 (ttm) cc_final: -0.0254 (pmm) REVERT: Z 103 LYS cc_start: 0.8235 (tttt) cc_final: 0.7507 (mmmt) REVERT: Z 112 MET cc_start: 0.9301 (mpp) cc_final: 0.8953 (mpp) REVERT: Z 138 TYR cc_start: 0.7298 (m-80) cc_final: 0.6892 (m-80) REVERT: Z 194 GLN cc_start: 0.9132 (mt0) cc_final: 0.8741 (tp-100) REVERT: Z 228 TYR cc_start: 0.7628 (p90) cc_final: 0.7251 (p90) REVERT: Z 256 GLN cc_start: 0.7973 (tp-100) cc_final: 0.7291 (mm-40) REVERT: a 278 MET cc_start: 0.6209 (ptm) cc_final: 0.5466 (mtm) REVERT: a 339 ARG cc_start: 0.5771 (mmt180) cc_final: 0.4460 (ptt180) REVERT: b 133 LYS cc_start: 0.7002 (pttm) cc_final: 0.6306 (tptt) REVERT: c 75 MET cc_start: 0.7514 (ttt) cc_final: 0.6952 (tmm) REVERT: c 198 ARG cc_start: 0.8238 (ttp-170) cc_final: 0.8028 (ttp-170) REVERT: c 216 MET cc_start: 0.7214 (ptm) cc_final: 0.6969 (ttp) REVERT: c 260 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8938 (pt0) REVERT: c 272 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8162 (tt) REVERT: d 1 MET cc_start: 0.4357 (ttt) cc_final: 0.3481 (tpp) REVERT: e 3 GLU cc_start: 0.8543 (tt0) cc_final: 0.7732 (mp0) REVERT: e 57 ARG cc_start: 0.7203 (mpt90) cc_final: 0.6882 (mmt180) REVERT: G 120 ASP cc_start: 0.8909 (m-30) cc_final: 0.8689 (t0) REVERT: G 155 ASP cc_start: 0.8360 (m-30) cc_final: 0.8093 (t0) REVERT: H 39 LYS cc_start: 0.7868 (tmtt) cc_final: 0.7470 (tttt) REVERT: H 118 MET cc_start: 0.7669 (ttm) cc_final: 0.7174 (ttp) REVERT: H 169 ASN cc_start: 0.8539 (m110) cc_final: 0.8234 (t0) REVERT: I 18 LEU cc_start: 0.8095 (mt) cc_final: 0.7298 (tt) REVERT: I 57 ASP cc_start: 0.6515 (m-30) cc_final: 0.6102 (m-30) REVERT: I 75 SER cc_start: 0.8107 (m) cc_final: 0.7850 (p) REVERT: I 136 TYR cc_start: 0.7154 (m-80) cc_final: 0.6546 (m-80) REVERT: J 177 THR cc_start: 0.6500 (p) cc_final: 0.6102 (p) REVERT: K 78 MET cc_start: 0.6621 (ppp) cc_final: 0.6388 (ppp) REVERT: K 84 ASP cc_start: 0.7106 (m-30) cc_final: 0.6254 (p0) REVERT: K 137 PHE cc_start: 0.8591 (m-10) cc_final: 0.8225 (m-80) REVERT: K 210 LEU cc_start: 0.7986 (tp) cc_final: 0.7694 (pt) REVERT: K 229 PHE cc_start: 0.8716 (t80) cc_final: 0.8349 (t80) REVERT: L 84 LEU cc_start: 0.8937 (tt) cc_final: 0.8703 (tt) REVERT: L 88 MET cc_start: 0.9256 (tpp) cc_final: 0.8829 (ptm) REVERT: L 98 VAL cc_start: 0.9278 (t) cc_final: 0.8870 (m) REVERT: L 100 ASP cc_start: 0.9526 (t0) cc_final: 0.9092 (m-30) REVERT: L 152 ASN cc_start: 0.8894 (m-40) cc_final: 0.8416 (p0) REVERT: M 40 ARG cc_start: 0.4999 (ptt180) cc_final: 0.4605 (ptt90) REVERT: M 140 TYR cc_start: 0.7401 (t80) cc_final: 0.7101 (t80) REVERT: M 177 GLU cc_start: 0.8770 (pt0) cc_final: 0.8069 (tp30) REVERT: M 197 ILE cc_start: 0.7869 (mm) cc_final: 0.7527 (tp) REVERT: N 98 ILE cc_start: 0.9169 (mm) cc_final: 0.8727 (pt) REVERT: P 56 LEU cc_start: 0.9290 (tp) cc_final: 0.8947 (mp) REVERT: P 59 ASP cc_start: 0.8613 (m-30) cc_final: 0.8265 (p0) REVERT: P 90 MET cc_start: 0.8775 (mtm) cc_final: 0.8136 (mmm) REVERT: P 117 PHE cc_start: 0.6984 (p90) cc_final: 0.6711 (p90) REVERT: P 126 LEU cc_start: 0.9228 (pp) cc_final: 0.8431 (tt) REVERT: P 149 MET cc_start: 0.5793 (mmm) cc_final: 0.5288 (tpp) REVERT: P 161 ASP cc_start: 0.7824 (m-30) cc_final: 0.7195 (p0) REVERT: P 171 MET cc_start: 0.9019 (mmm) cc_final: 0.8752 (tpt) REVERT: Q 31 ASP cc_start: 0.8645 (p0) cc_final: 0.8186 (m-30) REVERT: Q 75 LEU cc_start: 0.8477 (mt) cc_final: 0.8116 (tp) REVERT: R 35 ILE cc_start: 0.9195 (mt) cc_final: 0.8465 (mm) REVERT: R 71 LYS cc_start: 0.8832 (mtpp) cc_final: 0.8580 (tptt) REVERT: R 89 GLN cc_start: 0.8733 (pt0) cc_final: 0.8495 (tp40) REVERT: R 127 SER cc_start: 0.7760 (t) cc_final: 0.6831 (t) REVERT: R 190 ASP cc_start: 0.7932 (m-30) cc_final: 0.7424 (p0) REVERT: S 40 SER cc_start: 0.9155 (t) cc_final: 0.8848 (m) REVERT: S 144 MET cc_start: 0.9101 (mtt) cc_final: 0.8464 (ttm) REVERT: S 145 LEU cc_start: 0.9573 (mt) cc_final: 0.9267 (mt) REVERT: S 151 ASN cc_start: 0.8673 (t0) cc_final: 0.8172 (t0) REVERT: T 5 MET cc_start: 0.8787 (mmt) cc_final: 0.8535 (mpp) REVERT: T 7 THR cc_start: 0.8586 (p) cc_final: 0.8340 (t) REVERT: T 26 MET cc_start: 0.8429 (mtp) cc_final: 0.7706 (mpp) REVERT: T 43 MET cc_start: 0.8974 (ttp) cc_final: 0.8594 (tmm) REVERT: T 110 MET cc_start: 0.8920 (mtp) cc_final: 0.8269 (mmm) REVERT: T 168 LEU cc_start: 0.9216 (tt) cc_final: 0.8926 (pp) REVERT: T 173 MET cc_start: 0.9186 (tpp) cc_final: 0.8950 (tpp) REVERT: T 180 ASP cc_start: 0.8629 (t0) cc_final: 0.8001 (t70) REVERT: T 187 PHE cc_start: 0.8582 (p90) cc_final: 0.8052 (p90) REVERT: g 115 CYS cc_start: 0.8706 (t) cc_final: 0.7994 (p) REVERT: g 120 ASP cc_start: 0.9008 (m-30) cc_final: 0.8673 (m-30) REVERT: g 155 ASP cc_start: 0.7967 (t0) cc_final: 0.7701 (t0) REVERT: h 92 LYS cc_start: 0.8382 (mtpt) cc_final: 0.8021 (mtmm) REVERT: h 134 LEU cc_start: 0.8090 (mt) cc_final: 0.7782 (mt) REVERT: h 166 ASN cc_start: 0.9267 (t0) cc_final: 0.8945 (t0) REVERT: j 211 MET cc_start: 0.6291 (tmm) cc_final: 0.6075 (tmm) REVERT: k 90 ASP cc_start: 0.9223 (t70) cc_final: 0.8756 (t70) REVERT: k 183 GLU cc_start: 0.9237 (tp30) cc_final: 0.8996 (tp30) REVERT: k 203 LYS cc_start: 0.9046 (tmtt) cc_final: 0.8711 (pttt) REVERT: k 204 GLN cc_start: 0.8519 (mt0) cc_final: 0.7778 (tp40) REVERT: l 80 ASP cc_start: 0.8153 (m-30) cc_final: 0.7803 (t0) REVERT: l 88 MET cc_start: 0.8451 (tpp) cc_final: 0.8103 (tpt) REVERT: l 230 SER cc_start: 0.8929 (m) cc_final: 0.8626 (p) REVERT: m 27 MET cc_start: 0.8097 (mtt) cc_final: 0.7878 (mmt) REVERT: m 43 ASP cc_start: 0.8213 (p0) cc_final: 0.7844 (m-30) REVERT: m 150 MET cc_start: 0.7974 (tmm) cc_final: 0.7687 (tmm) REVERT: m 232 ARG cc_start: 0.8307 (mtp85) cc_final: 0.7772 (mtm-85) REVERT: n 4 MET cc_start: 0.8776 (tpp) cc_final: 0.8508 (tpp) REVERT: n 51 ASP cc_start: 0.8498 (m-30) cc_final: 0.8275 (p0) REVERT: n 57 ASP cc_start: 0.9046 (m-30) cc_final: 0.8839 (t70) REVERT: o 135 MET cc_start: 0.8467 (tpp) cc_final: 0.7960 (tpp) REVERT: p 28 PHE cc_start: 0.9208 (t80) cc_final: 0.8521 (t80) REVERT: p 95 LEU cc_start: 0.9577 (mt) cc_final: 0.9071 (tp) REVERT: p 144 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8318 (tt0) REVERT: p 158 MET cc_start: 0.7902 (tpp) cc_final: 0.7546 (tpp) REVERT: p 164 PHE cc_start: 0.8486 (t80) cc_final: 0.8249 (t80) REVERT: q 14 LEU cc_start: 0.8922 (tp) cc_final: 0.8671 (tp) REVERT: q 20 VAL cc_start: 0.6929 (t) cc_final: 0.6558 (t) REVERT: q 62 LYS cc_start: 0.9317 (mmmt) cc_final: 0.8827 (mmtm) REVERT: q 69 MET cc_start: 0.9468 (tpp) cc_final: 0.9143 (tpp) REVERT: q 118 MET cc_start: 0.7042 (mmm) cc_final: 0.6791 (mmm) REVERT: r 7 LYS cc_start: 0.7598 (pttt) cc_final: 0.7385 (ptmt) REVERT: r 65 ILE cc_start: 0.9066 (mm) cc_final: 0.8841 (mm) REVERT: r 86 MET cc_start: 0.8834 (mtp) cc_final: 0.8626 (mtp) REVERT: r 97 MET cc_start: 0.8130 (tmm) cc_final: 0.7657 (tmm) REVERT: r 105 ASP cc_start: 0.8662 (m-30) cc_final: 0.8429 (m-30) REVERT: r 115 ASP cc_start: 0.7463 (m-30) cc_final: 0.6546 (m-30) REVERT: r 140 ASP cc_start: 0.8548 (p0) cc_final: 0.7740 (t0) REVERT: s 69 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8894 (mm-30) REVERT: s 83 MET cc_start: 0.8209 (ttm) cc_final: 0.7975 (ttm) REVERT: t 3 ASN cc_start: 0.8787 (m-40) cc_final: 0.7764 (p0) REVERT: t 59 ASP cc_start: 0.8131 (m-30) cc_final: 0.7871 (m-30) REVERT: t 73 ASP cc_start: 0.8902 (m-30) cc_final: 0.8676 (t70) REVERT: t 96 MET cc_start: 0.8631 (tpp) cc_final: 0.8219 (tpp) REVERT: t 103 MET cc_start: 0.9080 (mmm) cc_final: 0.8867 (mmt) REVERT: t 133 GLU cc_start: 0.8525 (mt-10) cc_final: 0.7480 (pm20) REVERT: t 137 LEU cc_start: 0.9478 (mt) cc_final: 0.9219 (mt) REVERT: A 263 MET cc_start: 0.7116 (mtm) cc_final: 0.6399 (ptm) REVERT: A 273 PHE cc_start: 0.6831 (m-80) cc_final: 0.6346 (m-80) REVERT: A 318 LEU cc_start: 0.8471 (mt) cc_final: 0.7880 (mm) REVERT: A 377 CYS cc_start: 0.9211 (m) cc_final: 0.8746 (m) REVERT: B 184 TYR cc_start: 0.7191 (p90) cc_final: 0.6879 (p90) REVERT: B 250 VAL cc_start: 0.8869 (t) cc_final: 0.8631 (t) REVERT: B 251 VAL cc_start: 0.7710 (t) cc_final: 0.7478 (t) REVERT: B 272 ARG cc_start: 0.8159 (ttm170) cc_final: 0.7768 (tmt170) REVERT: B 309 MET cc_start: 0.8128 (ptt) cc_final: 0.7737 (ppp) REVERT: B 373 THR cc_start: 0.7614 (p) cc_final: 0.6760 (p) REVERT: C 121 TYR cc_start: 0.8670 (m-10) cc_final: 0.8397 (m-80) REVERT: C 139 MET cc_start: 0.3955 (mtm) cc_final: 0.3397 (mtt) REVERT: C 150 MET cc_start: 0.8160 (ptp) cc_final: 0.7777 (mmm) REVERT: C 327 ASP cc_start: 0.8944 (m-30) cc_final: 0.8692 (t70) REVERT: C 384 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8180 (pt0) REVERT: D 89 ILE cc_start: 0.7942 (mm) cc_final: 0.7688 (mm) REVERT: D 98 GLN cc_start: 0.6433 (tp-100) cc_final: 0.6142 (mm-40) REVERT: D 174 LYS cc_start: 0.4442 (mtmt) cc_final: 0.4188 (mtmt) REVERT: D 187 HIS cc_start: 0.8148 (m90) cc_final: 0.7877 (m90) REVERT: D 204 MET cc_start: 0.8136 (mtp) cc_final: 0.7684 (ttp) REVERT: D 309 MET cc_start: 0.6599 (mpp) cc_final: 0.5846 (mpp) REVERT: E 56 ILE cc_start: 0.9032 (mm) cc_final: 0.8783 (mt) REVERT: E 108 MET cc_start: 0.8070 (mmp) cc_final: 0.7603 (mmm) REVERT: E 261 LEU cc_start: 0.8385 (mt) cc_final: 0.8157 (mt) REVERT: E 272 ARG cc_start: 0.8414 (mtt180) cc_final: 0.7849 (ttm110) REVERT: F 74 LYS cc_start: 0.8160 (tptp) cc_final: 0.7952 (pttp) REVERT: F 88 TYR cc_start: 0.7721 (p90) cc_final: 0.7220 (p90) REVERT: F 89 LEU cc_start: 0.9126 (tp) cc_final: 0.8835 (tp) REVERT: F 310 MET cc_start: 0.7362 (ttp) cc_final: 0.7094 (tmm) REVERT: F 405 MET cc_start: 0.8121 (mtm) cc_final: 0.7663 (mpp) REVERT: F 421 MET cc_start: 0.6565 (mmp) cc_final: 0.5470 (mtt) REVERT: f 407 MET cc_start: 0.4730 (tpp) cc_final: 0.3892 (mmt) REVERT: f 414 LEU cc_start: 0.4969 (mt) cc_final: 0.4665 (tt) REVERT: f 477 MET cc_start: 0.0764 (ttm) cc_final: -0.0197 (ttp) REVERT: f 505 MET cc_start: -0.1148 (ttm) cc_final: -0.3049 (mtm) REVERT: f 686 LEU cc_start: 0.6731 (mm) cc_final: 0.6121 (tp) outliers start: 26 outliers final: 9 residues processed: 1509 average time/residue: 0.9252 time to fit residues: 2375.5937 Evaluate side-chains 1009 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 999 time to evaluate : 9.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1268 random chunks: chunk 639 optimal weight: 20.0000 chunk 357 optimal weight: 9.9990 chunk 958 optimal weight: 6.9990 chunk 784 optimal weight: 9.9990 chunk 317 optimal weight: 10.0000 chunk 1153 optimal weight: 7.9990 chunk 1246 optimal weight: 5.9990 chunk 1027 optimal weight: 8.9990 chunk 1143 optimal weight: 20.0000 chunk 393 optimal weight: 0.8980 chunk 925 optimal weight: 20.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 110 HIS ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 260 HIS V 326 GLN ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 184 GLN Z 174 HIS Z 231 GLN ** Z 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 129 GLN a 152 HIS ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 105 HIS ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 240 HIS ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 HIS L 190 HIS ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN ** P 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN ** S 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 65 GLN ** h 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 109 GLN ** h 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 152 GLN k 155 HIS ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 HIS o 153 ASN p 169 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 GLN ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 180 GLN f 327 ASN f 329 ASN f 364 GLN f 782 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 101622 Z= 0.252 Angle : 0.782 12.546 137458 Z= 0.405 Chirality : 0.047 0.268 15660 Planarity : 0.006 0.116 17770 Dihedral : 7.541 142.560 14082 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.20 % Favored : 89.61 % Rotamer: Outliers : 0.13 % Allowed : 4.43 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.20 % Twisted Proline : 0.67 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.07), residues: 12738 helix: -0.85 (0.07), residues: 5595 sheet: -1.14 (0.12), residues: 1661 loop : -2.88 (0.08), residues: 5482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP d 61 HIS 0.017 0.002 HIS f 566 PHE 0.036 0.002 PHE U 728 TYR 0.025 0.002 TYR F 437 ARG 0.017 0.001 ARG G 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1257 time to evaluate : 9.514 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: U 362 ASN cc_start: 0.6092 (t0) cc_final: 0.5641 (t0) REVERT: U 556 MET cc_start: 0.7471 (mmp) cc_final: 0.7246 (mmp) REVERT: U 588 MET cc_start: 0.8637 (ttp) cc_final: 0.8359 (ttt) REVERT: U 650 TYR cc_start: 0.9148 (t80) cc_final: 0.8819 (t80) REVERT: U 675 MET cc_start: 0.6494 (mmm) cc_final: 0.6222 (mmm) REVERT: U 728 PHE cc_start: 0.8747 (m-80) cc_final: 0.8338 (m-10) REVERT: U 793 LYS cc_start: 0.8047 (ttpp) cc_final: 0.7508 (mmtt) REVERT: V 139 MET cc_start: 0.5334 (mmm) cc_final: 0.4971 (ttt) REVERT: V 241 ARG cc_start: 0.5567 (mpp-170) cc_final: 0.4747 (tpp80) REVERT: V 336 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8257 (mm-30) REVERT: W 73 MET cc_start: 0.8904 (mmm) cc_final: 0.8618 (mmm) REVERT: W 85 GLU cc_start: 0.2920 (OUTLIER) cc_final: 0.2215 (mm-30) REVERT: W 94 ARG cc_start: 0.5003 (ttt-90) cc_final: 0.4456 (tpm170) REVERT: W 124 LEU cc_start: 0.7712 (mt) cc_final: 0.7255 (tt) REVERT: W 190 MET cc_start: 0.4546 (mpp) cc_final: 0.4195 (mmp) REVERT: W 315 MET cc_start: 0.4715 (pmm) cc_final: 0.1881 (mmm) REVERT: W 352 LYS cc_start: 0.8170 (mmtp) cc_final: 0.7734 (ptmm) REVERT: W 377 ARG cc_start: 0.6900 (ttt90) cc_final: 0.5997 (mpt-90) REVERT: W 428 TRP cc_start: 0.8363 (m100) cc_final: 0.7593 (t-100) REVERT: X 254 MET cc_start: -0.5724 (mtm) cc_final: -0.5936 (mtm) REVERT: X 283 GLN cc_start: 0.8152 (mt0) cc_final: 0.7930 (mp10) REVERT: X 337 ARG cc_start: 0.6696 (mtt180) cc_final: 0.6204 (tpm170) REVERT: X 363 ARG cc_start: 0.8214 (mtm110) cc_final: 0.7949 (ttt180) REVERT: X 368 MET cc_start: 0.6676 (mtt) cc_final: 0.5801 (mpp) REVERT: Y 40 GLU cc_start: 0.5408 (mm-30) cc_final: 0.5044 (pt0) REVERT: Y 104 MET cc_start: 0.6396 (tmm) cc_final: 0.5301 (ttt) REVERT: Y 319 MET cc_start: 0.6896 (mmm) cc_final: 0.6545 (mmm) REVERT: Y 379 ARG cc_start: 0.9143 (tpp-160) cc_final: 0.8730 (tpt-90) REVERT: Y 384 SER cc_start: 0.8633 (t) cc_final: 0.8380 (p) REVERT: Y 389 MET cc_start: 0.0338 (ttm) cc_final: -0.0062 (pmm) REVERT: Z 103 LYS cc_start: 0.8265 (tttt) cc_final: 0.8019 (mtpt) REVERT: Z 112 MET cc_start: 0.9378 (mpp) cc_final: 0.9142 (mpp) REVERT: Z 194 GLN cc_start: 0.9270 (mt0) cc_final: 0.8841 (tp-100) REVERT: Z 273 HIS cc_start: 0.8915 (m-70) cc_final: 0.8671 (m90) REVERT: a 278 MET cc_start: 0.6125 (ptm) cc_final: 0.5676 (mtm) REVERT: c 54 MET cc_start: 0.5119 (mtp) cc_final: 0.4802 (mtm) REVERT: c 57 MET cc_start: 0.8328 (mtm) cc_final: 0.8102 (ptp) REVERT: c 75 MET cc_start: 0.7631 (ttt) cc_final: 0.7223 (tmm) REVERT: c 198 ARG cc_start: 0.8214 (ttp-170) cc_final: 0.7961 (ttp-170) REVERT: c 216 MET cc_start: 0.7417 (ptm) cc_final: 0.6860 (ttp) REVERT: d 1 MET cc_start: 0.3626 (ttt) cc_final: 0.3371 (tpp) REVERT: e 3 GLU cc_start: 0.8499 (tt0) cc_final: 0.7687 (mp0) REVERT: G 120 ASP cc_start: 0.8934 (m-30) cc_final: 0.8700 (t0) REVERT: G 131 MET cc_start: 0.8160 (mpp) cc_final: 0.7568 (mpp) REVERT: G 155 ASP cc_start: 0.8311 (m-30) cc_final: 0.8005 (t70) REVERT: G 159 TYR cc_start: 0.8457 (t80) cc_final: 0.8190 (t80) REVERT: H 39 LYS cc_start: 0.7759 (tmtt) cc_final: 0.7367 (tttt) REVERT: H 118 MET cc_start: 0.7813 (ttm) cc_final: 0.7240 (ttp) REVERT: H 166 ASN cc_start: 0.8458 (m-40) cc_final: 0.8083 (m-40) REVERT: H 169 ASN cc_start: 0.8645 (m110) cc_final: 0.7937 (t0) REVERT: H 208 ILE cc_start: 0.8269 (pt) cc_final: 0.7417 (mt) REVERT: H 210 VAL cc_start: 0.8931 (t) cc_final: 0.8520 (t) REVERT: I 18 LEU cc_start: 0.8358 (mt) cc_final: 0.8065 (mt) REVERT: I 57 ASP cc_start: 0.6764 (m-30) cc_final: 0.6432 (m-30) REVERT: J 24 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8517 (mt-10) REVERT: J 211 MET cc_start: 0.7835 (mmm) cc_final: 0.7519 (mmm) REVERT: K 59 MET cc_start: 0.6719 (mtm) cc_final: 0.6485 (mtm) REVERT: K 78 MET cc_start: 0.6757 (ppp) cc_final: 0.6422 (ppp) REVERT: K 84 ASP cc_start: 0.7096 (m-30) cc_final: 0.6149 (p0) REVERT: K 137 PHE cc_start: 0.8575 (m-10) cc_final: 0.8257 (m-80) REVERT: K 228 MET cc_start: 0.7075 (pmm) cc_final: 0.6799 (pmm) REVERT: L 84 LEU cc_start: 0.8974 (tt) cc_final: 0.8742 (tt) REVERT: L 88 MET cc_start: 0.9284 (tpp) cc_final: 0.8867 (ptm) REVERT: L 152 ASN cc_start: 0.9022 (m-40) cc_final: 0.8427 (p0) REVERT: L 180 MET cc_start: 0.8280 (tpp) cc_final: 0.7982 (tpt) REVERT: L 190 HIS cc_start: 0.8140 (m90) cc_final: 0.7908 (m-70) REVERT: M 137 LEU cc_start: 0.8977 (tp) cc_final: 0.8635 (tp) REVERT: M 177 GLU cc_start: 0.8810 (pt0) cc_final: 0.8044 (tp30) REVERT: M 197 ILE cc_start: 0.8072 (mm) cc_final: 0.7765 (tp) REVERT: N 95 MET cc_start: 0.9022 (mpp) cc_final: 0.8659 (mpp) REVERT: N 98 ILE cc_start: 0.9175 (mm) cc_final: 0.8269 (tp) REVERT: N 120 MET cc_start: 0.8473 (tmm) cc_final: 0.7907 (tmm) REVERT: N 164 MET cc_start: 0.7676 (mtm) cc_final: 0.7390 (mtt) REVERT: O 146 MET cc_start: 0.7783 (ttm) cc_final: 0.7238 (ttm) REVERT: P 90 MET cc_start: 0.8742 (mtm) cc_final: 0.8156 (mmm) REVERT: P 117 PHE cc_start: 0.7058 (p90) cc_final: 0.6807 (p90) REVERT: P 126 LEU cc_start: 0.9067 (pp) cc_final: 0.8100 (tt) REVERT: P 149 MET cc_start: 0.5595 (mmm) cc_final: 0.5002 (tpp) REVERT: Q 31 ASP cc_start: 0.8616 (p0) cc_final: 0.8204 (m-30) REVERT: Q 82 ASN cc_start: 0.9009 (t0) cc_final: 0.8626 (t0) REVERT: Q 102 LEU cc_start: 0.9102 (mp) cc_final: 0.8867 (mm) REVERT: R 71 LYS cc_start: 0.8927 (mtpp) cc_final: 0.8475 (tptt) REVERT: R 97 MET cc_start: 0.7737 (mpp) cc_final: 0.7469 (mpp) REVERT: R 100 MET cc_start: 0.8383 (mpp) cc_final: 0.7704 (mpp) REVERT: R 190 ASP cc_start: 0.7817 (m-30) cc_final: 0.7228 (p0) REVERT: R 194 ASP cc_start: 0.8799 (m-30) cc_final: 0.8268 (p0) REVERT: S 18 GLU cc_start: 0.8235 (pm20) cc_final: 0.7856 (pm20) REVERT: S 144 MET cc_start: 0.9069 (mtt) cc_final: 0.8353 (ttm) REVERT: S 145 LEU cc_start: 0.9570 (mt) cc_final: 0.9256 (mt) REVERT: T 7 THR cc_start: 0.8624 (p) cc_final: 0.8324 (t) REVERT: T 26 MET cc_start: 0.8521 (mtp) cc_final: 0.7822 (mpp) REVERT: T 110 MET cc_start: 0.8943 (mtp) cc_final: 0.8229 (mmm) REVERT: T 180 ASP cc_start: 0.8458 (t0) cc_final: 0.7884 (t0) REVERT: T 187 PHE cc_start: 0.8650 (p90) cc_final: 0.8191 (p90) REVERT: g 80 MET cc_start: 0.6766 (mmm) cc_final: 0.6299 (mmm) REVERT: g 120 ASP cc_start: 0.9045 (m-30) cc_final: 0.8741 (m-30) REVERT: g 152 TYR cc_start: 0.7858 (m-80) cc_final: 0.7576 (m-10) REVERT: g 155 ASP cc_start: 0.8067 (t0) cc_final: 0.7669 (t0) REVERT: h 92 LYS cc_start: 0.8455 (mtpt) cc_final: 0.8047 (mtmt) REVERT: h 166 ASN cc_start: 0.9317 (t0) cc_final: 0.8965 (t0) REVERT: h 180 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6421 (pm20) REVERT: j 211 MET cc_start: 0.6571 (tmm) cc_final: 0.6274 (tmm) REVERT: k 90 ASP cc_start: 0.9037 (t70) cc_final: 0.8784 (t70) REVERT: k 203 LYS cc_start: 0.9080 (tmtt) cc_final: 0.8780 (pttt) REVERT: k 228 MET cc_start: 0.7189 (pmm) cc_final: 0.6877 (pmm) REVERT: l 4 ASN cc_start: 0.7739 (t0) cc_final: 0.7418 (m-40) REVERT: l 80 ASP cc_start: 0.8366 (m-30) cc_final: 0.7809 (t0) REVERT: l 88 MET cc_start: 0.8537 (tpp) cc_final: 0.8294 (tpt) REVERT: m 7 TYR cc_start: 0.6271 (m-10) cc_final: 0.6061 (m-10) REVERT: m 27 MET cc_start: 0.8285 (mtt) cc_final: 0.7862 (mmm) REVERT: m 43 ASP cc_start: 0.8401 (p0) cc_final: 0.8033 (m-30) REVERT: m 232 ARG cc_start: 0.8337 (mtp85) cc_final: 0.7789 (mtm-85) REVERT: n 4 MET cc_start: 0.8845 (tpp) cc_final: 0.8587 (tpp) REVERT: n 57 ASP cc_start: 0.9026 (m-30) cc_final: 0.8818 (t70) REVERT: n 119 MET cc_start: 0.8010 (mtt) cc_final: 0.6653 (mtt) REVERT: o 149 GLU cc_start: 0.8707 (tp30) cc_final: 0.8465 (tp30) REVERT: o 157 GLU cc_start: 0.9160 (tt0) cc_final: 0.8890 (mt-10) REVERT: p 28 PHE cc_start: 0.9293 (t80) cc_final: 0.8560 (t80) REVERT: p 95 LEU cc_start: 0.9515 (mt) cc_final: 0.9057 (tp) REVERT: p 158 MET cc_start: 0.7864 (tpp) cc_final: 0.7552 (tpp) REVERT: p 183 MET cc_start: 0.3898 (mtp) cc_final: 0.3456 (ptm) REVERT: q 20 VAL cc_start: 0.7000 (t) cc_final: 0.6574 (t) REVERT: q 35 MET cc_start: 0.5869 (mpp) cc_final: 0.5111 (pmm) REVERT: q 69 MET cc_start: 0.9503 (tpp) cc_final: 0.9179 (tpp) REVERT: q 118 MET cc_start: 0.6997 (mmm) cc_final: 0.6793 (mmm) REVERT: r 2 THR cc_start: 0.7970 (m) cc_final: 0.7765 (m) REVERT: r 93 MET cc_start: 0.8284 (mmm) cc_final: 0.7416 (mtp) REVERT: r 97 MET cc_start: 0.8083 (tmm) cc_final: 0.7573 (tmm) REVERT: r 105 ASP cc_start: 0.8662 (m-30) cc_final: 0.8436 (m-30) REVERT: s 69 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8836 (mm-30) REVERT: s 77 HIS cc_start: 0.8939 (m90) cc_final: 0.8623 (m90) REVERT: s 83 MET cc_start: 0.8230 (ttm) cc_final: 0.8012 (ttp) REVERT: t 3 ASN cc_start: 0.8836 (m-40) cc_final: 0.7547 (p0) REVERT: t 26 MET cc_start: 0.5756 (mmt) cc_final: 0.5389 (mmt) REVERT: t 73 ASP cc_start: 0.8907 (m-30) cc_final: 0.8640 (t70) REVERT: t 96 MET cc_start: 0.8553 (tpp) cc_final: 0.8286 (tpp) REVERT: t 103 MET cc_start: 0.9118 (mmm) cc_final: 0.8898 (mmt) REVERT: t 110 MET cc_start: 0.8446 (mmp) cc_final: 0.8046 (mmm) REVERT: t 133 GLU cc_start: 0.8701 (mt-10) cc_final: 0.7657 (pm20) REVERT: A 138 MET cc_start: 0.5669 (ttp) cc_final: 0.5392 (ttp) REVERT: A 263 MET cc_start: 0.7027 (mtm) cc_final: 0.6432 (ptm) REVERT: A 299 MET cc_start: 0.8264 (tmm) cc_final: 0.7972 (ppp) REVERT: A 318 LEU cc_start: 0.8021 (mt) cc_final: 0.7724 (pt) REVERT: B 184 TYR cc_start: 0.7335 (p90) cc_final: 0.7051 (p90) REVERT: B 270 LEU cc_start: 0.8972 (mt) cc_final: 0.8695 (mt) REVERT: B 272 ARG cc_start: 0.7952 (ttm170) cc_final: 0.7505 (tmt170) REVERT: B 309 MET cc_start: 0.8126 (ptt) cc_final: 0.7763 (ppp) REVERT: B 329 MET cc_start: 0.7934 (tpp) cc_final: 0.7666 (mmt) REVERT: C 121 TYR cc_start: 0.8669 (m-10) cc_final: 0.8335 (m-80) REVERT: C 139 MET cc_start: 0.4362 (mtm) cc_final: 0.3826 (mtp) REVERT: C 230 MET cc_start: 0.7058 (tpp) cc_final: 0.6302 (mmt) REVERT: C 232 ARG cc_start: 0.9317 (ppt170) cc_final: 0.9051 (ttm170) REVERT: C 327 ASP cc_start: 0.8917 (m-30) cc_final: 0.8619 (t70) REVERT: C 368 MET cc_start: 0.8779 (tmm) cc_final: 0.8341 (tmm) REVERT: C 374 ARG cc_start: 0.5735 (tpp-160) cc_final: 0.5130 (mmm160) REVERT: D 89 ILE cc_start: 0.8071 (mm) cc_final: 0.7783 (mm) REVERT: D 98 GLN cc_start: 0.6487 (tp-100) cc_final: 0.6059 (mm-40) REVERT: D 153 MET cc_start: 0.6266 (tmm) cc_final: 0.6053 (tmm) REVERT: D 179 GLU cc_start: 0.8117 (pt0) cc_final: 0.7651 (pp20) REVERT: D 187 HIS cc_start: 0.8128 (m90) cc_final: 0.7879 (m90) REVERT: D 204 MET cc_start: 0.8014 (mtp) cc_final: 0.7783 (ttp) REVERT: D 309 MET cc_start: 0.6669 (mpp) cc_final: 0.5915 (mpp) REVERT: E 56 ILE cc_start: 0.9093 (mm) cc_final: 0.8854 (mt) REVERT: E 108 MET cc_start: 0.8116 (mmp) cc_final: 0.7701 (mmm) REVERT: E 122 MET cc_start: 0.7697 (pmm) cc_final: 0.7309 (pmm) REVERT: E 264 MET cc_start: 0.6915 (mtt) cc_final: 0.6712 (mtt) REVERT: E 272 ARG cc_start: 0.8285 (mtt180) cc_final: 0.7700 (tpp80) REVERT: E 277 MET cc_start: 0.4996 (mpp) cc_final: 0.4219 (mpp) REVERT: F 405 MET cc_start: 0.8092 (mtm) cc_final: 0.7637 (mpp) REVERT: F 421 MET cc_start: 0.6846 (mmp) cc_final: 0.6000 (mtt) REVERT: f 178 LYS cc_start: 0.6051 (mtpt) cc_final: 0.4219 (mmtt) REVERT: f 477 MET cc_start: 0.1260 (ttm) cc_final: -0.0191 (ttp) REVERT: f 505 MET cc_start: -0.0990 (ttm) cc_final: -0.2890 (mtm) REVERT: f 686 LEU cc_start: 0.6752 (mm) cc_final: 0.6272 (tp) outliers start: 14 outliers final: 6 residues processed: 1270 average time/residue: 0.9660 time to fit residues: 2123.3021 Evaluate side-chains 925 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 918 time to evaluate : 9.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1268 random chunks: chunk 1139 optimal weight: 20.0000 chunk 867 optimal weight: 20.0000 chunk 598 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 550 optimal weight: 5.9990 chunk 774 optimal weight: 20.0000 chunk 1157 optimal weight: 1.9990 chunk 1225 optimal weight: 20.0000 chunk 604 optimal weight: 6.9990 chunk 1097 optimal weight: 7.9990 chunk 330 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 901 GLN V 110 HIS ** V 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 256 GLN ** Z 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 23 HIS a 86 GLN a 129 GLN ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 HIS ** c 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 34 ASN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** I 240 HIS J 116 GLN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 94 HIS j 154 HIS j 175 ASN k 155 HIS ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 28 ASN ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 168 GLN ** t 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 213 HIS ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN f 43 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 101622 Z= 0.207 Angle : 0.732 12.709 137458 Z= 0.377 Chirality : 0.046 0.392 15660 Planarity : 0.005 0.082 17770 Dihedral : 7.259 141.895 14082 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.60 % Favored : 90.26 % Rotamer: Outliers : 0.08 % Allowed : 3.48 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.20 % Twisted Proline : 0.45 % Twisted General : 0.11 % 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: -2.28 (0.07), residues: 12738 helix: -0.57 (0.07), residues: 5590 sheet: -0.94 (0.13), residues: 1606 loop : -2.70 (0.08), residues: 5542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP d 61 HIS 0.018 0.001 HIS f 301 PHE 0.058 0.002 PHE U 728 TYR 0.045 0.002 TYR P 147 ARG 0.011 0.001 ARG b 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1218 time to evaluate : 9.182 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: U 128 GLN cc_start: 0.7401 (mm110) cc_final: 0.7196 (tm-30) REVERT: U 362 ASN cc_start: 0.6391 (t0) cc_final: 0.6100 (t0) REVERT: U 556 MET cc_start: 0.7383 (mmp) cc_final: 0.7119 (mmp) REVERT: U 650 TYR cc_start: 0.9038 (t80) cc_final: 0.8812 (t80) REVERT: U 675 MET cc_start: 0.6517 (mmm) cc_final: 0.6290 (mmm) REVERT: U 728 PHE cc_start: 0.8614 (m-80) cc_final: 0.8051 (m-10) REVERT: U 738 ASP cc_start: 0.8827 (m-30) cc_final: 0.8446 (t0) REVERT: U 770 TRP cc_start: 0.6920 (m-90) cc_final: 0.6246 (m-90) REVERT: V 139 MET cc_start: 0.5376 (mmm) cc_final: 0.5086 (ttt) REVERT: V 241 ARG cc_start: 0.5582 (mpp-170) cc_final: 0.4832 (tpp80) REVERT: V 309 MET cc_start: 0.7008 (ptm) cc_final: 0.6588 (ptm) REVERT: V 336 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8241 (mm-30) REVERT: V 358 MET cc_start: 0.5487 (mtp) cc_final: 0.4826 (tpt) REVERT: V 489 MET cc_start: 0.8322 (mmp) cc_final: 0.8035 (mmm) REVERT: W 94 ARG cc_start: 0.4861 (ttt-90) cc_final: 0.4456 (tpm170) REVERT: W 114 GLU cc_start: 0.5508 (tm-30) cc_final: 0.5254 (tt0) REVERT: W 190 MET cc_start: 0.4566 (mpp) cc_final: 0.4273 (mmp) REVERT: W 315 MET cc_start: 0.4665 (pmm) cc_final: 0.1950 (mtt) REVERT: W 352 LYS cc_start: 0.8119 (mmtp) cc_final: 0.7742 (ptmm) REVERT: W 377 ARG cc_start: 0.6815 (ttt90) cc_final: 0.6183 (tpt170) REVERT: W 378 MET cc_start: 0.6653 (tpp) cc_final: 0.6427 (tpp) REVERT: W 428 TRP cc_start: 0.8208 (m100) cc_final: 0.7869 (t-100) REVERT: X 283 GLN cc_start: 0.8103 (mt0) cc_final: 0.7856 (mp10) REVERT: X 337 ARG cc_start: 0.6749 (mtt180) cc_final: 0.6240 (tpm170) REVERT: X 363 ARG cc_start: 0.8215 (mtm110) cc_final: 0.7841 (ttt180) REVERT: X 368 MET cc_start: 0.6766 (mtt) cc_final: 0.5884 (mpp) REVERT: X 402 GLU cc_start: 0.9055 (tp30) cc_final: 0.8848 (tp30) REVERT: X 406 ASN cc_start: 0.9079 (m110) cc_final: 0.8338 (m110) REVERT: Y 40 GLU cc_start: 0.5573 (mm-30) cc_final: 0.5195 (pt0) REVERT: Y 104 MET cc_start: 0.6468 (tmm) cc_final: 0.5452 (ttt) REVERT: Y 245 GLU cc_start: 0.7096 (pm20) cc_final: 0.6531 (tt0) REVERT: Y 319 MET cc_start: 0.6828 (mmm) cc_final: 0.6501 (mmm) REVERT: Y 367 GLN cc_start: 0.8931 (tp-100) cc_final: 0.8188 (mt0) REVERT: Y 379 ARG cc_start: 0.9120 (tpp-160) cc_final: 0.8772 (tpt-90) REVERT: Y 384 SER cc_start: 0.8605 (t) cc_final: 0.8358 (p) REVERT: Y 389 MET cc_start: 0.0260 (ttm) cc_final: -0.0250 (pmm) REVERT: Z 103 LYS cc_start: 0.8220 (tttt) cc_final: 0.7954 (mtpt) REVERT: Z 112 MET cc_start: 0.9389 (mpp) cc_final: 0.9149 (mpp) REVERT: Z 194 GLN cc_start: 0.9282 (mt0) cc_final: 0.8861 (tp-100) REVERT: Z 273 HIS cc_start: 0.8897 (m-70) cc_final: 0.8619 (m90) REVERT: b 42 ARG cc_start: 0.5196 (mpp-170) cc_final: 0.4425 (ttp-170) REVERT: c 54 MET cc_start: 0.5102 (mtp) cc_final: 0.4801 (mtm) REVERT: c 75 MET cc_start: 0.7767 (ttt) cc_final: 0.7289 (tmm) REVERT: c 216 MET cc_start: 0.7354 (ptm) cc_final: 0.6760 (ttp) REVERT: c 226 MET cc_start: 0.8413 (mpp) cc_final: 0.8100 (mpp) REVERT: c 255 TYR cc_start: 0.8248 (m-80) cc_final: 0.8009 (m-80) REVERT: c 260 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8857 (pt0) REVERT: d 1 MET cc_start: 0.3546 (ttt) cc_final: 0.3222 (tpp) REVERT: G 120 ASP cc_start: 0.8912 (m-30) cc_final: 0.8635 (t0) REVERT: G 131 MET cc_start: 0.8209 (mpp) cc_final: 0.7508 (mpp) REVERT: G 159 TYR cc_start: 0.8474 (t80) cc_final: 0.8173 (t80) REVERT: H 39 LYS cc_start: 0.7684 (tmtt) cc_final: 0.7287 (ttpt) REVERT: H 118 MET cc_start: 0.7780 (ttm) cc_final: 0.7206 (ttp) REVERT: H 166 ASN cc_start: 0.8443 (m-40) cc_final: 0.8080 (m-40) REVERT: H 169 ASN cc_start: 0.8557 (m110) cc_final: 0.7866 (t0) REVERT: I 57 ASP cc_start: 0.6761 (m-30) cc_final: 0.6479 (m-30) REVERT: J 24 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8485 (mt-10) REVERT: J 175 ASN cc_start: 0.8546 (m-40) cc_final: 0.8219 (t0) REVERT: J 211 MET cc_start: 0.7815 (mmm) cc_final: 0.7386 (mmm) REVERT: K 59 MET cc_start: 0.6679 (mtm) cc_final: 0.6331 (mtm) REVERT: K 76 CYS cc_start: 0.4181 (t) cc_final: 0.3580 (t) REVERT: K 78 MET cc_start: 0.6802 (ppp) cc_final: 0.6477 (ppp) REVERT: K 84 ASP cc_start: 0.7078 (m-30) cc_final: 0.6158 (p0) REVERT: K 137 PHE cc_start: 0.8596 (m-10) cc_final: 0.8217 (m-80) REVERT: L 84 LEU cc_start: 0.8998 (tt) cc_final: 0.8787 (tt) REVERT: L 88 MET cc_start: 0.9295 (tpp) cc_final: 0.8858 (ptm) REVERT: L 152 ASN cc_start: 0.9014 (m-40) cc_final: 0.8405 (p0) REVERT: L 180 MET cc_start: 0.8405 (tpp) cc_final: 0.7857 (tpt) REVERT: M 117 MET cc_start: 0.8953 (ptp) cc_final: 0.8577 (ptp) REVERT: M 137 LEU cc_start: 0.8996 (tp) cc_final: 0.8749 (tp) REVERT: M 177 GLU cc_start: 0.8807 (pt0) cc_final: 0.8008 (tp30) REVERT: M 197 ILE cc_start: 0.8076 (mm) cc_final: 0.7672 (tp) REVERT: O 146 MET cc_start: 0.7809 (ttm) cc_final: 0.7240 (ttm) REVERT: P 59 ASP cc_start: 0.8633 (m-30) cc_final: 0.8356 (t0) REVERT: P 90 MET cc_start: 0.8725 (mtm) cc_final: 0.8176 (mmm) REVERT: P 117 PHE cc_start: 0.7033 (p90) cc_final: 0.6775 (p90) REVERT: P 126 LEU cc_start: 0.9115 (pp) cc_final: 0.8267 (tt) REVERT: P 149 MET cc_start: 0.5690 (mmm) cc_final: 0.5178 (tpp) REVERT: P 171 MET cc_start: 0.9157 (tpp) cc_final: 0.8542 (tpp) REVERT: Q 2 GLU cc_start: 0.8478 (pm20) cc_final: 0.7424 (pp20) REVERT: Q 4 LEU cc_start: 0.8629 (mt) cc_final: 0.8253 (mt) REVERT: Q 31 ASP cc_start: 0.8613 (p0) cc_final: 0.8201 (m-30) REVERT: Q 62 LYS cc_start: 0.9108 (tmmt) cc_final: 0.8857 (tmmt) REVERT: Q 82 ASN cc_start: 0.8974 (t0) cc_final: 0.8594 (t0) REVERT: Q 102 LEU cc_start: 0.9111 (mp) cc_final: 0.8859 (mm) REVERT: R 35 ILE cc_start: 0.9258 (mm) cc_final: 0.9021 (mm) REVERT: R 71 LYS cc_start: 0.8717 (mtpp) cc_final: 0.8374 (tppt) REVERT: R 93 MET cc_start: 0.8175 (mtm) cc_final: 0.7471 (mpp) REVERT: R 100 MET cc_start: 0.8324 (mpp) cc_final: 0.7662 (mpp) REVERT: R 190 ASP cc_start: 0.7712 (m-30) cc_final: 0.7090 (p0) REVERT: S 144 MET cc_start: 0.8925 (mtt) cc_final: 0.8233 (tpt) REVERT: S 145 LEU cc_start: 0.9619 (mt) cc_final: 0.9357 (mt) REVERT: T 7 THR cc_start: 0.8513 (p) cc_final: 0.8209 (t) REVERT: T 26 MET cc_start: 0.8502 (mtp) cc_final: 0.7845 (mpp) REVERT: T 96 MET cc_start: 0.9583 (mmm) cc_final: 0.9192 (mmp) REVERT: T 110 MET cc_start: 0.8963 (mtp) cc_final: 0.8448 (mmm) REVERT: T 160 LEU cc_start: 0.8528 (tp) cc_final: 0.8276 (tp) REVERT: T 168 LEU cc_start: 0.9236 (tt) cc_final: 0.8983 (pp) REVERT: T 180 ASP cc_start: 0.8266 (t0) cc_final: 0.7721 (t0) REVERT: T 187 PHE cc_start: 0.8654 (p90) cc_final: 0.8105 (p90) REVERT: g 80 MET cc_start: 0.6616 (mmm) cc_final: 0.6127 (mmm) REVERT: g 120 ASP cc_start: 0.8942 (m-30) cc_final: 0.8633 (m-30) REVERT: g 152 TYR cc_start: 0.7811 (m-80) cc_final: 0.7547 (m-10) REVERT: g 155 ASP cc_start: 0.8074 (t0) cc_final: 0.7679 (t0) REVERT: g 159 TYR cc_start: 0.7540 (t80) cc_final: 0.6765 (t80) REVERT: h 79 MET cc_start: 0.5367 (ppp) cc_final: 0.5148 (ppp) REVERT: h 92 LYS cc_start: 0.8489 (mtpt) cc_final: 0.8118 (mtmm) REVERT: h 166 ASN cc_start: 0.9315 (t0) cc_final: 0.8969 (t0) REVERT: j 117 ARG cc_start: 0.9426 (ttt90) cc_final: 0.9120 (ttm-80) REVERT: j 211 MET cc_start: 0.6656 (tmm) cc_final: 0.6181 (tmm) REVERT: k 90 ASP cc_start: 0.9083 (t70) cc_final: 0.8801 (t70) REVERT: k 203 LYS cc_start: 0.9082 (tmtt) cc_final: 0.8819 (pttt) REVERT: k 204 GLN cc_start: 0.8469 (mt0) cc_final: 0.7651 (tp40) REVERT: l 4 ASN cc_start: 0.7693 (t0) cc_final: 0.7397 (m-40) REVERT: l 62 LYS cc_start: 0.7182 (mmtt) cc_final: 0.6751 (mptt) REVERT: l 80 ASP cc_start: 0.8368 (m-30) cc_final: 0.7737 (t0) REVERT: l 88 MET cc_start: 0.8521 (tpp) cc_final: 0.8295 (tpt) REVERT: m 7 TYR cc_start: 0.6566 (m-10) cc_final: 0.6359 (m-10) REVERT: m 27 MET cc_start: 0.8275 (mtt) cc_final: 0.7847 (mmm) REVERT: m 43 ASP cc_start: 0.8349 (p0) cc_final: 0.8041 (m-30) REVERT: m 75 MET cc_start: 0.9013 (mtp) cc_final: 0.8608 (mtm) REVERT: m 136 MET cc_start: 0.9092 (mmt) cc_final: 0.8785 (mmt) REVERT: n 4 MET cc_start: 0.8825 (tpp) cc_final: 0.8495 (tpp) REVERT: n 51 ASP cc_start: 0.8610 (m-30) cc_final: 0.8217 (p0) REVERT: n 86 MET cc_start: 0.8745 (ttm) cc_final: 0.8374 (ttp) REVERT: o 149 GLU cc_start: 0.8683 (tp30) cc_final: 0.8394 (tp30) REVERT: o 157 GLU cc_start: 0.9139 (tt0) cc_final: 0.8914 (mt-10) REVERT: p 28 PHE cc_start: 0.9326 (t80) cc_final: 0.8748 (t80) REVERT: p 56 LEU cc_start: 0.9337 (tp) cc_final: 0.9039 (mt) REVERT: p 95 LEU cc_start: 0.9436 (mt) cc_final: 0.8910 (tp) REVERT: p 96 TYR cc_start: 0.8359 (t80) cc_final: 0.7972 (t80) REVERT: p 127 ILE cc_start: 0.8999 (tp) cc_final: 0.8665 (tp) REVERT: p 158 MET cc_start: 0.8069 (tpp) cc_final: 0.7727 (tpp) REVERT: p 183 MET cc_start: 0.3711 (mtp) cc_final: 0.3493 (mtp) REVERT: q 20 VAL cc_start: 0.7004 (t) cc_final: 0.6383 (t) REVERT: q 35 MET cc_start: 0.5782 (mpp) cc_final: 0.5029 (pmm) REVERT: q 69 MET cc_start: 0.9536 (tpp) cc_final: 0.9230 (tpp) REVERT: r 2 THR cc_start: 0.8003 (m) cc_final: 0.7795 (m) REVERT: r 97 MET cc_start: 0.8041 (tmm) cc_final: 0.7581 (tmm) REVERT: r 105 ASP cc_start: 0.8778 (m-30) cc_final: 0.8541 (m-30) REVERT: s 69 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8884 (mm-30) REVERT: s 77 HIS cc_start: 0.8949 (m90) cc_final: 0.8689 (m90) REVERT: t 3 ASN cc_start: 0.8826 (m-40) cc_final: 0.8160 (t0) REVERT: t 60 PHE cc_start: 0.8682 (t80) cc_final: 0.8441 (t80) REVERT: t 73 ASP cc_start: 0.8868 (m-30) cc_final: 0.8506 (t70) REVERT: t 96 MET cc_start: 0.8539 (tpp) cc_final: 0.8287 (tpp) REVERT: A 138 MET cc_start: 0.5524 (ttp) cc_final: 0.5144 (ttp) REVERT: A 263 MET cc_start: 0.7094 (mtm) cc_final: 0.6416 (ptm) REVERT: A 273 PHE cc_start: 0.6730 (m-10) cc_final: 0.6455 (m-10) REVERT: A 299 MET cc_start: 0.8180 (tmm) cc_final: 0.7969 (ppp) REVERT: B 272 ARG cc_start: 0.7994 (ttm170) cc_final: 0.7491 (tmt170) REVERT: B 309 MET cc_start: 0.8156 (ptt) cc_final: 0.7775 (ppp) REVERT: B 329 MET cc_start: 0.8100 (mmp) cc_final: 0.7725 (mmp) REVERT: C 121 TYR cc_start: 0.8655 (m-10) cc_final: 0.8297 (m-80) REVERT: C 139 MET cc_start: 0.4404 (mtm) cc_final: 0.3951 (mtt) REVERT: C 230 MET cc_start: 0.6999 (tpp) cc_final: 0.6793 (mmt) REVERT: C 232 ARG cc_start: 0.9266 (ppt170) cc_final: 0.9045 (ttm170) REVERT: C 327 ASP cc_start: 0.8913 (m-30) cc_final: 0.8644 (t70) REVERT: C 374 ARG cc_start: 0.5945 (tpp-160) cc_final: 0.5258 (mmm160) REVERT: D 89 ILE cc_start: 0.8036 (mm) cc_final: 0.7730 (mm) REVERT: D 98 GLN cc_start: 0.6167 (tp-100) cc_final: 0.5897 (mm-40) REVERT: D 187 HIS cc_start: 0.8135 (m90) cc_final: 0.7869 (m90) REVERT: D 309 MET cc_start: 0.6839 (mpp) cc_final: 0.6047 (mpp) REVERT: D 384 MET cc_start: 0.8678 (ttt) cc_final: 0.8414 (ppp) REVERT: E 56 ILE cc_start: 0.9046 (mm) cc_final: 0.8841 (mt) REVERT: E 108 MET cc_start: 0.8058 (mmp) cc_final: 0.7651 (mmm) REVERT: E 122 MET cc_start: 0.7593 (pmm) cc_final: 0.7158 (pmm) REVERT: E 232 MET cc_start: 0.8998 (ttt) cc_final: 0.8768 (ttm) REVERT: E 277 MET cc_start: 0.4021 (mpp) cc_final: 0.2531 (mpp) REVERT: F 373 MET cc_start: 0.6255 (mpp) cc_final: 0.6027 (mpp) REVERT: F 405 MET cc_start: 0.7864 (mtm) cc_final: 0.7520 (mpp) REVERT: F 421 MET cc_start: 0.6805 (mmp) cc_final: 0.6088 (mtt) REVERT: F 425 LEU cc_start: 0.8853 (mp) cc_final: 0.8562 (tt) REVERT: f 222 ASP cc_start: 0.0933 (m-30) cc_final: 0.0501 (t70) REVERT: f 407 MET cc_start: 0.5073 (mmt) cc_final: 0.4521 (mmt) REVERT: f 477 MET cc_start: 0.1436 (ttm) cc_final: -0.0050 (ttp) REVERT: f 505 MET cc_start: -0.0935 (ttm) cc_final: -0.2723 (mtm) REVERT: f 670 MET cc_start: -0.1516 (tmm) cc_final: -0.2095 (tmm) REVERT: f 686 LEU cc_start: 0.6808 (mm) cc_final: 0.6403 (tp) outliers start: 8 outliers final: 5 residues processed: 1224 average time/residue: 0.9123 time to fit residues: 1934.2307 Evaluate side-chains 919 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 914 time to evaluate : 9.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1268 random chunks: chunk 1020 optimal weight: 7.9990 chunk 695 optimal weight: 7.9990 chunk 17 optimal weight: 30.0000 chunk 912 optimal weight: 8.9990 chunk 505 optimal weight: 20.0000 chunk 1045 optimal weight: 30.0000 chunk 847 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 625 optimal weight: 7.9990 chunk 1100 optimal weight: 0.1980 chunk 309 optimal weight: 0.8980 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 421 GLN ** U 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 901 GLN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 HIS ** V 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 288 HIS ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 367 GLN X 405 GLN ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 306 GLN Y 378 ASN ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 174 HIS Z 224 HIS Z 256 GLN ** Z 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 23 HIS a 129 GLN ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN ** 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** I 240 HIS J 92 GLN K 23 GLN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 190 HIS ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 169 GLN P 188 HIS ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 94 HIS ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 213 HIS ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 329 ASN f 747 GLN ** f 782 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 101622 Z= 0.197 Angle : 0.708 11.485 137458 Z= 0.365 Chirality : 0.045 0.260 15660 Planarity : 0.005 0.096 17770 Dihedral : 7.042 141.230 14082 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.63 % Favored : 90.26 % Rotamer: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.20 % Twisted Proline : 0.45 % Twisted General : 0.10 % 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: -2.05 (0.07), residues: 12738 helix: -0.38 (0.07), residues: 5622 sheet: -0.79 (0.13), residues: 1611 loop : -2.59 (0.08), residues: 5505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP d 61 HIS 0.017 0.001 HIS f 301 PHE 0.041 0.002 PHE U 728 TYR 0.029 0.002 TYR P 147 ARG 0.024 0.000 ARG C 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1168 time to evaluate : 9.307 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: U 362 ASN cc_start: 0.6465 (t0) cc_final: 0.6020 (t0) REVERT: U 560 MET cc_start: 0.8139 (mmp) cc_final: 0.7604 (tpt) REVERT: U 588 MET cc_start: 0.8705 (ttp) cc_final: 0.8433 (ttm) REVERT: U 650 TYR cc_start: 0.9066 (t80) cc_final: 0.8799 (t80) REVERT: U 675 MET cc_start: 0.6265 (mmt) cc_final: 0.5759 (mtp) REVERT: U 728 PHE cc_start: 0.8645 (m-80) cc_final: 0.8143 (m-10) REVERT: U 738 ASP cc_start: 0.8857 (m-30) cc_final: 0.8473 (t0) REVERT: U 770 TRP cc_start: 0.7093 (m-90) cc_final: 0.6337 (m-90) REVERT: V 40 GLU cc_start: 0.0657 (OUTLIER) cc_final: 0.0250 (tt0) REVERT: V 139 MET cc_start: 0.5413 (mmm) cc_final: 0.5029 (ttp) REVERT: V 241 ARG cc_start: 0.5687 (mpp-170) cc_final: 0.5121 (ttt180) REVERT: V 309 MET cc_start: 0.6962 (ptm) cc_final: 0.6544 (ptm) REVERT: V 311 ASN cc_start: 0.7474 (t0) cc_final: 0.6967 (t0) REVERT: V 336 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8268 (mm-30) REVERT: V 489 MET cc_start: 0.8255 (mmp) cc_final: 0.7948 (mmm) REVERT: W 73 MET cc_start: 0.8930 (mmm) cc_final: 0.8637 (mmm) REVERT: W 94 ARG cc_start: 0.5065 (ttt-90) cc_final: 0.4540 (tpm170) REVERT: W 114 GLU cc_start: 0.5515 (tm-30) cc_final: 0.5262 (tt0) REVERT: W 190 MET cc_start: 0.4596 (mpp) cc_final: 0.4359 (mmm) REVERT: W 315 MET cc_start: 0.5035 (pmm) cc_final: 0.2024 (mtt) REVERT: W 352 LYS cc_start: 0.8147 (mmtp) cc_final: 0.7780 (ptmm) REVERT: W 377 ARG cc_start: 0.6933 (ttt90) cc_final: 0.6276 (tpt170) REVERT: W 428 TRP cc_start: 0.8244 (m100) cc_final: 0.7188 (t60) REVERT: X 283 GLN cc_start: 0.8050 (mt0) cc_final: 0.7801 (mp10) REVERT: X 337 ARG cc_start: 0.6759 (mtt180) cc_final: 0.6202 (tpm170) REVERT: X 363 ARG cc_start: 0.8212 (mtm110) cc_final: 0.7760 (ttt180) REVERT: X 402 GLU cc_start: 0.9057 (tp30) cc_final: 0.8708 (tp30) REVERT: X 406 ASN cc_start: 0.9163 (m110) cc_final: 0.8321 (m110) REVERT: Y 104 MET cc_start: 0.6466 (tmm) cc_final: 0.5464 (ttt) REVERT: Y 245 GLU cc_start: 0.7079 (pm20) cc_final: 0.6502 (tt0) REVERT: Y 319 MET cc_start: 0.6856 (mmm) cc_final: 0.6538 (mmm) REVERT: Y 367 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8303 (mt0) REVERT: Y 379 ARG cc_start: 0.9158 (tpp-160) cc_final: 0.8765 (ttt90) REVERT: Y 384 SER cc_start: 0.8608 (t) cc_final: 0.8384 (p) REVERT: Y 389 MET cc_start: 0.0361 (ttm) cc_final: 0.0087 (pmm) REVERT: Z 78 MET cc_start: 0.8405 (mtt) cc_final: 0.8022 (mtt) REVERT: Z 81 MET cc_start: 0.9070 (ttp) cc_final: 0.8860 (tmm) REVERT: Z 103 LYS cc_start: 0.8153 (tttt) cc_final: 0.7881 (mtpt) REVERT: Z 112 MET cc_start: 0.9412 (mpp) cc_final: 0.9118 (mpp) REVERT: Z 194 GLN cc_start: 0.9307 (mt0) cc_final: 0.8888 (tp-100) REVERT: Z 273 HIS cc_start: 0.8963 (m-70) cc_final: 0.8706 (m90) REVERT: b 42 ARG cc_start: 0.5202 (mpp-170) cc_final: 0.4420 (ttp-170) REVERT: c 54 MET cc_start: 0.5211 (mtp) cc_final: 0.4907 (mtm) REVERT: c 75 MET cc_start: 0.7788 (ttt) cc_final: 0.7333 (tmm) REVERT: c 216 MET cc_start: 0.7334 (ptm) cc_final: 0.6746 (ttp) REVERT: c 226 MET cc_start: 0.8336 (mpp) cc_final: 0.8052 (mpp) REVERT: c 255 TYR cc_start: 0.8243 (m-80) cc_final: 0.7994 (m-80) REVERT: c 260 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8890 (pt0) REVERT: d 1 MET cc_start: 0.3498 (ttt) cc_final: 0.3211 (tpp) REVERT: d 230 GLN cc_start: 0.7352 (tp40) cc_final: 0.7030 (mp10) REVERT: G 120 ASP cc_start: 0.8903 (m-30) cc_final: 0.8601 (t0) REVERT: G 131 MET cc_start: 0.8140 (mpp) cc_final: 0.7407 (mpp) REVERT: H 39 LYS cc_start: 0.7622 (tmtt) cc_final: 0.7213 (ttpt) REVERT: H 166 ASN cc_start: 0.8419 (m-40) cc_final: 0.8025 (m-40) REVERT: H 169 ASN cc_start: 0.8554 (m110) cc_final: 0.7854 (t0) REVERT: I 18 LEU cc_start: 0.8357 (mt) cc_final: 0.7760 (mt) REVERT: I 57 ASP cc_start: 0.6879 (m-30) cc_final: 0.6342 (m-30) REVERT: J 3 TYR cc_start: 0.7669 (m-10) cc_final: 0.7448 (m-80) REVERT: J 71 MET cc_start: 0.8188 (tpt) cc_final: 0.7767 (tpp) REVERT: J 175 ASN cc_start: 0.8557 (m-40) cc_final: 0.8220 (t0) REVERT: J 211 MET cc_start: 0.8021 (mmm) cc_final: 0.7447 (mmm) REVERT: K 59 MET cc_start: 0.6609 (mtm) cc_final: 0.6286 (mtm) REVERT: K 78 MET cc_start: 0.6793 (ppp) cc_final: 0.6517 (ppp) REVERT: L 88 MET cc_start: 0.9294 (tpp) cc_final: 0.8868 (ptm) REVERT: L 100 ASP cc_start: 0.9509 (t0) cc_final: 0.9110 (m-30) REVERT: L 190 HIS cc_start: 0.8194 (m90) cc_final: 0.7980 (m-70) REVERT: M 137 LEU cc_start: 0.8974 (tp) cc_final: 0.8659 (tp) REVERT: M 140 TYR cc_start: 0.7435 (t80) cc_final: 0.7232 (t80) REVERT: M 177 GLU cc_start: 0.8816 (pt0) cc_final: 0.7962 (tp30) REVERT: M 197 ILE cc_start: 0.8019 (mm) cc_final: 0.7626 (tp) REVERT: N 51 ASP cc_start: 0.8955 (m-30) cc_final: 0.8680 (m-30) REVERT: N 84 LYS cc_start: 0.9425 (tmmt) cc_final: 0.9210 (tttt) REVERT: N 164 MET cc_start: 0.7226 (mtm) cc_final: 0.6939 (mtt) REVERT: O 146 MET cc_start: 0.7883 (ttm) cc_final: 0.7250 (ttm) REVERT: P 14 MET cc_start: 0.8171 (tpp) cc_final: 0.7964 (mmm) REVERT: P 59 ASP cc_start: 0.8624 (m-30) cc_final: 0.8389 (t0) REVERT: P 90 MET cc_start: 0.8754 (mtm) cc_final: 0.8205 (mmm) REVERT: P 117 PHE cc_start: 0.7029 (p90) cc_final: 0.6740 (p90) REVERT: P 126 LEU cc_start: 0.9070 (pp) cc_final: 0.8128 (tt) REVERT: P 149 MET cc_start: 0.5610 (mmm) cc_final: 0.5034 (tpp) REVERT: Q 2 GLU cc_start: 0.8428 (pm20) cc_final: 0.7379 (pp20) REVERT: Q 4 LEU cc_start: 0.8406 (mt) cc_final: 0.8132 (mt) REVERT: Q 31 ASP cc_start: 0.8559 (p0) cc_final: 0.8180 (m-30) REVERT: Q 82 ASN cc_start: 0.8982 (t0) cc_final: 0.8602 (t0) REVERT: Q 102 LEU cc_start: 0.9150 (mp) cc_final: 0.8920 (mm) REVERT: R 35 ILE cc_start: 0.9216 (mm) cc_final: 0.8708 (mm) REVERT: R 71 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8434 (tppt) REVERT: R 100 MET cc_start: 0.8280 (mpp) cc_final: 0.7631 (mpp) REVERT: S 144 MET cc_start: 0.8832 (mtt) cc_final: 0.8262 (tpt) REVERT: S 145 LEU cc_start: 0.9625 (mt) cc_final: 0.9358 (mt) REVERT: T 7 THR cc_start: 0.8555 (p) cc_final: 0.8255 (t) REVERT: T 26 MET cc_start: 0.8529 (mtp) cc_final: 0.7819 (mpp) REVERT: T 96 MET cc_start: 0.9376 (mmm) cc_final: 0.8982 (tpp) REVERT: T 110 MET cc_start: 0.8822 (mtp) cc_final: 0.8581 (mmm) REVERT: T 127 MET cc_start: 0.8566 (mtm) cc_final: 0.7877 (mtm) REVERT: T 160 LEU cc_start: 0.8508 (tp) cc_final: 0.8251 (tp) REVERT: T 168 LEU cc_start: 0.9243 (tt) cc_final: 0.8988 (pp) REVERT: T 180 ASP cc_start: 0.8193 (t0) cc_final: 0.7686 (t0) REVERT: T 187 PHE cc_start: 0.8629 (p90) cc_final: 0.8120 (p90) REVERT: g 80 MET cc_start: 0.6544 (mmm) cc_final: 0.5339 (mmm) REVERT: g 93 ARG cc_start: 0.9091 (mtm-85) cc_final: 0.8805 (mtt180) REVERT: g 120 ASP cc_start: 0.8968 (m-30) cc_final: 0.8637 (m-30) REVERT: g 152 TYR cc_start: 0.7756 (m-80) cc_final: 0.7489 (m-10) REVERT: g 155 ASP cc_start: 0.8130 (t0) cc_final: 0.7735 (t0) REVERT: g 159 TYR cc_start: 0.7568 (t80) cc_final: 0.6876 (t80) REVERT: h 79 MET cc_start: 0.5566 (ppp) cc_final: 0.5305 (ppp) REVERT: h 92 LYS cc_start: 0.8492 (mtpt) cc_final: 0.8044 (mtmm) REVERT: h 166 ASN cc_start: 0.9307 (t0) cc_final: 0.8959 (t0) REVERT: j 117 ARG cc_start: 0.9411 (ttt90) cc_final: 0.9166 (ttm-80) REVERT: j 211 MET cc_start: 0.6708 (tmm) cc_final: 0.6073 (tmm) REVERT: k 59 MET cc_start: 0.7990 (ptm) cc_final: 0.7692 (ptp) REVERT: k 90 ASP cc_start: 0.9070 (t70) cc_final: 0.8791 (t70) REVERT: k 103 TYR cc_start: 0.8938 (m-80) cc_final: 0.8423 (m-80) REVERT: k 203 LYS cc_start: 0.9057 (tmtt) cc_final: 0.8819 (pttt) REVERT: k 228 MET cc_start: 0.7206 (pmm) cc_final: 0.6869 (pmm) REVERT: l 62 LYS cc_start: 0.7235 (mmtt) cc_final: 0.6797 (mptt) REVERT: l 80 ASP cc_start: 0.8373 (m-30) cc_final: 0.7649 (t0) REVERT: l 88 MET cc_start: 0.8537 (tpp) cc_final: 0.8159 (tpt) REVERT: m 7 TYR cc_start: 0.6605 (m-10) cc_final: 0.6238 (m-10) REVERT: m 27 MET cc_start: 0.8296 (mtt) cc_final: 0.7852 (mmm) REVERT: m 43 ASP cc_start: 0.8337 (p0) cc_final: 0.8053 (m-30) REVERT: m 75 MET cc_start: 0.8919 (mtp) cc_final: 0.8451 (ptp) REVERT: m 136 MET cc_start: 0.8960 (mmt) cc_final: 0.8666 (mmt) REVERT: m 232 ARG cc_start: 0.8228 (mtt180) cc_final: 0.6604 (mtm-85) REVERT: n 86 MET cc_start: 0.8739 (ttm) cc_final: 0.8354 (ttp) REVERT: n 119 MET cc_start: 0.8342 (mtt) cc_final: 0.8117 (mtt) REVERT: o 149 GLU cc_start: 0.8696 (tp30) cc_final: 0.8407 (tp30) REVERT: p 28 PHE cc_start: 0.9350 (t80) cc_final: 0.8864 (t80) REVERT: p 56 LEU cc_start: 0.9349 (tp) cc_final: 0.9015 (mt) REVERT: p 95 LEU cc_start: 0.9364 (mt) cc_final: 0.8870 (tp) REVERT: p 96 TYR cc_start: 0.8446 (t80) cc_final: 0.8236 (t80) REVERT: p 127 ILE cc_start: 0.8959 (tp) cc_final: 0.8673 (tp) REVERT: p 158 MET cc_start: 0.8196 (tpp) cc_final: 0.7639 (tpp) REVERT: q 20 VAL cc_start: 0.6841 (t) cc_final: 0.6233 (t) REVERT: q 35 MET cc_start: 0.5780 (mpp) cc_final: 0.4980 (pmm) REVERT: q 62 LYS cc_start: 0.9221 (mmmt) cc_final: 0.8883 (mmmm) REVERT: q 69 MET cc_start: 0.9599 (tpp) cc_final: 0.9316 (tpp) REVERT: q 118 MET cc_start: 0.7613 (mmm) cc_final: 0.7311 (mmm) REVERT: q 144 ASP cc_start: 0.8483 (t0) cc_final: 0.8280 (t70) REVERT: r 2 THR cc_start: 0.7987 (m) cc_final: 0.7743 (m) REVERT: r 55 TRP cc_start: 0.9018 (m100) cc_final: 0.8342 (m100) REVERT: r 93 MET cc_start: 0.8112 (mmm) cc_final: 0.7411 (mtp) REVERT: r 97 MET cc_start: 0.8089 (tmm) cc_final: 0.7618 (tmm) REVERT: t 3 ASN cc_start: 0.8821 (m-40) cc_final: 0.7949 (t0) REVERT: t 73 ASP cc_start: 0.8865 (m-30) cc_final: 0.8521 (t70) REVERT: t 110 MET cc_start: 0.8544 (mmp) cc_final: 0.8049 (mmm) REVERT: t 173 MET cc_start: 0.8949 (tpp) cc_final: 0.8089 (mmt) REVERT: A 138 MET cc_start: 0.5464 (ttp) cc_final: 0.5153 (ttp) REVERT: A 263 MET cc_start: 0.7059 (mtm) cc_final: 0.6353 (ptm) REVERT: A 273 PHE cc_start: 0.6761 (m-10) cc_final: 0.6433 (m-10) REVERT: A 299 MET cc_start: 0.8277 (tmm) cc_final: 0.7976 (ppp) REVERT: B 272 ARG cc_start: 0.8008 (ttm170) cc_final: 0.7431 (tmt170) REVERT: B 309 MET cc_start: 0.8209 (ptt) cc_final: 0.7812 (ppp) REVERT: B 329 MET cc_start: 0.8272 (mmp) cc_final: 0.7818 (mmp) REVERT: C 121 TYR cc_start: 0.8651 (m-10) cc_final: 0.8286 (m-80) REVERT: C 139 MET cc_start: 0.4423 (mtm) cc_final: 0.3763 (ttm) REVERT: C 229 ARG cc_start: 0.7514 (mpp-170) cc_final: 0.6421 (mmp-170) REVERT: C 230 MET cc_start: 0.7272 (tpp) cc_final: 0.6797 (mmt) REVERT: C 232 ARG cc_start: 0.9233 (ppt170) cc_final: 0.8999 (ttm170) REVERT: C 327 ASP cc_start: 0.8896 (m-30) cc_final: 0.8628 (t70) REVERT: C 368 MET cc_start: 0.8841 (tmm) cc_final: 0.8625 (tmm) REVERT: C 374 ARG cc_start: 0.5868 (tpp-160) cc_final: 0.5147 (mmm160) REVERT: D 89 ILE cc_start: 0.8041 (mm) cc_final: 0.7730 (mm) REVERT: D 187 HIS cc_start: 0.8158 (m90) cc_final: 0.7885 (m90) REVERT: D 309 MET cc_start: 0.6542 (mpp) cc_final: 0.6184 (mpp) REVERT: D 316 THR cc_start: 0.7099 (p) cc_final: 0.6808 (t) REVERT: D 384 MET cc_start: 0.8671 (ttt) cc_final: 0.8435 (ppp) REVERT: E 56 ILE cc_start: 0.9015 (mm) cc_final: 0.8800 (mt) REVERT: E 108 MET cc_start: 0.7943 (mmp) cc_final: 0.7319 (mmm) REVERT: E 122 MET cc_start: 0.7603 (pmm) cc_final: 0.7142 (pmm) REVERT: E 277 MET cc_start: 0.4247 (mpp) cc_final: 0.3190 (mpp) REVERT: E 376 ASP cc_start: 0.8949 (t70) cc_final: 0.8552 (p0) REVERT: F 373 MET cc_start: 0.6248 (mpp) cc_final: 0.6037 (mpp) REVERT: F 405 MET cc_start: 0.7849 (mtm) cc_final: 0.7540 (mpp) REVERT: F 421 MET cc_start: 0.7013 (mmp) cc_final: 0.6335 (mtt) REVERT: f 178 LYS cc_start: 0.5961 (mtpt) cc_final: 0.5424 (tttm) REVERT: f 222 ASP cc_start: 0.0590 (m-30) cc_final: -0.0562 (p0) REVERT: f 407 MET cc_start: 0.5123 (mmt) cc_final: 0.4574 (mmt) REVERT: f 477 MET cc_start: 0.1444 (ttm) cc_final: -0.0081 (ttp) REVERT: f 505 MET cc_start: -0.0153 (ttp) cc_final: -0.2522 (mtm) REVERT: f 670 MET cc_start: -0.2085 (tmm) cc_final: -0.2291 (tmm) outliers start: 6 outliers final: 3 residues processed: 1174 average time/residue: 0.8898 time to fit residues: 1807.3483 Evaluate side-chains 905 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 901 time to evaluate : 9.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1268 random chunks: chunk 412 optimal weight: 5.9990 chunk 1103 optimal weight: 0.8980 chunk 242 optimal weight: 5.9990 chunk 719 optimal weight: 20.0000 chunk 302 optimal weight: 0.0170 chunk 1226 optimal weight: 20.0000 chunk 1018 optimal weight: 30.0000 chunk 568 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 405 optimal weight: 8.9990 chunk 644 optimal weight: 10.0000 overall best weight: 4.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 HIS ** V 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 242 HIS V 257 ASN ** V 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 218 ASN W 288 HIS W 362 ASN ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 367 GLN ** X 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 406 ASN ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 129 GLN ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 199 HIS ** c 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN ** 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 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 GLN ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 GLN ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 102 GLN ** h 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 94 HIS j 116 GLN k 155 HIS ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 168 GLN ** t 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 213 HIS ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 224 ASN f 378 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 101622 Z= 0.204 Angle : 0.709 13.092 137458 Z= 0.366 Chirality : 0.046 0.282 15660 Planarity : 0.005 0.089 17770 Dihedral : 6.916 139.886 14082 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.75 % Favored : 90.17 % Rotamer: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.20 % Twisted Proline : 0.45 % Twisted General : 0.10 % 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: 12738 helix: -0.24 (0.07), residues: 5615 sheet: -0.72 (0.13), residues: 1620 loop : -2.53 (0.08), residues: 5503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP d 61 HIS 0.021 0.001 HIS b 105 PHE 0.033 0.002 PHE U 728 TYR 0.031 0.002 TYR Y 54 ARG 0.017 0.001 ARG U 600 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1149 time to evaluate : 9.374 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: U 362 ASN cc_start: 0.6605 (t0) cc_final: 0.6239 (t0) REVERT: U 532 MET cc_start: 0.5266 (mtt) cc_final: 0.4942 (mpp) REVERT: U 650 TYR cc_start: 0.9025 (t80) cc_final: 0.8783 (t80) REVERT: U 728 PHE cc_start: 0.8633 (m-80) cc_final: 0.8121 (m-10) REVERT: U 738 ASP cc_start: 0.8847 (m-30) cc_final: 0.8311 (t0) REVERT: U 770 TRP cc_start: 0.7282 (m-90) cc_final: 0.6511 (m-90) REVERT: V 139 MET cc_start: 0.5452 (mmm) cc_final: 0.5079 (ttp) REVERT: V 309 MET cc_start: 0.7051 (ptm) cc_final: 0.6653 (ptm) REVERT: V 336 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8253 (mm-30) REVERT: W 94 ARG cc_start: 0.4952 (ttt-90) cc_final: 0.4471 (tpm170) REVERT: W 114 GLU cc_start: 0.5625 (tm-30) cc_final: 0.5398 (tt0) REVERT: W 190 MET cc_start: 0.4689 (mpp) cc_final: 0.4323 (mmp) REVERT: W 315 MET cc_start: 0.4607 (pmm) cc_final: 0.1749 (mmm) REVERT: W 326 MET cc_start: 0.7822 (mtm) cc_final: 0.7583 (mpp) REVERT: W 352 LYS cc_start: 0.8171 (mmtp) cc_final: 0.7831 (ptmm) REVERT: W 377 ARG cc_start: 0.6928 (ttt90) cc_final: 0.6243 (tpt170) REVERT: W 426 ASN cc_start: 0.9009 (m110) cc_final: 0.8783 (t0) REVERT: W 428 TRP cc_start: 0.8250 (m100) cc_final: 0.7140 (t60) REVERT: X 283 GLN cc_start: 0.7986 (mt0) cc_final: 0.7731 (mp10) REVERT: X 337 ARG cc_start: 0.6761 (mtt180) cc_final: 0.6197 (tpm170) REVERT: X 363 ARG cc_start: 0.8218 (mtm110) cc_final: 0.7754 (ttt180) REVERT: X 402 GLU cc_start: 0.9025 (tp30) cc_final: 0.8696 (tp30) REVERT: Y 40 GLU cc_start: 0.5557 (mm-30) cc_final: 0.5049 (pt0) REVERT: Y 104 MET cc_start: 0.6545 (tmm) cc_final: 0.5549 (ttt) REVERT: Y 245 GLU cc_start: 0.7134 (pm20) cc_final: 0.6600 (tt0) REVERT: Y 282 MET cc_start: 0.8278 (ppp) cc_final: 0.8007 (ppp) REVERT: Y 319 MET cc_start: 0.6911 (mmm) cc_final: 0.6576 (mmm) REVERT: Y 379 ARG cc_start: 0.9075 (tpp-160) cc_final: 0.8767 (ttt90) REVERT: Y 384 SER cc_start: 0.8623 (t) cc_final: 0.8401 (p) REVERT: Y 389 MET cc_start: 0.0376 (ttm) cc_final: -0.0000 (pmm) REVERT: Z 81 MET cc_start: 0.9119 (ttp) cc_final: 0.8891 (tmm) REVERT: Z 103 LYS cc_start: 0.8124 (tttt) cc_final: 0.7829 (mtpt) REVERT: Z 112 MET cc_start: 0.9427 (mpp) cc_final: 0.9129 (mpp) REVERT: Z 194 GLN cc_start: 0.9342 (mt0) cc_final: 0.8936 (tp-100) REVERT: Z 256 GLN cc_start: 0.8149 (tp-100) cc_final: 0.7558 (mm-40) REVERT: Z 273 HIS cc_start: 0.8955 (m-70) cc_final: 0.8746 (m90) REVERT: a 248 PHE cc_start: 0.8079 (t80) cc_final: 0.7868 (t80) REVERT: a 278 MET cc_start: 0.6007 (ptm) cc_final: 0.5691 (ptm) REVERT: c 54 MET cc_start: 0.5226 (mtp) cc_final: 0.5016 (mtm) REVERT: c 57 MET cc_start: 0.8674 (mtm) cc_final: 0.8431 (mtm) REVERT: c 75 MET cc_start: 0.7718 (ttt) cc_final: 0.7204 (tmm) REVERT: c 216 MET cc_start: 0.7333 (ptm) cc_final: 0.6753 (ttp) REVERT: c 226 MET cc_start: 0.8184 (mpp) cc_final: 0.7896 (mpp) REVERT: c 255 TYR cc_start: 0.8271 (m-80) cc_final: 0.8027 (m-80) REVERT: d 1 MET cc_start: 0.3337 (ttt) cc_final: 0.3061 (tpp) REVERT: d 105 PHE cc_start: 0.9020 (t80) cc_final: 0.8817 (t80) REVERT: d 230 GLN cc_start: 0.7427 (tp40) cc_final: 0.7067 (mp10) REVERT: G 120 ASP cc_start: 0.8917 (m-30) cc_final: 0.8529 (t0) REVERT: G 131 MET cc_start: 0.8149 (mpp) cc_final: 0.7503 (mpp) REVERT: H 39 LYS cc_start: 0.7578 (tmtt) cc_final: 0.7200 (ttpt) REVERT: H 92 LYS cc_start: 0.9682 (ttpt) cc_final: 0.9395 (tppt) REVERT: H 118 MET cc_start: 0.7759 (ttm) cc_final: 0.7537 (ttm) REVERT: H 166 ASN cc_start: 0.8417 (m110) cc_final: 0.8004 (m-40) REVERT: H 169 ASN cc_start: 0.8493 (m110) cc_final: 0.7737 (t0) REVERT: I 57 ASP cc_start: 0.6970 (m-30) cc_final: 0.6599 (m-30) REVERT: I 114 LEU cc_start: 0.9503 (tp) cc_final: 0.9171 (pp) REVERT: J 175 ASN cc_start: 0.8601 (m-40) cc_final: 0.8150 (t0) REVERT: J 176 TYR cc_start: 0.5751 (t80) cc_final: 0.4795 (t80) REVERT: J 211 MET cc_start: 0.7884 (mmm) cc_final: 0.7266 (mmm) REVERT: K 59 MET cc_start: 0.7432 (mtm) cc_final: 0.6428 (mpp) REVERT: K 78 MET cc_start: 0.6925 (ppp) cc_final: 0.6539 (ppp) REVERT: L 84 LEU cc_start: 0.9080 (tt) cc_final: 0.8836 (tt) REVERT: L 88 MET cc_start: 0.9295 (tpp) cc_final: 0.8879 (ptm) REVERT: L 99 PHE cc_start: 0.9370 (m-10) cc_final: 0.9141 (m-80) REVERT: L 100 ASP cc_start: 0.9507 (t0) cc_final: 0.9133 (m-30) REVERT: L 180 MET cc_start: 0.8454 (tpp) cc_final: 0.8064 (tpt) REVERT: M 17 ASP cc_start: 0.9183 (m-30) cc_final: 0.8933 (t0) REVERT: M 137 LEU cc_start: 0.9084 (tp) cc_final: 0.8820 (tp) REVERT: M 197 ILE cc_start: 0.8089 (mm) cc_final: 0.7720 (tp) REVERT: N 51 ASP cc_start: 0.9003 (m-30) cc_final: 0.8695 (m-30) REVERT: N 84 LYS cc_start: 0.9430 (tmmt) cc_final: 0.9201 (tttt) REVERT: N 164 MET cc_start: 0.7440 (mtm) cc_final: 0.7160 (mtt) REVERT: O 146 MET cc_start: 0.7898 (ttm) cc_final: 0.7255 (ttm) REVERT: P 45 MET cc_start: 0.8768 (mmp) cc_final: 0.8557 (mmm) REVERT: P 59 ASP cc_start: 0.8596 (m-30) cc_final: 0.8395 (t0) REVERT: P 90 MET cc_start: 0.8758 (mtm) cc_final: 0.8212 (mmm) REVERT: P 117 PHE cc_start: 0.7075 (p90) cc_final: 0.6810 (p90) REVERT: P 149 MET cc_start: 0.5686 (mmm) cc_final: 0.5057 (tpp) REVERT: Q 31 ASP cc_start: 0.8561 (p0) cc_final: 0.8205 (m-30) REVERT: Q 82 ASN cc_start: 0.8999 (t0) cc_final: 0.8595 (t0) REVERT: Q 102 LEU cc_start: 0.9198 (mp) cc_final: 0.8968 (mm) REVERT: R 71 LYS cc_start: 0.8753 (mtpp) cc_final: 0.8450 (tppt) REVERT: R 100 MET cc_start: 0.8260 (mpp) cc_final: 0.7681 (mpp) REVERT: S 91 MET cc_start: 0.9619 (mtt) cc_final: 0.9393 (mmm) REVERT: S 144 MET cc_start: 0.8734 (mtt) cc_final: 0.8345 (tpt) REVERT: S 145 LEU cc_start: 0.9658 (mt) cc_final: 0.9424 (mt) REVERT: T 7 THR cc_start: 0.8508 (p) cc_final: 0.8211 (t) REVERT: T 26 MET cc_start: 0.8580 (mtp) cc_final: 0.7869 (mpp) REVERT: T 96 MET cc_start: 0.9432 (mmm) cc_final: 0.9075 (tpp) REVERT: T 110 MET cc_start: 0.8898 (mtp) cc_final: 0.8607 (mmm) REVERT: T 127 MET cc_start: 0.8629 (mtm) cc_final: 0.7947 (mtm) REVERT: T 180 ASP cc_start: 0.8169 (t0) cc_final: 0.7685 (t0) REVERT: T 187 PHE cc_start: 0.8661 (p90) cc_final: 0.8139 (p90) REVERT: g 80 MET cc_start: 0.6341 (mmm) cc_final: 0.5973 (mmm) REVERT: g 120 ASP cc_start: 0.8967 (m-30) cc_final: 0.8660 (m-30) REVERT: g 138 MET cc_start: 0.7921 (tpp) cc_final: 0.7371 (tpp) REVERT: g 152 TYR cc_start: 0.7730 (m-80) cc_final: 0.7494 (m-10) REVERT: g 155 ASP cc_start: 0.8241 (t0) cc_final: 0.7820 (t0) REVERT: g 159 TYR cc_start: 0.7613 (t80) cc_final: 0.7005 (t80) REVERT: h 166 ASN cc_start: 0.9335 (t0) cc_final: 0.9015 (t0) REVERT: i 74 CYS cc_start: 0.8151 (p) cc_final: 0.7703 (t) REVERT: i 89 GLU cc_start: 0.9151 (mp0) cc_final: 0.8936 (mp0) REVERT: j 117 ARG cc_start: 0.9444 (ttt90) cc_final: 0.9211 (ttm-80) REVERT: j 211 MET cc_start: 0.6832 (tmm) cc_final: 0.6074 (tmm) REVERT: k 59 MET cc_start: 0.8048 (ptm) cc_final: 0.7704 (ptp) REVERT: k 90 ASP cc_start: 0.9076 (t70) cc_final: 0.8794 (t70) REVERT: k 103 TYR cc_start: 0.8939 (m-80) cc_final: 0.8324 (m-80) REVERT: k 166 ASP cc_start: 0.8121 (m-30) cc_final: 0.7899 (m-30) REVERT: k 203 LYS cc_start: 0.9079 (tmtt) cc_final: 0.8815 (pttt) REVERT: k 228 MET cc_start: 0.7242 (pmm) cc_final: 0.6958 (pmm) REVERT: l 4 ASN cc_start: 0.7246 (t0) cc_final: 0.6707 (m-40) REVERT: l 62 LYS cc_start: 0.7158 (mmtt) cc_final: 0.6688 (mptt) REVERT: l 80 ASP cc_start: 0.8436 (m-30) cc_final: 0.7518 (t0) REVERT: l 88 MET cc_start: 0.8492 (tpp) cc_final: 0.8142 (mtt) REVERT: l 97 PHE cc_start: 0.9067 (t80) cc_final: 0.8765 (t80) REVERT: m 7 TYR cc_start: 0.6574 (m-10) cc_final: 0.6245 (m-10) REVERT: m 27 MET cc_start: 0.8375 (mtt) cc_final: 0.7874 (mmm) REVERT: m 43 ASP cc_start: 0.8393 (p0) cc_final: 0.8151 (m-30) REVERT: m 75 MET cc_start: 0.8868 (mtp) cc_final: 0.8387 (ptp) REVERT: m 232 ARG cc_start: 0.8260 (mtt180) cc_final: 0.6584 (mtm-85) REVERT: n 4 MET cc_start: 0.8638 (tpt) cc_final: 0.8188 (tpp) REVERT: n 86 MET cc_start: 0.8761 (ttm) cc_final: 0.8143 (ttp) REVERT: n 119 MET cc_start: 0.8305 (mtt) cc_final: 0.8041 (mtt) REVERT: o 149 GLU cc_start: 0.8739 (tp30) cc_final: 0.8500 (tp30) REVERT: p 28 PHE cc_start: 0.9401 (t80) cc_final: 0.8841 (t80) REVERT: p 72 ASN cc_start: 0.8518 (m110) cc_final: 0.8234 (m-40) REVERT: p 95 LEU cc_start: 0.9343 (mt) cc_final: 0.8846 (tp) REVERT: p 127 ILE cc_start: 0.8959 (tp) cc_final: 0.8679 (tp) REVERT: p 149 MET cc_start: 0.8101 (mmp) cc_final: 0.6731 (mmp) REVERT: p 158 MET cc_start: 0.8404 (tpp) cc_final: 0.7979 (tpp) REVERT: q 20 VAL cc_start: 0.6825 (t) cc_final: 0.6246 (t) REVERT: q 26 VAL cc_start: 0.8863 (m) cc_final: 0.8262 (m) REVERT: q 62 LYS cc_start: 0.9199 (mmmt) cc_final: 0.8848 (mmmm) REVERT: q 69 MET cc_start: 0.9584 (tpp) cc_final: 0.9294 (tpp) REVERT: q 118 MET cc_start: 0.7558 (mmm) cc_final: 0.7140 (mmm) REVERT: r 93 MET cc_start: 0.8199 (mmm) cc_final: 0.7445 (mtp) REVERT: r 97 MET cc_start: 0.8099 (tmm) cc_final: 0.7613 (tmm) REVERT: s 69 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8843 (mm-30) REVERT: s 77 HIS cc_start: 0.8847 (m90) cc_final: 0.8495 (m90) REVERT: s 83 MET cc_start: 0.8110 (ttt) cc_final: 0.7836 (ttt) REVERT: t 3 ASN cc_start: 0.8830 (m-40) cc_final: 0.7980 (t0) REVERT: t 73 ASP cc_start: 0.8907 (m-30) cc_final: 0.8537 (t70) REVERT: t 99 ARG cc_start: 0.9160 (mmt180) cc_final: 0.8330 (mmm160) REVERT: t 104 ASN cc_start: 0.9159 (t0) cc_final: 0.8950 (t0) REVERT: t 110 MET cc_start: 0.8557 (mmp) cc_final: 0.8211 (mmm) REVERT: t 173 MET cc_start: 0.9006 (tpp) cc_final: 0.8106 (mmt) REVERT: A 138 MET cc_start: 0.5584 (ttp) cc_final: 0.5193 (ttp) REVERT: A 263 MET cc_start: 0.6932 (mtm) cc_final: 0.6307 (ptm) REVERT: A 273 PHE cc_start: 0.6787 (m-10) cc_final: 0.6437 (m-10) REVERT: A 299 MET cc_start: 0.8324 (tmm) cc_final: 0.7972 (ppp) REVERT: A 318 LEU cc_start: 0.8028 (mt) cc_final: 0.7682 (mt) REVERT: B 272 ARG cc_start: 0.7914 (ttm170) cc_final: 0.7360 (tmt170) REVERT: B 309 MET cc_start: 0.8221 (ptt) cc_final: 0.7828 (ppp) REVERT: B 329 MET cc_start: 0.8119 (mmp) cc_final: 0.7744 (mmp) REVERT: C 121 TYR cc_start: 0.8664 (m-10) cc_final: 0.8272 (m-80) REVERT: C 139 MET cc_start: 0.4539 (mtm) cc_final: 0.3970 (ttm) REVERT: C 229 ARG cc_start: 0.7330 (mpp-170) cc_final: 0.6256 (mmp80) REVERT: C 230 MET cc_start: 0.7756 (tpp) cc_final: 0.7316 (mmt) REVERT: C 232 ARG cc_start: 0.9204 (ppt170) cc_final: 0.8978 (ttm170) REVERT: C 278 ASN cc_start: 0.6310 (m-40) cc_final: 0.5953 (t0) REVERT: C 327 ASP cc_start: 0.8915 (m-30) cc_final: 0.8612 (t0) REVERT: C 374 ARG cc_start: 0.5895 (tpp-160) cc_final: 0.5281 (mmm160) REVERT: D 89 ILE cc_start: 0.8090 (mm) cc_final: 0.7765 (mm) REVERT: D 167 ILE cc_start: 0.6037 (mt) cc_final: 0.5121 (mt) REVERT: D 170 MET cc_start: 0.6074 (ptt) cc_final: 0.5756 (ptt) REVERT: D 187 HIS cc_start: 0.8081 (m90) cc_final: 0.7626 (m90) REVERT: D 246 MET cc_start: 0.8101 (mtm) cc_final: 0.7901 (mtm) REVERT: D 309 MET cc_start: 0.6619 (mpp) cc_final: 0.6352 (mpp) REVERT: E 56 ILE cc_start: 0.8989 (mm) cc_final: 0.8773 (mt) REVERT: E 108 MET cc_start: 0.7883 (mmp) cc_final: 0.7268 (mmm) REVERT: E 122 MET cc_start: 0.7572 (pmm) cc_final: 0.7034 (pmm) REVERT: E 277 MET cc_start: 0.3678 (mpp) cc_final: 0.2960 (mpp) REVERT: E 376 ASP cc_start: 0.8902 (t70) cc_final: 0.8520 (p0) REVERT: F 373 MET cc_start: 0.6335 (mpp) cc_final: 0.6122 (mpp) REVERT: F 405 MET cc_start: 0.7833 (mtm) cc_final: 0.7490 (mpp) REVERT: F 421 MET cc_start: 0.6934 (mmp) cc_final: 0.6239 (mtt) REVERT: f 178 LYS cc_start: 0.5974 (mtpt) cc_final: 0.5350 (tttm) REVERT: f 222 ASP cc_start: 0.0400 (m-30) cc_final: -0.0518 (p0) REVERT: f 407 MET cc_start: 0.5224 (mmt) cc_final: 0.4637 (mmt) REVERT: f 505 MET cc_start: -0.0150 (ttp) cc_final: -0.2535 (mtm) REVERT: f 581 GLU cc_start: -0.0090 (OUTLIER) cc_final: -0.3032 (mm-30) outliers start: 5 outliers final: 3 residues processed: 1154 average time/residue: 0.8948 time to fit residues: 1785.6861 Evaluate side-chains 893 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 889 time to evaluate : 9.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1268 random chunks: chunk 1182 optimal weight: 9.9990 chunk 138 optimal weight: 0.0170 chunk 699 optimal weight: 10.0000 chunk 895 optimal weight: 20.0000 chunk 694 optimal weight: 5.9990 chunk 1032 optimal weight: 0.0060 chunk 685 optimal weight: 20.0000 chunk 1222 optimal weight: 1.9990 chunk 764 optimal weight: 0.0970 chunk 745 optimal weight: 8.9990 chunk 564 optimal weight: 30.0000 overall best weight: 1.6236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN U 721 HIS ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 HIS ** V 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 257 ASN ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 288 HIS ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 367 GLN X 405 GLN ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 174 HIS ** Z 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 129 GLN ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 105 HIS c 30 GLN ** c 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 190 HIS ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 94 HIS ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 33 GLN ** p 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 85 ASN ** t 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 GLN D 294 ASN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 GLN ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 101622 Z= 0.168 Angle : 0.690 13.071 137458 Z= 0.350 Chirality : 0.045 0.387 15660 Planarity : 0.005 0.081 17770 Dihedral : 6.726 147.958 14082 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.96 % Favored : 90.99 % Rotamer: Outliers : 0.04 % Allowed : 1.72 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.20 % Twisted Proline : 0.45 % Twisted General : 0.09 % 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: -1.71 (0.07), residues: 12738 helix: -0.08 (0.07), residues: 5601 sheet: -0.67 (0.13), residues: 1640 loop : -2.42 (0.08), residues: 5497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP d 61 HIS 0.014 0.001 HIS f 301 PHE 0.037 0.001 PHE f 675 TYR 0.029 0.001 TYR A 420 ARG 0.009 0.000 ARG l 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1167 time to evaluate : 9.602 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: U 221 ILE cc_start: 0.2002 (pt) cc_final: 0.1731 (pt) REVERT: U 362 ASN cc_start: 0.6654 (t0) cc_final: 0.6158 (t0) REVERT: U 654 MET cc_start: 0.8482 (ppp) cc_final: 0.8275 (ppp) REVERT: U 728 PHE cc_start: 0.8620 (m-80) cc_final: 0.7944 (m-10) REVERT: U 738 ASP cc_start: 0.8896 (m-30) cc_final: 0.8397 (t0) REVERT: U 770 TRP cc_start: 0.7248 (m-90) cc_final: 0.6348 (m-90) REVERT: V 37 MET cc_start: 0.6234 (tpt) cc_final: 0.5906 (mmm) REVERT: V 139 MET cc_start: 0.5628 (mmm) cc_final: 0.5260 (ttp) REVERT: V 302 TYR cc_start: 0.3913 (m-10) cc_final: 0.3663 (m-80) REVERT: V 309 MET cc_start: 0.7000 (ptm) cc_final: 0.6620 (ptm) REVERT: V 336 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8287 (mm-30) REVERT: V 489 MET cc_start: 0.8262 (mmt) cc_final: 0.7977 (mmm) REVERT: W 73 MET cc_start: 0.8928 (mmm) cc_final: 0.8585 (mmm) REVERT: W 94 ARG cc_start: 0.4922 (ttt-90) cc_final: 0.4368 (tpm170) REVERT: W 114 GLU cc_start: 0.5818 (tm-30) cc_final: 0.5593 (tt0) REVERT: W 190 MET cc_start: 0.4647 (mpp) cc_final: 0.4436 (mmm) REVERT: W 312 MET cc_start: -0.4416 (ttm) cc_final: -0.5898 (tpp) REVERT: W 315 MET cc_start: 0.4570 (pmm) cc_final: 0.3111 (mmm) REVERT: W 326 MET cc_start: 0.7853 (mtm) cc_final: 0.7620 (mpp) REVERT: W 352 LYS cc_start: 0.8162 (mmtp) cc_final: 0.7860 (ptmm) REVERT: W 377 ARG cc_start: 0.7001 (ttt90) cc_final: 0.6356 (tpt170) REVERT: W 428 TRP cc_start: 0.8039 (m100) cc_final: 0.7222 (t60) REVERT: X 283 GLN cc_start: 0.7990 (mt0) cc_final: 0.7735 (mp10) REVERT: X 337 ARG cc_start: 0.6663 (mtt180) cc_final: 0.6147 (tpm170) REVERT: X 363 ARG cc_start: 0.8202 (mtm110) cc_final: 0.7824 (ttt180) REVERT: Y 104 MET cc_start: 0.6475 (tmm) cc_final: 0.5461 (ttt) REVERT: Y 105 MET cc_start: 0.2762 (ppp) cc_final: 0.2161 (ppp) REVERT: Y 245 GLU cc_start: 0.7005 (pm20) cc_final: 0.6598 (tt0) REVERT: Y 319 MET cc_start: 0.6910 (mmm) cc_final: 0.6594 (mmm) REVERT: Y 379 ARG cc_start: 0.9070 (tpp-160) cc_final: 0.8806 (ttt90) REVERT: Y 384 SER cc_start: 0.8584 (t) cc_final: 0.8347 (p) REVERT: Z 103 LYS cc_start: 0.8082 (tttt) cc_final: 0.7763 (mtpt) REVERT: Z 112 MET cc_start: 0.9416 (mpp) cc_final: 0.9051 (mpp) REVERT: Z 194 GLN cc_start: 0.9340 (mt0) cc_final: 0.8910 (tp-100) REVERT: Z 273 HIS cc_start: 0.8867 (m-70) cc_final: 0.8645 (m-70) REVERT: a 141 MET cc_start: -0.0151 (mmp) cc_final: -0.0913 (tpp) REVERT: a 278 MET cc_start: 0.5933 (ptm) cc_final: 0.5652 (ptm) REVERT: a 333 MET cc_start: 0.6638 (mmm) cc_final: 0.5580 (ptp) REVERT: a 339 ARG cc_start: 0.5640 (mmt180) cc_final: 0.4795 (mmt180) REVERT: b 38 HIS cc_start: 0.6312 (m90) cc_final: 0.5968 (m-70) REVERT: b 145 GLU cc_start: 0.3844 (tm-30) cc_final: 0.3413 (mp0) REVERT: c 57 MET cc_start: 0.8699 (mtm) cc_final: 0.8359 (ptp) REVERT: c 216 MET cc_start: 0.7172 (ptm) cc_final: 0.6583 (ttp) REVERT: c 255 TYR cc_start: 0.8250 (m-80) cc_final: 0.8001 (m-80) REVERT: c 260 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8872 (pt0) REVERT: d 1 MET cc_start: 0.3245 (ttt) cc_final: 0.2969 (tpp) REVERT: d 230 GLN cc_start: 0.7341 (tp40) cc_final: 0.6693 (mp10) REVERT: G 120 ASP cc_start: 0.8887 (m-30) cc_final: 0.8522 (t0) REVERT: G 131 MET cc_start: 0.7995 (mpp) cc_final: 0.7303 (mpp) REVERT: H 39 LYS cc_start: 0.7523 (tmtt) cc_final: 0.7145 (ttpt) REVERT: H 118 MET cc_start: 0.7687 (ttm) cc_final: 0.7417 (ttm) REVERT: H 166 ASN cc_start: 0.8338 (m110) cc_final: 0.7923 (m-40) REVERT: H 169 ASN cc_start: 0.8513 (m110) cc_final: 0.7835 (t0) REVERT: I 57 ASP cc_start: 0.6894 (m-30) cc_final: 0.6469 (m-30) REVERT: J 175 ASN cc_start: 0.8547 (m-40) cc_final: 0.8176 (t0) REVERT: J 176 TYR cc_start: 0.5760 (t80) cc_final: 0.5110 (t80) REVERT: J 211 MET cc_start: 0.7774 (mmm) cc_final: 0.7156 (mmm) REVERT: K 78 MET cc_start: 0.6943 (ppp) cc_final: 0.6694 (ppp) REVERT: L 84 LEU cc_start: 0.9066 (tt) cc_final: 0.8813 (tt) REVERT: L 88 MET cc_start: 0.9298 (tpp) cc_final: 0.8972 (ptm) REVERT: L 91 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8767 (mm-30) REVERT: L 99 PHE cc_start: 0.9371 (m-10) cc_final: 0.9139 (m-80) REVERT: L 100 ASP cc_start: 0.9506 (t0) cc_final: 0.9139 (m-30) REVERT: L 180 MET cc_start: 0.8417 (tpp) cc_final: 0.8194 (tpp) REVERT: M 137 LEU cc_start: 0.9079 (tp) cc_final: 0.8873 (tp) REVERT: M 197 ILE cc_start: 0.7955 (mm) cc_final: 0.7612 (tp) REVERT: N 51 ASP cc_start: 0.8959 (m-30) cc_final: 0.8657 (m-30) REVERT: N 84 LYS cc_start: 0.9443 (tmmt) cc_final: 0.9204 (tttt) REVERT: N 164 MET cc_start: 0.7466 (mtm) cc_final: 0.7225 (mtt) REVERT: O 146 MET cc_start: 0.7941 (ttm) cc_final: 0.7195 (ttm) REVERT: P 14 MET cc_start: 0.8057 (tpp) cc_final: 0.7749 (mmm) REVERT: P 45 MET cc_start: 0.8806 (mmp) cc_final: 0.8556 (mmm) REVERT: P 59 ASP cc_start: 0.8654 (m-30) cc_final: 0.8381 (t0) REVERT: P 90 MET cc_start: 0.8763 (mtm) cc_final: 0.8240 (mmm) REVERT: P 117 PHE cc_start: 0.7044 (p90) cc_final: 0.6760 (p90) REVERT: P 149 MET cc_start: 0.5651 (mmm) cc_final: 0.5197 (tpp) REVERT: P 171 MET cc_start: 0.9011 (tpp) cc_final: 0.8340 (ttm) REVERT: Q 2 GLU cc_start: 0.8255 (pm20) cc_final: 0.7136 (pp20) REVERT: Q 4 LEU cc_start: 0.8352 (mt) cc_final: 0.7972 (mt) REVERT: Q 28 MET cc_start: 0.8768 (mtm) cc_final: 0.8447 (mpp) REVERT: Q 82 ASN cc_start: 0.8901 (t0) cc_final: 0.8536 (t0) REVERT: Q 102 LEU cc_start: 0.9151 (mp) cc_final: 0.8894 (mm) REVERT: R 97 MET cc_start: 0.6344 (mpp) cc_final: 0.6137 (mpp) REVERT: R 100 MET cc_start: 0.8233 (mpp) cc_final: 0.7653 (mpp) REVERT: S 91 MET cc_start: 0.9589 (mtt) cc_final: 0.9344 (mmm) REVERT: S 144 MET cc_start: 0.8663 (mtt) cc_final: 0.8289 (tpt) REVERT: S 145 LEU cc_start: 0.9667 (mt) cc_final: 0.9435 (mt) REVERT: T 7 THR cc_start: 0.8459 (p) cc_final: 0.8202 (t) REVERT: T 26 MET cc_start: 0.8603 (mtp) cc_final: 0.7885 (mpp) REVERT: T 96 MET cc_start: 0.9389 (mmm) cc_final: 0.9049 (tpp) REVERT: T 110 MET cc_start: 0.8865 (mtp) cc_final: 0.8615 (mmm) REVERT: T 127 MET cc_start: 0.8549 (mtm) cc_final: 0.7842 (mtm) REVERT: T 160 LEU cc_start: 0.8486 (tp) cc_final: 0.8262 (tp) REVERT: T 180 ASP cc_start: 0.8047 (t0) cc_final: 0.7591 (t0) REVERT: T 187 PHE cc_start: 0.8636 (p90) cc_final: 0.8086 (p90) REVERT: g 69 LEU cc_start: 0.8770 (mm) cc_final: 0.8078 (tp) REVERT: g 80 MET cc_start: 0.6168 (mmm) cc_final: 0.5869 (mmm) REVERT: g 115 CYS cc_start: 0.8548 (t) cc_final: 0.7813 (p) REVERT: g 120 ASP cc_start: 0.8895 (m-30) cc_final: 0.8556 (m-30) REVERT: g 138 MET cc_start: 0.7965 (tpp) cc_final: 0.7412 (tpp) REVERT: g 155 ASP cc_start: 0.8256 (t0) cc_final: 0.7824 (t0) REVERT: g 159 TYR cc_start: 0.7613 (t80) cc_final: 0.7010 (t80) REVERT: h 92 LYS cc_start: 0.8506 (mtpt) cc_final: 0.8076 (mtmm) REVERT: h 166 ASN cc_start: 0.9303 (t0) cc_final: 0.8985 (t0) REVERT: i 74 CYS cc_start: 0.8169 (p) cc_final: 0.7801 (t) REVERT: j 117 ARG cc_start: 0.9449 (ttt90) cc_final: 0.9150 (ttm-80) REVERT: j 211 MET cc_start: 0.6751 (tmm) cc_final: 0.5945 (tmm) REVERT: k 59 MET cc_start: 0.8009 (ptm) cc_final: 0.7664 (ptp) REVERT: k 90 ASP cc_start: 0.9053 (t70) cc_final: 0.8771 (t70) REVERT: k 103 TYR cc_start: 0.8902 (m-80) cc_final: 0.8330 (m-80) REVERT: k 166 ASP cc_start: 0.8109 (m-30) cc_final: 0.7883 (m-30) REVERT: l 4 ASN cc_start: 0.7137 (t0) cc_final: 0.6669 (m-40) REVERT: l 80 ASP cc_start: 0.8344 (m-30) cc_final: 0.7488 (t0) REVERT: l 228 ASP cc_start: 0.8870 (m-30) cc_final: 0.8442 (t0) REVERT: m 7 TYR cc_start: 0.6510 (m-10) cc_final: 0.6194 (m-10) REVERT: m 27 MET cc_start: 0.8352 (mtt) cc_final: 0.7840 (mmm) REVERT: m 43 ASP cc_start: 0.8309 (p0) cc_final: 0.8070 (m-30) REVERT: m 75 MET cc_start: 0.8848 (mtp) cc_final: 0.8452 (ptp) REVERT: m 136 MET cc_start: 0.9000 (mmt) cc_final: 0.8648 (mmt) REVERT: m 232 ARG cc_start: 0.8241 (mtt180) cc_final: 0.6569 (mtm-85) REVERT: n 4 MET cc_start: 0.8694 (tpt) cc_final: 0.8090 (tpp) REVERT: n 119 MET cc_start: 0.8307 (mtt) cc_final: 0.8000 (mtt) REVERT: o 94 ILE cc_start: 0.8735 (tt) cc_final: 0.8504 (tp) REVERT: o 149 GLU cc_start: 0.8724 (tp30) cc_final: 0.8440 (tp30) REVERT: p 28 PHE cc_start: 0.9403 (t80) cc_final: 0.8931 (t80) REVERT: p 72 ASN cc_start: 0.8392 (m110) cc_final: 0.8102 (m-40) REVERT: p 95 LEU cc_start: 0.9257 (mt) cc_final: 0.8743 (tp) REVERT: p 127 ILE cc_start: 0.8947 (tp) cc_final: 0.8684 (tp) REVERT: p 149 MET cc_start: 0.8121 (mmp) cc_final: 0.6630 (mmp) REVERT: p 150 CYS cc_start: 0.9118 (m) cc_final: 0.8866 (m) REVERT: p 158 MET cc_start: 0.8447 (tpp) cc_final: 0.8092 (tpp) REVERT: q 20 VAL cc_start: 0.6778 (t) cc_final: 0.6164 (t) REVERT: q 26 VAL cc_start: 0.8852 (m) cc_final: 0.8264 (m) REVERT: q 44 LEU cc_start: 0.9298 (tp) cc_final: 0.9008 (tp) REVERT: q 62 LYS cc_start: 0.9233 (mmpt) cc_final: 0.8908 (mttp) REVERT: q 118 MET cc_start: 0.7421 (mmm) cc_final: 0.6922 (mmm) REVERT: r 86 MET cc_start: 0.9264 (mmp) cc_final: 0.8627 (ttt) REVERT: r 93 MET cc_start: 0.8198 (mmm) cc_final: 0.7495 (mtp) REVERT: r 97 MET cc_start: 0.8085 (tmm) cc_final: 0.7639 (tmm) REVERT: s 69 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8926 (mm-30) REVERT: s 76 LYS cc_start: 0.9397 (tttm) cc_final: 0.9153 (tptp) REVERT: s 83 MET cc_start: 0.8051 (ttt) cc_final: 0.7735 (ttt) REVERT: t 3 ASN cc_start: 0.8817 (m-40) cc_final: 0.8077 (t0) REVERT: t 73 ASP cc_start: 0.8897 (m-30) cc_final: 0.8551 (t70) REVERT: t 99 ARG cc_start: 0.9292 (mmt180) cc_final: 0.8420 (mmm160) REVERT: t 110 MET cc_start: 0.8519 (mmp) cc_final: 0.8131 (mmm) REVERT: t 173 MET cc_start: 0.8978 (tpp) cc_final: 0.8127 (mmt) REVERT: A 138 MET cc_start: 0.5416 (ttp) cc_final: 0.5077 (ttp) REVERT: A 157 ILE cc_start: 0.5770 (tp) cc_final: 0.5460 (mt) REVERT: A 263 MET cc_start: 0.7001 (mtm) cc_final: 0.6343 (ptm) REVERT: A 273 PHE cc_start: 0.6634 (m-10) cc_final: 0.6391 (m-10) REVERT: A 299 MET cc_start: 0.8309 (tmm) cc_final: 0.7966 (ppp) REVERT: A 318 LEU cc_start: 0.8108 (mt) cc_final: 0.7761 (mt) REVERT: B 102 LEU cc_start: 0.6702 (mt) cc_final: 0.6340 (mt) REVERT: B 210 TYR cc_start: 0.8181 (m-80) cc_final: 0.7739 (m-80) REVERT: B 309 MET cc_start: 0.8216 (ptt) cc_final: 0.7820 (ppp) REVERT: B 329 MET cc_start: 0.8301 (mmp) cc_final: 0.7893 (mmp) REVERT: C 121 TYR cc_start: 0.8500 (m-10) cc_final: 0.8149 (m-80) REVERT: C 139 MET cc_start: 0.4358 (mtm) cc_final: 0.3826 (mtm) REVERT: C 229 ARG cc_start: 0.7230 (mpp-170) cc_final: 0.6380 (mmp80) REVERT: C 230 MET cc_start: 0.7913 (tpp) cc_final: 0.7524 (mmt) REVERT: C 327 ASP cc_start: 0.8898 (m-30) cc_final: 0.8591 (t0) REVERT: D 89 ILE cc_start: 0.8006 (mm) cc_final: 0.7704 (mm) REVERT: D 124 LEU cc_start: 0.8650 (mm) cc_final: 0.8433 (mt) REVERT: D 146 GLU cc_start: 0.7505 (pp20) cc_final: 0.7290 (pm20) REVERT: D 167 ILE cc_start: 0.6201 (mt) cc_final: 0.5506 (mt) REVERT: D 170 MET cc_start: 0.6469 (ptt) cc_final: 0.6126 (ptt) REVERT: D 187 HIS cc_start: 0.8110 (m90) cc_final: 0.7848 (m90) REVERT: D 246 MET cc_start: 0.8065 (mtm) cc_final: 0.7849 (mtm) REVERT: D 309 MET cc_start: 0.6799 (mpp) cc_final: 0.6386 (mpp) REVERT: D 316 THR cc_start: 0.6897 (p) cc_final: 0.6606 (t) REVERT: E 108 MET cc_start: 0.7700 (mmp) cc_final: 0.7068 (mmm) REVERT: E 122 MET cc_start: 0.7509 (pmm) cc_final: 0.7150 (pmm) REVERT: E 232 MET cc_start: 0.8931 (ttp) cc_final: 0.8630 (ttt) REVERT: E 277 MET cc_start: 0.4182 (mpp) cc_final: 0.3678 (mpp) REVERT: E 376 ASP cc_start: 0.8876 (t70) cc_final: 0.8487 (p0) REVERT: F 125 LYS cc_start: 0.9632 (ttmt) cc_final: 0.9307 (pttm) REVERT: F 373 MET cc_start: 0.6341 (mpp) cc_final: 0.6109 (mpp) REVERT: F 405 MET cc_start: 0.7805 (mtm) cc_final: 0.7529 (mpp) REVERT: F 421 MET cc_start: 0.6845 (mmp) cc_final: 0.6229 (mtt) REVERT: f 178 LYS cc_start: 0.5908 (mtpt) cc_final: 0.4134 (mmtt) REVERT: f 222 ASP cc_start: 0.0038 (m-30) cc_final: -0.0468 (p0) REVERT: f 407 MET cc_start: 0.5207 (mmt) cc_final: 0.4836 (mmt) REVERT: f 505 MET cc_start: -0.0341 (ttp) cc_final: -0.2706 (mtm) outliers start: 4 outliers final: 3 residues processed: 1171 average time/residue: 0.8876 time to fit residues: 1805.9053 Evaluate side-chains 900 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 897 time to evaluate : 9.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1268 random chunks: chunk 756 optimal weight: 30.0000 chunk 488 optimal weight: 3.9990 chunk 729 optimal weight: 7.9990 chunk 368 optimal weight: 7.9990 chunk 240 optimal weight: 7.9990 chunk 236 optimal weight: 20.0000 chunk 776 optimal weight: 30.0000 chunk 832 optimal weight: 0.5980 chunk 604 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 chunk 960 optimal weight: 7.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 HIS ** V 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 252 ASN V 257 ASN V 299 GLN V 453 HIS ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 229 GLN ** Z 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 129 GLN ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 34 ASN d 97 GLN d 109 GLN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 23 GLN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 190 HIS ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 GLN O 193 ASN ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 94 HIS k 155 HIS ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 101622 Z= 0.211 Angle : 0.713 14.254 137458 Z= 0.365 Chirality : 0.046 0.311 15660 Planarity : 0.005 0.080 17770 Dihedral : 6.700 146.723 14082 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.80 % Favored : 90.13 % Rotamer: Outliers : 0.05 % Allowed : 1.28 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.20 % Twisted Proline : 0.45 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.07), residues: 12738 helix: -0.04 (0.07), residues: 5603 sheet: -0.67 (0.13), residues: 1622 loop : -2.41 (0.08), residues: 5513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP d 61 HIS 0.015 0.001 HIS f 301 PHE 0.044 0.002 PHE d 71 TYR 0.030 0.002 TYR g 125 ARG 0.040 0.001 ARG n 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1092 time to evaluate : 9.400 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: U 106 ASP cc_start: 0.8967 (t0) cc_final: 0.8454 (m-30) REVERT: U 221 ILE cc_start: 0.2024 (pt) cc_final: 0.1691 (pt) REVERT: U 362 ASN cc_start: 0.6778 (t0) cc_final: 0.6397 (t0) REVERT: U 650 TYR cc_start: 0.9100 (t80) cc_final: 0.8864 (t80) REVERT: U 728 PHE cc_start: 0.8528 (m-80) cc_final: 0.8157 (m-10) REVERT: U 738 ASP cc_start: 0.8884 (m-30) cc_final: 0.8373 (t0) REVERT: U 770 TRP cc_start: 0.7338 (m-90) cc_final: 0.6505 (m-90) REVERT: V 139 MET cc_start: 0.5646 (mmm) cc_final: 0.5291 (ttp) REVERT: V 302 TYR cc_start: 0.3900 (m-10) cc_final: 0.3615 (m-80) REVERT: V 309 MET cc_start: 0.6971 (ptm) cc_final: 0.6583 (ptm) REVERT: V 336 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8265 (mm-30) REVERT: V 489 MET cc_start: 0.8317 (mmt) cc_final: 0.8049 (mmm) REVERT: W 73 MET cc_start: 0.8911 (mmm) cc_final: 0.8637 (mmm) REVERT: W 114 GLU cc_start: 0.5853 (tm-30) cc_final: 0.5593 (tt0) REVERT: W 303 LYS cc_start: 0.7719 (mmmt) cc_final: 0.7369 (mmtt) REVERT: W 315 MET cc_start: 0.4608 (pmm) cc_final: 0.2015 (mmm) REVERT: W 352 LYS cc_start: 0.8158 (mmtp) cc_final: 0.7873 (ptmm) REVERT: W 375 MET cc_start: 0.7967 (mmm) cc_final: 0.7590 (mmm) REVERT: W 377 ARG cc_start: 0.7152 (ttt90) cc_final: 0.6463 (tpt170) REVERT: W 378 MET cc_start: 0.6405 (tpp) cc_final: 0.6010 (tpp) REVERT: W 428 TRP cc_start: 0.8151 (m100) cc_final: 0.7405 (t60) REVERT: X 283 GLN cc_start: 0.7980 (mt0) cc_final: 0.7722 (mp10) REVERT: X 337 ARG cc_start: 0.6610 (mtt180) cc_final: 0.6099 (tpm170) REVERT: X 363 ARG cc_start: 0.8210 (mtm110) cc_final: 0.7756 (ttt180) REVERT: X 402 GLU cc_start: 0.9067 (tp30) cc_final: 0.8680 (tp30) REVERT: Y 104 MET cc_start: 0.6529 (tmm) cc_final: 0.5529 (ttt) REVERT: Y 105 MET cc_start: 0.2593 (ppp) cc_final: 0.1981 (ppp) REVERT: Y 245 GLU cc_start: 0.7038 (pm20) cc_final: 0.6594 (tt0) REVERT: Y 319 MET cc_start: 0.6977 (mmm) cc_final: 0.6639 (mmm) REVERT: Y 379 ARG cc_start: 0.9055 (tpp-160) cc_final: 0.8812 (tpt-90) REVERT: Y 384 SER cc_start: 0.8658 (t) cc_final: 0.8429 (p) REVERT: Y 389 MET cc_start: 0.2148 (mtm) cc_final: 0.1811 (pmm) REVERT: Z 103 LYS cc_start: 0.8039 (tttt) cc_final: 0.7718 (mtpt) REVERT: Z 112 MET cc_start: 0.9399 (mpp) cc_final: 0.9069 (mpp) REVERT: Z 194 GLN cc_start: 0.9333 (mt0) cc_final: 0.8987 (tp-100) REVERT: a 278 MET cc_start: 0.5988 (ptm) cc_final: 0.5749 (ptm) REVERT: a 339 ARG cc_start: 0.5801 (mmt180) cc_final: 0.5323 (mmt180) REVERT: b 42 ARG cc_start: 0.4897 (mpp-170) cc_final: 0.4244 (ttp80) REVERT: b 145 GLU cc_start: 0.3849 (tm-30) cc_final: 0.3459 (mp0) REVERT: c 54 MET cc_start: 0.5565 (mtt) cc_final: 0.4876 (mtm) REVERT: c 216 MET cc_start: 0.7299 (ptm) cc_final: 0.6697 (ttp) REVERT: c 226 MET cc_start: 0.7999 (mpp) cc_final: 0.7735 (mpp) REVERT: c 255 TYR cc_start: 0.8262 (m-80) cc_final: 0.8030 (m-80) REVERT: c 260 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8925 (pt0) REVERT: d 1 MET cc_start: 0.3220 (ttt) cc_final: 0.2934 (tpp) REVERT: d 230 GLN cc_start: 0.7149 (tp40) cc_final: 0.6620 (mp10) REVERT: G 120 ASP cc_start: 0.8956 (m-30) cc_final: 0.8582 (t0) REVERT: G 131 MET cc_start: 0.8095 (mpp) cc_final: 0.7407 (mpp) REVERT: H 39 LYS cc_start: 0.7476 (tmtt) cc_final: 0.7073 (ttpt) REVERT: H 118 MET cc_start: 0.7730 (ttm) cc_final: 0.7521 (ttm) REVERT: H 166 ASN cc_start: 0.8371 (m110) cc_final: 0.7959 (m-40) REVERT: H 169 ASN cc_start: 0.8492 (m110) cc_final: 0.7717 (t0) REVERT: I 57 ASP cc_start: 0.6877 (m-30) cc_final: 0.6152 (m-30) REVERT: J 3 TYR cc_start: 0.7511 (m-80) cc_final: 0.7291 (m-80) REVERT: J 71 MET cc_start: 0.8074 (tpp) cc_final: 0.7243 (tpp) REVERT: J 175 ASN cc_start: 0.8556 (m-40) cc_final: 0.8113 (t0) REVERT: J 176 TYR cc_start: 0.5878 (t80) cc_final: 0.5197 (t80) REVERT: J 211 MET cc_start: 0.7825 (mmm) cc_final: 0.7202 (mmm) REVERT: K 78 MET cc_start: 0.7030 (ppp) cc_final: 0.6746 (ppp) REVERT: L 88 MET cc_start: 0.9320 (tpp) cc_final: 0.8789 (tpp) REVERT: L 99 PHE cc_start: 0.9407 (m-10) cc_final: 0.9119 (m-10) REVERT: L 100 ASP cc_start: 0.9498 (t0) cc_final: 0.9142 (m-30) REVERT: L 180 MET cc_start: 0.8454 (tpp) cc_final: 0.8073 (tpt) REVERT: M 117 MET cc_start: 0.9078 (ptp) cc_final: 0.8653 (ptp) REVERT: M 197 ILE cc_start: 0.8092 (mm) cc_final: 0.7754 (tp) REVERT: N 51 ASP cc_start: 0.8997 (m-30) cc_final: 0.8696 (m-30) REVERT: N 93 ASP cc_start: 0.8383 (m-30) cc_final: 0.8181 (m-30) REVERT: O 146 MET cc_start: 0.8065 (ttm) cc_final: 0.7379 (ttm) REVERT: P 45 MET cc_start: 0.8794 (mmp) cc_final: 0.8569 (mmm) REVERT: P 59 ASP cc_start: 0.8586 (m-30) cc_final: 0.8363 (t0) REVERT: P 90 MET cc_start: 0.8756 (mtm) cc_final: 0.8219 (mmm) REVERT: P 117 PHE cc_start: 0.7070 (p90) cc_final: 0.6770 (p90) REVERT: P 126 LEU cc_start: 0.9124 (pp) cc_final: 0.8151 (tt) REVERT: P 149 MET cc_start: 0.5789 (mmm) cc_final: 0.5230 (tpp) REVERT: P 171 MET cc_start: 0.9069 (tpp) cc_final: 0.8580 (tpp) REVERT: Q 2 GLU cc_start: 0.8361 (pm20) cc_final: 0.7285 (tm-30) REVERT: Q 28 MET cc_start: 0.8835 (mtm) cc_final: 0.8460 (mpp) REVERT: Q 82 ASN cc_start: 0.8954 (t0) cc_final: 0.8568 (t0) REVERT: Q 102 LEU cc_start: 0.9199 (mp) cc_final: 0.8959 (mm) REVERT: R 54 PHE cc_start: 0.8897 (t80) cc_final: 0.8674 (t80) REVERT: R 97 MET cc_start: 0.6661 (mpp) cc_final: 0.6455 (mpp) REVERT: R 100 MET cc_start: 0.8263 (mpp) cc_final: 0.7710 (mpp) REVERT: S 83 MET cc_start: 0.8329 (mmp) cc_final: 0.8100 (mmp) REVERT: S 144 MET cc_start: 0.8630 (mtt) cc_final: 0.8297 (tpt) REVERT: S 145 LEU cc_start: 0.9692 (mt) cc_final: 0.9463 (mt) REVERT: T 7 THR cc_start: 0.8539 (p) cc_final: 0.8254 (t) REVERT: T 26 MET cc_start: 0.8632 (mtp) cc_final: 0.7917 (mpp) REVERT: T 96 MET cc_start: 0.9413 (mmm) cc_final: 0.9091 (tpp) REVERT: T 110 MET cc_start: 0.8842 (mtp) cc_final: 0.8582 (mmm) REVERT: T 127 MET cc_start: 0.8574 (mtm) cc_final: 0.7931 (mtm) REVERT: T 160 LEU cc_start: 0.8424 (tp) cc_final: 0.8202 (tp) REVERT: T 180 ASP cc_start: 0.8102 (t0) cc_final: 0.7546 (t0) REVERT: T 187 PHE cc_start: 0.8707 (p90) cc_final: 0.8106 (p90) REVERT: g 69 LEU cc_start: 0.8512 (mm) cc_final: 0.8233 (mp) REVERT: g 80 MET cc_start: 0.6074 (mmm) cc_final: 0.5773 (mmm) REVERT: g 120 ASP cc_start: 0.8894 (m-30) cc_final: 0.8555 (m-30) REVERT: g 138 MET cc_start: 0.7919 (tpp) cc_final: 0.7189 (tpp) REVERT: g 152 TYR cc_start: 0.7780 (m-80) cc_final: 0.7488 (m-10) REVERT: g 155 ASP cc_start: 0.8184 (t0) cc_final: 0.7817 (t0) REVERT: g 159 TYR cc_start: 0.7587 (t80) cc_final: 0.6476 (m-10) REVERT: h 92 LYS cc_start: 0.8521 (mtpt) cc_final: 0.8102 (mtmm) REVERT: h 166 ASN cc_start: 0.9341 (t0) cc_final: 0.9035 (t0) REVERT: j 117 ARG cc_start: 0.9426 (ttt90) cc_final: 0.9200 (ttm-80) REVERT: j 211 MET cc_start: 0.6880 (tmm) cc_final: 0.6042 (tmm) REVERT: k 59 MET cc_start: 0.8134 (ptm) cc_final: 0.7760 (ptp) REVERT: k 90 ASP cc_start: 0.9078 (t70) cc_final: 0.8808 (t70) REVERT: k 103 TYR cc_start: 0.8912 (m-80) cc_final: 0.8284 (m-80) REVERT: k 166 ASP cc_start: 0.8142 (m-30) cc_final: 0.7936 (m-30) REVERT: k 228 MET cc_start: 0.7180 (pmm) cc_final: 0.6739 (pmm) REVERT: l 62 LYS cc_start: 0.7165 (mmtt) cc_final: 0.6685 (mptt) REVERT: l 80 ASP cc_start: 0.8434 (m-30) cc_final: 0.7616 (t0) REVERT: l 228 ASP cc_start: 0.8889 (m-30) cc_final: 0.8404 (t0) REVERT: m 7 TYR cc_start: 0.6635 (m-10) cc_final: 0.6287 (m-10) REVERT: m 27 MET cc_start: 0.8381 (mtt) cc_final: 0.7866 (mmm) REVERT: m 75 MET cc_start: 0.8818 (mtp) cc_final: 0.8447 (ptp) REVERT: m 232 ARG cc_start: 0.8278 (mtt180) cc_final: 0.6617 (mtm-85) REVERT: n 4 MET cc_start: 0.8711 (tpt) cc_final: 0.8066 (tpp) REVERT: n 119 MET cc_start: 0.8374 (mtt) cc_final: 0.8036 (mtt) REVERT: o 82 MET cc_start: 0.7983 (ttm) cc_final: 0.7699 (tmm) REVERT: o 94 ILE cc_start: 0.8706 (tt) cc_final: 0.8479 (tp) REVERT: o 149 GLU cc_start: 0.8771 (tp30) cc_final: 0.8539 (tp30) REVERT: p 28 PHE cc_start: 0.9444 (t80) cc_final: 0.9011 (t80) REVERT: p 95 LEU cc_start: 0.9229 (mt) cc_final: 0.8746 (tp) REVERT: p 149 MET cc_start: 0.8335 (mmp) cc_final: 0.6902 (mmp) REVERT: p 150 CYS cc_start: 0.9150 (m) cc_final: 0.8886 (m) REVERT: p 158 MET cc_start: 0.8593 (tpp) cc_final: 0.8061 (tpp) REVERT: q 20 VAL cc_start: 0.6816 (t) cc_final: 0.6600 (t) REVERT: q 26 VAL cc_start: 0.8858 (m) cc_final: 0.8279 (m) REVERT: q 35 MET cc_start: 0.6258 (mpp) cc_final: 0.5381 (pmm) REVERT: q 69 MET cc_start: 0.9583 (tpp) cc_final: 0.9284 (tpp) REVERT: q 118 MET cc_start: 0.7393 (mmm) cc_final: 0.7147 (mmm) REVERT: r 55 TRP cc_start: 0.8787 (m100) cc_final: 0.8582 (m100) REVERT: r 86 MET cc_start: 0.9265 (mmp) cc_final: 0.8704 (ttt) REVERT: r 93 MET cc_start: 0.8140 (mmm) cc_final: 0.7370 (mtp) REVERT: r 97 MET cc_start: 0.8040 (tmm) cc_final: 0.7545 (tmm) REVERT: s 69 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8925 (mm-30) REVERT: s 76 LYS cc_start: 0.9433 (tttm) cc_final: 0.9184 (tppt) REVERT: s 83 MET cc_start: 0.8135 (ttt) cc_final: 0.7793 (ttt) REVERT: t 3 ASN cc_start: 0.8859 (m-40) cc_final: 0.8097 (t0) REVERT: t 73 ASP cc_start: 0.8951 (m-30) cc_final: 0.8579 (t70) REVERT: t 99 ARG cc_start: 0.9208 (mmt180) cc_final: 0.8358 (mmm160) REVERT: t 110 MET cc_start: 0.8591 (mmp) cc_final: 0.8193 (mmm) REVERT: t 169 VAL cc_start: 0.9246 (t) cc_final: 0.8833 (p) REVERT: t 173 MET cc_start: 0.9047 (tpp) cc_final: 0.8164 (mmt) REVERT: A 138 MET cc_start: 0.5577 (ttp) cc_final: 0.5333 (ttt) REVERT: A 186 LYS cc_start: 0.8916 (mttt) cc_final: 0.8467 (mtmm) REVERT: A 263 MET cc_start: 0.6947 (mtm) cc_final: 0.6318 (ptm) REVERT: A 273 PHE cc_start: 0.6658 (m-10) cc_final: 0.6386 (m-80) REVERT: A 299 MET cc_start: 0.8317 (tmm) cc_final: 0.7942 (ppp) REVERT: A 318 LEU cc_start: 0.8097 (mt) cc_final: 0.7746 (mt) REVERT: A 429 TYR cc_start: 0.5007 (p90) cc_final: 0.4362 (p90) REVERT: B 210 TYR cc_start: 0.8255 (m-80) cc_final: 0.7835 (m-80) REVERT: B 309 MET cc_start: 0.8227 (ptt) cc_final: 0.7835 (ppp) REVERT: B 329 MET cc_start: 0.8125 (mmp) cc_final: 0.7722 (mmm) REVERT: C 139 MET cc_start: 0.4426 (mtm) cc_final: 0.3900 (mtm) REVERT: C 229 ARG cc_start: 0.7139 (mpp-170) cc_final: 0.6153 (mmp80) REVERT: C 293 MET cc_start: 0.7776 (tpt) cc_final: 0.7537 (tpt) REVERT: C 298 ILE cc_start: 0.8795 (mt) cc_final: 0.8526 (mt) REVERT: C 327 ASP cc_start: 0.8905 (m-30) cc_final: 0.8584 (t0) REVERT: C 374 ARG cc_start: 0.5904 (tpp-160) cc_final: 0.5250 (mmm160) REVERT: D 89 ILE cc_start: 0.8142 (mm) cc_final: 0.7820 (mm) REVERT: D 167 ILE cc_start: 0.6109 (mt) cc_final: 0.5551 (mt) REVERT: D 170 MET cc_start: 0.6548 (ptt) cc_final: 0.6159 (ptt) REVERT: D 187 HIS cc_start: 0.8014 (m90) cc_final: 0.7569 (m90) REVERT: D 246 MET cc_start: 0.8127 (mtm) cc_final: 0.7878 (mtm) REVERT: D 309 MET cc_start: 0.6836 (mpp) cc_final: 0.6479 (mpp) REVERT: E 108 MET cc_start: 0.7701 (mmp) cc_final: 0.7252 (mmm) REVERT: E 232 MET cc_start: 0.8936 (ttp) cc_final: 0.8711 (ttt) REVERT: E 277 MET cc_start: 0.4225 (mpp) cc_final: 0.3816 (mpp) REVERT: E 376 ASP cc_start: 0.8884 (t70) cc_final: 0.8503 (p0) REVERT: F 373 MET cc_start: 0.6332 (mpp) cc_final: 0.6114 (mpp) REVERT: F 421 MET cc_start: 0.6836 (mmp) cc_final: 0.6257 (mtt) REVERT: f 222 ASP cc_start: -0.0030 (m-30) cc_final: -0.0610 (p0) REVERT: f 407 MET cc_start: 0.5259 (mmt) cc_final: 0.4667 (mmt) REVERT: f 477 MET cc_start: 0.0897 (mmt) cc_final: -0.1712 (ttp) REVERT: f 505 MET cc_start: -0.0373 (ttp) cc_final: -0.2714 (mtt) outliers start: 5 outliers final: 4 residues processed: 1097 average time/residue: 0.8736 time to fit residues: 1684.2841 Evaluate side-chains 861 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 857 time to evaluate : 9.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1268 random chunks: chunk 1111 optimal weight: 20.0000 chunk 1170 optimal weight: 20.0000 chunk 1068 optimal weight: 20.0000 chunk 1138 optimal weight: 10.0000 chunk 685 optimal weight: 7.9990 chunk 496 optimal weight: 20.0000 chunk 894 optimal weight: 30.0000 chunk 349 optimal weight: 30.0000 chunk 1029 optimal weight: 0.5980 chunk 1077 optimal weight: 8.9990 chunk 1134 optimal weight: 3.9990 overall best weight: 6.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 421 GLN U 463 ASN U 721 HIS ** U 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 880 ASN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 HIS ** V 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 257 ASN V 452 ASN ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 235 GLN ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 422 ASN ** X 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 174 HIS Z 229 GLN ** Z 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 GLN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 GLN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 ASN ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 GLN ** h 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN ** i 123 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** ** n 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 33 GLN ** p 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 72 ASN q 8 GLN q 87 ASN t 47 ASN ** t 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 HIS ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 327 ASN f 329 ASN f 752 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 101622 Z= 0.244 Angle : 0.746 11.543 137458 Z= 0.384 Chirality : 0.046 0.411 15660 Planarity : 0.005 0.080 17770 Dihedral : 6.842 150.934 14082 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 22.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.44 % Favored : 89.48 % Rotamer: Outliers : 0.06 % Allowed : 0.91 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.20 % Twisted Proline : 0.45 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.07), residues: 12738 helix: -0.14 (0.07), residues: 5616 sheet: -0.83 (0.13), residues: 1675 loop : -2.41 (0.08), residues: 5447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP d 61 HIS 0.016 0.001 HIS X 322 PHE 0.045 0.002 PHE d 71 TYR 0.037 0.002 TYR d 132 ARG 0.010 0.001 ARG a 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1062 time to evaluate : 9.390 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: U 106 ASP cc_start: 0.8956 (t0) cc_final: 0.8431 (m-30) REVERT: U 221 ILE cc_start: 0.2100 (pt) cc_final: 0.1676 (pt) REVERT: U 362 ASN cc_start: 0.6980 (t0) cc_final: 0.6510 (t0) REVERT: U 650 TYR cc_start: 0.9029 (t80) cc_final: 0.8794 (t80) REVERT: U 738 ASP cc_start: 0.8945 (m-30) cc_final: 0.8429 (t0) REVERT: U 757 MET cc_start: 0.7524 (ptp) cc_final: 0.7191 (ptp) REVERT: U 770 TRP cc_start: 0.7481 (m-90) cc_final: 0.6712 (m-90) REVERT: V 139 MET cc_start: 0.5768 (mmm) cc_final: 0.5364 (ttp) REVERT: V 302 TYR cc_start: 0.3859 (m-10) cc_final: 0.3579 (m-80) REVERT: V 309 MET cc_start: 0.7042 (ptm) cc_final: 0.6665 (ptm) REVERT: V 336 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8239 (mm-30) REVERT: W 114 GLU cc_start: 0.5962 (tm-30) cc_final: 0.5730 (tt0) REVERT: W 303 LYS cc_start: 0.7825 (mmmt) cc_final: 0.7448 (mttt) REVERT: W 315 MET cc_start: 0.4587 (pmm) cc_final: 0.1921 (mmm) REVERT: W 352 LYS cc_start: 0.8189 (mmtp) cc_final: 0.7878 (ptmm) REVERT: W 375 MET cc_start: 0.8190 (mmm) cc_final: 0.7715 (mmm) REVERT: W 377 ARG cc_start: 0.7196 (ttt90) cc_final: 0.6130 (mtt-85) REVERT: W 428 TRP cc_start: 0.8182 (m100) cc_final: 0.7354 (t60) REVERT: X 283 GLN cc_start: 0.8041 (mt0) cc_final: 0.7809 (mp10) REVERT: X 337 ARG cc_start: 0.6590 (mtt180) cc_final: 0.6050 (tpm170) REVERT: X 402 GLU cc_start: 0.9036 (tp30) cc_final: 0.8643 (tp30) REVERT: Y 42 MET cc_start: 0.3680 (ptt) cc_final: 0.3249 (ppp) REVERT: Y 104 MET cc_start: 0.6566 (tmm) cc_final: 0.5446 (ttm) REVERT: Y 105 MET cc_start: 0.2641 (ppp) cc_final: 0.2090 (ppp) REVERT: Y 245 GLU cc_start: 0.7063 (pm20) cc_final: 0.6616 (tt0) REVERT: Y 319 MET cc_start: 0.7008 (mmm) cc_final: 0.6673 (mmm) REVERT: Y 374 ASP cc_start: 0.8109 (m-30) cc_final: 0.7904 (m-30) REVERT: Y 384 SER cc_start: 0.8726 (t) cc_final: 0.8506 (p) REVERT: Y 389 MET cc_start: 0.1869 (mtm) cc_final: 0.1628 (pmm) REVERT: Z 103 LYS cc_start: 0.8014 (tttt) cc_final: 0.7686 (mtpt) REVERT: Z 256 GLN cc_start: 0.8253 (tp-100) cc_final: 0.7727 (mm-40) REVERT: a 278 MET cc_start: 0.6023 (ptm) cc_final: 0.5746 (ptm) REVERT: a 339 ARG cc_start: 0.5833 (mmt180) cc_final: 0.5310 (mmt180) REVERT: a 363 MET cc_start: 0.8860 (tmm) cc_final: 0.8314 (ppp) REVERT: b 42 ARG cc_start: 0.4776 (mpp-170) cc_final: 0.3834 (ttp80) REVERT: c 190 GLN cc_start: 0.8034 (mm110) cc_final: 0.7058 (tt0) REVERT: c 216 MET cc_start: 0.7351 (ptm) cc_final: 0.6865 (ttp) REVERT: c 226 MET cc_start: 0.7826 (mpp) cc_final: 0.7587 (mpp) REVERT: c 255 TYR cc_start: 0.8308 (m-80) cc_final: 0.8072 (m-80) REVERT: c 260 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8982 (pt0) REVERT: d 230 GLN cc_start: 0.7023 (tp40) cc_final: 0.6460 (mp10) REVERT: e 44 ASP cc_start: 0.6818 (t0) cc_final: 0.6347 (m-30) REVERT: G 120 ASP cc_start: 0.8965 (m-30) cc_final: 0.8599 (t0) REVERT: H 118 MET cc_start: 0.7743 (ttm) cc_final: 0.7505 (ttm) REVERT: H 166 ASN cc_start: 0.8382 (m110) cc_final: 0.7946 (m-40) REVERT: H 169 ASN cc_start: 0.8464 (m110) cc_final: 0.7612 (t0) REVERT: I 57 ASP cc_start: 0.7041 (m-30) cc_final: 0.6757 (m-30) REVERT: J 3 TYR cc_start: 0.7657 (m-80) cc_final: 0.7455 (m-80) REVERT: J 71 MET cc_start: 0.7925 (tpp) cc_final: 0.7084 (tpp) REVERT: J 175 ASN cc_start: 0.8511 (m-40) cc_final: 0.7954 (t0) REVERT: J 211 MET cc_start: 0.7807 (mmm) cc_final: 0.7213 (mmm) REVERT: K 78 MET cc_start: 0.7112 (ppp) cc_final: 0.6743 (ppp) REVERT: L 88 MET cc_start: 0.9310 (tpp) cc_final: 0.8890 (tpp) REVERT: L 91 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8743 (mm-30) REVERT: L 99 PHE cc_start: 0.9415 (m-10) cc_final: 0.9210 (m-10) REVERT: L 100 ASP cc_start: 0.9490 (t0) cc_final: 0.9147 (m-30) REVERT: L 180 MET cc_start: 0.8488 (tpp) cc_final: 0.8079 (tpt) REVERT: L 190 HIS cc_start: 0.8234 (m-70) cc_final: 0.7997 (m-70) REVERT: N 51 ASP cc_start: 0.9005 (m-30) cc_final: 0.8672 (m-30) REVERT: O 54 MET cc_start: 0.9385 (tmm) cc_final: 0.9119 (tmm) REVERT: O 146 MET cc_start: 0.8136 (ttm) cc_final: 0.7406 (ttm) REVERT: P 45 MET cc_start: 0.8807 (mmp) cc_final: 0.8591 (mmm) REVERT: P 90 MET cc_start: 0.8752 (mtm) cc_final: 0.8221 (mmm) REVERT: P 117 PHE cc_start: 0.7110 (p90) cc_final: 0.6775 (p90) REVERT: P 149 MET cc_start: 0.5999 (mmm) cc_final: 0.5487 (tpp) REVERT: P 171 MET cc_start: 0.9051 (tpp) cc_final: 0.8571 (tpp) REVERT: Q 4 LEU cc_start: 0.8501 (mt) cc_final: 0.8009 (mp) REVERT: Q 28 MET cc_start: 0.8861 (mtm) cc_final: 0.8471 (mpp) REVERT: Q 58 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8620 (mt-10) REVERT: Q 82 ASN cc_start: 0.8958 (t0) cc_final: 0.8579 (t0) REVERT: Q 102 LEU cc_start: 0.9279 (mp) cc_final: 0.9061 (mm) REVERT: R 97 MET cc_start: 0.6786 (mpp) cc_final: 0.6515 (mpp) REVERT: R 100 MET cc_start: 0.8251 (mpp) cc_final: 0.7718 (mpp) REVERT: S 144 MET cc_start: 0.8611 (mtt) cc_final: 0.8278 (tpt) REVERT: S 145 LEU cc_start: 0.9690 (mt) cc_final: 0.9450 (mt) REVERT: T 7 THR cc_start: 0.8554 (p) cc_final: 0.8250 (t) REVERT: T 26 MET cc_start: 0.8720 (mtp) cc_final: 0.8045 (mpp) REVERT: T 96 MET cc_start: 0.9371 (mmm) cc_final: 0.9137 (tpp) REVERT: T 110 MET cc_start: 0.8821 (mtp) cc_final: 0.8537 (mpp) REVERT: T 125 VAL cc_start: 0.9389 (t) cc_final: 0.8937 (t) REVERT: T 127 MET cc_start: 0.8693 (mtm) cc_final: 0.8067 (mtt) REVERT: T 160 LEU cc_start: 0.8445 (tp) cc_final: 0.8244 (tp) REVERT: T 180 ASP cc_start: 0.8329 (t0) cc_final: 0.7741 (t0) REVERT: g 69 LEU cc_start: 0.8555 (mm) cc_final: 0.8320 (mp) REVERT: g 115 CYS cc_start: 0.8570 (t) cc_final: 0.7952 (p) REVERT: g 120 ASP cc_start: 0.8959 (m-30) cc_final: 0.8584 (m-30) REVERT: g 138 MET cc_start: 0.8061 (tpp) cc_final: 0.7610 (tpp) REVERT: g 152 TYR cc_start: 0.7660 (m-80) cc_final: 0.7346 (m-10) REVERT: g 155 ASP cc_start: 0.8228 (t0) cc_final: 0.7844 (t0) REVERT: g 159 TYR cc_start: 0.7643 (t80) cc_final: 0.6662 (m-10) REVERT: h 92 LYS cc_start: 0.8548 (mtpt) cc_final: 0.8129 (mtmm) REVERT: h 166 ASN cc_start: 0.9378 (t0) cc_final: 0.9096 (t0) REVERT: i 74 CYS cc_start: 0.8630 (m) cc_final: 0.8191 (m) REVERT: j 117 ARG cc_start: 0.9462 (ttt90) cc_final: 0.9230 (ttm-80) REVERT: j 211 MET cc_start: 0.6973 (tmm) cc_final: 0.6105 (tmm) REVERT: k 90 ASP cc_start: 0.9060 (t70) cc_final: 0.8789 (t70) REVERT: k 103 TYR cc_start: 0.8940 (m-80) cc_final: 0.8488 (m-80) REVERT: k 166 ASP cc_start: 0.8179 (m-30) cc_final: 0.7962 (m-30) REVERT: k 226 PHE cc_start: 0.9126 (m-80) cc_final: 0.8513 (t80) REVERT: k 228 MET cc_start: 0.7272 (pmm) cc_final: 0.6837 (pmm) REVERT: l 62 LYS cc_start: 0.7247 (mmtt) cc_final: 0.6702 (mptt) REVERT: l 77 LEU cc_start: 0.7838 (mt) cc_final: 0.7553 (tp) REVERT: l 228 ASP cc_start: 0.8968 (m-30) cc_final: 0.8488 (t0) REVERT: m 7 TYR cc_start: 0.6708 (m-10) cc_final: 0.6345 (m-10) REVERT: m 27 MET cc_start: 0.8429 (mtt) cc_final: 0.7887 (mmm) REVERT: m 232 ARG cc_start: 0.8431 (mtt180) cc_final: 0.6839 (mtm-85) REVERT: n 4 MET cc_start: 0.8639 (tpt) cc_final: 0.7976 (tpp) REVERT: n 86 MET cc_start: 0.8812 (tmm) cc_final: 0.8382 (tmm) REVERT: n 119 MET cc_start: 0.8540 (mtt) cc_final: 0.8091 (mtt) REVERT: o 82 MET cc_start: 0.8081 (ttm) cc_final: 0.7754 (tmm) REVERT: o 149 GLU cc_start: 0.8762 (tp30) cc_final: 0.8506 (tp30) REVERT: p 28 PHE cc_start: 0.9465 (t80) cc_final: 0.9095 (t80) REVERT: p 96 TYR cc_start: 0.8316 (t80) cc_final: 0.7950 (t80) REVERT: p 149 MET cc_start: 0.8509 (mmp) cc_final: 0.6958 (mmt) REVERT: p 150 CYS cc_start: 0.9150 (m) cc_final: 0.8899 (m) REVERT: p 158 MET cc_start: 0.8810 (tpp) cc_final: 0.7975 (tpp) REVERT: q 8 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7434 (pp30) REVERT: q 26 VAL cc_start: 0.8830 (m) cc_final: 0.8254 (m) REVERT: q 35 MET cc_start: 0.6318 (mpp) cc_final: 0.6098 (mpp) REVERT: q 62 LYS cc_start: 0.9183 (mmpt) cc_final: 0.8856 (mmtm) REVERT: q 69 MET cc_start: 0.9553 (tpp) cc_final: 0.9238 (tpp) REVERT: q 118 MET cc_start: 0.7396 (mmm) cc_final: 0.6962 (tpp) REVERT: q 144 ASP cc_start: 0.8688 (t0) cc_final: 0.8464 (t0) REVERT: r 55 TRP cc_start: 0.8885 (m100) cc_final: 0.8467 (m100) REVERT: r 86 MET cc_start: 0.9295 (mmp) cc_final: 0.8792 (ttt) REVERT: r 93 MET cc_start: 0.8223 (mmm) cc_final: 0.7392 (mtp) REVERT: r 97 MET cc_start: 0.8052 (tmm) cc_final: 0.7549 (tmm) REVERT: s 76 LYS cc_start: 0.9420 (tttm) cc_final: 0.9176 (tptp) REVERT: s 83 MET cc_start: 0.8184 (ttt) cc_final: 0.7879 (ttt) REVERT: t 3 ASN cc_start: 0.8888 (m-40) cc_final: 0.8104 (t0) REVERT: t 73 ASP cc_start: 0.8979 (m-30) cc_final: 0.8589 (t70) REVERT: t 99 ARG cc_start: 0.9167 (mmt180) cc_final: 0.8405 (mmm160) REVERT: t 110 MET cc_start: 0.8636 (mmp) cc_final: 0.8250 (mmm) REVERT: A 186 LYS cc_start: 0.9008 (mttt) cc_final: 0.8775 (mttm) REVERT: A 273 PHE cc_start: 0.6718 (m-10) cc_final: 0.6437 (m-80) REVERT: A 318 LEU cc_start: 0.8053 (mt) cc_final: 0.7757 (mt) REVERT: A 332 MET cc_start: 0.7456 (tmm) cc_final: 0.7230 (tmm) REVERT: A 429 TYR cc_start: 0.5131 (p90) cc_final: 0.4504 (p90) REVERT: B 210 TYR cc_start: 0.8269 (m-80) cc_final: 0.7941 (m-80) REVERT: B 309 MET cc_start: 0.8254 (ptt) cc_final: 0.7820 (ppp) REVERT: B 310 LEU cc_start: 0.9413 (tp) cc_final: 0.9068 (mt) REVERT: B 329 MET cc_start: 0.8376 (mmp) cc_final: 0.7981 (mmm) REVERT: C 139 MET cc_start: 0.4562 (mtm) cc_final: 0.4056 (mtm) REVERT: C 229 ARG cc_start: 0.7045 (mpp-170) cc_final: 0.5987 (mmp80) REVERT: C 298 ILE cc_start: 0.8760 (mt) cc_final: 0.8503 (mt) REVERT: C 327 ASP cc_start: 0.8875 (m-30) cc_final: 0.8527 (t0) REVERT: C 374 ARG cc_start: 0.5903 (tpp-160) cc_final: 0.5237 (mmm160) REVERT: D 89 ILE cc_start: 0.8334 (mm) cc_final: 0.8034 (mm) REVERT: D 167 ILE cc_start: 0.6089 (mt) cc_final: 0.5600 (mt) REVERT: D 170 MET cc_start: 0.6635 (ptt) cc_final: 0.6242 (ptt) REVERT: D 246 MET cc_start: 0.8165 (mtm) cc_final: 0.7883 (mtm) REVERT: D 309 MET cc_start: 0.6923 (mpp) cc_final: 0.6544 (mpp) REVERT: E 108 MET cc_start: 0.7793 (mmp) cc_final: 0.7328 (mmm) REVERT: E 232 MET cc_start: 0.8949 (ttp) cc_final: 0.8739 (ttm) REVERT: E 277 MET cc_start: 0.4637 (mpp) cc_final: 0.4311 (mpp) REVERT: E 376 ASP cc_start: 0.8896 (t70) cc_final: 0.8517 (p0) REVERT: F 373 MET cc_start: 0.6672 (mpp) cc_final: 0.6411 (mpp) REVERT: F 421 MET cc_start: 0.6760 (mmp) cc_final: 0.6117 (mtt) REVERT: f 133 MET cc_start: 0.4284 (mmt) cc_final: 0.4015 (mtp) REVERT: f 222 ASP cc_start: 0.0107 (m-30) cc_final: -0.0630 (p0) REVERT: f 407 MET cc_start: 0.5078 (mmt) cc_final: 0.4434 (mmt) REVERT: f 416 MET cc_start: -0.1654 (mtp) cc_final: -0.2158 (mtp) REVERT: f 505 MET cc_start: -0.0519 (ttp) cc_final: -0.2742 (mtm) REVERT: f 670 MET cc_start: -0.3581 (tmm) cc_final: -0.4172 (ttt) outliers start: 6 outliers final: 3 residues processed: 1068 average time/residue: 0.9101 time to fit residues: 1700.1618 Evaluate side-chains 850 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 846 time to evaluate : 9.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1268 random chunks: chunk 747 optimal weight: 8.9990 chunk 1204 optimal weight: 9.9990 chunk 735 optimal weight: 5.9990 chunk 571 optimal weight: 5.9990 chunk 837 optimal weight: 30.0000 chunk 1263 optimal weight: 0.0370 chunk 1162 optimal weight: 6.9990 chunk 1005 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 777 optimal weight: 30.0000 chunk 616 optimal weight: 8.9990 overall best weight: 5.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 721 HIS ** U 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 HIS ** V 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 257 ASN ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 84 ASN ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 229 GLN ** Z 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 129 GLN ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 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 220 ASN ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 GLN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 152 GLN ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 87 ASN ** t 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 327 ASN ** f 782 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 101622 Z= 0.215 Angle : 0.730 13.591 137458 Z= 0.374 Chirality : 0.046 0.622 15660 Planarity : 0.005 0.080 17770 Dihedral : 6.786 151.175 14082 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.22 % Favored : 89.72 % Rotamer: Outliers : 0.03 % Allowed : 0.47 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.20 % Twisted Proline : 0.45 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.07), residues: 12738 helix: -0.10 (0.07), residues: 5614 sheet: -0.82 (0.13), residues: 1669 loop : -2.39 (0.08), residues: 5455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP d 61 HIS 0.014 0.001 HIS f 301 PHE 0.047 0.002 PHE b 21 TYR 0.028 0.002 TYR F 437 ARG 0.011 0.001 ARG A 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25476 Ramachandran restraints generated. 12738 Oldfield, 0 Emsley, 12738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1042 time to evaluate : 9.402 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: U 106 ASP cc_start: 0.8960 (t0) cc_final: 0.8432 (m-30) REVERT: U 221 ILE cc_start: 0.2139 (pt) cc_final: 0.1722 (pt) REVERT: U 362 ASN cc_start: 0.6966 (t0) cc_final: 0.6511 (t0) REVERT: U 738 ASP cc_start: 0.8928 (m-30) cc_final: 0.8432 (t0) REVERT: U 757 MET cc_start: 0.7573 (ptp) cc_final: 0.7249 (ptp) REVERT: V 139 MET cc_start: 0.5891 (mmm) cc_final: 0.5488 (ttp) REVERT: V 302 TYR cc_start: 0.3925 (m-10) cc_final: 0.3681 (m-80) REVERT: V 309 MET cc_start: 0.6985 (ptm) cc_final: 0.6593 (ptm) REVERT: V 336 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8256 (mm-30) REVERT: V 489 MET cc_start: 0.8308 (mmp) cc_final: 0.8051 (mmm) REVERT: W 16 MET cc_start: 0.4382 (mmp) cc_final: 0.3983 (ptp) REVERT: W 73 MET cc_start: 0.8891 (mmm) cc_final: 0.8650 (mmm) REVERT: W 114 GLU cc_start: 0.5993 (tm-30) cc_final: 0.5765 (tt0) REVERT: W 124 LEU cc_start: 0.7483 (mt) cc_final: 0.6886 (tt) REVERT: W 315 MET cc_start: 0.4554 (pmm) cc_final: 0.1929 (mmm) REVERT: W 352 LYS cc_start: 0.8190 (mmtp) cc_final: 0.7882 (ptmm) REVERT: W 375 MET cc_start: 0.8263 (mmm) cc_final: 0.7803 (mmm) REVERT: W 377 ARG cc_start: 0.7164 (ttt90) cc_final: 0.6112 (mtt90) REVERT: W 428 TRP cc_start: 0.8177 (m100) cc_final: 0.7267 (t60) REVERT: X 283 GLN cc_start: 0.8043 (mt0) cc_final: 0.7785 (mp10) REVERT: X 337 ARG cc_start: 0.6491 (mtt180) cc_final: 0.6001 (tpm170) REVERT: X 406 ASN cc_start: 0.9237 (m110) cc_final: 0.8867 (m110) REVERT: Y 73 MET cc_start: 0.3208 (mmp) cc_final: 0.2653 (mtt) REVERT: Y 104 MET cc_start: 0.6483 (tmm) cc_final: 0.5555 (ttt) REVERT: Y 105 MET cc_start: 0.2698 (ppp) cc_final: 0.2164 (ppp) REVERT: Y 245 GLU cc_start: 0.7021 (pm20) cc_final: 0.6606 (tt0) REVERT: Y 319 MET cc_start: 0.7069 (mmm) cc_final: 0.6737 (mmm) REVERT: Y 367 GLN cc_start: 0.9010 (tp-100) cc_final: 0.8298 (mt0) REVERT: Y 384 SER cc_start: 0.8767 (t) cc_final: 0.8514 (p) REVERT: a 278 MET cc_start: 0.6042 (ptm) cc_final: 0.5686 (ptm) REVERT: a 339 ARG cc_start: 0.5899 (mmt180) cc_final: 0.5013 (mmt180) REVERT: b 1 MET cc_start: 0.1155 (mtp) cc_final: 0.0934 (mtp) REVERT: b 42 ARG cc_start: 0.4937 (mpp-170) cc_final: 0.3904 (ttp80) REVERT: c 216 MET cc_start: 0.7323 (ptm) cc_final: 0.6720 (ttp) REVERT: c 226 MET cc_start: 0.7810 (mpp) cc_final: 0.7578 (mpp) REVERT: c 255 TYR cc_start: 0.8317 (m-80) cc_final: 0.8079 (m-80) REVERT: c 260 GLU cc_start: 0.9259 (mt-10) cc_final: 0.9028 (pt0) REVERT: d 230 GLN cc_start: 0.7050 (tp40) cc_final: 0.6478 (mp10) REVERT: G 120 ASP cc_start: 0.8946 (m-30) cc_final: 0.8581 (t0) REVERT: G 131 MET cc_start: 0.8092 (mpp) cc_final: 0.7333 (mpp) REVERT: G 216 GLU cc_start: 0.8221 (mp0) cc_final: 0.7885 (mp0) REVERT: H 166 ASN cc_start: 0.8371 (m110) cc_final: 0.7925 (m-40) REVERT: H 169 ASN cc_start: 0.8454 (m110) cc_final: 0.7636 (t0) REVERT: J 71 MET cc_start: 0.7834 (tpp) cc_final: 0.7018 (tpp) REVERT: J 175 ASN cc_start: 0.8485 (m-40) cc_final: 0.7878 (t0) REVERT: J 211 MET cc_start: 0.7882 (mmm) cc_final: 0.7236 (mmm) REVERT: K 78 MET cc_start: 0.7121 (ppp) cc_final: 0.6827 (ppp) REVERT: K 95 GLU cc_start: 0.9021 (mp0) cc_final: 0.8801 (mp0) REVERT: L 88 MET cc_start: 0.9309 (tpp) cc_final: 0.8918 (tpp) REVERT: L 91 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8718 (mm-30) REVERT: L 99 PHE cc_start: 0.9423 (m-10) cc_final: 0.9204 (m-10) REVERT: L 100 ASP cc_start: 0.9490 (t0) cc_final: 0.9149 (m-30) REVERT: L 180 MET cc_start: 0.8465 (tpp) cc_final: 0.8190 (tpp) REVERT: L 190 HIS cc_start: 0.8216 (m-70) cc_final: 0.7968 (m-70) REVERT: N 51 ASP cc_start: 0.9007 (m-30) cc_final: 0.8698 (m-30) REVERT: N 147 MET cc_start: 0.7581 (ttm) cc_final: 0.7281 (ttt) REVERT: O 54 MET cc_start: 0.9380 (tmm) cc_final: 0.9145 (tmm) REVERT: O 146 MET cc_start: 0.8213 (ttm) cc_final: 0.7525 (ttm) REVERT: P 90 MET cc_start: 0.8774 (mtm) cc_final: 0.8245 (mmm) REVERT: P 117 PHE cc_start: 0.7052 (p90) cc_final: 0.6679 (p90) REVERT: P 149 MET cc_start: 0.6056 (mmm) cc_final: 0.5486 (tpp) REVERT: P 171 MET cc_start: 0.9044 (tpp) cc_final: 0.8553 (tpp) REVERT: Q 4 LEU cc_start: 0.8390 (mt) cc_final: 0.8086 (mt) REVERT: Q 28 MET cc_start: 0.8897 (mtm) cc_final: 0.8500 (mpp) REVERT: Q 82 ASN cc_start: 0.8966 (t0) cc_final: 0.8602 (t0) REVERT: Q 102 LEU cc_start: 0.9216 (mp) cc_final: 0.8987 (mm) REVERT: R 100 MET cc_start: 0.8231 (mpp) cc_final: 0.7711 (mpp) REVERT: S 144 MET cc_start: 0.8498 (mtt) cc_final: 0.8040 (tpp) REVERT: S 145 LEU cc_start: 0.9682 (mt) cc_final: 0.9295 (mt) REVERT: T 7 THR cc_start: 0.8546 (p) cc_final: 0.8273 (t) REVERT: T 26 MET cc_start: 0.8658 (mtp) cc_final: 0.8056 (mpp) REVERT: T 96 MET cc_start: 0.9350 (mmm) cc_final: 0.9144 (tpp) REVERT: T 110 MET cc_start: 0.8854 (mtp) cc_final: 0.8608 (mmm) REVERT: T 127 MET cc_start: 0.8665 (mtm) cc_final: 0.7987 (mtt) REVERT: T 180 ASP cc_start: 0.8307 (t0) cc_final: 0.7723 (t70) REVERT: g 69 LEU cc_start: 0.8620 (mm) cc_final: 0.8418 (mp) REVERT: g 80 MET cc_start: 0.6193 (mmm) cc_final: 0.5546 (mmm) REVERT: g 120 ASP cc_start: 0.8986 (m-30) cc_final: 0.8628 (m-30) REVERT: g 138 MET cc_start: 0.8070 (tpp) cc_final: 0.7372 (tpp) REVERT: g 152 TYR cc_start: 0.7630 (m-80) cc_final: 0.7188 (m-10) REVERT: g 155 ASP cc_start: 0.8273 (t0) cc_final: 0.7944 (t0) REVERT: g 159 TYR cc_start: 0.7540 (t80) cc_final: 0.6647 (m-10) REVERT: h 92 LYS cc_start: 0.8558 (mtpt) cc_final: 0.8133 (mtmm) REVERT: h 166 ASN cc_start: 0.9383 (t0) cc_final: 0.9101 (t0) REVERT: i 74 CYS cc_start: 0.8619 (m) cc_final: 0.8166 (m) REVERT: j 117 ARG cc_start: 0.9460 (ttt90) cc_final: 0.9225 (ttm-80) REVERT: j 211 MET cc_start: 0.6866 (tmm) cc_final: 0.6005 (tmm) REVERT: k 90 ASP cc_start: 0.9055 (t70) cc_final: 0.8764 (t70) REVERT: k 103 TYR cc_start: 0.8921 (m-80) cc_final: 0.8474 (m-80) REVERT: k 203 LYS cc_start: 0.9145 (tmtt) cc_final: 0.8862 (pttt) REVERT: k 226 PHE cc_start: 0.9146 (m-80) cc_final: 0.8518 (t80) REVERT: k 228 MET cc_start: 0.7347 (pmm) cc_final: 0.6903 (pmm) REVERT: l 62 LYS cc_start: 0.7288 (mmtt) cc_final: 0.6765 (mptt) REVERT: l 77 LEU cc_start: 0.7992 (mt) cc_final: 0.7704 (tp) REVERT: l 172 LEU cc_start: 0.9319 (mm) cc_final: 0.9049 (pp) REVERT: m 7 TYR cc_start: 0.6596 (m-10) cc_final: 0.6234 (m-10) REVERT: m 27 MET cc_start: 0.8419 (mtt) cc_final: 0.7883 (mmm) REVERT: m 136 MET cc_start: 0.9087 (mmt) cc_final: 0.8738 (mmt) REVERT: m 232 ARG cc_start: 0.8420 (mtt180) cc_final: 0.6938 (mtm-85) REVERT: n 4 MET cc_start: 0.8641 (tpt) cc_final: 0.7954 (tpp) REVERT: n 119 MET cc_start: 0.8517 (mtt) cc_final: 0.8021 (mtt) REVERT: o 82 MET cc_start: 0.8112 (ttm) cc_final: 0.7850 (tmm) REVERT: o 135 MET cc_start: 0.8053 (tpt) cc_final: 0.7379 (tmm) REVERT: o 149 GLU cc_start: 0.8774 (tp30) cc_final: 0.8512 (tp30) REVERT: p 11 VAL cc_start: 0.9165 (t) cc_final: 0.8816 (p) REVERT: p 28 PHE cc_start: 0.9455 (t80) cc_final: 0.9083 (t80) REVERT: p 88 MET cc_start: 0.9120 (mmm) cc_final: 0.8847 (tpp) REVERT: p 96 TYR cc_start: 0.8369 (t80) cc_final: 0.8019 (t80) REVERT: p 109 ILE cc_start: 0.9067 (mm) cc_final: 0.8865 (mm) REVERT: p 149 MET cc_start: 0.8450 (mmp) cc_final: 0.6987 (mmt) REVERT: p 150 CYS cc_start: 0.9121 (m) cc_final: 0.8853 (m) REVERT: p 158 MET cc_start: 0.8863 (tpp) cc_final: 0.7967 (tpp) REVERT: p 183 MET cc_start: 0.3181 (mtp) cc_final: 0.2684 (mpp) REVERT: q 62 LYS cc_start: 0.9134 (mmpt) cc_final: 0.8517 (mttp) REVERT: q 69 MET cc_start: 0.9574 (tpp) cc_final: 0.9272 (tpp) REVERT: q 118 MET cc_start: 0.7436 (mmm) cc_final: 0.6987 (tpp) REVERT: r 55 TRP cc_start: 0.8807 (m100) cc_final: 0.8370 (m100) REVERT: r 86 MET cc_start: 0.9280 (mmp) cc_final: 0.8803 (ttt) REVERT: r 93 MET cc_start: 0.8243 (mmm) cc_final: 0.7401 (mtp) REVERT: r 97 MET cc_start: 0.8030 (tmm) cc_final: 0.7554 (tmm) REVERT: s 69 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8787 (mm-30) REVERT: s 83 MET cc_start: 0.8160 (ttt) cc_final: 0.7834 (ttt) REVERT: t 3 ASN cc_start: 0.8913 (m-40) cc_final: 0.8111 (t0) REVERT: t 73 ASP cc_start: 0.8982 (m-30) cc_final: 0.8590 (t70) REVERT: t 110 MET cc_start: 0.8627 (mmp) cc_final: 0.8250 (mmm) REVERT: A 186 LYS cc_start: 0.9008 (mttt) cc_final: 0.8570 (mtmm) REVERT: A 332 MET cc_start: 0.7499 (tmm) cc_final: 0.7249 (tmm) REVERT: A 429 TYR cc_start: 0.5165 (p90) cc_final: 0.4618 (p90) REVERT: B 210 TYR cc_start: 0.8248 (m-80) cc_final: 0.7872 (m-80) REVERT: B 309 MET cc_start: 0.8286 (ptt) cc_final: 0.7856 (ppp) REVERT: B 310 LEU cc_start: 0.9404 (tp) cc_final: 0.9071 (mt) REVERT: B 329 MET cc_start: 0.8229 (mmp) cc_final: 0.7854 (mmm) REVERT: B 373 THR cc_start: 0.7478 (p) cc_final: 0.7185 (p) REVERT: C 139 MET cc_start: 0.4641 (mtm) cc_final: 0.3982 (ttm) REVERT: C 229 ARG cc_start: 0.7012 (mpp-170) cc_final: 0.5905 (mmp-170) REVERT: C 293 MET cc_start: 0.7654 (tpt) cc_final: 0.7361 (tpt) REVERT: C 298 ILE cc_start: 0.8723 (mt) cc_final: 0.8450 (mt) REVERT: C 327 ASP cc_start: 0.8894 (m-30) cc_final: 0.8557 (t0) REVERT: C 374 ARG cc_start: 0.5891 (tpp-160) cc_final: 0.5209 (mmm160) REVERT: D 57 GLN cc_start: 0.8521 (tp-100) cc_final: 0.7720 (mt0) REVERT: D 89 ILE cc_start: 0.8318 (mm) cc_final: 0.8015 (mm) REVERT: D 167 ILE cc_start: 0.6115 (mt) cc_final: 0.5648 (mt) REVERT: D 170 MET cc_start: 0.6636 (ptt) cc_final: 0.6264 (ptt) REVERT: D 309 MET cc_start: 0.7034 (mpp) cc_final: 0.6469 (mmp) REVERT: E 108 MET cc_start: 0.7807 (mmp) cc_final: 0.7357 (mmm) REVERT: E 232 MET cc_start: 0.8957 (ttp) cc_final: 0.8738 (ttm) REVERT: E 277 MET cc_start: 0.4664 (mpp) cc_final: 0.4351 (mpp) REVERT: E 376 ASP cc_start: 0.8883 (t70) cc_final: 0.8500 (p0) REVERT: F 373 MET cc_start: 0.6646 (mpp) cc_final: 0.6374 (mpp) REVERT: F 421 MET cc_start: 0.6703 (mmp) cc_final: 0.6172 (mtt) REVERT: f 133 MET cc_start: 0.4393 (mmt) cc_final: 0.4191 (mtp) REVERT: f 222 ASP cc_start: 0.0091 (m-30) cc_final: -0.0751 (p0) REVERT: f 407 MET cc_start: 0.4999 (mmt) cc_final: 0.4386 (mmt) REVERT: f 477 MET cc_start: 0.0939 (mmt) cc_final: -0.1478 (ttp) REVERT: f 505 MET cc_start: -0.0750 (ttp) cc_final: -0.2979 (mtm) outliers start: 3 outliers final: 3 residues processed: 1045 average time/residue: 0.9151 time to fit residues: 1668.2662 Evaluate side-chains 844 residues out of total 10972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 841 time to evaluate : 9.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1268 random chunks: chunk 799 optimal weight: 0.4980 chunk 1071 optimal weight: 8.9990 chunk 308 optimal weight: 3.9990 chunk 927 optimal weight: 20.0000 chunk 148 optimal weight: 0.0970 chunk 279 optimal weight: 40.0000 chunk 1007 optimal weight: 0.9990 chunk 421 optimal weight: 9.9990 chunk 1034 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 185 optimal weight: 40.0000 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 721 HIS ** U 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 HIS ** V 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 185 GLN V 257 ASN ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 454 ASN X 406 ASN ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 22 HIS Z 174 HIS Z 229 GLN ** a 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 129 GLN ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 190 GLN ** c 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN G 75 ASN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** I 220 ASN ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 GLN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 148 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** ** m 101 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** ** p 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.068104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.057823 restraints weight = 822404.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.059202 restraints weight = 523014.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.059835 restraints weight = 352591.742| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.5916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 101622 Z= 0.177 Angle : 0.702 12.269 137458 Z= 0.357 Chirality : 0.046 0.513 15660 Planarity : 0.005 0.080 17770 Dihedral : 6.613 151.208 14082 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.37 % Favored : 90.56 % Rotamer: Outliers : 0.04 % Allowed : 0.42 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.22 % Cis-general : 0.19 % Twisted Proline : 0.45 % Twisted General : 0.07 % 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: -1.57 (0.07), residues: 12738 helix: 0.04 (0.07), residues: 5622 sheet: -0.69 (0.13), residues: 1650 loop : -2.32 (0.08), residues: 5466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP d 61 HIS 0.012 0.001 HIS f 301 PHE 0.040 0.002 PHE b 21 TYR 0.033 0.001 TYR A 420 ARG 0.012 0.000 ARG n 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31269.68 seconds wall clock time: 548 minutes 11.56 seconds (32891.56 seconds total)