Starting phenix.real_space_refine on Tue Mar 26 22:45:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t0g_8334/03_2024/5t0g_8334_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t0g_8334/03_2024/5t0g_8334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t0g_8334/03_2024/5t0g_8334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t0g_8334/03_2024/5t0g_8334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t0g_8334/03_2024/5t0g_8334_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t0g_8334/03_2024/5t0g_8334_updated.pdb" } resolution = 4.4 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 Anisotropic ADP refinement not supported. Converting 72278 atoms to isotropic. 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 18 5.49 5 S 449 5.16 5 C 49139 2.51 5 N 13382 2.21 5 O 14811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "H ARG 4": "NH1" <-> "NH2" Residue "H TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 249": "NH1" <-> "NH2" Residue "K ARG 20": "NH1" <-> "NH2" Residue "K PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "L ARG 157": "NH1" <-> "NH2" Residue "L TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "M GLU 234": "OE1" <-> "OE2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ASP 347": "OD1" <-> "OD2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 303": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 411": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 283": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D ASP 410": "OD1" <-> "OD2" Residue "E ASP 116": "OD1" <-> "OD2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "E TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 223": "NH1" <-> "NH2" Residue "E GLU 252": "OE1" <-> "OE2" Residue "E ARG 255": "NH1" <-> "NH2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E ARG 281": "NH1" <-> "NH2" Residue "E ARG 356": "NH1" <-> "NH2" Residue "F TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 238": "NH1" <-> "NH2" Residue "F ARG 269": "NH1" <-> "NH2" Residue "F ARG 295": "NH1" <-> "NH2" Residue "F ARG 334": "NH1" <-> "NH2" Residue "F ARG 347": "NH1" <-> "NH2" Residue "F ARG 350": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C ARG 258": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 334": "NH1" <-> "NH2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "C ARG 374": "NH1" <-> "NH2" Residue "U GLU 40": "OE1" <-> "OE2" 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 "U PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 36": "OE1" <-> "OE2" 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 TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 357": "NH1" <-> "NH2" Residue "W ARG 364": "NH1" <-> "NH2" Residue "X TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 137": "NH1" <-> "NH2" Residue "Y TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 176": "NH1" <-> "NH2" Residue "Y ARG 177": "NH1" <-> "NH2" Residue "Y ARG 179": "NH1" <-> "NH2" Residue "Y PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 173": "OE1" <-> "OE2" Residue "Z TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 267": "NH1" <-> "NH2" Residue "a ASP 187": "OD1" <-> "OD2" 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 "b GLU 134": "OE1" <-> "OE2" Residue "b ASP 164": "OD1" <-> "OD2" Residue "c ARG 68": "NH1" <-> "NH2" Residue "c ARG 104": "NH1" <-> "NH2" Residue "c PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 146": "OD1" <-> "OD2" 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 "f PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 604": "NH1" <-> "NH2" Residue "f TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 77800 Number of models: 1 Model: "" Number of chains: 39 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: {'CIS': 1, 'PTRANS': 8, 'TRANS': 230} 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: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1713 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 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: {'CIS': 3, 'PTRANS': 5, 'TRANS': 241} 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': 1, 'PTRANS': 6, 'TRANS': 231} 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: {'CIS': 4, 'PTRANS': 7, 'TRANS': 216} 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: {'CIS': 1, 'PTRANS': 10, 'TRANS': 226} 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: {'PCIS': 1, 'PTRANS': 8, '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: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2835 Classifications: {'peptide': 361} Link IDs: {'CIS': 12, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 325} Chain: "B" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2662 Classifications: {'peptide': 341} Link IDs: {'CIS': 14, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 310} 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': 13, 'PCIS': 5, 'PTRANS': 12, 'TRANS': 349} Chain: "E" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2790 Classifications: {'peptide': 353} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 16, 'TRANS': 331} Chain: "F" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2863 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'CIS': 13, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain breaks: 1 Chain: "C" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3015 Classifications: {'peptide': 384} Link IDs: {'CIS': 9, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 358} Chain: "U" Number of atoms: 6287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6287 Classifications: {'peptide': 806} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 25, 'TRANS': 776} Chain breaks: 3 Chain: "V" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3852 Classifications: {'peptide': 480} Link IDs: {'CIS': 22, 'PTRANS': 22, 'TRANS': 435} 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: {'CIS': 14, 'PTRANS': 8, 'TRANS': 433} Chain: "X" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3009 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 369} Chain: "Y" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3115 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'CIS': 6, 'PTRANS': 7, 'TRANS': 364} Chain: "Z" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'CIS': 13, 'PCIS': 2, 'PTRANS': 7, 'TRANS': 263} 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: {'CIS': 8, 'PTRANS': 12, 'TRANS': 352} Chain: "b" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1458 Classifications: {'peptide': 191} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 178} Chain: "c" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2260 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Link IDs: {'CIS': 8, 'PCIS': 3, 'PTRANS': 7, 'TRANS': 268} 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: {'CIS': 14, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 231} 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: {'CIS': 3, 'PTRANS': 1, 'TRANS': 35} Chain breaks: 1 Chain: "f" Number of atoms: 5331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5331 Classifications: {'peptide': 694} Link IDs: {'CIS': 25, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 647} Chain breaks: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ALA X 359 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA X 359 " occ=0.50 residue: pdb=" N GLN X 380 " occ=0.50 ... (7 atoms not shown) pdb=" NE2 GLN X 380 " occ=0.50 residue: pdb=" N GLY Z 30 " occ=0.38 ... (2 atoms not shown) pdb=" O GLY Z 30 " occ=0.38 residue: pdb=" N ILE b 90 " occ=0.46 ... (6 atoms not shown) pdb=" CD1 ILE b 90 " occ=0.46 residue: pdb=" N SER b 115 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER b 115 " occ=0.70 residue: pdb=" N ILE b 140 " occ=0.39 ... (6 atoms not shown) pdb=" CD1 ILE b 140 " occ=0.39 residue: pdb=" N VAL b 173 " occ=0.89 ... (5 atoms not shown) pdb=" CG2 VAL b 173 " occ=0.89 residue: pdb=" N GLY b 191 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY b 191 " occ=0.50 residue: pdb=" N ILE d 63 " occ=0.78 ... (6 atoms not shown) pdb=" CD1 ILE d 63 " occ=0.78 residue: pdb=" N SER d 70 " occ=0.95 ... (4 atoms not shown) pdb=" OG SER d 70 " occ=0.95 residue: pdb=" N MET d 95 " occ=0.66 ... (6 atoms not shown) pdb=" CE MET d 95 " occ=0.66 residue: pdb=" N MET d 144 " occ=0.52 ... (6 atoms not shown) pdb=" CE MET d 144 " occ=0.52 Time building chain proxies: 28.72, per 1000 atoms: 0.37 Number of scatterers: 77800 At special positions: 0 Unit cell: (282.08, 207.26, 228.76, 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 449 16.00 P 18 15.00 O 14811 8.00 N 13382 7.00 C 49139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 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=0, symmetry=0 Time building additional restraints: 22.79 Conformation dependent library (CDL) restraints added in 10.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 401 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 115 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 113 " 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18600 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 405 helices and 57 sheets defined 49.6% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.42 Creating SS restraints... Processing helix chain 'G' and resid 23 through 34 removed outlier: 3.564A pdb=" N LYS G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 104 removed outlier: 3.743A pdb=" N SER G 89 " --> pdb=" O ALA G 85 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN G 90 " --> pdb=" O ASP G 86 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN G 92 " --> pdb=" O ARG G 88 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG G 93 " --> pdb=" O SER G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 127 removed outlier: 3.778A pdb=" N LYS G 116 " --> pdb=" O ASP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 183 removed outlier: 3.823A pdb=" N SER G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS G 181 " --> pdb=" O SER G 177 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS G 182 " --> pdb=" O PHE G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 205 removed outlier: 4.008A pdb=" N ILE G 199 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR G 200 " --> pdb=" O GLU G 196 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL G 205 " --> pdb=" O CYS G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 242 Processing helix chain 'H' and resid 20 through 30 Processing helix chain 'H' and resid 81 through 100 removed outlier: 3.608A pdb=" N VAL H 85 " --> pdb=" O PRO H 81 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU H 86 " --> pdb=" O ASP H 82 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN H 95 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN H 96 " --> pdb=" O LYS H 92 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR H 97 " --> pdb=" O LEU H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 123 removed outlier: 3.517A pdb=" N GLN H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 177 removed outlier: 3.501A pdb=" N THR H 172 " --> pdb=" O VAL H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 198 removed outlier: 4.258A pdb=" N SER H 198 " --> pdb=" O THR H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 229 Processing helix chain 'I' and resid 3 through 5 No H-bonds generated for 'chain 'I' and resid 3 through 5' Processing helix chain 'I' and resid 19 through 29 removed outlier: 3.532A pdb=" N TYR I 23 " --> pdb=" O TYR I 19 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA I 27 " --> pdb=" O TYR I 23 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE I 28 " --> pdb=" O ALA I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 100 removed outlier: 3.771A pdb=" N LEU I 86 " --> pdb=" O ASP I 82 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN I 88 " --> pdb=" O ASN I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 123 removed outlier: 3.669A pdb=" N TYR I 121 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR I 122 " --> pdb=" O LYS I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 177 removed outlier: 4.033A pdb=" N ALA I 170 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS I 176 " --> pdb=" O SER I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 197 Processing helix chain 'I' and resid 230 through 249 removed outlier: 3.856A pdb=" N GLN I 235 " --> pdb=" O LYS I 231 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU I 236 " --> pdb=" O GLU I 232 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG I 249 " --> pdb=" O ALA I 245 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 27 removed outlier: 3.754A pdb=" N GLN J 23 " --> pdb=" O VAL J 19 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 96 removed outlier: 4.103A pdb=" N ILE J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL J 83 " --> pdb=" O ASP J 79 " (cutoff:3.500A) 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 removed outlier: 3.703A pdb=" N GLU J 173 " --> pdb=" O ARG J 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 196 removed outlier: 3.738A pdb=" N LYS J 189 " --> pdb=" O ASP J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 238 Processing helix chain 'K' and resid 22 through 31 removed outlier: 3.876A pdb=" N GLU K 29 " --> pdb=" O GLU K 25 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA K 30 " --> pdb=" O TYR K 26 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE K 31 " --> pdb=" O ALA K 27 " (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 82 through 103 removed outlier: 3.868A pdb=" N THR K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU K 88 " --> pdb=" O ASP K 84 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS K 91 " --> pdb=" O THR K 87 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL K 94 " --> pdb=" O ASP K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 118 removed outlier: 3.941A pdb=" N THR K 113 " --> pdb=" O VAL K 109 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 184 removed outlier: 3.581A pdb=" N GLU K 183 " --> pdb=" O SER K 179 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 205 removed outlier: 3.595A pdb=" N LYS K 196 " --> pdb=" O LYS K 192 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU K 199 " --> pdb=" O ILE K 195 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE K 200 " --> pdb=" O LYS K 196 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE K 201 " --> pdb=" O SER K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 240 removed outlier: 3.503A pdb=" N VAL K 237 " --> pdb=" O GLU K 233 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS K 239 " --> pdb=" O GLU K 235 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 7 No H-bonds generated for 'chain 'L' and resid 5 through 7' Processing helix chain 'L' and resid 20 through 31 removed outlier: 3.547A pdb=" N ALA L 28 " --> pdb=" O TYR L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 97 removed outlier: 3.706A pdb=" N SER L 95 " --> pdb=" O GLU L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 120 removed outlier: 3.875A pdb=" N SER L 110 " --> pdb=" O SER L 106 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU L 111 " --> pdb=" O ARG L 107 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE L 112 " --> pdb=" O LEU L 108 " (cutoff:3.500A) removed outlier: 4.019A 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 176 removed outlier: 3.505A pdb=" N TYR L 171 " --> pdb=" O SER L 167 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ARG L 174 " --> pdb=" O THR L 170 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS L 175 " --> pdb=" O TYR L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 196 removed outlier: 3.930A pdb=" N LYS L 189 " --> pdb=" O ASN L 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA L 194 " --> pdb=" O HIS L 190 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU L 195 " --> pdb=" O GLY L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 233 Proline residue: L 231 - end of helix Processing helix chain 'M' and resid 21 through 31 removed outlier: 3.530A pdb=" N LYS M 28 " --> pdb=" O GLU M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 101 Processing helix chain 'M' and resid 108 through 123 removed outlier: 3.601A pdb=" N TYR M 118 " --> pdb=" O ARG M 114 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR M 123 " --> pdb=" O VAL M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 178 removed outlier: 4.720A pdb=" N GLU M 175 " --> pdb=" O ALA M 171 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE M 176 " --> pdb=" O ALA M 172 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU M 177 " --> pdb=" O LYS M 173 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 199 removed outlier: 4.275A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE M 196 " --> pdb=" O GLU M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'N' and resid 49 through 70 Processing helix chain 'N' and resid 76 through 90 removed outlier: 3.652A pdb=" N LEU N 82 " --> pdb=" O THR N 78 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE N 83 " --> pdb=" O ALA N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 133 removed outlier: 3.518A pdb=" N SER N 133 " --> pdb=" O SER N 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 130 through 133' Processing helix chain 'N' and resid 136 through 142 removed outlier: 4.067A pdb=" N ALA N 141 " --> pdb=" O GLY N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 166 removed outlier: 3.630A pdb=" N GLN N 154 " --> pdb=" O GLU N 150 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA N 163 " --> pdb=" O ALA N 159 " (cutoff:3.500A) 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 removed outlier: 3.672A pdb=" N VAL O 137 " --> pdb=" O ALA O 133 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP O 140 " --> pdb=" O ALA O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 148 through 165 removed outlier: 3.587A pdb=" N GLY O 162 " --> pdb=" O ALA O 158 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE O 164 " --> pdb=" O ALA O 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 7 removed outlier: 4.710A pdb=" N ASN P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 3 through 7' Processing helix chain 'P' and resid 57 through 77 Processing helix chain 'P' and resid 84 through 96 Processing helix chain 'P' and resid 144 through 153 removed outlier: 3.731A pdb=" N GLU P 151 " --> pdb=" O TYR P 147 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER P 152 " --> pdb=" O GLY P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 160 through 175 Processing helix chain 'Q' and resid 50 through 71 removed outlier: 3.797A pdb=" N VAL Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL Q 64 " --> pdb=" O ILE Q 60 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET Q 69 " --> pdb=" O GLN Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 92 removed outlier: 3.709A pdb=" N ASN Q 87 " --> pdb=" O PHE Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 145 removed outlier: 3.899A pdb=" N PHE Q 137 " --> pdb=" O TYR Q 134 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU Q 140 " --> pdb=" O PHE Q 137 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER Q 141 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE Q 142 " --> pdb=" O THR Q 139 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU Q 143 " --> pdb=" O LEU Q 140 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP Q 144 " --> pdb=" O SER Q 141 " (cutoff:3.500A) Processing helix chain 'Q' and resid 153 through 167 removed outlier: 3.843A pdb=" N LYS Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS Q 163 " --> pdb=" O LEU Q 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 69 removed outlier: 3.766A pdb=" N GLN R 62 " --> pdb=" O LEU R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 90 removed outlier: 3.739A pdb=" N GLN R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 142 removed outlier: 3.879A pdb=" N TYR R 136 " --> pdb=" O VAL R 133 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY R 137 " --> pdb=" O TYR R 134 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET R 139 " --> pdb=" O TYR R 136 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP R 140 " --> pdb=" O GLY R 137 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG R 141 " --> pdb=" O VAL R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 166 removed outlier: 3.836A pdb=" N ASP R 154 " --> pdb=" O GLU R 150 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE R 160 " --> pdb=" O ALA R 156 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG R 166 " --> pdb=" O GLN R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 200 removed outlier: 4.641A pdb=" N GLU R 197 " --> pdb=" O ALA R 193 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS R 198 " --> pdb=" O ASP R 194 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 58 through 79 removed outlier: 3.732A pdb=" N LYS S 73 " --> pdb=" O GLU S 69 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET S 74 " --> pdb=" O ALA S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 102 removed outlier: 3.672A pdb=" N ALA S 89 " --> pdb=" O THR S 85 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA S 90 " --> pdb=" O GLY S 86 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG S 99 " --> pdb=" O ILE S 95 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG S 100 " --> pdb=" O LEU S 96 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N PHE S 101 " --> pdb=" O TYR S 97 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE S 102 " --> pdb=" O SER S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 140 through 143 removed outlier: 4.144A pdb=" N ALA S 143 " --> pdb=" O SER S 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 140 through 143' Processing helix chain 'S' and resid 146 through 152 Processing helix chain 'S' and resid 168 through 183 removed outlier: 3.629A pdb=" N ARG S 173 " --> pdb=" O ASP S 169 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER S 181 " --> pdb=" O ASP S 177 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 77 removed outlier: 3.890A pdb=" N ILE T 72 " --> pdb=" O GLY T 68 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU T 74 " --> pdb=" O MET T 70 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU T 77 " --> pdb=" O ASP T 73 " (cutoff:3.500A) Processing helix chain 'T' and resid 85 through 102 removed outlier: 3.836A pdb=" N SER T 101 " --> pdb=" O TYR T 97 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS T 102 " --> pdb=" O SER T 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 144 Processing helix chain 'T' and resid 146 through 156 removed outlier: 3.690A pdb=" N LYS T 156 " --> pdb=" O GLU T 152 " (cutoff:3.500A) Processing helix chain 'T' and resid 162 through 179 removed outlier: 3.768A pdb=" N VAL T 169 " --> pdb=" O ALA T 165 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU T 170 " --> pdb=" O ARG T 166 " (cutoff:3.500A) Processing helix chain 'T' and resid 210 through 212 No H-bonds generated for 'chain 'T' and resid 210 through 212' Processing helix chain 'A' and resid 74 through 88 removed outlier: 3.704A pdb=" N ALA A 82 " --> pdb=" O TRP A 78 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASP A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LYS A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLN A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.829A pdb=" N VAL A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.573A pdb=" N ALA A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 252 through 266 removed outlier: 3.728A pdb=" N LEU A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) 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 292 through 306 removed outlier: 3.689A pdb=" N THR A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 336 Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 348 through 360 removed outlier: 4.373A pdb=" N THR A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N HIS A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.603A pdb=" N ARG A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 398 removed outlier: 3.803A pdb=" N GLY A 393 " --> pdb=" O CYS A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 423 removed outlier: 3.526A pdb=" N LEU A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 431 No H-bonds generated for 'chain 'A' and resid 428 through 431' Processing helix chain 'B' and resid 94 through 103 removed outlier: 3.836A pdb=" N ASP B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASP B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 144 No H-bonds generated for 'chain 'B' and resid 141 through 144' Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 191 through 203 removed outlier: 4.788A pdb=" N GLU B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 212 No H-bonds generated for 'chain 'B' and resid 209 through 212' Processing helix chain 'B' and resid 232 through 243 removed outlier: 3.761A pdb=" N LYS B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 removed outlier: 3.588A pdb=" N GLN B 257 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 removed outlier: 4.040A pdb=" N LEU B 266 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 269 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 271 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 273 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 316 Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 358 through 369 Processing helix chain 'B' and resid 380 through 386 removed outlier: 3.648A pdb=" N ILE B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 408 removed outlier: 3.520A pdb=" N CYS B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 432 removed outlier: 3.654A pdb=" N ASN B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 46 Processing helix chain 'D' and resid 49 through 81 removed outlier: 3.782A pdb=" N GLU D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU D 78 " --> pdb=" O HIS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 179 removed outlier: 3.745A pdb=" N GLU D 176 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU D 179 " --> pdb=" O GLN D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 189 through 194 Processing helix chain 'D' and resid 212 through 222 removed outlier: 3.545A pdb=" N VAL D 219 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA D 220 " --> pdb=" O LYS D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 256 Proline residue: D 244 - end of helix Processing helix chain 'D' and resid 267 through 269 No H-bonds generated for 'chain 'D' and resid 267 through 269' Processing helix chain 'D' and resid 278 through 299 removed outlier: 3.902A pdb=" N ALA D 281 " --> pdb=" O GLN D 278 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 290 " --> pdb=" O ARG D 287 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 292 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET D 296 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 322 No H-bonds generated for 'chain 'D' and resid 319 through 322' Processing helix chain 'D' and resid 338 through 351 removed outlier: 3.620A pdb=" N ILE D 348 " --> pdb=" O ILE D 344 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 367 through 369 No H-bonds generated for 'chain 'D' and resid 367 through 369' Processing helix chain 'D' and resid 375 through 387 Processing helix chain 'D' and resid 396 through 405 removed outlier: 3.575A pdb=" N LYS D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.994A pdb=" N TYR D 417 " --> pdb=" O HIS D 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 89 through 92 No H-bonds generated for 'chain 'E' and resid 89 through 92' Processing helix chain 'E' and resid 118 through 121 No H-bonds generated for 'chain 'E' and resid 118 through 121' Processing helix chain 'E' and resid 130 through 134 Processing helix chain 'E' and resid 139 through 154 removed outlier: 3.916A pdb=" N GLU E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 157 through 162 removed outlier: 3.683A pdb=" N VAL E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 191 Processing helix chain 'E' and resid 200 through 202 No H-bonds generated for 'chain 'E' and resid 200 through 202' Processing helix chain 'E' and resid 210 through 224 removed outlier: 3.617A pdb=" N TYR E 221 " --> pdb=" O MET E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 238 No H-bonds generated for 'chain 'E' and resid 235 through 238' Processing helix chain 'E' and resid 249 through 264 removed outlier: 3.715A pdb=" N GLN E 254 " --> pdb=" O ASP E 250 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU E 259 " --> pdb=" O ARG E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 306 through 317 Processing helix chain 'E' and resid 328 through 334 Processing helix chain 'E' and resid 340 through 357 removed outlier: 3.514A pdb=" N ILE E 355 " --> pdb=" O GLY E 351 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG E 356 " --> pdb=" O MET E 352 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 380 Processing helix chain 'F' and resid 64 through 83 removed outlier: 3.604A pdb=" N ASN F 76 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL F 82 " --> pdb=" O LYS F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 170 through 173 No H-bonds generated for 'chain 'F' and resid 170 through 173' Processing helix chain 'F' and resid 185 through 187 No H-bonds generated for 'chain 'F' and resid 185 through 187' Processing helix chain 'F' and resid 192 through 215 removed outlier: 3.712A pdb=" N GLN F 196 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU F 197 " --> pdb=" O LYS F 193 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 198 " --> pdb=" O GLN F 194 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE F 202 " --> pdb=" O LEU F 198 " (cutoff:3.500A) Proline residue: F 205 - end of helix removed outlier: 3.914A pdb=" N LYS F 209 " --> pdb=" O PRO F 205 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLU F 210 " --> pdb=" O MET F 206 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LYS F 211 " --> pdb=" O ASN F 207 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN F 214 " --> pdb=" O GLU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 244 removed outlier: 3.727A pdb=" N ALA F 241 " --> pdb=" O ALA F 237 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA F 242 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN F 243 " --> pdb=" O ALA F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 263 through 277 removed outlier: 3.783A pdb=" N LEU F 274 " --> pdb=" O ASP F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 291 No H-bonds generated for 'chain 'F' and resid 288 through 291' Processing helix chain 'F' and resid 302 through 319 removed outlier: 4.050A pdb=" N GLU F 305 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU F 311 " --> pdb=" O ARG F 308 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU F 314 " --> pdb=" O LEU F 311 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY F 319 " --> pdb=" O GLN F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 324 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 359 through 369 removed outlier: 3.514A pdb=" N MET F 366 " --> pdb=" O ARG F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 386 Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.612A pdb=" N GLY F 404 " --> pdb=" O CYS F 400 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 406 " --> pdb=" O GLU F 402 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA F 407 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU F 408 " --> pdb=" O GLY F 404 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG F 409 " --> pdb=" O MET F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 427 removed outlier: 3.825A pdb=" N MET F 421 " --> pdb=" O HIS F 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 67 removed outlier: 3.845A pdb=" N LEU C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 42 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU C 45 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 removed outlier: 3.746A pdb=" N MET C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) 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: 3.562A pdb=" N GLU C 160 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU C 163 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.632A 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 178 removed outlier: 4.413A pdb=" N GLU C 176 " --> pdb=" O GLU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 207 removed outlier: 3.895A pdb=" N ALA C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 223 No H-bonds generated for 'chain 'C' and resid 220 through 223' Processing helix chain 'C' and resid 233 through 240 Processing helix chain 'C' and resid 261 through 282 removed outlier: 3.849A pdb=" N GLU C 268 " --> pdb=" O GLY C 264 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.608A pdb=" N ALA C 304 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 335 removed outlier: 4.019A pdb=" N ASP C 327 " --> pdb=" O GLU C 323 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LYS C 335 " --> pdb=" O ILE C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 349 removed outlier: 3.807A pdb=" N ALA C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU C 349 " --> pdb=" O ARG C 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 344 through 349' Processing helix chain 'C' and resid 357 through 372 removed outlier: 3.565A pdb=" N GLY C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET C 368 " --> pdb=" O THR C 364 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 392 removed outlier: 3.733A pdb=" N ALA C 386 " --> pdb=" O ASP C 382 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 13 Processing helix chain 'U' and resid 17 through 34 removed outlier: 3.957A pdb=" N GLU U 21 " --> pdb=" O GLN U 18 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN U 28 " --> pdb=" O HIS U 25 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL U 31 " --> pdb=" O ASN U 28 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ASN U 32 " --> pdb=" O ALA U 29 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP U 33 " --> pdb=" O VAL U 30 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE U 34 " --> pdb=" O VAL U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 38 No H-bonds generated for 'chain 'U' and resid 36 through 38' Processing helix chain 'U' and resid 42 through 50 removed outlier: 4.234A pdb=" N VAL U 47 " --> pdb=" O ASP U 43 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU U 48 " --> pdb=" O LYS U 44 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 70 removed outlier: 4.062A pdb=" N LEU U 62 " --> pdb=" O GLN U 58 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL U 63 " --> pdb=" O PHE U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 84 removed outlier: 3.718A pdb=" N TYR U 80 " --> pdb=" O GLU U 76 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY U 83 " --> pdb=" O ASN U 79 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 89 No H-bonds generated for 'chain 'U' and resid 86 through 89' Processing helix chain 'U' and resid 96 through 117 removed outlier: 3.607A pdb=" N ILE U 100 " --> pdb=" O TYR U 96 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP U 117 " --> pdb=" O VAL U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 143 removed outlier: 4.058A pdb=" N VAL U 134 " --> pdb=" O LEU U 130 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN U 135 " --> pdb=" O GLU U 131 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG U 140 " --> pdb=" O LYS U 136 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS U 141 " --> pdb=" O MET U 137 " (cutoff:3.500A) Processing helix chain 'U' and resid 147 through 156 removed outlier: 3.998A pdb=" N ILE U 151 " --> pdb=" O TYR U 147 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY U 152 " --> pdb=" O LYS U 148 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA U 154 " --> pdb=" O ALA U 150 " (cutoff:3.500A) Processing helix chain 'U' and resid 160 through 167 removed outlier: 3.675A pdb=" N LYS U 165 " --> pdb=" O ASP U 161 " (cutoff:3.500A) Processing helix chain 'U' and resid 176 through 187 removed outlier: 3.966A pdb=" N LEU U 181 " --> pdb=" O LEU U 177 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS U 182 " --> pdb=" O ALA U 178 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER U 186 " --> pdb=" O LYS U 182 " (cutoff:3.500A) Processing helix chain 'U' and resid 194 through 207 removed outlier: 3.818A pdb=" N VAL U 200 " --> pdb=" O LYS U 196 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU U 201 " --> pdb=" O VAL U 197 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL U 202 " --> pdb=" O LEU U 198 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS U 203 " --> pdb=" O ARG U 199 " (cutoff:3.500A) Processing helix chain 'U' and resid 214 through 223 Processing helix chain 'U' and resid 226 through 239 removed outlier: 3.716A pdb=" N ASP U 231 " --> pdb=" O GLN U 227 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE U 232 " --> pdb=" O ALA U 228 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU U 233 " --> pdb=" O VAL U 229 " (cutoff:3.500A) Processing helix chain 'U' and resid 244 through 255 removed outlier: 3.665A pdb=" N GLN U 247 " --> pdb=" O MET U 244 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE U 248 " --> pdb=" O ALA U 245 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS U 249 " --> pdb=" O TYR U 246 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE U 250 " --> pdb=" O GLN U 247 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP U 251 " --> pdb=" O ILE U 248 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU U 254 " --> pdb=" O ASP U 251 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER U 255 " --> pdb=" O LEU U 252 " (cutoff:3.500A) Processing helix chain 'U' and resid 258 through 268 removed outlier: 3.870A pdb=" N GLN U 266 " --> pdb=" O SER U 262 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN U 267 " --> pdb=" O SER U 263 " (cutoff:3.500A) Processing helix chain 'U' and resid 321 through 330 removed outlier: 3.875A pdb=" N MET U 325 " --> pdb=" O GLN U 321 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE U 326 " --> pdb=" O THR U 322 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS U 327 " --> pdb=" O LEU U 323 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE U 328 " --> pdb=" O LYS U 324 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU U 329 " --> pdb=" O MET U 325 " (cutoff:3.500A) Processing helix chain 'U' and resid 332 through 345 Processing helix chain 'U' and resid 350 through 359 removed outlier: 4.568A pdb=" N ALA U 359 " --> pdb=" O ASN U 355 " (cutoff:3.500A) Processing helix chain 'U' and resid 365 through 376 removed outlier: 4.111A pdb=" N VAL U 370 " --> pdb=" O HIS U 366 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE U 375 " --> pdb=" O ILE U 371 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET U 376 " --> pdb=" O ALA U 372 " (cutoff:3.500A) Processing helix chain 'U' and resid 385 through 388 No H-bonds generated for 'chain 'U' and resid 385 through 388' Processing helix chain 'U' and resid 391 through 395 Processing helix chain 'U' and resid 398 through 411 removed outlier: 3.758A pdb=" N LYS U 401 " --> pdb=" O ASN U 398 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE U 402 " --> pdb=" O TRP U 399 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR U 405 " --> pdb=" O PHE U 402 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA U 406 " --> pdb=" O THR U 403 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU U 408 " --> pdb=" O THR U 405 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 425 removed outlier: 3.997A pdb=" N MET U 423 " --> pdb=" O ALA U 419 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA U 424 " --> pdb=" O LEU U 420 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N THR U 425 " --> pdb=" O GLN U 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 419 through 425' Processing helix chain 'U' and resid 428 through 431 No H-bonds generated for 'chain 'U' and resid 428 through 431' Processing helix chain 'U' and resid 436 through 449 removed outlier: 3.852A pdb=" N GLY U 442 " --> pdb=" O GLN U 438 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU U 443 " --> pdb=" O GLU U 439 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR U 444 " --> pdb=" O GLY U 440 " (cutoff:3.500A) Processing helix chain 'U' and resid 456 through 466 removed outlier: 3.712A pdb=" N ASN U 463 " --> pdb=" O ASP U 459 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN U 464 " --> pdb=" O TYR U 460 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS U 466 " --> pdb=" O LEU U 462 " (cutoff:3.500A) Processing helix chain 'U' and resid 472 through 484 removed outlier: 4.167A pdb=" N GLY U 476 " --> pdb=" O ILE U 472 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU U 479 " --> pdb=" O HIS U 475 " (cutoff:3.500A) Processing helix chain 'U' and resid 492 through 503 removed outlier: 3.644A pdb=" N LEU U 496 " --> pdb=" O ASP U 492 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS U 498 " --> pdb=" O TYR U 494 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR U 499 " --> pdb=" O ASP U 495 " (cutoff:3.500A) Processing helix chain 'U' and resid 509 through 519 removed outlier: 3.530A pdb=" N GLY U 517 " --> pdb=" O GLY U 513 " (cutoff:3.500A) Processing helix chain 'U' and resid 526 through 535 Processing helix chain 'U' and resid 542 through 555 Processing helix chain 'U' and resid 560 through 572 removed outlier: 3.900A pdb=" N ALA U 563 " --> pdb=" O MET U 560 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA U 565 " --> pdb=" O GLU U 562 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU U 568 " --> pdb=" O ALA U 565 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS U 571 " --> pdb=" O GLU U 568 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG U 572 " --> pdb=" O SER U 569 " (cutoff:3.500A) Processing helix chain 'U' and resid 576 through 589 removed outlier: 3.722A pdb=" N MET U 583 " --> pdb=" O ARG U 579 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR U 584 " --> pdb=" O ARG U 580 " (cutoff:3.500A) Processing helix chain 'U' and resid 597 through 608 removed outlier: 4.470A pdb=" N ARG U 601 " --> pdb=" O LYS U 597 " (cutoff:3.500A) Processing helix chain 'U' and resid 612 through 628 removed outlier: 3.691A pdb=" N VAL U 619 " --> pdb=" O ARG U 615 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER U 621 " --> pdb=" O ALA U 617 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU U 622 " --> pdb=" O ALA U 618 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE U 627 " --> pdb=" O GLY U 623 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ARG U 628 " --> pdb=" O PHE U 624 " (cutoff:3.500A) Processing helix chain 'U' and resid 630 through 637 Proline residue: U 634 - end of helix Processing helix chain 'U' and resid 640 through 642 No H-bonds generated for 'chain 'U' and resid 640 through 642' Processing helix chain 'U' and resid 646 through 659 removed outlier: 3.604A pdb=" N LEU U 656 " --> pdb=" O ALA U 652 " (cutoff:3.500A) Processing helix chain 'U' and resid 666 through 677 Proline residue: U 674 - end of helix removed outlier: 4.289A pdb=" N ASN U 677 " --> pdb=" O GLU U 673 " (cutoff:3.500A) Processing helix chain 'U' and resid 681 through 694 removed outlier: 3.509A pdb=" N GLN U 685 " --> pdb=" O ASN U 681 " (cutoff:3.500A) Processing helix chain 'U' and resid 705 through 718 removed outlier: 3.708A pdb=" N LEU U 712 " --> pdb=" O GLN U 708 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER U 714 " --> pdb=" O ARG U 710 " (cutoff:3.500A) Processing helix chain 'U' and resid 724 through 737 removed outlier: 4.031A pdb=" N GLY U 729 " --> pdb=" O MET U 725 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA U 730 " --> pdb=" O ALA U 726 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE U 731 " --> pdb=" O LYS U 727 " (cutoff:3.500A) Processing helix chain 'U' and resid 757 through 767 Processing helix chain 'U' and resid 773 through 782 removed outlier: 3.675A pdb=" N LEU U 779 " --> pdb=" O SER U 776 " (cutoff:3.500A) Processing helix chain 'V' and resid 19 through 52 Proline residue: V 26 - end of helix Proline residue: V 29 - end of helix Proline residue: V 32 - end of helix removed outlier: 4.172A pdb=" N MET V 37 " --> pdb=" O GLN V 33 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU V 40 " --> pdb=" O GLU V 36 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA V 41 " --> pdb=" O MET V 37 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY V 49 " --> pdb=" O GLY V 45 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP V 52 " --> pdb=" O THR V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 61 through 73 Processing helix chain 'V' and resid 87 through 94 removed outlier: 3.798A pdb=" N GLU V 90 " --> pdb=" O SER V 87 " (cutoff:3.500A) Proline residue: V 91 - end of helix Processing helix chain 'V' and resid 101 through 120 removed outlier: 3.824A pdb=" N SER V 105 " --> pdb=" O LEU V 101 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ARG V 106 " --> pdb=" O PRO V 102 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG V 107 " --> pdb=" O SER V 103 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL V 112 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS V 115 " --> pdb=" O TYR V 111 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA V 116 " --> pdb=" O VAL V 112 " (cutoff:3.500A) Processing helix chain 'V' and resid 128 through 135 removed outlier: 3.507A pdb=" N LEU V 132 " --> pdb=" O ASP V 129 " (cutoff:3.500A) Proline residue: V 133 - end of helix Processing helix chain 'V' and resid 137 through 141 Processing helix chain 'V' and resid 148 through 165 Proline residue: V 158 - end of helix Proline residue: V 161 - end of helix removed outlier: 4.634A pdb=" N GLU V 164 " --> pdb=" O LEU V 160 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA V 165 " --> pdb=" O PRO V 161 " (cutoff:3.500A) Processing helix chain 'V' and resid 172 through 191 Processing helix chain 'V' and resid 199 through 220 removed outlier: 4.270A pdb=" N LEU V 205 " --> pdb=" O ARG V 201 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL V 206 " --> pdb=" O ALA V 202 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE V 220 " --> pdb=" O ARG V 216 " (cutoff:3.500A) Processing helix chain 'V' and resid 226 through 238 Processing helix chain 'V' and resid 246 through 260 removed outlier: 3.556A pdb=" N ASN V 252 " --> pdb=" O ALA V 248 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN V 257 " --> pdb=" O LEU V 253 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS V 260 " --> pdb=" O ARG V 256 " (cutoff:3.500A) Processing helix chain 'V' and resid 265 through 272 removed outlier: 3.998A pdb=" N LYS V 269 " --> pdb=" O ASP V 265 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU V 270 " --> pdb=" O GLN V 266 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL V 271 " --> pdb=" O ALA V 267 " (cutoff:3.500A) Processing helix chain 'V' and resid 282 through 298 removed outlier: 3.978A pdb=" N ARG V 287 " --> pdb=" O GLU V 284 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR V 292 " --> pdb=" O LEU V 289 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS V 296 " --> pdb=" O GLY V 293 " (cutoff:3.500A) Processing helix chain 'V' and resid 302 through 314 removed outlier: 3.850A pdb=" N ARG V 307 " --> pdb=" O SER V 303 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR V 308 " --> pdb=" O GLU V 304 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 324 through 339 removed outlier: 3.800A pdb=" N HIS V 329 " --> pdb=" O LYS V 325 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE V 333 " --> pdb=" O HIS V 329 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL V 334 " --> pdb=" O LYS V 330 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL V 335 " --> pdb=" O LEU V 331 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU V 336 " --> pdb=" O LEU V 332 " (cutoff:3.500A) Processing helix chain 'V' and resid 345 through 348 Processing helix chain 'V' and resid 351 through 368 removed outlier: 4.297A pdb=" N ARG V 355 " --> pdb=" O PRO V 351 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER V 356 " --> pdb=" O SER V 352 " (cutoff:3.500A) Proline residue: V 359 - end of helix Processing helix chain 'V' and resid 372 through 389 removed outlier: 3.767A pdb=" N VAL V 378 " --> pdb=" O LYS V 374 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU V 379 " --> pdb=" O PHE V 375 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP V 380 " --> pdb=" O ASN V 376 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLU V 384 " --> pdb=" O ASP V 380 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LYS V 385 " --> pdb=" O GLN V 381 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE V 386 " --> pdb=" O PHE V 382 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA V 388 " --> pdb=" O GLU V 384 " (cutoff:3.500A) Processing helix chain 'V' and resid 391 through 413 removed outlier: 4.187A pdb=" N ILE V 396 " --> pdb=" O THR V 393 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU V 398 " --> pdb=" O ILE V 395 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG V 399 " --> pdb=" O ILE V 396 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS V 400 " --> pdb=" O ARG V 397 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE V 403 " --> pdb=" O HIS V 400 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL V 407 " --> pdb=" O LYS V 404 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER V 413 " --> pdb=" O ILE V 410 " (cutoff:3.500A) Processing helix chain 'V' and resid 419 through 422 No H-bonds generated for 'chain 'V' and resid 419 through 422' Processing helix chain 'V' and resid 431 through 443 removed outlier: 3.855A pdb=" N GLU V 435 " --> pdb=" O PRO V 431 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE V 436 " --> pdb=" O GLU V 432 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL V 438 " --> pdb=" O ALA V 434 " (cutoff:3.500A) Processing helix chain 'V' and resid 467 through 494 removed outlier: 4.715A pdb=" N GLU V 471 " --> pdb=" O SER V 468 " (cutoff:3.500A) Proline residue: V 472 - end of helix removed outlier: 3.525A pdb=" N HIS V 477 " --> pdb=" O LEU V 474 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE V 480 " --> pdb=" O HIS V 477 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER V 481 " --> pdb=" O GLN V 478 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU V 484 " --> pdb=" O SER V 481 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS V 492 " --> pdb=" O MET V 489 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA V 493 " --> pdb=" O SER V 490 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 18 removed outlier: 3.745A pdb=" N GLU W 7 " --> pdb=" O ASP W 3 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL W 14 " --> pdb=" O ASP W 10 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS W 15 " --> pdb=" O GLY W 11 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET W 16 " --> pdb=" O ARG W 12 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU W 17 " --> pdb=" O ILE W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 22 through 37 removed outlier: 3.536A pdb=" N LEU W 28 " --> pdb=" O VAL W 24 " (cutoff:3.500A) Proline residue: W 29 - end of helix removed outlier: 3.634A pdb=" N LEU W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA W 35 " --> pdb=" O CYS W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 43 through 64 removed outlier: 3.619A pdb=" N VAL W 61 " --> pdb=" O ALA W 57 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 84 removed outlier: 3.516A pdb=" N CYS W 74 " --> pdb=" O VAL W 71 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU W 76 " --> pdb=" O MET W 73 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TRP W 80 " --> pdb=" O ALA W 77 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP W 81 " --> pdb=" O LYS W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 114 removed outlier: 3.675A pdb=" N GLN W 99 " --> pdb=" O SER W 95 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU W 113 " --> pdb=" O CYS W 109 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 132 removed outlier: 3.654A pdb=" N LEU W 122 " --> pdb=" O LEU W 118 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARG W 129 " --> pdb=" O ILE W 125 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET W 130 " --> pdb=" O ASP W 126 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL W 131 " --> pdb=" O THR W 127 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR W 132 " --> pdb=" O LEU W 128 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 155 removed outlier: 3.771A pdb=" N ARG W 144 " --> pdb=" O ILE W 140 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU W 145 " --> pdb=" O GLU W 141 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR W 146 " --> pdb=" O ARG W 142 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA W 150 " --> pdb=" O THR W 146 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR W 151 " --> pdb=" O LYS W 147 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE W 152 " --> pdb=" O THR W 148 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS W 153 " --> pdb=" O LEU W 149 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN W 155 " --> pdb=" O THR W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 159 through 171 removed outlier: 3.731A pdb=" N ILE W 165 " --> pdb=" O GLU W 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU W 166 " --> pdb=" O ALA W 162 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN W 170 " --> pdb=" O LEU W 166 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL W 171 " --> pdb=" O GLN W 167 " (cutoff:3.500A) Processing helix chain 'W' and resid 181 through 186 Processing helix chain 'W' and resid 188 through 196 removed outlier: 3.962A pdb=" N LEU W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA W 195 " --> pdb=" O ARG W 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 199 through 210 removed outlier: 3.669A pdb=" N ILE W 204 " --> pdb=" O ILE W 200 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE W 209 " --> pdb=" O ILE W 205 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN W 210 " --> pdb=" O SER W 206 " (cutoff:3.500A) Processing helix chain 'W' and resid 222 through 236 removed outlier: 3.755A pdb=" N TYR W 227 " --> pdb=" O LYS W 223 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN W 228 " --> pdb=" O LEU W 224 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU W 229 " --> pdb=" O LYS W 225 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN W 232 " --> pdb=" O ASN W 228 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU W 233 " --> pdb=" O LEU W 229 " (cutoff:3.500A) Processing helix chain 'W' and resid 242 through 256 removed outlier: 3.977A pdb=" N HIS W 246 " --> pdb=" O SER W 242 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG W 248 " --> pdb=" O CYS W 244 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA W 249 " --> pdb=" O LYS W 245 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP W 252 " --> pdb=" O ARG W 248 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR W 253 " --> pdb=" O ALA W 249 " (cutoff:3.500A) Proline residue: W 254 - end of helix Processing helix chain 'W' and resid 261 through 276 removed outlier: 3.771A pdb=" N LYS W 268 " --> pdb=" O GLN W 264 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TYR W 273 " --> pdb=" O SER W 269 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N VAL W 274 " --> pdb=" O VAL W 270 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ILE W 275 " --> pdb=" O VAL W 271 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU W 276 " --> pdb=" O LEU W 272 " (cutoff:3.500A) Processing helix chain 'W' and resid 281 through 290 removed outlier: 3.628A pdb=" N ASP W 285 " --> pdb=" O ASN W 281 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS W 288 " --> pdb=" O SER W 284 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG W 289 " --> pdb=" O ASP W 285 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE W 290 " --> pdb=" O LEU W 286 " (cutoff:3.500A) Processing helix chain 'W' and resid 296 through 298 No H-bonds generated for 'chain 'W' and resid 296 through 298' Processing helix chain 'W' and resid 301 through 309 removed outlier: 3.645A pdb=" N PHE W 309 " --> pdb=" O LEU W 305 " (cutoff:3.500A) Processing helix chain 'W' and resid 317 through 324 Processing helix chain 'W' and resid 335 through 340 Processing helix chain 'W' and resid 344 through 369 removed outlier: 3.553A pdb=" N ARG W 364 " --> pdb=" O GLU W 360 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE W 365 " --> pdb=" O HIS W 361 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET W 366 " --> pdb=" O ASN W 362 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS W 368 " --> pdb=" O ARG W 364 " (cutoff:3.500A) Processing helix chain 'W' and resid 375 through 382 removed outlier: 3.560A pdb=" N GLN W 380 " --> pdb=" O LYS W 376 " (cutoff:3.500A) Processing helix chain 'W' and resid 386 through 398 Processing helix chain 'W' and resid 423 through 455 removed outlier: 4.266A pdb=" N SER W 437 " --> pdb=" O ASN W 433 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU W 438 " --> pdb=" O SER W 434 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR W 442 " --> pdb=" O LEU W 438 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR W 443 " --> pdb=" O VAL W 439 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE W 446 " --> pdb=" O THR W 442 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA W 447 " --> pdb=" O THR W 443 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU W 455 " --> pdb=" O MET W 451 " (cutoff:3.500A) Processing helix chain 'X' and resid 44 through 60 removed outlier: 3.804A pdb=" N SER X 49 " --> pdb=" O VAL X 45 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE X 50 " --> pdb=" O LYS X 46 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU X 51 " --> pdb=" O GLU X 47 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 79 removed outlier: 3.706A pdb=" N LEU X 69 " --> pdb=" O GLU X 65 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS X 71 " --> pdb=" O GLY X 67 " (cutoff:3.500A) Proline residue: X 75 - end of helix removed outlier: 3.758A pdb=" N ASN X 78 " --> pdb=" O ARG X 74 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER X 79 " --> pdb=" O PRO X 75 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 97 removed outlier: 3.741A pdb=" N ARG X 87 " --> pdb=" O ALA X 83 " (cutoff:3.500A) Processing helix chain 'X' and resid 103 through 120 removed outlier: 4.017A pdb=" N VAL X 107 " --> pdb=" O THR X 103 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU X 108 " --> pdb=" O GLY X 104 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU X 111 " --> pdb=" O VAL X 107 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU X 112 " --> pdb=" O GLU X 108 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 140 removed outlier: 3.773A pdb=" N ALA X 128 " --> pdb=" O PHE X 124 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER X 135 " --> pdb=" O ALA X 131 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP X 139 " --> pdb=" O SER X 135 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR X 140 " --> pdb=" O LEU X 136 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 159 removed outlier: 3.950A pdb=" N GLY X 150 " --> pdb=" O ALA X 146 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER X 151 " --> pdb=" O LEU X 147 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN X 152 " --> pdb=" O HIS X 148 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG X 155 " --> pdb=" O SER X 151 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU X 156 " --> pdb=" O GLN X 152 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS X 159 " --> pdb=" O ARG X 155 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 179 removed outlier: 3.635A pdb=" N GLU X 168 " --> pdb=" O ALA X 164 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU X 172 " --> pdb=" O GLU X 168 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS X 175 " --> pdb=" O LEU X 171 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR X 176 " --> pdb=" O LEU X 172 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR X 177 " --> pdb=" O GLU X 173 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N HIS X 178 " --> pdb=" O SER X 174 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA X 179 " --> pdb=" O LYS X 175 " (cutoff:3.500A) Processing helix chain 'X' and resid 183 through 199 removed outlier: 3.956A pdb=" N SER X 192 " --> pdb=" O ALA X 188 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA X 193 " --> pdb=" O ALA X 189 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR X 195 " --> pdb=" O THR X 191 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN X 198 " --> pdb=" O ARG X 194 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA X 199 " --> pdb=" O THR X 195 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 221 removed outlier: 3.914A pdb=" N MET X 212 " --> pdb=" O ALA X 208 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN X 213 " --> pdb=" O THR X 209 " (cutoff:3.500A) Processing helix chain 'X' and resid 227 through 239 removed outlier: 3.530A pdb=" N PHE X 232 " --> pdb=" O ALA X 228 " (cutoff:3.500A) Processing helix chain 'X' and resid 244 through 260 removed outlier: 3.549A pdb=" N THR X 249 " --> pdb=" O PRO X 245 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU X 251 " --> pdb=" O ALA X 247 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS X 252 " --> pdb=" O ILE X 248 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR X 253 " --> pdb=" O THR X 249 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET X 254 " --> pdb=" O SER X 250 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 271 removed outlier: 3.802A pdb=" N GLN X 268 " --> pdb=" O GLU X 265 " (cutoff:3.500A) Processing helix chain 'X' and resid 274 through 278 removed outlier: 4.015A pdb=" N ARG X 278 " --> pdb=" O LYS X 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 274 through 278' Processing helix chain 'X' and resid 282 through 296 removed outlier: 3.502A pdb=" N ALA X 286 " --> pdb=" O ARG X 282 " (cutoff:3.500A) Processing helix chain 'X' and resid 299 through 308 removed outlier: 3.558A pdb=" N THR X 307 " --> pdb=" O GLU X 303 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP X 308 " --> pdb=" O LYS X 304 " (cutoff:3.500A) Processing helix chain 'X' and resid 310 through 313 No H-bonds generated for 'chain 'X' and resid 310 through 313' Processing helix chain 'X' and resid 319 through 340 removed outlier: 3.547A pdb=" N LEU X 323 " --> pdb=" O ILE X 319 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU X 332 " --> pdb=" O ASP X 328 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG X 337 " --> pdb=" O GLN X 333 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL X 338 " --> pdb=" O ASN X 334 " (cutoff:3.500A) Processing helix chain 'X' and resid 347 through 354 removed outlier: 3.644A pdb=" N SER X 352 " --> pdb=" O GLU X 348 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU X 353 " --> pdb=" O HIS X 349 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE X 354 " --> pdb=" O ILE X 350 " (cutoff:3.500A) Processing helix chain 'X' and resid 358 through 370 Processing helix chain 'X' and resid 394 through 421 removed outlier: 3.827A pdb=" N ALA X 399 " --> pdb=" O LYS X 395 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU X 402 " --> pdb=" O GLU X 398 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN X 405 " --> pdb=" O LEU X 401 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER X 408 " --> pdb=" O ILE X 404 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR X 415 " --> pdb=" O VAL X 411 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN X 416 " --> pdb=" O ASP X 412 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU X 421 " --> pdb=" O LYS X 417 " (cutoff:3.500A) Processing helix chain 'Y' and resid 14 through 27 removed outlier: 3.823A pdb=" N ILE Y 19 " --> pdb=" O PRO Y 15 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 44 removed outlier: 3.596A pdb=" N ASP Y 39 " --> pdb=" O ALA Y 35 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU Y 40 " --> pdb=" O ALA Y 36 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 59 removed outlier: 4.076A pdb=" N GLU Y 55 " --> pdb=" O PRO Y 52 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA Y 56 " --> pdb=" O TYR Y 53 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS Y 58 " --> pdb=" O GLU Y 55 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS Y 59 " --> pdb=" O ALA Y 56 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 91 removed outlier: 4.377A pdb=" N LYS Y 72 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET Y 73 " --> pdb=" O LEU Y 70 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS Y 75 " --> pdb=" O LYS Y 72 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA Y 76 " --> pdb=" O MET Y 73 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN Y 77 " --> pdb=" O LYS Y 74 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU Y 80 " --> pdb=" O ASN Y 77 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS Y 82 " --> pdb=" O ASP Y 79 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG Y 83 " --> pdb=" O GLU Y 80 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP Y 85 " --> pdb=" O LYS Y 82 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU Y 86 " --> pdb=" O ARG Y 83 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU Y 88 " --> pdb=" O ASP Y 85 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU Y 89 " --> pdb=" O GLU Y 86 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP Y 90 " --> pdb=" O GLU Y 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 101 through 113 removed outlier: 3.926A pdb=" N ALA Y 106 " --> pdb=" O ASP Y 102 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS Y 107 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 129 removed outlier: 3.615A pdb=" N ARG Y 125 " --> pdb=" O LEU Y 121 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP Y 129 " --> pdb=" O ARG Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 134 through 150 Processing helix chain 'Y' and resid 157 through 168 removed outlier: 3.777A pdb=" N THR Y 161 " --> pdb=" O ILE Y 157 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU Y 162 " --> pdb=" O THR Y 158 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER Y 166 " --> pdb=" O GLU Y 162 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU Y 167 " --> pdb=" O LYS Y 163 " (cutoff:3.500A) Processing helix chain 'Y' and resid 175 through 190 removed outlier: 3.511A pdb=" N GLY Y 185 " --> pdb=" O LYS Y 181 " (cutoff:3.500A) Processing helix chain 'Y' and resid 195 through 207 removed outlier: 5.321A pdb=" N ASP Y 203 " --> pdb=" O GLU Y 199 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N THR Y 204 " --> pdb=" O LEU Y 200 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL Y 205 " --> pdb=" O PHE Y 201 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER Y 206 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N THR Y 207 " --> pdb=" O ASP Y 203 " (cutoff:3.500A) Processing helix chain 'Y' and resid 216 through 227 removed outlier: 3.633A pdb=" N VAL Y 226 " --> pdb=" O TYR Y 222 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER Y 227 " --> pdb=" O THR Y 223 " (cutoff:3.500A) Processing helix chain 'Y' and resid 233 through 240 Processing helix chain 'Y' and resid 245 through 252 removed outlier: 4.441A pdb=" N VAL Y 249 " --> pdb=" O GLU Y 245 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU Y 250 " --> pdb=" O ILE Y 246 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 265 removed outlier: 3.713A pdb=" N TYR Y 259 " --> pdb=" O ALA Y 255 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU Y 260 " --> pdb=" O VAL Y 256 " (cutoff:3.500A) Processing helix chain 'Y' and resid 270 through 284 removed outlier: 3.510A pdb=" N LYS Y 284 " --> pdb=" O GLN Y 280 " (cutoff:3.500A) Processing helix chain 'Y' and resid 292 through 308 removed outlier: 4.050A pdb=" N ARG Y 297 " --> pdb=" O ARG Y 293 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG Y 300 " --> pdb=" O VAL Y 296 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN Y 306 " --> pdb=" O HIS Y 302 " (cutoff:3.500A) Processing helix chain 'Y' and resid 316 through 323 removed outlier: 3.890A pdb=" N GLU Y 321 " --> pdb=" O GLY Y 317 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA Y 322 " --> pdb=" O TYR Y 318 " (cutoff:3.500A) Processing helix chain 'Y' and resid 329 through 339 Processing helix chain 'Y' and resid 363 through 386 removed outlier: 3.590A pdb=" N GLU Y 368 " --> pdb=" O TRP Y 364 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR Y 369 " --> pdb=" O GLN Y 365 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE Y 370 " --> pdb=" O TYR Y 366 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU Y 375 " --> pdb=" O LYS Y 371 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS Y 382 " --> pdb=" O ASN Y 378 " (cutoff:3.500A) Processing helix chain 'Z' and resid 13 through 29 removed outlier: 3.649A pdb=" N HIS Z 22 " --> pdb=" O SER Z 18 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS Z 28 " --> pdb=" O ASN Z 24 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL Z 29 " --> pdb=" O ARG Z 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 85 Processing helix chain 'Z' and resid 103 through 114 removed outlier: 3.558A pdb=" N ILE Z 106 " --> pdb=" O LYS Z 103 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE Z 108 " --> pdb=" O ASP Z 105 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN Z 109 " --> pdb=" O ILE Z 106 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS Z 113 " --> pdb=" O GLU Z 110 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG Z 114 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) Processing helix chain 'Z' and resid 167 through 176 removed outlier: 3.789A pdb=" N GLY Z 171 " --> pdb=" O ALA Z 167 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL Z 172 " --> pdb=" O GLU Z 168 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU Z 176 " --> pdb=" O VAL Z 172 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 216 removed outlier: 3.903A pdb=" N ILE Z 191 " --> pdb=" O LEU Z 187 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR Z 192 " --> pdb=" O SER Z 188 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY Z 197 " --> pdb=" O ASN Z 193 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER Z 203 " --> pdb=" O LYS Z 199 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL Z 215 " --> pdb=" O TYR Z 211 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA Z 216 " --> pdb=" O LEU Z 212 " (cutoff:3.500A) Processing helix chain 'Z' and resid 226 through 236 removed outlier: 3.697A pdb=" N LEU Z 230 " --> pdb=" O ILE Z 226 " (cutoff:3.500A) Processing helix chain 'Z' and resid 244 through 289 removed outlier: 4.083A pdb=" N TYR Z 250 " --> pdb=" O LYS Z 247 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU Z 251 " --> pdb=" O ALA Z 248 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR Z 253 " --> pdb=" O TYR Z 250 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL Z 258 " --> pdb=" O ASP Z 255 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG Z 267 " --> pdb=" O SER Z 264 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER Z 268 " --> pdb=" O LEU Z 265 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA Z 271 " --> pdb=" O SER Z 268 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN Z 274 " --> pdb=" O ALA Z 271 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE Z 276 " --> pdb=" O HIS Z 273 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN Z 277 " --> pdb=" O ASN Z 274 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE Z 280 " --> pdb=" O ASN Z 277 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG Z 283 " --> pdb=" O ILE Z 280 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASP Z 284 " --> pdb=" O ALA Z 281 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA Z 285 " --> pdb=" O ASN Z 282 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS Z 287 " --> pdb=" O ASP Z 284 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS Z 288 " --> pdb=" O ALA Z 285 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 10 Processing helix chain 'a' and resid 18 through 28 removed outlier: 3.783A pdb=" N HIS a 23 " --> pdb=" O ALA a 20 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU a 26 " --> pdb=" O HIS a 23 " (cutoff:3.500A) Processing helix chain 'a' and resid 35 through 46 Processing helix chain 'a' and resid 54 through 68 removed outlier: 4.469A pdb=" N LEU a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE a 67 " --> pdb=" O PHE a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 87 removed outlier: 3.773A pdb=" N HIS a 82 " --> pdb=" O GLU a 78 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG a 85 " --> pdb=" O LEU a 81 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN a 86 " --> pdb=" O HIS a 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 103 removed outlier: 3.673A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE a 96 " --> pdb=" O VAL a 92 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 124 removed outlier: 3.509A pdb=" N LEU a 123 " --> pdb=" O GLY a 119 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN a 124 " --> pdb=" O ALA a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 131 through 142 removed outlier: 3.726A pdb=" N ASP a 137 " --> pdb=" O GLU a 133 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL a 138 " --> pdb=" O THR a 134 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU a 139 " --> pdb=" O ILE a 135 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU a 140 " --> pdb=" O GLU a 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 150 through 165 removed outlier: 3.795A pdb=" N ARG a 154 " --> pdb=" O SER a 150 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU a 158 " --> pdb=" O ARG a 154 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR a 163 " --> pdb=" O SER a 159 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR a 165 " --> pdb=" O LYS a 161 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 182 removed outlier: 3.828A pdb=" N TYR a 173 " --> pdb=" O HIS a 169 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS a 174 " --> pdb=" O ALA a 170 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG a 178 " --> pdb=" O LYS a 174 " (cutoff:3.500A) Processing helix chain 'a' and resid 190 through 206 removed outlier: 4.347A pdb=" N GLU a 195 " --> pdb=" O SER a 191 " (cutoff:3.500A) 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: 3.890A pdb=" N SER a 224 " --> pdb=" O PRO a 220 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU a 225 " --> pdb=" O VAL a 221 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR a 228 " --> pdb=" O SER a 224 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 241 Processing helix chain 'a' and resid 249 through 256 removed outlier: 4.430A pdb=" N ALA a 254 " --> pdb=" O THR a 250 " (cutoff:3.500A) Processing helix chain 'a' and resid 265 through 283 removed outlier: 3.982A pdb=" N GLN a 273 " --> pdb=" O LEU a 269 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU a 277 " --> pdb=" O GLN a 273 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N MET a 278 " --> pdb=" O LEU a 274 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU a 279 " --> pdb=" O LEU a 275 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE a 282 " --> pdb=" O MET a 278 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 299 Processing helix chain 'a' and resid 307 through 317 removed outlier: 3.745A pdb=" N ALA a 314 " --> pdb=" O LEU a 310 " (cutoff:3.500A) Processing helix chain 'a' and resid 343 through 370 removed outlier: 3.745A pdb=" N TRP a 356 " --> pdb=" O ARG a 352 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS a 357 " --> pdb=" O LEU a 353 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP a 359 " --> pdb=" O PHE a 355 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU a 366 " --> pdb=" O SER a 362 " (cutoff:3.500A) Processing helix chain 'b' and resid 14 through 16 No H-bonds generated for 'chain 'b' and resid 14 through 16' Processing helix chain 'b' and resid 25 through 43 Processing helix chain 'b' and resid 69 through 75 Processing helix chain 'b' and resid 87 through 98 removed outlier: 4.167A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA b 93 " --> pdb=" O GLY b 89 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 134 removed outlier: 3.568A pdb=" N LYS b 133 " --> pdb=" O LYS b 129 " (cutoff:3.500A) Processing helix chain 'b' and resid 152 through 160 Processing helix chain 'b' and resid 180 through 189 removed outlier: 3.788A pdb=" N SER b 185 " --> pdb=" O ASP b 181 " (cutoff:3.500A) removed outlier: 4.598A 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 48 removed outlier: 3.907A pdb=" N LEU c 39 " --> pdb=" O SER c 35 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY c 48 " --> pdb=" O HIS c 44 " (cutoff:3.500A) 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 124 through 136 removed outlier: 3.589A pdb=" N ASN c 128 " --> pdb=" O GLY c 124 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR c 129 " --> pdb=" O VAL c 125 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER c 132 " --> pdb=" O ASN c 128 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA c 135 " --> pdb=" O GLN c 131 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU c 136 " --> pdb=" O SER c 132 " (cutoff:3.500A) Processing helix chain 'c' and resid 178 through 185 Processing helix chain 'c' and resid 194 through 196 No H-bonds generated for 'chain 'c' and resid 194 through 196' Processing helix chain 'c' and resid 211 through 225 removed outlier: 3.746A pdb=" N HIS c 221 " --> pdb=" O LEU c 217 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TRP c 225 " --> pdb=" O HIS c 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 233 through 241 Processing helix chain 'c' and resid 245 through 263 removed outlier: 3.584A pdb=" N GLU c 260 " --> pdb=" O ASN c 256 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU c 262 " --> pdb=" O ALA c 258 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 273 removed outlier: 4.049A pdb=" N ALA c 271 " --> pdb=" O PRO c 267 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE c 272 " --> pdb=" O GLU c 268 " (cutoff:3.500A) Processing helix chain 'c' and resid 287 through 307 removed outlier: 4.075A pdb=" N LEU c 304 " --> pdb=" O LEU c 300 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP c 305 " --> pdb=" O ALA c 301 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR c 306 " --> pdb=" O ALA c 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 10 removed outlier: 4.462A pdb=" N ASN d 10 " --> pdb=" O GLY d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 32 removed outlier: 4.049A pdb=" N LEU d 28 " --> pdb=" O GLY d 24 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL d 29 " --> pdb=" O ARG d 25 " (cutoff:3.500A) Processing helix chain 'd' and resid 42 through 64 removed outlier: 4.509A pdb=" N GLN d 47 " --> pdb=" O THR d 44 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU d 50 " --> pdb=" O GLN d 47 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP d 53 " --> pdb=" O LEU d 50 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE d 57 " --> pdb=" O ILE d 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP d 61 " --> pdb=" O GLY d 58 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE d 63 " --> pdb=" O GLN d 60 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU d 64 " --> pdb=" O TRP d 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 82 Processing helix chain 'd' and resid 95 through 109 removed outlier: 4.124A pdb=" N LEU d 99 " --> pdb=" O MET d 95 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY d 100 " --> pdb=" O HIS d 96 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN d 102 " --> pdb=" O LEU d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 112 through 121 removed outlier: 3.744A pdb=" N HIS d 116 " --> pdb=" O VAL d 112 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU d 119 " --> pdb=" O PHE d 115 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU d 120 " --> pdb=" O HIS d 116 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG d 121 " --> pdb=" O THR d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 123 through 128 removed outlier: 3.872A pdb=" N ILE d 127 " --> pdb=" O PRO d 123 " (cutoff:3.500A) Processing helix chain 'd' and resid 131 through 143 Proline residue: d 136 - end of helix Processing helix chain 'd' and resid 149 through 154 Processing helix chain 'd' and resid 164 through 182 removed outlier: 3.950A pdb=" N ILE d 169 " --> pdb=" O PHE d 165 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU d 177 " --> pdb=" O THR d 173 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA d 179 " --> pdb=" O ARG d 175 " (cutoff:3.500A) Processing helix chain 'd' and resid 191 through 198 removed outlier: 3.920A pdb=" N ILE d 197 " --> pdb=" O GLU d 193 " (cutoff:3.500A) Processing helix chain 'd' and resid 205 through 212 Processing helix chain 'd' and resid 237 through 254 removed outlier: 4.195A pdb=" N GLU d 241 " --> pdb=" O ILE d 237 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL d 246 " --> pdb=" O LEU d 242 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 53 removed outlier: 4.001A pdb=" N VAL e 48 " --> pdb=" O ASP e 44 " (cutoff:3.500A) Processing helix chain 'e' and resid 61 through 69 removed outlier: 4.552A pdb=" N MET e 67 " --> pdb=" O HIS e 63 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLU e 68 " --> pdb=" O GLY e 64 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR e 69 " --> pdb=" O TYR e 65 " (cutoff:3.500A) Processing helix chain 'f' and resid 16 through 19 No H-bonds generated for 'chain 'f' and resid 16 through 19' Processing helix chain 'f' and resid 22 through 26 Processing helix chain 'f' and resid 29 through 37 removed outlier: 3.679A pdb=" N VAL f 33 " --> pdb=" O LYS f 30 " (cutoff:3.500A) Proline residue: f 34 - end of helix removed outlier: 4.126A pdb=" N MET f 37 " --> pdb=" O PRO f 34 " (cutoff:3.500A) Processing helix chain 'f' and resid 46 through 57 removed outlier: 4.338A pdb=" N ILE f 52 " --> pdb=" O LEU f 49 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL f 55 " --> pdb=" O ILE f 52 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET f 57 " --> pdb=" O GLN f 54 " (cutoff:3.500A) Processing helix chain 'f' and resid 63 through 67 Processing helix chain 'f' and resid 83 through 97 removed outlier: 3.595A pdb=" N PHE f 97 " --> pdb=" O ALA f 93 " (cutoff:3.500A) Processing helix chain 'f' and resid 115 through 128 removed outlier: 4.002A pdb=" N SER f 125 " --> pdb=" O ASP f 121 " (cutoff:3.500A) Processing helix chain 'f' and resid 135 through 139 Processing helix chain 'f' and resid 142 through 148 removed outlier: 3.804A pdb=" N GLU f 147 " --> pdb=" O GLY f 143 " (cutoff:3.500A) Processing helix chain 'f' and resid 165 through 179 removed outlier: 3.790A pdb=" N ASN f 170 " --> pdb=" O GLN f 166 " (cutoff:3.500A) Processing helix chain 'f' and resid 186 through 191 removed outlier: 3.817A pdb=" N ILE f 189 " --> pdb=" O PRO f 186 " (cutoff:3.500A) Processing helix chain 'f' and resid 197 through 205 Processing helix chain 'f' and resid 213 through 223 removed outlier: 3.930A pdb=" N SER f 216 " --> pdb=" O LEU f 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE f 217 " --> pdb=" O ALA f 214 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL f 218 " --> pdb=" O SER f 215 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASN f 219 " --> pdb=" O SER f 216 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLY f 220 " --> pdb=" O PHE f 217 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN f 223 " --> pdb=" O GLY f 220 " (cutoff:3.500A) Processing helix chain 'f' and resid 228 through 237 Processing helix chain 'f' and resid 245 through 247 No H-bonds generated for 'chain 'f' and resid 245 through 247' Processing helix chain 'f' and resid 252 through 264 Processing helix chain 'f' and resid 271 through 280 removed outlier: 4.038A pdb=" N TYR f 280 " --> pdb=" O SER f 276 " (cutoff:3.500A) Processing helix chain 'f' and resid 290 through 296 Processing helix chain 'f' and resid 302 through 313 removed outlier: 3.516A pdb=" N LEU f 306 " --> pdb=" O PRO f 302 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N HIS f 313 " --> pdb=" O ASP f 309 " (cutoff:3.500A) Processing helix chain 'f' and resid 319 through 332 removed outlier: 3.582A pdb=" N GLY f 327 " --> pdb=" O ILE f 323 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR f 330 " --> pdb=" O LEU f 326 " (cutoff:3.500A) Processing helix chain 'f' and resid 343 through 347 Processing helix chain 'f' and resid 357 through 367 removed outlier: 3.753A pdb=" N CYS f 363 " --> pdb=" O THR f 359 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY f 364 " --> pdb=" O ALA f 360 " (cutoff:3.500A) Processing helix chain 'f' and resid 374 through 385 Processing helix chain 'f' and resid 396 through 402 Proline residue: f 400 - end of helix No H-bonds generated for 'chain 'f' and resid 396 through 402' Processing helix chain 'f' and resid 415 through 419 Processing helix chain 'f' and resid 422 through 424 No H-bonds generated for 'chain 'f' and resid 422 through 424' Processing helix chain 'f' and resid 429 through 439 removed outlier: 4.293A pdb=" N VAL f 436 " --> pdb=" O ALA f 432 " (cutoff:3.500A) Processing helix chain 'f' and resid 449 through 458 Processing helix chain 'f' and resid 465 through 476 Processing helix chain 'f' and resid 482 through 486 Processing helix chain 'f' and resid 495 through 504 removed outlier: 3.504A pdb=" N ALA f 499 " --> pdb=" O VAL f 495 " (cutoff:3.500A) Processing helix chain 'f' and resid 513 through 521 removed outlier: 3.952A pdb=" N LEU f 520 " --> pdb=" O PHE f 516 " (cutoff:3.500A) Processing helix chain 'f' and resid 527 through 536 Proline residue: f 532 - end of helix removed outlier: 4.707A pdb=" N LEU f 535 " --> pdb=" O VAL f 531 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA f 536 " --> pdb=" O PRO f 532 " (cutoff:3.500A) Processing helix chain 'f' and resid 538 through 540 No H-bonds generated for 'chain 'f' and resid 538 through 540' Processing helix chain 'f' and resid 543 through 555 removed outlier: 4.201A pdb=" N LEU f 548 " --> pdb=" O ARG f 544 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP f 549 " --> pdb=" O LEU f 545 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS f 553 " --> pdb=" O ASP f 549 " (cutoff:3.500A) Processing helix chain 'f' and resid 560 through 570 Processing helix chain 'f' and resid 580 through 589 removed outlier: 4.114A pdb=" N ARG f 587 " --> pdb=" O ALA f 583 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLN f 588 " --> pdb=" O ALA f 584 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU f 589 " --> pdb=" O MET f 585 " (cutoff:3.500A) Processing helix chain 'f' and resid 597 through 605 Processing helix chain 'f' and resid 623 through 634 removed outlier: 3.526A pdb=" N ALA f 633 " --> pdb=" O MET f 629 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL f 634 " --> pdb=" O SER f 630 " (cutoff:3.500A) Processing helix chain 'f' and resid 640 through 655 removed outlier: 4.495A pdb=" N ASP f 646 " --> pdb=" O SER f 643 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL f 647 " --> pdb=" O PHE f 644 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN f 649 " --> pdb=" O ASP f 646 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU f 652 " --> pdb=" O ASN f 649 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY f 653 " --> pdb=" O ILE f 650 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS f 654 " --> pdb=" O ILE f 651 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER f 655 " --> pdb=" O LEU f 652 " (cutoff:3.500A) Processing helix chain 'f' and resid 671 through 682 removed outlier: 3.664A pdb=" N ASP f 675 " --> pdb=" O LEU f 671 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG f 679 " --> pdb=" O ASP f 675 " (cutoff:3.500A) Proline residue: f 680 - end of helix Processing helix chain 'f' and resid 687 through 693 Processing sheet with id= A, first strand: chain 'G' and resid 40 through 43 Processing sheet with id= B, first strand: chain 'G' and resid 159 through 162 removed outlier: 4.152A pdb=" N TYR G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP G 155 " --> pdb=" O TYR G 159 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY G 148 " --> pdb=" O ASP G 144 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE G 141 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N GLY G 77 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N CYS G 78 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LYS G 71 " --> pdb=" O CYS G 78 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N MET G 80 " --> pdb=" O LEU G 69 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU G 69 " --> pdb=" O MET G 80 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 160 through 163 removed outlier: 3.508A pdb=" N GLY H 43 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU H 209 " --> pdb=" O THR H 48 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE H 212 " --> pdb=" O ARG H 219 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.825A pdb=" N LEU H 134 " --> pdb=" O SER H 149 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN H 140 " --> pdb=" O ARG H 143 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'I' and resid 34 through 36 removed outlier: 4.065A pdb=" N ALA I 46 " --> pdb=" O LEU I 35 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'I' and resid 135 through 140 removed outlier: 3.708A pdb=" N GLY I 138 " --> pdb=" O GLN I 146 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 33 through 35 removed outlier: 3.696A pdb=" N GLY J 34 " --> pdb=" O ASN J 159 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 40 through 42 Processing sheet with id= I, first strand: chain 'J' and resid 62 through 64 Processing sheet with id= J, first strand: chain 'J' and resid 132 through 136 removed outlier: 3.597A pdb=" N ARG J 143 " --> pdb=" O GLY J 135 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 37 through 41 removed outlier: 3.532A pdb=" N GLU K 216 " --> pdb=" O VAL K 50 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'K' and resid 74 through 77 Processing sheet with id= M, first strand: chain 'L' and resid 158 through 161 removed outlier: 3.894A pdb=" N ILE L 214 " --> pdb=" O THR L 222 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR L 222 " --> pdb=" O ILE L 214 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 135 through 138 Processing sheet with id= O, first strand: chain 'M' and resid 36 through 39 Processing sheet with id= P, first strand: chain 'M' and resid 44 through 53 removed outlier: 4.676A pdb=" N ALA M 208 " --> pdb=" O VAL M 53 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'M' and resid 76 through 79 removed outlier: 3.686A pdb=" N ALA M 76 " --> pdb=" O MET M 136 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'N' and resid 125 through 128 removed outlier: 3.888A pdb=" N GLY N 11 " --> pdb=" O PHE N 8 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA N 180 " --> pdb=" O GLY N 183 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'N' and resid 41 through 44 Processing sheet with id= T, first strand: chain 'N' and resid 20 through 22 removed outlier: 5.654A pdb=" N THR N 22 " --> pdb=" O ILE N 26 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE N 26 " --> pdb=" O THR N 22 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'O' and resid 124 through 128 removed outlier: 5.843A pdb=" N THR O 2 " --> pdb=" O ASP O 17 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP O 17 " --> pdb=" O THR O 2 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY O 11 " --> pdb=" O TYR O 8 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU O 175 " --> pdb=" O LEU O 186 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'O' and resid 119 through 121 removed outlier: 3.535A pdb=" N LEU O 98 " --> pdb=" O ILE O 113 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA O 97 " --> pdb=" O ALA O 46 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N CYS O 43 " --> pdb=" O PHE O 36 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N PHE O 36 " --> pdb=" O CYS O 43 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY O 45 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ILE O 34 " --> pdb=" O GLY O 45 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'O' and resid 20 through 22 removed outlier: 5.509A pdb=" N GLU O 22 " --> pdb=" O VAL O 26 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL O 26 " --> pdb=" O GLU O 22 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'P' and resid 136 through 140 removed outlier: 6.036A pdb=" N ALA P 10 " --> pdb=" O ASP P 25 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'P' and resid 49 through 52 removed outlier: 3.709A pdb=" N ALA P 110 " --> pdb=" O TYR P 50 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'P' and resid 28 through 30 removed outlier: 5.763A pdb=" N ILE P 30 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N MET P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Q' and resid 5 through 8 removed outlier: 3.755A pdb=" N VAL Q 15 " --> pdb=" O ARG Q 181 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Q' and resid 35 through 37 removed outlier: 3.738A pdb=" N ALA Q 105 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Q' and resid 116 through 118 Processing sheet with id= AD, first strand: chain 'R' and resid 3 through 7 removed outlier: 3.517A pdb=" N PHE R 6 " --> pdb=" O ILE R 13 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA R 16 " --> pdb=" O ASN R 175 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N HIS R 178 " --> pdb=" O ARG R 186 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ARG R 186 " --> pdb=" O HIS R 178 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'R' and resid 100 through 104 removed outlier: 3.864A pdb=" N GLY R 103 " --> pdb=" O GLY R 110 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY R 110 " --> pdb=" O GLY R 103 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'S' and resid 135 through 139 removed outlier: 5.604A pdb=" N THR S 11 " --> pdb=" O ASP S 26 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'S' and resid 43 through 45 removed outlier: 3.578A pdb=" N GLY S 53 " --> pdb=" O ILE S 109 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE S 109 " --> pdb=" O GLY S 53 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE S 110 " --> pdb=" O TYR S 122 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY S 112 " --> pdb=" O ALA S 120 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'T' and resid 136 through 138 removed outlier: 3.503A pdb=" N GLY T 13 " --> pdb=" O LEU T 137 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY T 19 " --> pdb=" O PHE T 16 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA T 24 " --> pdb=" O GLN T 188 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'T' and resid 42 through 45 removed outlier: 3.838A pdb=" N TYR T 132 " --> pdb=" O TYR T 124 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'A' and resid 121 through 123 removed outlier: 3.811A pdb=" N ALA A 104 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASN A 114 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE A 102 " --> pdb=" O ASN A 114 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'A' and resid 213 through 215 removed outlier: 4.155A pdb=" N PHE A 215 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'A' and resid 238 through 240 removed outlier: 7.172A pdb=" N LEU A 318 " --> pdb=" O PHE A 274 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'B' and resid 149 through 153 removed outlier: 6.847A pdb=" N ILE B 122 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'B' and resid 222 through 225 removed outlier: 3.513A pdb=" N THR B 331 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'D' and resid 110 through 114 removed outlier: 3.546A pdb=" N GLU D 94 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLY D 104 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N PHE D 92 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP D 141 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N HIS D 133 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU D 139 " --> pdb=" O HIS D 133 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'D' and resid 330 through 332 removed outlier: 7.212A pdb=" N ILE D 331 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEU D 203 " --> pdb=" O ILE D 331 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL D 307 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N MET D 204 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N MET D 309 " --> pdb=" O MET D 204 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ILE D 308 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE D 262 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ALA D 310 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE D 264 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ALA D 226 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE D 263 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE D 228 " --> pdb=" O PHE D 263 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP D 265 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N VAL D 230 " --> pdb=" O ASP D 265 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'E' and resid 97 through 100 removed outlier: 6.563A pdb=" N ILE E 70 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'E' and resid 170 through 173 removed outlier: 6.477A pdb=" N ARG E 297 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N TYR E 173 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE E 299 " --> pdb=" O TYR E 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'E' and resid 195 through 198 removed outlier: 5.830A pdb=" N ILE E 229 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL E 198 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N PHE E 231 " --> pdb=" O VAL E 198 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS E 274 " --> pdb=" O ILE E 230 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N MET E 232 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE E 276 " --> pdb=" O MET E 232 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'F' and resid 121 through 125 Processing sheet with id= AU, first strand: chain 'F' and resid 247 through 250 removed outlier: 4.156A pdb=" N VAL F 223 " --> pdb=" O VAL F 328 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA F 330 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU F 224 " --> pdb=" O ASP F 349 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS F 351 " --> pdb=" O LEU F 224 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N TYR F 226 " --> pdb=" O LYS F 351 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLU F 353 " --> pdb=" O TYR F 226 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'C' and resid 113 through 116 removed outlier: 7.238A pdb=" N LEU C 86 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ALA C 79 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LYS C 84 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'C' and resid 313 through 316 removed outlier: 3.544A pdb=" N TYR C 189 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL C 291 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU C 188 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N MET C 293 " --> pdb=" O LEU C 188 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS C 290 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR C 210 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N PHE C 247 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE C 212 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'U' and resid 744 through 746 Processing sheet with id= AY, first strand: chain 'W' and resid 404 through 406 Processing sheet with id= AZ, first strand: chain 'Y' and resid 346 through 348 removed outlier: 3.503A pdb=" N ILE Y 353 " --> pdb=" O ASP Y 348 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'Z' and resid 159 through 163 removed outlier: 6.725A pdb=" N LEU Z 48 " --> pdb=" O VAL Z 10 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N HIS Z 12 " --> pdb=" O LEU Z 48 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL Z 50 " --> pdb=" O HIS Z 12 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER Z 51 " --> pdb=" O LEU Z 40 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU Z 40 " --> pdb=" O SER Z 51 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N SER Z 53 " --> pdb=" O VAL Z 38 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL Z 38 " --> pdb=" O SER Z 53 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA Z 55 " --> pdb=" O VAL Z 36 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N VAL Z 36 " --> pdb=" O ALA Z 55 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY Z 93 " --> pdb=" O LEU Z 39 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLY Z 41 " --> pdb=" O ILE Z 91 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE Z 91 " --> pdb=" O GLY Z 41 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL Z 120 " --> pdb=" O TRP Z 94 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N HIS Z 96 " --> pdb=" O VAL Z 120 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL Z 122 " --> pdb=" O HIS Z 96 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'Z' and resid 138 through 142 removed outlier: 4.130A pdb=" N VAL Z 141 " --> pdb=" O THR Z 154 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR Z 154 " --> pdb=" O VAL Z 141 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'b' and resid 49 through 53 removed outlier: 9.561A pdb=" N GLY b 50 " --> pdb=" O GLU b 4 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR b 6 " --> pdb=" O GLY b 50 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N ILE b 52 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL b 8 " --> pdb=" O ILE b 52 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LYS b 106 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N MET b 7 " --> pdb=" O LYS b 106 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ARG b 108 " --> pdb=" O MET b 7 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N CYS b 9 " --> pdb=" O ARG b 108 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE b 110 " --> pdb=" O CYS b 9 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN b 137 " --> pdb=" O ILE b 109 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N ALA b 111 " --> pdb=" O ASN b 137 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASP b 139 " --> pdb=" O ALA b 111 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N VAL b 113 " --> pdb=" O ASP b 139 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE b 141 " --> pdb=" O VAL b 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= BC Processing sheet with id= BD, first strand: chain 'c' and resid 204 through 207 removed outlier: 3.621A pdb=" N ILE c 33 " --> pdb=" O ASN c 206 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL c 67 " --> pdb=" O TYR c 32 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG c 68 " --> pdb=" O GLU c 60 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU c 58 " --> pdb=" O ILE c 70 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL c 72 " --> pdb=" O LEU c 56 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU c 56 " --> pdb=" O VAL c 72 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA c 74 " --> pdb=" O MET c 54 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N MET c 54 " --> pdb=" O ALA c 74 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLY c 59 " --> pdb=" O VAL c 108 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL c 108 " --> pdb=" O GLY c 59 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL c 145 " --> pdb=" O HIS c 113 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'c' and resid 160 through 162 2963 hydrogen bonds defined for protein. 7950 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: 27.79 Time building geometry restraints manager: 25.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 23066 1.34 - 1.46: 14346 1.46 - 1.58: 40928 1.58 - 1.70: 34 1.70 - 1.82: 754 Bond restraints: 79128 Sorted by residual: bond pdb=" C LEU a 145 " pdb=" N PRO a 146 " ideal model delta sigma weight residual 1.334 1.565 -0.231 2.34e-02 1.83e+03 9.72e+01 bond pdb=" C4 ATP E 401 " pdb=" C5 ATP E 401 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.59e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.43e+01 bond pdb=" C4 ATP F 501 " pdb=" C5 ATP F 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.39e+01 ... (remaining 79123 not shown) Histogram of bond angle deviations from ideal: 98.82 - 106.83: 2079 106.83 - 114.84: 47293 114.84 - 122.85: 51019 122.85 - 130.86: 6284 130.86 - 138.87: 310 Bond angle restraints: 106985 Sorted by residual: angle pdb=" PB ATP E 401 " pdb=" O3B ATP E 401 " pdb=" PG ATP E 401 " ideal model delta sigma weight residual 139.87 117.17 22.70 1.00e+00 1.00e+00 5.15e+02 angle pdb=" PB ATP F 501 " pdb=" O3B ATP F 501 " pdb=" PG ATP F 501 " ideal model delta sigma weight residual 139.87 117.29 22.58 1.00e+00 1.00e+00 5.10e+02 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 114.50 22.33 1.00e+00 1.00e+00 4.99e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 118.75 21.12 1.00e+00 1.00e+00 4.46e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 118.79 21.08 1.00e+00 1.00e+00 4.44e+02 ... (remaining 106980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 45484 17.91 - 35.81: 2360 35.81 - 53.72: 454 53.72 - 71.63: 83 71.63 - 89.53: 62 Dihedral angle restraints: 48443 sinusoidal: 19596 harmonic: 28847 Sorted by residual: dihedral pdb=" CA HIS C 171 " pdb=" C HIS C 171 " pdb=" N PRO C 172 " pdb=" CA PRO C 172 " ideal model delta harmonic sigma weight residual -180.00 -146.83 -33.17 0 5.00e+00 4.00e-02 4.40e+01 dihedral pdb=" CA ASP D 148 " pdb=" C ASP D 148 " pdb=" N SER D 149 " pdb=" CA SER D 149 " ideal model delta harmonic sigma weight residual 0.00 -32.18 32.18 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA SER c 243 " pdb=" C SER c 243 " pdb=" N VAL c 244 " pdb=" CA VAL c 244 " ideal model delta harmonic sigma weight residual 0.00 -31.20 31.20 0 5.00e+00 4.00e-02 3.89e+01 ... (remaining 48440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.248: 12168 0.248 - 0.496: 7 0.496 - 0.744: 1 0.744 - 0.992: 0 0.992 - 1.240: 1 Chirality restraints: 12177 Sorted by residual: chirality pdb=" CG LEU C 167 " pdb=" CB LEU C 167 " pdb=" CD1 LEU C 167 " pdb=" CD2 LEU C 167 " both_signs ideal model delta sigma weight residual False -2.59 -1.35 -1.24 2.00e-01 2.50e+01 3.84e+01 chirality pdb=" CB ILE Z 222 " pdb=" CA ILE Z 222 " pdb=" CG1 ILE Z 222 " pdb=" CG2 ILE Z 222 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.14e+00 chirality pdb=" CA GLU f 459 " pdb=" N GLU f 459 " pdb=" C GLU f 459 " pdb=" CB GLU f 459 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 12174 not shown) Planarity restraints: 13802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 175 " 0.025 2.00e-02 2.50e+03 3.63e-02 2.31e+01 pdb=" CG PHE C 175 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE C 175 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE C 175 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE C 175 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE C 175 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE C 175 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 158 " -0.054 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO A 159 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP d 215 " 0.025 2.00e-02 2.50e+03 1.63e-02 6.64e+00 pdb=" CG TRP d 215 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP d 215 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP d 215 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP d 215 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP d 215 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP d 215 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP d 215 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP d 215 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP d 215 " 0.007 2.00e-02 2.50e+03 ... (remaining 13799 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 283 2.39 - 3.02: 45780 3.02 - 3.65: 120818 3.65 - 4.27: 179004 4.27 - 4.90: 282164 Nonbonded interactions: 628049 Sorted by model distance: nonbonded pdb=" OD1 ASN a 13 " pdb=" CG PRO a 19 " model vdw 1.763 3.440 nonbonded pdb=" OD2 ASP B 117 " pdb=" NE2 GLN f 588 " model vdw 1.786 2.520 nonbonded pdb=" O TYR Z 261 " pdb=" CD1 LEU Z 265 " model vdw 1.860 3.460 nonbonded pdb=" O LEU W 47 " pdb=" OE1 GLU W 51 " model vdw 1.972 3.040 nonbonded pdb=" OG SER J 11 " pdb=" O HIS J 15 " model vdw 2.016 2.440 ... (remaining 628044 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.650 Construct map_model_manager: 0.040 Extract box with map and model: 12.430 Check model and map are aligned: 0.770 Set scattering table: 0.470 Process input model: 164.710 Find NCS groups from input model: 3.050 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 188.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5668 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 : 0.005 0.231 79128 Z= 0.295 Angle : 0.933 22.696 106985 Z= 0.552 Chirality : 0.048 1.240 12177 Planarity : 0.005 0.082 13802 Dihedral : 11.891 89.531 29840 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.50 % Favored : 91.71 % Rotamer: Outliers : 0.10 % Allowed : 8.74 % Favored : 91.17 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 6.55 % Cis-general : 2.02 % Twisted Proline : 0.28 % Twisted General : 0.02 % 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: -3.88 (0.07), residues: 9841 helix: -3.16 (0.05), residues: 4600 sheet: -1.21 (0.14), residues: 1077 loop : -2.04 (0.09), residues: 4164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP d 215 HIS 0.018 0.002 HIS c 172 PHE 0.078 0.002 PHE C 175 TYR 0.025 0.002 TYR f 441 ARG 0.016 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2655 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 2647 time to evaluate : 6.625 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: G 13 ILE cc_start: 0.8610 (pt) cc_final: 0.8249 (pt) REVERT: G 26 GLU cc_start: 0.8955 (pt0) cc_final: 0.8746 (pt0) REVERT: G 37 LEU cc_start: 0.8682 (tp) cc_final: 0.8432 (tt) REVERT: G 61 LEU cc_start: 0.7104 (tt) cc_final: 0.6791 (tt) REVERT: G 100 ASN cc_start: 0.8465 (m-40) cc_final: 0.8032 (m-40) REVERT: G 125 TYR cc_start: 0.8878 (m-80) cc_final: 0.8476 (m-80) REVERT: G 156 PRO cc_start: 0.8278 (Cg_endo) cc_final: 0.7951 (Cg_exo) REVERT: H 74 LEU cc_start: 0.7875 (tt) cc_final: 0.7622 (pt) REVERT: H 150 ASP cc_start: 0.6976 (p0) cc_final: 0.6749 (p0) REVERT: H 165 LYS cc_start: 0.8345 (mttt) cc_final: 0.8039 (mtmm) REVERT: H 175 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8115 (tp30) REVERT: I 5 TYR cc_start: 0.7452 (m-80) cc_final: 0.7136 (m-80) REVERT: I 8 ARG cc_start: 0.7606 (mtt180) cc_final: 0.7147 (mtp180) REVERT: I 26 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8408 (mt-10) REVERT: I 71 ASP cc_start: 0.7985 (m-30) cc_final: 0.7605 (m-30) REVERT: I 82 ASP cc_start: 0.6938 (t0) cc_final: 0.6326 (t0) REVERT: I 89 GLU cc_start: 0.8856 (tp30) cc_final: 0.8575 (mm-30) REVERT: I 93 ILE cc_start: 0.9088 (mp) cc_final: 0.8810 (mm) REVERT: I 96 ARG cc_start: 0.9429 (ptp-170) cc_final: 0.9025 (mtp85) REVERT: I 100 GLN cc_start: 0.8966 (tt0) cc_final: 0.8591 (tp40) REVERT: I 108 GLU cc_start: 0.8338 (mp0) cc_final: 0.7975 (pt0) REVERT: I 121 TYR cc_start: 0.7540 (m-80) cc_final: 0.7270 (m-80) REVERT: I 148 TYR cc_start: 0.5351 (m-80) cc_final: 0.4617 (m-80) REVERT: I 220 ASN cc_start: 0.7552 (p0) cc_final: 0.7131 (t0) REVERT: I 225 ILE cc_start: 0.7984 (mt) cc_final: 0.7466 (mt) REVERT: I 243 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8190 (mt-10) REVERT: J 13 ASP cc_start: 0.7445 (p0) cc_final: 0.6312 (t0) REVERT: J 18 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8031 (mm-40) REVERT: J 54 GLN cc_start: 0.7119 (mm-40) cc_final: 0.6707 (pm20) REVERT: J 66 ASP cc_start: 0.6792 (t0) cc_final: 0.6167 (t0) REVERT: J 84 ILE cc_start: 0.7861 (mt) cc_final: 0.7657 (mm) REVERT: J 238 GLU cc_start: 0.6061 (mt-10) cc_final: 0.5760 (pp20) REVERT: K 21 LEU cc_start: 0.8292 (mt) cc_final: 0.7827 (tp) REVERT: K 29 GLU cc_start: 0.8765 (tp30) cc_final: 0.8377 (mt-10) REVERT: K 66 LYS cc_start: 0.6780 (tptt) cc_final: 0.6437 (tptt) REVERT: K 108 THR cc_start: 0.8004 (p) cc_final: 0.7799 (p) REVERT: K 190 THR cc_start: 0.7637 (p) cc_final: 0.7312 (t) REVERT: L 16 GLN cc_start: 0.9329 (mt0) cc_final: 0.8977 (mm-40) REVERT: L 26 MET cc_start: 0.7399 (mmt) cc_final: 0.6812 (mmm) REVERT: L 51 ARG cc_start: 0.7276 (mtm180) cc_final: 0.6830 (tmm160) REVERT: L 88 MET cc_start: 0.8176 (tpt) cc_final: 0.7888 (tpt) REVERT: L 91 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7926 (pt0) REVERT: L 115 LYS cc_start: 0.7599 (tptt) cc_final: 0.7185 (tptm) REVERT: L 152 ASN cc_start: 0.7113 (m-40) cc_final: 0.6455 (m-40) REVERT: L 178 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8097 (pt0) REVERT: L 181 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7694 (mp0) REVERT: M 34 SER cc_start: 0.5944 (p) cc_final: 0.5633 (t) REVERT: M 50 GLU cc_start: 0.6861 (tt0) cc_final: 0.5877 (tp30) REVERT: M 69 VAL cc_start: 0.6958 (t) cc_final: 0.4935 (p) REVERT: M 122 TYR cc_start: 0.7445 (m-80) cc_final: 0.7235 (m-80) REVERT: M 180 GLN cc_start: 0.6593 (mm-40) cc_final: 0.6274 (mm-40) REVERT: N 46 SER cc_start: 0.5495 (m) cc_final: 0.5229 (t) REVERT: N 66 HIS cc_start: 0.8183 (t-90) cc_final: 0.7792 (t-170) REVERT: N 71 ASN cc_start: 0.7970 (t0) cc_final: 0.7188 (m-40) REVERT: N 73 PRO cc_start: 0.7773 (Cg_exo) cc_final: 0.7416 (Cg_endo) REVERT: N 77 HIS cc_start: 0.8227 (t-90) cc_final: 0.7495 (p90) REVERT: N 89 ARG cc_start: 0.8368 (ttt90) cc_final: 0.7922 (ttm110) REVERT: N 119 MET cc_start: 0.5701 (ptm) cc_final: 0.5216 (mtt) REVERT: N 162 LEU cc_start: 0.3519 (mt) cc_final: 0.2876 (tt) REVERT: N 185 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7973 (mp0) REVERT: O 35 HIS cc_start: 0.4226 (m90) cc_final: 0.3922 (m90) REVERT: O 100 LEU cc_start: 0.7351 (tp) cc_final: 0.6958 (tt) REVERT: O 113 ILE cc_start: 0.8399 (mt) cc_final: 0.7996 (mp) REVERT: O 114 TYR cc_start: 0.8237 (m-10) cc_final: 0.7639 (m-10) REVERT: O 127 MET cc_start: 0.2858 (mmm) cc_final: 0.2338 (mmt) REVERT: O 135 MET cc_start: 0.5398 (tpp) cc_final: 0.4892 (ttt) REVERT: O 147 GLU cc_start: 0.6643 (mm-30) cc_final: 0.5897 (tm-30) REVERT: O 212 LEU cc_start: 0.7563 (mt) cc_final: 0.7314 (mt) REVERT: P 11 VAL cc_start: 0.5772 (t) cc_final: 0.5441 (p) REVERT: P 49 LEU cc_start: 0.8304 (tt) cc_final: 0.8069 (tp) REVERT: P 69 PHE cc_start: 0.9043 (t80) cc_final: 0.8727 (t80) REVERT: P 117 PHE cc_start: 0.7789 (p90) cc_final: 0.7264 (p90) REVERT: P 183 MET cc_start: 0.6602 (mmm) cc_final: 0.5930 (mmm) REVERT: P 199 THR cc_start: 0.7457 (p) cc_final: 0.6945 (p) REVERT: Q 12 TYR cc_start: 0.6169 (p90) cc_final: 0.5732 (p90) REVERT: Q 134 TYR cc_start: 0.6889 (m-10) cc_final: 0.5529 (t80) REVERT: Q 158 GLU cc_start: 0.9076 (tp30) cc_final: 0.8660 (mt-10) REVERT: Q 161 ARG cc_start: 0.6512 (mmt180) cc_final: 0.6287 (mtt-85) REVERT: R 1 THR cc_start: 0.7002 (m) cc_final: 0.6671 (m) REVERT: R 7 LYS cc_start: 0.7072 (pttt) cc_final: 0.6822 (ptmt) REVERT: R 36 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8099 (mp0) REVERT: R 41 LEU cc_start: 0.7194 (mt) cc_final: 0.6783 (tp) REVERT: R 55 TRP cc_start: 0.7764 (m100) cc_final: 0.7226 (m100) REVERT: R 95 LEU cc_start: 0.4212 (mt) cc_final: 0.3962 (mm) REVERT: R 191 ASN cc_start: 0.6634 (t0) cc_final: 0.6428 (p0) REVERT: S 13 LEU cc_start: 0.7463 (tp) cc_final: 0.7195 (tp) REVERT: S 163 HIS cc_start: 0.4315 (m-70) cc_final: 0.4081 (p90) REVERT: S 172 MET cc_start: 0.7984 (mmm) cc_final: 0.7746 (mmm) REVERT: T 50 MET cc_start: 0.7761 (ttp) cc_final: 0.6782 (tmm) REVERT: T 63 LEU cc_start: 0.9271 (mt) cc_final: 0.8815 (pp) REVERT: T 86 ARG cc_start: 0.7645 (mtp-110) cc_final: 0.7403 (tpt170) REVERT: T 89 HIS cc_start: 0.7937 (t-90) cc_final: 0.7701 (t70) REVERT: T 127 MET cc_start: 0.4015 (ttp) cc_final: 0.3168 (ppp) REVERT: T 211 ILE cc_start: 0.5880 (pt) cc_final: 0.5527 (tt) REVERT: T 214 MET cc_start: 0.1270 (mtt) cc_final: 0.0213 (ppp) REVERT: A 87 LEU cc_start: 0.8325 (pp) cc_final: 0.7891 (pp) REVERT: A 94 GLN cc_start: 0.7394 (tp-100) cc_final: 0.6919 (tt0) REVERT: A 127 ASP cc_start: 0.8718 (m-30) cc_final: 0.8477 (t0) REVERT: A 153 LEU cc_start: 0.8217 (pt) cc_final: 0.7834 (pt) REVERT: A 192 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7445 (mp0) REVERT: A 249 TYR cc_start: 0.8472 (t80) cc_final: 0.8271 (t80) REVERT: A 256 MET cc_start: 0.8206 (ttm) cc_final: 0.7855 (mmm) REVERT: A 273 PHE cc_start: 0.6847 (t80) cc_final: 0.6373 (t80) REVERT: A 278 ASP cc_start: 0.7923 (p0) cc_final: 0.7336 (p0) REVERT: A 285 PHE cc_start: 0.6923 (p90) cc_final: 0.6267 (p90) REVERT: A 300 LEU cc_start: 0.8903 (mt) cc_final: 0.8687 (mt) REVERT: A 301 GLU cc_start: 0.7567 (tt0) cc_final: 0.7142 (pt0) REVERT: A 355 PHE cc_start: 0.8565 (m-10) cc_final: 0.8039 (m-80) REVERT: A 362 MET cc_start: 0.7365 (ttt) cc_final: 0.6645 (tmm) REVERT: B 182 GLU cc_start: 0.7299 (mm-30) cc_final: 0.7054 (mp0) REVERT: B 251 VAL cc_start: 0.7527 (t) cc_final: 0.6544 (m) REVERT: B 314 ASN cc_start: 0.8763 (t0) cc_final: 0.8503 (m-40) REVERT: B 349 ARG cc_start: 0.7983 (tpt170) cc_final: 0.7115 (mtm180) REVERT: B 365 PHE cc_start: 0.8391 (t80) cc_final: 0.8128 (t80) REVERT: B 385 MET cc_start: 0.8034 (ttt) cc_final: 0.7812 (mmm) REVERT: B 427 LEU cc_start: 0.8561 (tp) cc_final: 0.8102 (tp) REVERT: D 54 LEU cc_start: 0.8714 (mt) cc_final: 0.8248 (tp) REVERT: D 68 LEU cc_start: 0.8786 (tp) cc_final: 0.8551 (mt) REVERT: D 73 LEU cc_start: 0.9125 (mt) cc_final: 0.8903 (tt) REVERT: D 142 VAL cc_start: 0.7024 (m) cc_final: 0.6793 (m) REVERT: D 153 MET cc_start: 0.8077 (tpp) cc_final: 0.7549 (tpt) REVERT: D 203 LEU cc_start: 0.9280 (tp) cc_final: 0.8807 (mp) REVERT: D 288 ILE cc_start: 0.8658 (mt) cc_final: 0.8304 (mt) REVERT: D 302 ASN cc_start: 0.6513 (m-40) cc_final: 0.6143 (m-40) REVERT: D 318 ASP cc_start: 0.7716 (m-30) cc_final: 0.7001 (t70) REVERT: D 321 LEU cc_start: 0.8856 (mt) cc_final: 0.8549 (mp) REVERT: D 352 MET cc_start: 0.7144 (mtt) cc_final: 0.6600 (ptm) REVERT: D 361 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8497 (tp30) REVERT: D 381 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8478 (mt-10) REVERT: E 51 GLN cc_start: 0.7690 (mm110) cc_final: 0.6731 (pp30) REVERT: E 61 LEU cc_start: 0.8081 (mt) cc_final: 0.7678 (mt) REVERT: E 75 ASN cc_start: 0.7435 (m110) cc_final: 0.7228 (p0) REVERT: E 114 GLU cc_start: 0.8382 (pt0) cc_final: 0.7631 (mm-30) REVERT: E 120 TYR cc_start: 0.7214 (m-10) cc_final: 0.6942 (m-80) REVERT: E 164 ILE cc_start: 0.7653 (tp) cc_final: 0.6421 (mt) REVERT: E 213 ARG cc_start: 0.8330 (ptt90) cc_final: 0.8095 (tmm160) REVERT: E 216 ARG cc_start: 0.8618 (mtm180) cc_final: 0.8396 (mtt180) REVERT: E 242 ARG cc_start: 0.5188 (ptt-90) cc_final: 0.4741 (tpt90) REVERT: E 254 GLN cc_start: 0.8523 (mm-40) cc_final: 0.7954 (tp-100) REVERT: E 277 MET cc_start: 0.8061 (mtt) cc_final: 0.7674 (mtt) REVERT: E 295 LEU cc_start: 0.7793 (mt) cc_final: 0.7050 (mt) REVERT: E 356 ARG cc_start: 0.7710 (mtp180) cc_final: 0.7481 (ptp-170) REVERT: F 76 ASN cc_start: 0.7414 (t160) cc_final: 0.6859 (m-40) REVERT: F 98 ASP cc_start: 0.6821 (t0) cc_final: 0.6312 (p0) REVERT: F 123 VAL cc_start: 0.8642 (t) cc_final: 0.8383 (t) REVERT: F 225 MET cc_start: 0.5064 (ttt) cc_final: 0.4596 (ptt) REVERT: F 235 LEU cc_start: 0.7592 (mp) cc_final: 0.7062 (tt) REVERT: F 251 LEU cc_start: 0.8275 (tp) cc_final: 0.8026 (tp) REVERT: F 261 ILE cc_start: 0.6633 (pt) cc_final: 0.5592 (pt) REVERT: F 263 ASP cc_start: 0.7520 (m-30) cc_final: 0.6884 (m-30) REVERT: F 288 LEU cc_start: 0.9107 (tp) cc_final: 0.8638 (mp) REVERT: F 305 GLU cc_start: 0.7280 (mt-10) cc_final: 0.7004 (pm20) REVERT: F 311 LEU cc_start: 0.9089 (mt) cc_final: 0.8776 (tt) REVERT: F 366 MET cc_start: 0.8628 (ttp) cc_final: 0.8317 (tmm) REVERT: F 430 LYS cc_start: 0.6207 (mtmm) cc_final: 0.5752 (ptmt) REVERT: F 436 GLN cc_start: 0.7408 (mt0) cc_final: 0.6729 (tp40) REVERT: C 23 TYR cc_start: 0.6383 (t80) cc_final: 0.6034 (t80) REVERT: C 49 ARG cc_start: 0.9146 (mmm-85) cc_final: 0.8909 (ptm160) REVERT: C 80 MET cc_start: 0.7291 (mmp) cc_final: 0.6375 (mpp) REVERT: C 81 ASP cc_start: 0.8785 (p0) cc_final: 0.8528 (p0) REVERT: C 88 LYS cc_start: 0.9067 (tttp) cc_final: 0.8736 (tptp) REVERT: C 101 LYS cc_start: 0.8152 (pttm) cc_final: 0.7934 (pptt) REVERT: C 139 MET cc_start: 0.7974 (mmp) cc_final: 0.7586 (tpp) REVERT: C 145 ASP cc_start: 0.8497 (m-30) cc_final: 0.7810 (t70) REVERT: C 159 LYS cc_start: 0.8835 (tptp) cc_final: 0.8164 (mmmt) REVERT: C 163 GLU cc_start: 0.7244 (mp0) cc_final: 0.6494 (pm20) REVERT: C 188 LEU cc_start: 0.7649 (mp) cc_final: 0.6995 (mt) REVERT: C 201 ARG cc_start: 0.8592 (ttt90) cc_final: 0.8140 (tpt90) REVERT: C 211 PHE cc_start: 0.7534 (t80) cc_final: 0.7139 (t80) REVERT: C 219 LEU cc_start: 0.8473 (tm) cc_final: 0.8000 (mp) REVERT: C 237 MET cc_start: 0.9023 (mmm) cc_final: 0.8623 (mmp) REVERT: C 240 GLU cc_start: 0.8846 (tt0) cc_final: 0.8026 (mt-10) REVERT: C 241 HIS cc_start: 0.8391 (m-70) cc_final: 0.7905 (t-170) REVERT: C 275 GLU cc_start: 0.8851 (pt0) cc_final: 0.8486 (mm-30) REVERT: C 315 ILE cc_start: 0.7518 (mt) cc_final: 0.7283 (mt) REVERT: C 368 MET cc_start: 0.8842 (mmp) cc_final: 0.8108 (ptt) REVERT: C 369 TYR cc_start: 0.8608 (m-80) cc_final: 0.8016 (m-80) REVERT: C 372 ARG cc_start: 0.9082 (ttt-90) cc_final: 0.8356 (mtp180) REVERT: U 87 LEU cc_start: 0.6957 (mt) cc_final: 0.6455 (tt) REVERT: U 176 MET cc_start: 0.6903 (mtp) cc_final: 0.6214 (mmm) REVERT: U 188 MET cc_start: 0.4731 (tpp) cc_final: 0.4499 (ppp) REVERT: U 345 ASN cc_start: 0.6300 (t160) cc_final: 0.5806 (t0) REVERT: U 423 MET cc_start: 0.6763 (mtt) cc_final: 0.6290 (mmm) REVERT: U 426 TYR cc_start: 0.5006 (m-10) cc_final: 0.4008 (m-10) REVERT: U 479 LEU cc_start: 0.7078 (mp) cc_final: 0.6736 (mt) REVERT: U 483 LEU cc_start: 0.7778 (tp) cc_final: 0.7391 (tp) REVERT: U 573 ASP cc_start: 0.7066 (t0) cc_final: 0.6139 (t0) REVERT: U 574 LYS cc_start: 0.6721 (pttm) cc_final: 0.6428 (mmmt) REVERT: U 638 SER cc_start: 0.8734 (t) cc_final: 0.8407 (p) REVERT: U 642 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7977 (pt0) REVERT: U 650 TYR cc_start: 0.8232 (t80) cc_final: 0.7798 (t80) REVERT: U 723 ASP cc_start: 0.6128 (m-30) cc_final: 0.5853 (p0) REVERT: U 764 LEU cc_start: 0.8520 (pp) cc_final: 0.8241 (pp) REVERT: U 770 TRP cc_start: 0.5698 (m-90) cc_final: 0.4986 (m-10) REVERT: U 894 MET cc_start: 0.3655 (ptp) cc_final: 0.3275 (ptp) REVERT: U 896 GLU cc_start: 0.7212 (pt0) cc_final: 0.6576 (mm-30) REVERT: V 36 GLU cc_start: 0.6195 (pp20) cc_final: 0.5242 (pt0) REVERT: V 140 ASP cc_start: 0.7510 (m-30) cc_final: 0.6996 (m-30) REVERT: V 378 VAL cc_start: 0.6283 (t) cc_final: 0.5510 (p) REVERT: V 385 LYS cc_start: 0.7296 (tptt) cc_final: 0.6685 (ptmt) REVERT: V 437 ILE cc_start: 0.9355 (mp) cc_final: 0.9151 (tp) REVERT: V 444 ASP cc_start: 0.8489 (m-30) cc_final: 0.8012 (t0) REVERT: V 452 ASN cc_start: 0.6911 (t0) cc_final: 0.6710 (p0) REVERT: V 489 MET cc_start: 0.8766 (mmp) cc_final: 0.8061 (ppp) REVERT: W 36 LYS cc_start: 0.8557 (mttt) cc_final: 0.8304 (mmtt) REVERT: W 37 GLU cc_start: 0.6200 (mt-10) cc_final: 0.4945 (tt0) REVERT: W 101 VAL cc_start: 0.8319 (t) cc_final: 0.8083 (m) REVERT: W 130 MET cc_start: 0.8112 (mmp) cc_final: 0.7266 (tmm) REVERT: W 145 LEU cc_start: 0.8329 (mt) cc_final: 0.8068 (mt) REVERT: W 169 LEU cc_start: 0.6933 (mt) cc_final: 0.5608 (mt) REVERT: W 184 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7208 (tt0) REVERT: W 185 PHE cc_start: 0.7896 (t80) cc_final: 0.7350 (t80) REVERT: W 214 PHE cc_start: 0.8498 (t80) cc_final: 0.8272 (p90) REVERT: W 221 LYS cc_start: 0.8770 (pttp) cc_final: 0.8498 (tttt) REVERT: W 222 LEU cc_start: 0.8143 (tp) cc_final: 0.7769 (tp) REVERT: W 312 MET cc_start: 0.6092 (tpt) cc_final: 0.4822 (tpt) REVERT: W 348 GLU cc_start: 0.8353 (tp30) cc_final: 0.8017 (tm-30) REVERT: W 375 MET cc_start: 0.8383 (tpt) cc_final: 0.7898 (ptm) REVERT: W 451 MET cc_start: 0.6998 (mmt) cc_final: 0.6720 (tpt) REVERT: X 194 ARG cc_start: 0.5512 (mmm-85) cc_final: 0.4877 (ttt-90) REVERT: X 211 ASP cc_start: 0.7789 (m-30) cc_final: 0.7245 (m-30) REVERT: X 232 PHE cc_start: 0.7226 (m-80) cc_final: 0.6900 (m-10) REVERT: X 282 ARG cc_start: 0.7596 (mmm-85) cc_final: 0.7338 (mmm160) REVERT: X 296 ASN cc_start: 0.7403 (m-40) cc_final: 0.7188 (m-40) REVERT: X 309 TYR cc_start: 0.5705 (m-10) cc_final: 0.4529 (m-10) REVERT: X 321 THR cc_start: 0.8194 (m) cc_final: 0.7925 (m) REVERT: X 322 HIS cc_start: 0.5421 (m90) cc_final: 0.4825 (p90) REVERT: X 407 MET cc_start: 0.8929 (mmt) cc_final: 0.8705 (tmm) REVERT: X 416 ASN cc_start: 0.8526 (m-40) cc_final: 0.8241 (p0) REVERT: Y 22 LEU cc_start: 0.8212 (mp) cc_final: 0.7808 (mt) REVERT: Y 32 ARG cc_start: 0.7012 (tpt90) cc_final: 0.5709 (ptp-110) REVERT: Y 34 ASP cc_start: 0.8231 (p0) cc_final: 0.7997 (p0) REVERT: Y 38 ARG cc_start: 0.8652 (mtm-85) cc_final: 0.8238 (ppt170) REVERT: Y 55 GLU cc_start: 0.7053 (mp0) cc_final: 0.6293 (pt0) REVERT: Y 73 MET cc_start: 0.8209 (mtp) cc_final: 0.8005 (mmt) REVERT: Y 99 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8544 (tm-30) REVERT: Y 102 ASP cc_start: 0.9202 (t0) cc_final: 0.8954 (t0) REVERT: Y 107 LYS cc_start: 0.8072 (mtmm) cc_final: 0.7801 (tptm) REVERT: Y 110 TYR cc_start: 0.8174 (t80) cc_final: 0.7771 (t80) REVERT: Y 124 PHE cc_start: 0.8345 (m-10) cc_final: 0.7845 (m-80) REVERT: Y 143 TYR cc_start: 0.8376 (m-80) cc_final: 0.8068 (m-80) REVERT: Y 199 GLU cc_start: 0.9012 (tp30) cc_final: 0.8805 (tm-30) REVERT: Y 211 TYR cc_start: 0.3870 (p90) cc_final: 0.3562 (p90) REVERT: Y 217 LYS cc_start: 0.9183 (ttpt) cc_final: 0.8957 (mttt) REVERT: Y 222 TYR cc_start: 0.8514 (m-10) cc_final: 0.8267 (m-80) REVERT: Y 247 LEU cc_start: 0.8355 (tp) cc_final: 0.8054 (tp) REVERT: Y 282 MET cc_start: 0.6893 (tpp) cc_final: 0.6670 (mmt) REVERT: Y 288 PHE cc_start: 0.6144 (m-80) cc_final: 0.5780 (m-10) REVERT: Y 319 MET cc_start: 0.7571 (mmp) cc_final: 0.6755 (mmm) REVERT: Z 9 VAL cc_start: 0.8197 (m) cc_final: 0.7926 (p) REVERT: Z 54 PHE cc_start: 0.7758 (p90) cc_final: 0.7376 (p90) REVERT: Z 75 LEU cc_start: 0.8405 (tt) cc_final: 0.8095 (mp) REVERT: Z 85 VAL cc_start: 0.8031 (p) cc_final: 0.7628 (t) REVERT: Z 123 ILE cc_start: 0.7249 (mt) cc_final: 0.7046 (mp) REVERT: Z 169 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7425 (mp0) REVERT: Z 193 ASN cc_start: 0.8875 (m-40) cc_final: 0.8554 (m110) REVERT: Z 196 HIS cc_start: 0.8832 (p-80) cc_final: 0.8355 (t-90) REVERT: Z 222 ILE cc_start: 0.6017 (tp) cc_final: 0.5678 (tp) REVERT: Z 227 ILE cc_start: 0.7635 (mm) cc_final: 0.7417 (mm) REVERT: Z 257 MET cc_start: 0.6658 (tpt) cc_final: 0.6055 (ttp) REVERT: a 121 LEU cc_start: 0.8454 (mp) cc_final: 0.7996 (tt) REVERT: a 135 ILE cc_start: 0.8102 (mt) cc_final: 0.7850 (pt) REVERT: a 141 MET cc_start: 0.8139 (mmm) cc_final: 0.7904 (mmm) REVERT: a 144 ASN cc_start: 0.8558 (m-40) cc_final: 0.8337 (p0) REVERT: a 223 GLU cc_start: 0.7291 (pt0) cc_final: 0.7084 (tt0) REVERT: a 320 VAL cc_start: 0.6639 (p) cc_final: 0.5990 (t) REVERT: a 342 ASP cc_start: 0.7020 (m-30) cc_final: 0.6361 (m-30) REVERT: a 345 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7771 (mt0) REVERT: b 7 MET cc_start: 0.7807 (tpt) cc_final: 0.6490 (tpp) REVERT: b 56 ASN cc_start: 0.6178 (t0) cc_final: 0.5693 (m110) REVERT: b 57 ASP cc_start: 0.7981 (t0) cc_final: 0.7305 (t0) REVERT: b 109 ILE cc_start: 0.7659 (mt) cc_final: 0.7443 (mt) REVERT: b 121 GLU cc_start: 0.8327 (pt0) cc_final: 0.8110 (tm-30) REVERT: b 134 GLU cc_start: 0.4552 (mt-10) cc_final: 0.4179 (mt-10) REVERT: c 41 MET cc_start: 0.8707 (mmm) cc_final: 0.7775 (mmm) REVERT: c 104 ARG cc_start: 0.6616 (mtp180) cc_final: 0.6331 (tpt170) REVERT: c 112 TYR cc_start: 0.6633 (p90) cc_final: 0.5390 (p90) REVERT: c 166 ASN cc_start: 0.7713 (m110) cc_final: 0.7460 (t0) REVERT: c 230 THR cc_start: 0.3406 (p) cc_final: 0.2450 (m) REVERT: c 269 GLN cc_start: 0.7933 (mt0) cc_final: 0.7528 (tp-100) REVERT: c 282 ARG cc_start: 0.3851 (ptt90) cc_final: 0.3013 (ptt180) REVERT: c 283 HIS cc_start: 0.6021 (p-80) cc_final: 0.5204 (t-170) REVERT: c 292 MET cc_start: 0.9299 (mmm) cc_final: 0.8539 (ppp) REVERT: d 1 MET cc_start: 0.3696 (ttt) cc_final: 0.3226 (ptm) REVERT: d 9 TRP cc_start: 0.7769 (t60) cc_final: 0.7229 (t60) REVERT: d 35 PHE cc_start: 0.7260 (t80) cc_final: 0.7029 (t80) REVERT: d 75 MET cc_start: 0.4327 (tpt) cc_final: 0.3454 (tpt) REVERT: d 241 GLU cc_start: 0.7998 (pt0) cc_final: 0.7561 (tp30) REVERT: f 116 MET cc_start: 0.5523 (mmp) cc_final: 0.5300 (tpt) REVERT: f 155 TYR cc_start: 0.2735 (t80) cc_final: 0.2489 (t80) REVERT: f 384 MET cc_start: 0.2768 (mmm) cc_final: 0.2293 (mtm) REVERT: f 446 ASN cc_start: 0.3831 (t0) cc_final: 0.3575 (m-40) REVERT: f 495 VAL cc_start: 0.3092 (t) cc_final: 0.2849 (p) REVERT: f 602 MET cc_start: 0.2371 (tpt) cc_final: 0.2119 (tpp) REVERT: f 629 MET cc_start: -0.0075 (ptp) cc_final: -0.0841 (tpp) REVERT: f 666 MET cc_start: 0.1436 (ttp) cc_final: -0.0303 (ttp) REVERT: f 667 GLN cc_start: 0.3741 (mm110) cc_final: 0.3328 (mp10) outliers start: 8 outliers final: 2 residues processed: 2652 average time/residue: 0.7408 time to fit residues: 3236.7045 Evaluate side-chains 1316 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1314 time to evaluate : 6.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 828 optimal weight: 8.9990 chunk 743 optimal weight: 1.9990 chunk 412 optimal weight: 3.9990 chunk 253 optimal weight: 30.0000 chunk 501 optimal weight: 4.9990 chunk 397 optimal weight: 0.8980 chunk 768 optimal weight: 4.9990 chunk 297 optimal weight: 10.0000 chunk 467 optimal weight: 10.0000 chunk 572 optimal weight: 20.0000 chunk 890 optimal weight: 20.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 92 GLN H 112 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 GLN J 146 GLN ** K 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 HIS ** K 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 196 HIS T 69 GLN T 162 GLN A 103 ASN A 197 HIS B 193 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 ASN ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 ASN E 51 GLN E 124 HIS E 262 ASN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 GLN ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN C 377 HIS ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 111 GLN U 128 GLN U 258 GLN U 345 ASN ** U 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 595 ASN U 698 GLN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 177 ASN ** V 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 247 GLN V 257 ASN ** V 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 459 GLN V 473 GLN V 477 HIS ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 433 ASN ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 44 GLN ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 225 GLN Z 229 GLN ** a 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 273 GLN b 79 GLN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 172 HIS ** c 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 190 GLN c 221 HIS d 245 GLN ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 212 ASN f 228 GLN f 237 ASN f 269 GLN f 298 ASN f 316 ASN ** f 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 372 ASN ** f 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 491 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5728 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 79128 Z= 0.238 Angle : 0.827 14.693 106985 Z= 0.427 Chirality : 0.047 0.322 12177 Planarity : 0.005 0.105 13802 Dihedral : 6.650 88.848 10988 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.19 % Favored : 94.39 % Rotamer: Outliers : 0.29 % Allowed : 4.52 % Favored : 95.20 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 6.55 % Cis-general : 2.00 % Twisted Proline : 0.57 % Twisted General : 0.04 % 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: -2.64 (0.07), residues: 9841 helix: -1.84 (0.06), residues: 4713 sheet: -0.78 (0.15), residues: 1030 loop : -1.72 (0.09), residues: 4098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP T 107 HIS 0.012 0.001 HIS M 72 PHE 0.038 0.002 PHE C 175 TYR 0.029 0.002 TYR f 441 ARG 0.020 0.001 ARG D 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1657 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1633 time to evaluate : 6.577 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: G 26 GLU cc_start: 0.8814 (pt0) cc_final: 0.8475 (pt0) REVERT: G 70 PHE cc_start: 0.7993 (m-10) cc_final: 0.7679 (m-80) REVERT: G 80 MET cc_start: 0.8170 (mmp) cc_final: 0.6693 (mmp) REVERT: G 125 TYR cc_start: 0.8876 (m-10) cc_final: 0.8574 (m-80) REVERT: G 174 GLU cc_start: 0.8119 (mp0) cc_final: 0.7796 (pm20) REVERT: H 10 LEU cc_start: 0.7022 (pp) cc_final: 0.5777 (mt) REVERT: H 79 MET cc_start: 0.8562 (pmm) cc_final: 0.8049 (tpt) REVERT: H 82 ASP cc_start: 0.8553 (m-30) cc_final: 0.8116 (m-30) REVERT: H 165 LYS cc_start: 0.8346 (mttt) cc_final: 0.8104 (mtmm) REVERT: H 175 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8322 (tp30) REVERT: I 8 ARG cc_start: 0.7520 (mtt180) cc_final: 0.7216 (mtm110) REVERT: I 14 PRO cc_start: 0.8975 (Cg_exo) cc_final: 0.8629 (Cg_endo) REVERT: I 26 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8430 (mt-10) REVERT: I 89 GLU cc_start: 0.8834 (tp30) cc_final: 0.8597 (mm-30) REVERT: I 93 ILE cc_start: 0.9116 (mm) cc_final: 0.8861 (mm) REVERT: I 96 ARG cc_start: 0.9481 (ptp-170) cc_final: 0.9083 (mtp85) REVERT: I 100 GLN cc_start: 0.8811 (tt0) cc_final: 0.8229 (tm-30) REVERT: I 107 CYS cc_start: 0.8192 (m) cc_final: 0.7975 (p) REVERT: I 136 TYR cc_start: 0.7207 (m-80) cc_final: 0.6993 (m-80) REVERT: I 220 ASN cc_start: 0.7549 (p0) cc_final: 0.7213 (t0) REVERT: I 243 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8126 (mp0) REVERT: J 24 GLU cc_start: 0.8641 (tp30) cc_final: 0.8273 (tt0) REVERT: J 134 VAL cc_start: 0.8122 (t) cc_final: 0.7869 (t) REVERT: K 21 LEU cc_start: 0.8279 (mt) cc_final: 0.7684 (tp) REVERT: K 29 GLU cc_start: 0.8927 (tp30) cc_final: 0.8512 (mt-10) REVERT: K 156 MET cc_start: 0.5717 (ppp) cc_final: 0.5288 (ppp) REVERT: L 27 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6825 (mt-10) REVERT: L 88 MET cc_start: 0.8230 (tpt) cc_final: 0.7941 (tpt) REVERT: L 91 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8002 (pt0) REVERT: L 179 PHE cc_start: 0.7782 (m-10) cc_final: 0.7380 (m-10) REVERT: L 181 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7661 (mp0) REVERT: M 34 SER cc_start: 0.6055 (p) cc_final: 0.5712 (t) REVERT: M 47 PHE cc_start: 0.7126 (m-10) cc_final: 0.6342 (m-80) REVERT: M 50 GLU cc_start: 0.6909 (tt0) cc_final: 0.5731 (tp30) REVERT: M 69 VAL cc_start: 0.5642 (t) cc_final: 0.4771 (p) REVERT: M 75 MET cc_start: 0.6206 (mmm) cc_final: 0.5382 (mmm) REVERT: M 136 MET cc_start: 0.5608 (mtt) cc_final: 0.4671 (mtm) REVERT: N 73 PRO cc_start: 0.7883 (Cg_exo) cc_final: 0.7606 (Cg_endo) REVERT: N 77 HIS cc_start: 0.8083 (t-90) cc_final: 0.7637 (t70) REVERT: N 78 THR cc_start: 0.7013 (m) cc_final: 0.6441 (m) REVERT: N 95 MET cc_start: 0.2222 (ptm) cc_final: 0.1224 (ptm) REVERT: N 119 MET cc_start: 0.5735 (ptm) cc_final: 0.4989 (mtt) REVERT: N 147 MET cc_start: 0.6898 (mmm) cc_final: 0.6693 (mmm) REVERT: N 162 LEU cc_start: 0.3897 (mt) cc_final: 0.3426 (tt) REVERT: O 28 ASP cc_start: 0.6326 (t0) cc_final: 0.6081 (t0) REVERT: O 35 HIS cc_start: 0.4304 (m90) cc_final: 0.3826 (m90) REVERT: O 114 TYR cc_start: 0.8136 (m-10) cc_final: 0.7583 (m-10) REVERT: O 127 MET cc_start: 0.2918 (mmm) cc_final: 0.2681 (mmt) REVERT: O 135 MET cc_start: 0.5385 (tpp) cc_final: 0.4990 (ttt) REVERT: O 147 GLU cc_start: 0.6745 (mm-30) cc_final: 0.6110 (tm-30) REVERT: P 39 PHE cc_start: 0.6376 (t80) cc_final: 0.6087 (t80) REVERT: P 69 PHE cc_start: 0.8987 (t80) cc_final: 0.8778 (t80) REVERT: P 88 MET cc_start: 0.9239 (tmm) cc_final: 0.9018 (tmm) REVERT: P 117 PHE cc_start: 0.7520 (p90) cc_final: 0.7258 (p90) REVERT: P 158 MET cc_start: 0.2617 (mtm) cc_final: 0.2412 (ttm) REVERT: P 197 THR cc_start: 0.7312 (m) cc_final: 0.6543 (m) REVERT: Q 69 MET cc_start: 0.6846 (mtp) cc_final: 0.6363 (tpt) REVERT: Q 92 LEU cc_start: 0.7919 (tp) cc_final: 0.7440 (mt) REVERT: Q 104 LEU cc_start: 0.8575 (tp) cc_final: 0.8325 (tp) REVERT: Q 161 ARG cc_start: 0.6634 (mmt180) cc_final: 0.6094 (mmt90) REVERT: R 67 GLU cc_start: 0.7919 (tt0) cc_final: 0.7576 (tp30) REVERT: R 83 LEU cc_start: 0.8126 (tt) cc_final: 0.7832 (tp) REVERT: R 86 MET cc_start: 0.7684 (ttm) cc_final: 0.7262 (ppp) REVERT: S 13 LEU cc_start: 0.7141 (tp) cc_final: 0.6929 (tp) REVERT: S 122 TYR cc_start: 0.7495 (m-80) cc_final: 0.7127 (m-80) REVERT: S 163 HIS cc_start: 0.4466 (m-70) cc_final: 0.4138 (p90) REVERT: S 198 VAL cc_start: 0.7073 (t) cc_final: 0.6770 (t) REVERT: T 43 MET cc_start: 0.7420 (mmm) cc_final: 0.7141 (mmm) REVERT: T 50 MET cc_start: 0.7751 (ttp) cc_final: 0.6689 (tmm) REVERT: T 75 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8878 (pp20) REVERT: T 98 SER cc_start: 0.8706 (t) cc_final: 0.8109 (p) REVERT: T 162 GLN cc_start: 0.8078 (tt0) cc_final: 0.7693 (tt0) REVERT: T 211 ILE cc_start: 0.5990 (pt) cc_final: 0.5674 (tt) REVERT: T 214 MET cc_start: 0.1236 (mtt) cc_final: 0.0084 (ppp) REVERT: A 78 TRP cc_start: 0.4678 (p-90) cc_final: 0.4317 (p-90) REVERT: A 117 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7864 (pt0) REVERT: A 138 MET cc_start: 0.5403 (ttt) cc_final: 0.5065 (ttm) REVERT: A 225 CYS cc_start: 0.8650 (m) cc_final: 0.8350 (m) REVERT: A 255 ARG cc_start: 0.8481 (mmp80) cc_final: 0.8187 (mmp80) REVERT: A 285 PHE cc_start: 0.6745 (p90) cc_final: 0.6413 (p90) REVERT: A 301 GLU cc_start: 0.7372 (tt0) cc_final: 0.7158 (pt0) REVERT: A 318 LEU cc_start: 0.8903 (tp) cc_final: 0.8386 (tp) REVERT: A 362 MET cc_start: 0.7539 (ttt) cc_final: 0.6427 (tmm) REVERT: B 141 LYS cc_start: 0.8297 (pttt) cc_final: 0.7871 (mttt) REVERT: B 251 VAL cc_start: 0.7575 (t) cc_final: 0.7119 (m) REVERT: B 255 LEU cc_start: 0.7319 (pp) cc_final: 0.7037 (pp) REVERT: B 256 ILE cc_start: 0.7695 (pt) cc_final: 0.7372 (pt) REVERT: B 349 ARG cc_start: 0.7579 (tpt170) cc_final: 0.7227 (mtt90) REVERT: B 384 ILE cc_start: 0.7219 (pt) cc_final: 0.6616 (pt) REVERT: B 385 MET cc_start: 0.8101 (ttt) cc_final: 0.7801 (mmm) REVERT: B 390 LEU cc_start: 0.6793 (mt) cc_final: 0.6555 (mt) REVERT: B 404 LEU cc_start: 0.8856 (mt) cc_final: 0.8422 (mt) REVERT: D 54 LEU cc_start: 0.8311 (mt) cc_final: 0.7971 (tp) REVERT: D 68 LEU cc_start: 0.8878 (tp) cc_final: 0.8639 (mt) REVERT: D 81 ARG cc_start: 0.7148 (tmt170) cc_final: 0.6289 (ttm110) REVERT: D 170 MET cc_start: 0.8217 (ptm) cc_final: 0.6844 (tpp) REVERT: D 179 GLU cc_start: 0.8908 (pt0) cc_final: 0.8546 (pt0) REVERT: D 214 MET cc_start: 0.6944 (mtm) cc_final: 0.6004 (mmm) REVERT: D 217 LYS cc_start: 0.8003 (mttt) cc_final: 0.7648 (ttmt) REVERT: D 237 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7684 (tm-30) REVERT: D 283 ARG cc_start: 0.9189 (ttt-90) cc_final: 0.8602 (mtp180) REVERT: D 309 MET cc_start: 0.7873 (mmm) cc_final: 0.7540 (tpp) REVERT: D 318 ASP cc_start: 0.7519 (m-30) cc_final: 0.7174 (t70) REVERT: D 361 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8430 (tp30) REVERT: D 381 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8473 (mt-10) REVERT: E 51 GLN cc_start: 0.7557 (mm-40) cc_final: 0.6455 (pp30) REVERT: E 69 PHE cc_start: 0.8070 (m-80) cc_final: 0.7828 (m-80) REVERT: E 114 GLU cc_start: 0.7965 (pt0) cc_final: 0.7481 (tp30) REVERT: E 168 LYS cc_start: 0.7070 (ptpt) cc_final: 0.6649 (tptt) REVERT: E 242 ARG cc_start: 0.5243 (ptt-90) cc_final: 0.4997 (tpt90) REVERT: E 254 GLN cc_start: 0.8798 (mm-40) cc_final: 0.7792 (tp-100) REVERT: E 295 LEU cc_start: 0.7553 (mt) cc_final: 0.6785 (mt) REVERT: F 124 ILE cc_start: 0.9143 (mm) cc_final: 0.8934 (pt) REVERT: F 130 GLN cc_start: 0.8382 (mm-40) cc_final: 0.8056 (mm-40) REVERT: F 225 MET cc_start: 0.5196 (ttt) cc_final: 0.4759 (ptt) REVERT: F 235 LEU cc_start: 0.7986 (mp) cc_final: 0.7506 (tt) REVERT: F 306 VAL cc_start: 0.8528 (t) cc_final: 0.8324 (t) REVERT: F 388 THR cc_start: 0.8104 (p) cc_final: 0.7764 (p) REVERT: F 430 LYS cc_start: 0.6091 (mtmm) cc_final: 0.5714 (ptmt) REVERT: C 23 TYR cc_start: 0.6403 (t80) cc_final: 0.5997 (t80) REVERT: C 44 ARG cc_start: 0.7933 (tpt90) cc_final: 0.7664 (tmt170) REVERT: C 49 ARG cc_start: 0.9000 (mmm-85) cc_final: 0.8781 (ptm160) REVERT: C 67 GLN cc_start: 0.6262 (tp-100) cc_final: 0.5698 (tm-30) REVERT: C 139 MET cc_start: 0.7948 (mmp) cc_final: 0.7520 (tpp) REVERT: C 145 ASP cc_start: 0.8562 (m-30) cc_final: 0.7928 (t70) REVERT: C 154 LEU cc_start: 0.8978 (mt) cc_final: 0.8762 (mt) REVERT: C 159 LYS cc_start: 0.8808 (tptp) cc_final: 0.8249 (mmmt) REVERT: C 163 GLU cc_start: 0.7199 (mp0) cc_final: 0.6143 (pt0) REVERT: C 171 HIS cc_start: 0.8371 (m90) cc_final: 0.7995 (m90) REVERT: C 211 PHE cc_start: 0.7377 (t80) cc_final: 0.7166 (t80) REVERT: C 237 MET cc_start: 0.8902 (mmm) cc_final: 0.8694 (mmp) REVERT: C 240 GLU cc_start: 0.8891 (tt0) cc_final: 0.7693 (mm-30) REVERT: C 241 HIS cc_start: 0.8278 (m-70) cc_final: 0.7652 (t-170) REVERT: C 275 GLU cc_start: 0.8765 (pt0) cc_final: 0.8403 (mm-30) REVERT: C 278 ASN cc_start: 0.8298 (m-40) cc_final: 0.7609 (m-40) REVERT: C 315 ILE cc_start: 0.7462 (mt) cc_final: 0.7228 (mt) REVERT: C 368 MET cc_start: 0.8882 (mmp) cc_final: 0.8240 (ptt) REVERT: C 369 TYR cc_start: 0.8483 (m-80) cc_final: 0.8206 (m-80) REVERT: C 372 ARG cc_start: 0.9121 (ttt-90) cc_final: 0.8369 (mtp180) REVERT: C 391 MET cc_start: 0.8390 (tmm) cc_final: 0.8027 (tmm) REVERT: U 87 LEU cc_start: 0.6927 (mt) cc_final: 0.6439 (tt) REVERT: U 106 ASP cc_start: 0.7932 (m-30) cc_final: 0.7686 (m-30) REVERT: U 212 ASP cc_start: 0.5684 (t0) cc_final: 0.5214 (m-30) REVERT: U 235 LYS cc_start: 0.7529 (mttt) cc_final: 0.7221 (mptt) REVERT: U 510 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7105 (pm20) REVERT: U 554 LEU cc_start: 0.8664 (tt) cc_final: 0.8237 (mm) REVERT: U 573 ASP cc_start: 0.7013 (t0) cc_final: 0.6407 (t0) REVERT: U 574 LYS cc_start: 0.6845 (pttm) cc_final: 0.6256 (mmmt) REVERT: U 626 LEU cc_start: 0.8879 (mm) cc_final: 0.8635 (tp) REVERT: U 638 SER cc_start: 0.8750 (t) cc_final: 0.8444 (p) REVERT: U 650 TYR cc_start: 0.7941 (t80) cc_final: 0.7735 (t80) REVERT: U 675 MET cc_start: 0.8553 (mmm) cc_final: 0.8351 (tpp) REVERT: U 693 LEU cc_start: 0.8890 (mm) cc_final: 0.8506 (tp) REVERT: U 757 MET cc_start: 0.7003 (tmm) cc_final: 0.6558 (tmm) REVERT: U 770 TRP cc_start: 0.5410 (m-90) cc_final: 0.4806 (m-10) REVERT: V 346 LEU cc_start: 0.6238 (pp) cc_final: 0.5977 (mp) REVERT: V 444 ASP cc_start: 0.8502 (m-30) cc_final: 0.8043 (t0) REVERT: V 454 GLU cc_start: 0.8243 (tp30) cc_final: 0.7995 (mp0) REVERT: V 489 MET cc_start: 0.8717 (mmp) cc_final: 0.8133 (ttp) REVERT: W 37 GLU cc_start: 0.6342 (mt-10) cc_final: 0.5084 (tt0) REVERT: W 101 VAL cc_start: 0.8751 (t) cc_final: 0.8506 (t) REVERT: W 130 MET cc_start: 0.8164 (mmp) cc_final: 0.7451 (tmm) REVERT: W 221 LYS cc_start: 0.8513 (pttp) cc_final: 0.8278 (tttt) REVERT: W 225 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8502 (tmtt) REVERT: W 308 LEU cc_start: 0.8536 (tp) cc_final: 0.7653 (mt) REVERT: W 348 GLU cc_start: 0.8248 (tp30) cc_final: 0.7922 (tm-30) REVERT: W 352 LYS cc_start: 0.8392 (mmtp) cc_final: 0.8188 (mmmt) REVERT: W 375 MET cc_start: 0.8503 (tpt) cc_final: 0.8096 (mtm) REVERT: W 428 TRP cc_start: 0.8670 (m100) cc_final: 0.8391 (m100) REVERT: W 436 MET cc_start: 0.8743 (mmm) cc_final: 0.8516 (ttp) REVERT: W 451 MET cc_start: 0.6806 (mmt) cc_final: 0.6542 (tpt) REVERT: X 195 THR cc_start: 0.7520 (t) cc_final: 0.7040 (m) REVERT: X 211 ASP cc_start: 0.7516 (m-30) cc_final: 0.7133 (m-30) REVERT: X 234 GLU cc_start: 0.8353 (tp30) cc_final: 0.8101 (tt0) REVERT: X 282 ARG cc_start: 0.7779 (mmm-85) cc_final: 0.7251 (mmm160) REVERT: X 301 ASP cc_start: 0.8630 (m-30) cc_final: 0.8424 (m-30) REVERT: X 309 TYR cc_start: 0.6233 (m-10) cc_final: 0.5992 (m-10) REVERT: X 349 HIS cc_start: 0.8904 (m90) cc_final: 0.8698 (m90) REVERT: X 388 PHE cc_start: 0.6812 (p90) cc_final: 0.6583 (p90) REVERT: X 416 ASN cc_start: 0.8456 (m-40) cc_final: 0.8221 (p0) REVERT: Y 32 ARG cc_start: 0.6984 (tpt90) cc_final: 0.5881 (ptp-170) REVERT: Y 34 ASP cc_start: 0.8551 (p0) cc_final: 0.8275 (p0) REVERT: Y 38 ARG cc_start: 0.8744 (mtm-85) cc_final: 0.8336 (ppt170) REVERT: Y 55 GLU cc_start: 0.7051 (mp0) cc_final: 0.6301 (pt0) REVERT: Y 73 MET cc_start: 0.8269 (mtp) cc_final: 0.7852 (mmt) REVERT: Y 77 ASN cc_start: 0.7693 (t0) cc_final: 0.7425 (m-40) REVERT: Y 99 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8471 (tm-30) REVERT: Y 102 ASP cc_start: 0.9155 (t0) cc_final: 0.8652 (t0) REVERT: Y 124 PHE cc_start: 0.7865 (m-10) cc_final: 0.7658 (m-80) REVERT: Y 143 TYR cc_start: 0.8185 (m-80) cc_final: 0.7943 (m-80) REVERT: Y 188 CYS cc_start: 0.8216 (m) cc_final: 0.7960 (m) REVERT: Y 217 LYS cc_start: 0.9264 (ttpt) cc_final: 0.9061 (mttt) REVERT: Y 222 TYR cc_start: 0.8435 (m-10) cc_final: 0.8130 (m-80) REVERT: Y 319 MET cc_start: 0.7742 (mmp) cc_final: 0.7316 (mmm) REVERT: Y 371 LYS cc_start: 0.9129 (mmtt) cc_final: 0.8883 (ptmt) REVERT: Y 375 LEU cc_start: 0.8988 (tt) cc_final: 0.8436 (mm) REVERT: Z 35 VAL cc_start: 0.5066 (t) cc_final: 0.4354 (p) REVERT: Z 75 LEU cc_start: 0.8298 (tt) cc_final: 0.7842 (mp) REVERT: Z 81 MET cc_start: 0.8757 (mmp) cc_final: 0.8397 (mmm) REVERT: Z 112 MET cc_start: 0.8408 (ptp) cc_final: 0.8081 (pmm) REVERT: Z 169 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7226 (mp0) REVERT: Z 221 PRO cc_start: 0.7292 (Cg_exo) cc_final: 0.6387 (Cg_endo) REVERT: Z 255 ASP cc_start: 0.7474 (t70) cc_final: 0.7158 (m-30) REVERT: Z 257 MET cc_start: 0.6862 (tpt) cc_final: 0.6282 (ttp) REVERT: a 121 LEU cc_start: 0.8463 (mp) cc_final: 0.8022 (tt) REVERT: a 247 ARG cc_start: 0.8132 (mmt180) cc_final: 0.7229 (mmt90) REVERT: a 312 MET cc_start: 0.8677 (mmt) cc_final: 0.8303 (mmt) REVERT: a 342 ASP cc_start: 0.6844 (m-30) cc_final: 0.6345 (m-30) REVERT: b 56 ASN cc_start: 0.6125 (t0) cc_final: 0.5647 (m110) REVERT: b 57 ASP cc_start: 0.7874 (t0) cc_final: 0.7180 (t0) REVERT: b 121 GLU cc_start: 0.8318 (pt0) cc_final: 0.8069 (tm-30) REVERT: c 57 MET cc_start: 0.7639 (mmt) cc_final: 0.6925 (tpp) REVERT: c 71 ASP cc_start: 0.8233 (t70) cc_final: 0.8013 (t70) REVERT: c 95 MET cc_start: 0.8724 (mmp) cc_final: 0.8445 (mmm) REVERT: c 200 TYR cc_start: 0.7243 (m-80) cc_final: 0.6968 (m-80) REVERT: c 255 TYR cc_start: 0.8576 (m-10) cc_final: 0.8338 (m-10) REVERT: c 292 MET cc_start: 0.9274 (mmm) cc_final: 0.8520 (ppp) REVERT: c 303 MET cc_start: 0.8781 (mmm) cc_final: 0.8391 (mpp) REVERT: d 1 MET cc_start: 0.3330 (ttt) cc_final: 0.3122 (ptm) REVERT: d 35 PHE cc_start: 0.6700 (t80) cc_final: 0.6383 (t80) REVERT: d 75 MET cc_start: 0.3664 (tpt) cc_final: 0.2944 (tpt) REVERT: d 206 MET cc_start: 0.6693 (ptm) cc_final: 0.6335 (ptm) REVERT: d 241 GLU cc_start: 0.8115 (pt0) cc_final: 0.7660 (tp30) REVERT: f 112 MET cc_start: 0.0812 (ptt) cc_final: -0.1063 (mmp) REVERT: f 135 MET cc_start: -0.0023 (pmm) cc_final: -0.3819 (ttt) REVERT: f 384 MET cc_start: 0.2753 (mmm) cc_final: 0.2274 (mtm) REVERT: f 446 ASN cc_start: 0.3756 (t0) cc_final: 0.3473 (m110) REVERT: f 570 MET cc_start: 0.6929 (ptm) cc_final: 0.5262 (tpp) REVERT: f 572 MET cc_start: 0.2522 (tpt) cc_final: 0.1938 (tpt) REVERT: f 602 MET cc_start: 0.2150 (tpt) cc_final: 0.1795 (tpp) REVERT: f 629 MET cc_start: 0.0357 (ptp) cc_final: -0.0385 (mmt) REVERT: f 666 MET cc_start: 0.1109 (ttp) cc_final: 0.0882 (ttp) outliers start: 24 outliers final: 3 residues processed: 1653 average time/residue: 0.6851 time to fit residues: 1920.3695 Evaluate side-chains 1101 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1097 time to evaluate : 6.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 495 optimal weight: 20.0000 chunk 276 optimal weight: 7.9990 chunk 741 optimal weight: 0.8980 chunk 606 optimal weight: 30.0000 chunk 245 optimal weight: 50.0000 chunk 892 optimal weight: 20.0000 chunk 964 optimal weight: 8.9990 chunk 794 optimal weight: 0.2980 chunk 885 optimal weight: 10.0000 chunk 304 optimal weight: 2.9990 chunk 715 optimal weight: 30.0000 overall best weight: 4.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN H 109 GLN H 148 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 221 GLN ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 HIS ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 188 HIS ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 247 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS E 262 ASN ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 GLN ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN C 40 GLN C 278 ASN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN ** U 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 128 GLN U 149 GLN U 258 GLN U 345 ASN U 346 ASN ** U 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 880 ASN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 GLN ** V 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 400 HIS V 473 GLN ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 292 GLN ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 306 GLN Z 44 GLN ** Z 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 ASN ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 273 GLN b 79 GLN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 HIS ** c 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 4 GLN ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 293 ASN ** f 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 79128 Z= 0.229 Angle : 0.784 13.864 106985 Z= 0.405 Chirality : 0.045 0.294 12177 Planarity : 0.005 0.098 13802 Dihedral : 6.418 85.858 10988 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.84 % Favored : 93.74 % Rotamer: Outliers : 0.23 % Allowed : 4.70 % Favored : 95.08 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 6.55 % Cis-general : 2.01 % Twisted Proline : 0.57 % Twisted General : 0.03 % 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: -2.07 (0.08), residues: 9841 helix: -1.22 (0.07), residues: 4690 sheet: -0.68 (0.15), residues: 1039 loop : -1.57 (0.09), residues: 4112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP P 154 HIS 0.014 0.001 HIS L 20 PHE 0.041 0.002 PHE C 235 TYR 0.025 0.002 TYR V 213 ARG 0.021 0.001 ARG M 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1415 time to evaluate : 6.430 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: G 70 PHE cc_start: 0.8007 (m-10) cc_final: 0.7738 (m-80) REVERT: G 80 MET cc_start: 0.8289 (mmp) cc_final: 0.6901 (mmp) REVERT: G 125 TYR cc_start: 0.8789 (m-10) cc_final: 0.8485 (m-80) REVERT: G 174 GLU cc_start: 0.8129 (mp0) cc_final: 0.7926 (pm20) REVERT: H 79 MET cc_start: 0.8533 (pmm) cc_final: 0.8097 (tpt) REVERT: H 82 ASP cc_start: 0.8544 (m-30) cc_final: 0.8293 (m-30) REVERT: H 165 LYS cc_start: 0.8342 (mttt) cc_final: 0.8082 (mtmm) REVERT: H 175 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8251 (tp30) REVERT: I 26 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8405 (mt-10) REVERT: I 68 LEU cc_start: 0.8283 (mt) cc_final: 0.8083 (tp) REVERT: I 89 GLU cc_start: 0.8812 (tp30) cc_final: 0.8483 (mm-30) REVERT: I 96 ARG cc_start: 0.9481 (ptp-170) cc_final: 0.9041 (mtp85) REVERT: I 100 GLN cc_start: 0.8838 (tt0) cc_final: 0.8366 (tp40) REVERT: I 119 GLN cc_start: 0.9015 (tt0) cc_final: 0.8678 (tp40) REVERT: I 148 TYR cc_start: 0.5396 (m-80) cc_final: 0.4958 (m-80) REVERT: I 220 ASN cc_start: 0.7596 (p0) cc_final: 0.7268 (t0) REVERT: I 243 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8132 (mp0) REVERT: J 24 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8604 (tt0) REVERT: K 21 LEU cc_start: 0.8061 (mt) cc_final: 0.7647 (tp) REVERT: K 28 ILE cc_start: 0.8885 (mm) cc_final: 0.8655 (pt) REVERT: K 29 GLU cc_start: 0.8967 (tp30) cc_final: 0.8586 (mt-10) REVERT: K 228 MET cc_start: 0.5826 (ttm) cc_final: 0.5449 (mmt) REVERT: L 27 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7772 (mt-10) REVERT: L 88 MET cc_start: 0.8428 (tpt) cc_final: 0.8024 (tpt) REVERT: L 91 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8154 (pt0) REVERT: L 181 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7695 (mp0) REVERT: M 34 SER cc_start: 0.6292 (p) cc_final: 0.6090 (t) REVERT: M 47 PHE cc_start: 0.7253 (m-10) cc_final: 0.6502 (m-80) REVERT: M 50 GLU cc_start: 0.7017 (tt0) cc_final: 0.5870 (tp30) REVERT: M 69 VAL cc_start: 0.5875 (t) cc_final: 0.5653 (p) REVERT: M 75 MET cc_start: 0.6184 (mmm) cc_final: 0.5957 (mmm) REVERT: M 136 MET cc_start: 0.5741 (mtt) cc_final: 0.5306 (mtt) REVERT: N 73 PRO cc_start: 0.8088 (Cg_exo) cc_final: 0.7836 (Cg_endo) REVERT: N 77 HIS cc_start: 0.7926 (t-90) cc_final: 0.7608 (t70) REVERT: N 78 THR cc_start: 0.7213 (m) cc_final: 0.6985 (m) REVERT: N 95 MET cc_start: 0.2805 (ptm) cc_final: 0.2120 (ptm) REVERT: N 120 MET cc_start: 0.7078 (mmt) cc_final: 0.6617 (mmm) REVERT: N 162 LEU cc_start: 0.4282 (mt) cc_final: 0.3773 (tt) REVERT: O 28 ASP cc_start: 0.6378 (t0) cc_final: 0.6097 (t0) REVERT: O 35 HIS cc_start: 0.4096 (m90) cc_final: 0.3831 (m90) REVERT: O 114 TYR cc_start: 0.8071 (m-10) cc_final: 0.7466 (m-10) REVERT: O 127 MET cc_start: 0.3136 (mmm) cc_final: 0.2835 (mmt) REVERT: O 135 MET cc_start: 0.5712 (tpp) cc_final: 0.5201 (ttt) REVERT: P 34 MET cc_start: -0.0016 (ptp) cc_final: -0.1138 (tpt) REVERT: P 45 MET cc_start: 0.8478 (tpt) cc_final: 0.8122 (tpt) REVERT: P 69 PHE cc_start: 0.9091 (t80) cc_final: 0.8811 (t80) REVERT: P 88 MET cc_start: 0.9255 (tmm) cc_final: 0.9002 (tmm) REVERT: P 149 MET cc_start: 0.2908 (mmt) cc_final: 0.2681 (mmt) REVERT: P 183 MET cc_start: 0.7508 (mmt) cc_final: 0.7041 (mmt) REVERT: Q 92 LEU cc_start: 0.7776 (tp) cc_final: 0.7319 (mt) REVERT: R 83 LEU cc_start: 0.8435 (tt) cc_final: 0.7978 (tp) REVERT: S 13 LEU cc_start: 0.7189 (tp) cc_final: 0.6980 (tp) REVERT: S 163 HIS cc_start: 0.4671 (m-70) cc_final: 0.4037 (p90) REVERT: T 43 MET cc_start: 0.7347 (mmm) cc_final: 0.7101 (mmm) REVERT: T 50 MET cc_start: 0.7762 (ttp) cc_final: 0.6656 (tmm) REVERT: T 98 SER cc_start: 0.8440 (t) cc_final: 0.8035 (p) REVERT: T 211 ILE cc_start: 0.5992 (pt) cc_final: 0.5653 (tt) REVERT: T 214 MET cc_start: 0.1104 (mtt) cc_final: -0.0065 (ppp) REVERT: A 138 MET cc_start: 0.5651 (ttt) cc_final: 0.5421 (ttt) REVERT: A 225 CYS cc_start: 0.8707 (m) cc_final: 0.8414 (m) REVERT: A 252 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7123 (tt0) REVERT: A 256 MET cc_start: 0.7614 (mmp) cc_final: 0.7365 (mmm) REVERT: A 285 PHE cc_start: 0.6760 (p90) cc_final: 0.6424 (p90) REVERT: A 318 LEU cc_start: 0.8854 (tp) cc_final: 0.8324 (tp) REVERT: A 362 MET cc_start: 0.7586 (ttt) cc_final: 0.6517 (tmm) REVERT: B 155 LYS cc_start: 0.8147 (mmtm) cc_final: 0.7795 (ttmm) REVERT: B 163 LEU cc_start: 0.8488 (mp) cc_final: 0.7917 (tp) REVERT: B 251 VAL cc_start: 0.7673 (t) cc_final: 0.6881 (m) REVERT: B 287 ILE cc_start: 0.8200 (mt) cc_final: 0.7817 (mt) REVERT: B 306 GLN cc_start: 0.8781 (tt0) cc_final: 0.8532 (tm-30) REVERT: B 349 ARG cc_start: 0.8023 (tpt170) cc_final: 0.7110 (mtt90) REVERT: B 384 ILE cc_start: 0.7244 (pt) cc_final: 0.6638 (pt) REVERT: B 385 MET cc_start: 0.8075 (ttt) cc_final: 0.7824 (mmt) REVERT: B 404 LEU cc_start: 0.8816 (mt) cc_final: 0.8400 (mt) REVERT: D 68 LEU cc_start: 0.8803 (tp) cc_final: 0.8546 (mt) REVERT: D 81 ARG cc_start: 0.7099 (tmt170) cc_final: 0.6285 (ttm110) REVERT: D 170 MET cc_start: 0.8185 (ptm) cc_final: 0.6710 (tpt) REVERT: D 179 GLU cc_start: 0.8952 (pt0) cc_final: 0.8628 (pt0) REVERT: D 214 MET cc_start: 0.6849 (mtm) cc_final: 0.5899 (mmm) REVERT: D 240 LEU cc_start: 0.7588 (pp) cc_final: 0.7344 (pp) REVERT: D 283 ARG cc_start: 0.9066 (ttt-90) cc_final: 0.8552 (mtp180) REVERT: D 361 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8423 (tp30) REVERT: D 381 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8551 (mt-10) REVERT: E 51 GLN cc_start: 0.7569 (mm-40) cc_final: 0.6561 (pp30) REVERT: E 69 PHE cc_start: 0.7989 (m-80) cc_final: 0.7764 (m-80) REVERT: E 114 GLU cc_start: 0.7910 (pt0) cc_final: 0.7492 (tp30) REVERT: E 168 LYS cc_start: 0.7145 (ptpt) cc_final: 0.6684 (tptt) REVERT: E 210 GLU cc_start: 0.7609 (tm-30) cc_final: 0.6682 (tm-30) REVERT: E 242 ARG cc_start: 0.5591 (ptt-90) cc_final: 0.4875 (tpt90) REVERT: E 253 ILE cc_start: 0.8643 (mp) cc_final: 0.8443 (mm) REVERT: E 258 MET cc_start: 0.8768 (mpp) cc_final: 0.8147 (mmt) REVERT: E 262 ASN cc_start: 0.8473 (t0) cc_final: 0.8206 (p0) REVERT: E 295 LEU cc_start: 0.7871 (mt) cc_final: 0.7574 (mt) REVERT: E 327 ASP cc_start: 0.6213 (t70) cc_final: 0.4643 (p0) REVERT: F 225 MET cc_start: 0.5124 (ttt) cc_final: 0.4771 (ptt) REVERT: F 235 LEU cc_start: 0.8026 (mp) cc_final: 0.7559 (tt) REVERT: F 259 MET cc_start: 0.7980 (mmm) cc_final: 0.7579 (mmm) REVERT: F 430 LYS cc_start: 0.6072 (mtmm) cc_final: 0.5005 (tttp) REVERT: C 23 TYR cc_start: 0.6338 (t80) cc_final: 0.5568 (t80) REVERT: C 49 ARG cc_start: 0.9054 (mmm-85) cc_final: 0.8766 (ptm160) REVERT: C 67 GLN cc_start: 0.6245 (tp-100) cc_final: 0.6018 (tm-30) REVERT: C 80 MET cc_start: 0.7473 (mpp) cc_final: 0.7123 (mpp) REVERT: C 139 MET cc_start: 0.7957 (mmp) cc_final: 0.7402 (tpp) REVERT: C 145 ASP cc_start: 0.8596 (m-30) cc_final: 0.8157 (t70) REVERT: C 154 LEU cc_start: 0.8987 (mt) cc_final: 0.8767 (mt) REVERT: C 159 LYS cc_start: 0.8813 (tptp) cc_final: 0.8230 (mmmt) REVERT: C 163 GLU cc_start: 0.7105 (mp0) cc_final: 0.6136 (pt0) REVERT: C 171 HIS cc_start: 0.8212 (m90) cc_final: 0.7868 (m90) REVERT: C 211 PHE cc_start: 0.7104 (t80) cc_final: 0.6771 (t80) REVERT: C 241 HIS cc_start: 0.8225 (m-70) cc_final: 0.7913 (t-170) REVERT: C 275 GLU cc_start: 0.8684 (pt0) cc_final: 0.8310 (mm-30) REVERT: C 278 ASN cc_start: 0.8347 (m110) cc_final: 0.7908 (m-40) REVERT: C 315 ILE cc_start: 0.7746 (mt) cc_final: 0.7518 (mt) REVERT: C 351 MET cc_start: 0.8274 (tmm) cc_final: 0.8041 (tmm) REVERT: C 368 MET cc_start: 0.8971 (mmp) cc_final: 0.8282 (ptt) REVERT: C 369 TYR cc_start: 0.8448 (m-80) cc_final: 0.8226 (m-80) REVERT: C 372 ARG cc_start: 0.9194 (ttt-90) cc_final: 0.8434 (mtp180) REVERT: C 385 MET cc_start: 0.7693 (mmm) cc_final: 0.7477 (mmm) REVERT: C 391 MET cc_start: 0.8313 (tmm) cc_final: 0.7892 (tmm) REVERT: U 87 LEU cc_start: 0.7034 (mt) cc_final: 0.6504 (tt) REVERT: U 128 GLN cc_start: 0.8853 (tp40) cc_final: 0.7501 (pm20) REVERT: U 212 ASP cc_start: 0.5848 (t0) cc_final: 0.5253 (m-30) REVERT: U 235 LYS cc_start: 0.7522 (mttt) cc_final: 0.7219 (mptt) REVERT: U 355 ASN cc_start: 0.8262 (m110) cc_final: 0.7935 (t0) REVERT: U 448 LEU cc_start: 0.8260 (mt) cc_final: 0.7795 (mm) REVERT: U 510 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7206 (pm20) REVERT: U 532 MET cc_start: 0.7900 (mtp) cc_final: 0.7041 (ttm) REVERT: U 548 LEU cc_start: 0.7707 (mt) cc_final: 0.7311 (mt) REVERT: U 573 ASP cc_start: 0.7111 (t0) cc_final: 0.6542 (t0) REVERT: U 574 LYS cc_start: 0.7231 (pttm) cc_final: 0.6300 (mmmt) REVERT: U 583 MET cc_start: 0.8978 (mtp) cc_final: 0.8637 (tmm) REVERT: U 638 SER cc_start: 0.8811 (t) cc_final: 0.8491 (p) REVERT: U 642 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7964 (pt0) REVERT: U 650 TYR cc_start: 0.7933 (t80) cc_final: 0.7722 (t80) REVERT: U 693 LEU cc_start: 0.8868 (mm) cc_final: 0.8548 (tp) REVERT: U 757 MET cc_start: 0.7085 (tmm) cc_final: 0.6569 (tmm) REVERT: U 764 LEU cc_start: 0.8196 (pp) cc_final: 0.7981 (pp) REVERT: U 770 TRP cc_start: 0.5372 (m-90) cc_final: 0.4797 (m-10) REVERT: V 360 TYR cc_start: 0.6135 (t80) cc_final: 0.5755 (t80) REVERT: V 444 ASP cc_start: 0.8483 (m-30) cc_final: 0.8074 (t0) REVERT: V 454 GLU cc_start: 0.8549 (tp30) cc_final: 0.7899 (mp0) REVERT: V 489 MET cc_start: 0.8736 (mmp) cc_final: 0.8198 (ttp) REVERT: V 495 ARG cc_start: 0.7364 (mpt90) cc_final: 0.7127 (mpp80) REVERT: W 37 GLU cc_start: 0.6422 (mt-10) cc_final: 0.4927 (tt0) REVERT: W 130 MET cc_start: 0.8183 (mmp) cc_final: 0.7542 (ppp) REVERT: W 221 LYS cc_start: 0.8730 (pttp) cc_final: 0.8489 (ttmt) REVERT: W 308 LEU cc_start: 0.8571 (tp) cc_final: 0.7717 (mt) REVERT: W 312 MET cc_start: 0.5461 (tpt) cc_final: 0.5111 (tpt) REVERT: W 348 GLU cc_start: 0.8246 (tp30) cc_final: 0.7908 (tm-30) REVERT: W 352 LYS cc_start: 0.8567 (mmtp) cc_final: 0.8219 (mmmt) REVERT: W 366 MET cc_start: 0.6391 (mtp) cc_final: 0.6185 (mtp) REVERT: W 375 MET cc_start: 0.8536 (tpt) cc_final: 0.7764 (tmm) REVERT: W 428 TRP cc_start: 0.8708 (m100) cc_final: 0.8381 (m100) REVERT: W 432 LEU cc_start: 0.9348 (mt) cc_final: 0.9097 (mp) REVERT: W 436 MET cc_start: 0.8759 (mmm) cc_final: 0.8419 (mmp) REVERT: W 451 MET cc_start: 0.6633 (mmt) cc_final: 0.6100 (mtt) REVERT: W 453 HIS cc_start: 0.8858 (m90) cc_final: 0.8651 (m90) REVERT: X 211 ASP cc_start: 0.7555 (m-30) cc_final: 0.7130 (p0) REVERT: X 234 GLU cc_start: 0.8344 (tp30) cc_final: 0.8016 (pt0) REVERT: X 260 MET cc_start: 0.7163 (mmp) cc_final: 0.6869 (mmp) REVERT: X 282 ARG cc_start: 0.7689 (mmm-85) cc_final: 0.7145 (mmm160) REVERT: X 309 TYR cc_start: 0.6266 (m-10) cc_final: 0.5913 (m-10) REVERT: X 349 HIS cc_start: 0.8946 (m90) cc_final: 0.8733 (m90) REVERT: X 407 MET cc_start: 0.8957 (tmm) cc_final: 0.8608 (mmt) REVERT: Y 32 ARG cc_start: 0.6991 (tpt90) cc_final: 0.5864 (ptp-170) REVERT: Y 34 ASP cc_start: 0.8599 (p0) cc_final: 0.8319 (p0) REVERT: Y 38 ARG cc_start: 0.8830 (mtm-85) cc_final: 0.8330 (ppt90) REVERT: Y 55 GLU cc_start: 0.7080 (mp0) cc_final: 0.6317 (pt0) REVERT: Y 73 MET cc_start: 0.8025 (mtp) cc_final: 0.7522 (mmt) REVERT: Y 77 ASN cc_start: 0.7804 (t0) cc_final: 0.7465 (m-40) REVERT: Y 99 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8352 (tm-30) REVERT: Y 102 ASP cc_start: 0.9166 (t0) cc_final: 0.8948 (t0) REVERT: Y 105 MET cc_start: 0.7389 (ptp) cc_final: 0.6543 (ptp) REVERT: Y 124 PHE cc_start: 0.7914 (m-10) cc_final: 0.7699 (m-80) REVERT: Y 188 CYS cc_start: 0.8117 (m) cc_final: 0.7892 (m) REVERT: Y 222 TYR cc_start: 0.8542 (m-10) cc_final: 0.8289 (m-80) REVERT: Y 299 MET cc_start: 0.7412 (mmm) cc_final: 0.7070 (mmm) REVERT: Y 319 MET cc_start: 0.7813 (mmp) cc_final: 0.7590 (mmm) REVERT: Y 371 LYS cc_start: 0.9158 (mmtt) cc_final: 0.8953 (ptmt) REVERT: Z 35 VAL cc_start: 0.4953 (t) cc_final: 0.4347 (p) REVERT: Z 75 LEU cc_start: 0.8297 (tt) cc_final: 0.7795 (mp) REVERT: Z 81 MET cc_start: 0.8664 (mmp) cc_final: 0.8427 (mmm) REVERT: Z 112 MET cc_start: 0.8412 (ptp) cc_final: 0.8062 (pmm) REVERT: Z 169 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7309 (mm-30) REVERT: Z 221 PRO cc_start: 0.7488 (Cg_exo) cc_final: 0.7111 (Cg_endo) REVERT: Z 255 ASP cc_start: 0.7569 (t70) cc_final: 0.7184 (m-30) REVERT: Z 257 MET cc_start: 0.7057 (tpt) cc_final: 0.6691 (mmm) REVERT: a 121 LEU cc_start: 0.8472 (mp) cc_final: 0.8007 (tt) REVERT: a 161 LYS cc_start: 0.8371 (mmpt) cc_final: 0.7777 (tptp) REVERT: a 180 LEU cc_start: 0.8637 (mt) cc_final: 0.8333 (pp) REVERT: a 247 ARG cc_start: 0.8187 (mmt180) cc_final: 0.7313 (mmt180) REVERT: a 312 MET cc_start: 0.8584 (mmt) cc_final: 0.8263 (mmt) REVERT: b 52 ILE cc_start: 0.7978 (pt) cc_final: 0.7534 (tp) REVERT: b 57 ASP cc_start: 0.7777 (t0) cc_final: 0.7438 (t0) REVERT: b 121 GLU cc_start: 0.8244 (pt0) cc_final: 0.8027 (tm-30) REVERT: c 95 MET cc_start: 0.8759 (mmp) cc_final: 0.8515 (mmp) REVERT: c 200 TYR cc_start: 0.7180 (m-80) cc_final: 0.6855 (m-80) REVERT: c 234 TYR cc_start: 0.7241 (m-10) cc_final: 0.6989 (m-80) REVERT: c 292 MET cc_start: 0.9215 (mmm) cc_final: 0.8453 (ppp) REVERT: c 303 MET cc_start: 0.8845 (mmm) cc_final: 0.8496 (mpp) REVERT: d 1 MET cc_start: 0.3382 (ttt) cc_final: 0.2624 (ptm) REVERT: d 75 MET cc_start: 0.3877 (tpt) cc_final: 0.3238 (tpt) REVERT: d 206 MET cc_start: 0.6724 (ptm) cc_final: 0.6503 (ptm) REVERT: d 252 GLN cc_start: 0.8763 (mt0) cc_final: 0.8558 (mp10) REVERT: f 112 MET cc_start: 0.0871 (ptt) cc_final: -0.1095 (mmp) REVERT: f 135 MET cc_start: -0.0392 (pmm) cc_final: -0.3081 (ttt) REVERT: f 162 MET cc_start: 0.3734 (mmp) cc_final: 0.3001 (tpp) REVERT: f 384 MET cc_start: 0.2415 (mmm) cc_final: 0.1969 (mtm) REVERT: f 446 ASN cc_start: 0.3920 (t0) cc_final: 0.3567 (m110) REVERT: f 570 MET cc_start: 0.6979 (ptm) cc_final: 0.5198 (tpp) REVERT: f 572 MET cc_start: 0.2406 (tpt) cc_final: 0.1641 (mmm) REVERT: f 602 MET cc_start: 0.1933 (tpt) cc_final: 0.1540 (tpp) REVERT: f 629 MET cc_start: 0.0500 (ptp) cc_final: -0.0342 (mmt) outliers start: 19 outliers final: 3 residues processed: 1427 average time/residue: 0.6655 time to fit residues: 1626.5612 Evaluate side-chains 1020 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1017 time to evaluate : 6.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 881 optimal weight: 0.9990 chunk 670 optimal weight: 9.9990 chunk 463 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 425 optimal weight: 4.9990 chunk 599 optimal weight: 20.0000 chunk 895 optimal weight: 7.9990 chunk 948 optimal weight: 5.9990 chunk 467 optimal weight: 0.7980 chunk 848 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN G 123 GLN H 109 GLN H 148 GLN I 95 GLN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN N 66 HIS N 77 HIS ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 72 ASN ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 70 ASN T 162 GLN T 185 ASN A 88 GLN A 103 ASN A 247 GLN B 154 HIS ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS E 262 ASN ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN U 25 HIS U 28 ASN U 145 HIS U 345 ASN U 377 HIS U 421 GLN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 473 GLN ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 454 ASN ** X 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 ASN ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 258 GLN Z 44 GLN ** Z 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 256 GLN ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 273 GLN a 345 GLN b 79 GLN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 HIS ** c 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 298 GLN d 228 GLN e 6 GLN f 293 ASN ** f 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5822 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 79128 Z= 0.200 Angle : 0.758 13.688 106985 Z= 0.389 Chirality : 0.045 0.295 12177 Planarity : 0.005 0.098 13802 Dihedral : 6.353 88.621 10988 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.53 % Favored : 94.06 % Rotamer: Outliers : 0.07 % Allowed : 3.97 % Favored : 95.96 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 6.55 % Cis-general : 2.01 % Twisted Proline : 0.28 % Twisted General : 0.03 % 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: -1.78 (0.08), residues: 9841 helix: -0.92 (0.07), residues: 4673 sheet: -0.61 (0.15), residues: 1053 loop : -1.50 (0.09), residues: 4115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP U 35 HIS 0.019 0.001 HIS Z 196 PHE 0.028 0.002 PHE C 175 TYR 0.034 0.001 TYR Z 211 ARG 0.009 0.000 ARG c 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1362 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1356 time to evaluate : 6.514 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: G 61 LEU cc_start: 0.7516 (tt) cc_final: 0.7055 (tt) REVERT: G 70 PHE cc_start: 0.7987 (m-10) cc_final: 0.7714 (m-80) REVERT: G 80 MET cc_start: 0.8304 (mmp) cc_final: 0.6928 (mmp) REVERT: G 125 TYR cc_start: 0.8614 (m-10) cc_final: 0.8275 (m-80) REVERT: H 79 MET cc_start: 0.8547 (pmm) cc_final: 0.8116 (tpt) REVERT: H 82 ASP cc_start: 0.8582 (m-30) cc_final: 0.8359 (m-30) REVERT: H 165 LYS cc_start: 0.8299 (mttt) cc_final: 0.8044 (mtmm) REVERT: H 175 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8286 (tp30) REVERT: I 26 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8416 (mt-10) REVERT: I 89 GLU cc_start: 0.8783 (tp30) cc_final: 0.8404 (mm-30) REVERT: I 96 ARG cc_start: 0.9471 (ptp-170) cc_final: 0.9043 (mtp85) REVERT: I 100 GLN cc_start: 0.8845 (tt0) cc_final: 0.8377 (tp40) REVERT: I 136 TYR cc_start: 0.7463 (m-80) cc_final: 0.7149 (m-80) REVERT: I 148 TYR cc_start: 0.5524 (m-80) cc_final: 0.4952 (m-80) REVERT: I 220 ASN cc_start: 0.7574 (p0) cc_final: 0.7272 (t0) REVERT: I 243 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8178 (tm-30) REVERT: J 217 LEU cc_start: 0.5791 (pp) cc_final: 0.5427 (pp) REVERT: K 28 ILE cc_start: 0.8923 (mm) cc_final: 0.8710 (pt) REVERT: K 29 GLU cc_start: 0.8902 (tp30) cc_final: 0.8601 (mt-10) REVERT: K 66 LYS cc_start: 0.7089 (tptt) cc_final: 0.6818 (tptt) REVERT: K 114 GLN cc_start: 0.7554 (pm20) cc_final: 0.7294 (tp-100) REVERT: K 228 MET cc_start: 0.5882 (ttm) cc_final: 0.5504 (mmt) REVERT: L 27 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7796 (mt-10) REVERT: L 178 GLU cc_start: 0.8352 (pt0) cc_final: 0.8066 (pm20) REVERT: L 181 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7866 (mp0) REVERT: L 185 ASN cc_start: 0.8199 (m-40) cc_final: 0.7981 (m110) REVERT: M 37 ILE cc_start: 0.6799 (pt) cc_final: 0.6491 (pt) REVERT: M 47 PHE cc_start: 0.7158 (m-10) cc_final: 0.6447 (m-80) REVERT: M 50 GLU cc_start: 0.7164 (tt0) cc_final: 0.6037 (tp30) REVERT: M 69 VAL cc_start: 0.5972 (t) cc_final: 0.5539 (p) REVERT: M 75 MET cc_start: 0.6281 (mmm) cc_final: 0.5670 (mmm) REVERT: M 136 MET cc_start: 0.5768 (mtt) cc_final: 0.5037 (mtp) REVERT: N 73 PRO cc_start: 0.8133 (Cg_exo) cc_final: 0.7892 (Cg_endo) REVERT: N 77 HIS cc_start: 0.7870 (t70) cc_final: 0.7502 (t70) REVERT: N 78 THR cc_start: 0.7441 (m) cc_final: 0.7214 (m) REVERT: N 162 LEU cc_start: 0.4515 (mt) cc_final: 0.3943 (tt) REVERT: O 28 ASP cc_start: 0.6486 (t0) cc_final: 0.6211 (t0) REVERT: O 48 THR cc_start: 0.7239 (m) cc_final: 0.6849 (t) REVERT: O 114 TYR cc_start: 0.8032 (m-10) cc_final: 0.7447 (m-10) REVERT: O 127 MET cc_start: 0.3229 (mmm) cc_final: 0.2995 (mmt) REVERT: O 135 MET cc_start: 0.5911 (tpp) cc_final: 0.5315 (ttt) REVERT: P 34 MET cc_start: 0.0185 (ptp) cc_final: -0.1052 (tpt) REVERT: P 45 MET cc_start: 0.8711 (tpt) cc_final: 0.8455 (tpt) REVERT: P 69 PHE cc_start: 0.9107 (t80) cc_final: 0.8746 (t80) REVERT: P 88 MET cc_start: 0.9218 (tmm) cc_final: 0.8929 (tmm) REVERT: Q 92 LEU cc_start: 0.7790 (tp) cc_final: 0.7300 (mt) REVERT: Q 167 LEU cc_start: 0.7955 (mt) cc_final: 0.7631 (mt) REVERT: R 63 CYS cc_start: 0.9346 (m) cc_final: 0.8710 (t) REVERT: R 86 MET cc_start: 0.6799 (ptt) cc_final: 0.6466 (ppp) REVERT: S 13 LEU cc_start: 0.7128 (tp) cc_final: 0.6916 (tp) REVERT: S 163 HIS cc_start: 0.4635 (m-70) cc_final: 0.4005 (p-80) REVERT: T 43 MET cc_start: 0.7501 (mmm) cc_final: 0.7153 (mmm) REVERT: T 50 MET cc_start: 0.7804 (ttp) cc_final: 0.6756 (tmm) REVERT: T 98 SER cc_start: 0.8468 (t) cc_final: 0.8047 (p) REVERT: T 110 MET cc_start: 0.7753 (mpp) cc_final: 0.7099 (mpp) REVERT: T 211 ILE cc_start: 0.5872 (pt) cc_final: 0.5557 (tt) REVERT: T 214 MET cc_start: 0.1374 (mtt) cc_final: 0.0181 (ppp) REVERT: A 99 THR cc_start: 0.8458 (p) cc_final: 0.8188 (t) REVERT: A 138 MET cc_start: 0.5858 (ttt) cc_final: 0.5616 (ttt) REVERT: A 225 CYS cc_start: 0.8780 (m) cc_final: 0.8339 (t) REVERT: A 249 TYR cc_start: 0.7910 (t80) cc_final: 0.7678 (t80) REVERT: A 285 PHE cc_start: 0.6740 (p90) cc_final: 0.6431 (p90) REVERT: A 300 LEU cc_start: 0.9166 (mt) cc_final: 0.8646 (mt) REVERT: A 318 LEU cc_start: 0.8727 (tp) cc_final: 0.8377 (tp) REVERT: A 362 MET cc_start: 0.7532 (ttt) cc_final: 0.6493 (tmm) REVERT: B 107 MET cc_start: 0.4352 (ptm) cc_final: 0.3237 (ppp) REVERT: B 109 VAL cc_start: 0.8036 (t) cc_final: 0.7770 (t) REVERT: B 162 VAL cc_start: 0.5592 (t) cc_final: 0.5121 (t) REVERT: B 163 LEU cc_start: 0.8271 (mp) cc_final: 0.7679 (tp) REVERT: B 251 VAL cc_start: 0.7695 (t) cc_final: 0.6968 (m) REVERT: B 264 PRO cc_start: 0.6701 (Cg_endo) cc_final: 0.3964 (Cg_exo) REVERT: B 306 GLN cc_start: 0.8781 (tt0) cc_final: 0.8535 (tm-30) REVERT: B 311 GLU cc_start: 0.7788 (tp30) cc_final: 0.7423 (tt0) REVERT: B 327 VAL cc_start: 0.9358 (m) cc_final: 0.9116 (p) REVERT: B 329 MET cc_start: 0.8584 (tpt) cc_final: 0.8201 (mpp) REVERT: B 349 ARG cc_start: 0.7538 (tpt170) cc_final: 0.7046 (mtt90) REVERT: B 385 MET cc_start: 0.8082 (ttt) cc_final: 0.7820 (mmt) REVERT: B 404 LEU cc_start: 0.8812 (mt) cc_final: 0.8408 (mt) REVERT: D 143 LEU cc_start: 0.5693 (tt) cc_final: 0.5395 (tt) REVERT: D 170 MET cc_start: 0.8134 (ptm) cc_final: 0.6708 (tpt) REVERT: D 179 GLU cc_start: 0.8973 (pt0) cc_final: 0.8504 (pt0) REVERT: D 214 MET cc_start: 0.6835 (mtm) cc_final: 0.5918 (mmm) REVERT: D 240 LEU cc_start: 0.7463 (pp) cc_final: 0.7233 (pp) REVERT: D 283 ARG cc_start: 0.9049 (ttt-90) cc_final: 0.8641 (mtp180) REVERT: D 352 MET cc_start: 0.7869 (mtt) cc_final: 0.7634 (mmm) REVERT: D 361 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8429 (tp30) REVERT: D 381 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8596 (mt-10) REVERT: E 50 LEU cc_start: 0.7473 (mt) cc_final: 0.7238 (mt) REVERT: E 51 GLN cc_start: 0.7575 (mm-40) cc_final: 0.6563 (pp30) REVERT: E 69 PHE cc_start: 0.7971 (m-80) cc_final: 0.7714 (m-80) REVERT: E 114 GLU cc_start: 0.8067 (pt0) cc_final: 0.7581 (tp30) REVERT: E 164 ILE cc_start: 0.7183 (tp) cc_final: 0.6980 (mt) REVERT: E 216 ARG cc_start: 0.8231 (ptp-110) cc_final: 0.7391 (tmm-80) REVERT: E 242 ARG cc_start: 0.5533 (ptt-90) cc_final: 0.4875 (tpt90) REVERT: E 255 ARG cc_start: 0.9180 (ptp-170) cc_final: 0.8738 (ptt-90) REVERT: E 258 MET cc_start: 0.8854 (mpp) cc_final: 0.8221 (mmt) REVERT: E 327 ASP cc_start: 0.6290 (t70) cc_final: 0.4929 (p0) REVERT: F 225 MET cc_start: 0.5045 (ttt) cc_final: 0.4690 (ptt) REVERT: F 235 LEU cc_start: 0.8081 (mp) cc_final: 0.7788 (tp) REVERT: F 288 LEU cc_start: 0.9113 (tp) cc_final: 0.8738 (mp) REVERT: F 391 PHE cc_start: 0.7858 (m-80) cc_final: 0.7056 (t80) REVERT: C 23 TYR cc_start: 0.6573 (t80) cc_final: 0.5824 (t80) REVERT: C 49 ARG cc_start: 0.9051 (mmm-85) cc_final: 0.8800 (ptm160) REVERT: C 67 GLN cc_start: 0.6373 (tp-100) cc_final: 0.6081 (tm-30) REVERT: C 80 MET cc_start: 0.7335 (mpp) cc_final: 0.7068 (mpp) REVERT: C 139 MET cc_start: 0.7934 (mmp) cc_final: 0.7354 (tpp) REVERT: C 145 ASP cc_start: 0.8580 (m-30) cc_final: 0.8110 (t70) REVERT: C 171 HIS cc_start: 0.8226 (m90) cc_final: 0.7892 (m90) REVERT: C 211 PHE cc_start: 0.7120 (t80) cc_final: 0.6604 (t80) REVERT: C 240 GLU cc_start: 0.8782 (tt0) cc_final: 0.8276 (tp30) REVERT: C 275 GLU cc_start: 0.8736 (pt0) cc_final: 0.8358 (mm-30) REVERT: C 278 ASN cc_start: 0.8400 (m110) cc_final: 0.7989 (m-40) REVERT: C 315 ILE cc_start: 0.7731 (mt) cc_final: 0.7515 (mt) REVERT: C 351 MET cc_start: 0.8320 (tmm) cc_final: 0.8017 (tmm) REVERT: C 368 MET cc_start: 0.8998 (mmp) cc_final: 0.8334 (ptt) REVERT: C 372 ARG cc_start: 0.9210 (ttt-90) cc_final: 0.8483 (mtp85) REVERT: C 391 MET cc_start: 0.8310 (tmm) cc_final: 0.8061 (tmm) REVERT: U 128 GLN cc_start: 0.8902 (tp40) cc_final: 0.8186 (mm-40) REVERT: U 212 ASP cc_start: 0.6110 (t0) cc_final: 0.5302 (m-30) REVERT: U 235 LYS cc_start: 0.7479 (mttt) cc_final: 0.7056 (mptt) REVERT: U 355 ASN cc_start: 0.8326 (m110) cc_final: 0.7976 (t0) REVERT: U 532 MET cc_start: 0.7657 (mtp) cc_final: 0.6864 (ttm) REVERT: U 548 LEU cc_start: 0.7727 (mt) cc_final: 0.7328 (mt) REVERT: U 574 LYS cc_start: 0.7421 (pttm) cc_final: 0.6342 (mmmt) REVERT: U 583 MET cc_start: 0.9003 (mtp) cc_final: 0.8704 (tmm) REVERT: U 642 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7928 (pt0) REVERT: U 650 TYR cc_start: 0.7897 (t80) cc_final: 0.7668 (t80) REVERT: U 693 LEU cc_start: 0.8831 (mm) cc_final: 0.8505 (tp) REVERT: U 770 TRP cc_start: 0.5293 (m-90) cc_final: 0.4685 (m-10) REVERT: V 331 LEU cc_start: 0.8876 (mm) cc_final: 0.8628 (tp) REVERT: V 444 ASP cc_start: 0.8487 (m-30) cc_final: 0.8085 (t0) REVERT: V 454 GLU cc_start: 0.8598 (tp30) cc_final: 0.7978 (mp0) REVERT: V 489 MET cc_start: 0.8723 (mmp) cc_final: 0.8203 (ttp) REVERT: W 130 MET cc_start: 0.8116 (mmp) cc_final: 0.7554 (tmm) REVERT: W 145 LEU cc_start: 0.7725 (mt) cc_final: 0.7327 (mt) REVERT: W 271 VAL cc_start: 0.7917 (p) cc_final: 0.7605 (p) REVERT: W 308 LEU cc_start: 0.8611 (tp) cc_final: 0.7940 (mt) REVERT: W 348 GLU cc_start: 0.8214 (tp30) cc_final: 0.7803 (tm-30) REVERT: W 375 MET cc_start: 0.8454 (tpt) cc_final: 0.7465 (tmm) REVERT: W 428 TRP cc_start: 0.8732 (m100) cc_final: 0.8387 (m100) REVERT: W 436 MET cc_start: 0.8741 (mmm) cc_final: 0.8497 (ttp) REVERT: W 451 MET cc_start: 0.6500 (mmt) cc_final: 0.5810 (ttm) REVERT: W 453 HIS cc_start: 0.8868 (m90) cc_final: 0.8653 (m90) REVERT: X 260 MET cc_start: 0.7132 (mmp) cc_final: 0.6887 (mmp) REVERT: X 282 ARG cc_start: 0.7678 (mmm-85) cc_final: 0.7363 (mmm160) REVERT: X 349 HIS cc_start: 0.8956 (m90) cc_final: 0.8738 (m90) REVERT: X 407 MET cc_start: 0.8964 (tmm) cc_final: 0.8609 (mmt) REVERT: Y 32 ARG cc_start: 0.6939 (tpt90) cc_final: 0.5814 (ptp-170) REVERT: Y 34 ASP cc_start: 0.8665 (p0) cc_final: 0.8376 (p0) REVERT: Y 38 ARG cc_start: 0.8874 (mtm-85) cc_final: 0.8402 (ptt90) REVERT: Y 55 GLU cc_start: 0.7072 (mp0) cc_final: 0.6337 (pt0) REVERT: Y 71 ASN cc_start: 0.6920 (m-40) cc_final: 0.5982 (t0) REVERT: Y 73 MET cc_start: 0.7878 (mtp) cc_final: 0.7319 (mmt) REVERT: Y 77 ASN cc_start: 0.7762 (t0) cc_final: 0.7380 (m-40) REVERT: Y 102 ASP cc_start: 0.9185 (t0) cc_final: 0.8950 (t0) REVERT: Y 105 MET cc_start: 0.7725 (ptp) cc_final: 0.7081 (ptp) REVERT: Y 124 PHE cc_start: 0.7961 (m-10) cc_final: 0.7694 (m-80) REVERT: Y 188 CYS cc_start: 0.8045 (m) cc_final: 0.7819 (m) REVERT: Y 371 LYS cc_start: 0.9157 (mmtt) cc_final: 0.8952 (pttt) REVERT: Z 35 VAL cc_start: 0.4597 (t) cc_final: 0.4070 (p) REVERT: Z 75 LEU cc_start: 0.8335 (tt) cc_final: 0.7888 (mp) REVERT: Z 81 MET cc_start: 0.8625 (mmp) cc_final: 0.8415 (mmm) REVERT: Z 112 MET cc_start: 0.8345 (ptp) cc_final: 0.8011 (pmm) REVERT: Z 169 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7291 (mm-30) REVERT: Z 176 LEU cc_start: 0.8454 (pp) cc_final: 0.8025 (mt) REVERT: Z 187 LEU cc_start: 0.7542 (mp) cc_final: 0.7165 (pp) REVERT: Z 221 PRO cc_start: 0.7561 (Cg_exo) cc_final: 0.6852 (Cg_endo) REVERT: Z 247 LYS cc_start: 0.8206 (mptt) cc_final: 0.7921 (mtmm) REVERT: a 121 LEU cc_start: 0.8455 (mp) cc_final: 0.7987 (tt) REVERT: a 124 ASN cc_start: 0.6928 (m-40) cc_final: 0.6123 (t0) REVERT: a 161 LYS cc_start: 0.8376 (mmpt) cc_final: 0.7753 (tptp) REVERT: a 312 MET cc_start: 0.8566 (mmt) cc_final: 0.8247 (mmt) REVERT: b 52 ILE cc_start: 0.7936 (pt) cc_final: 0.7477 (tp) REVERT: b 57 ASP cc_start: 0.7771 (t0) cc_final: 0.7421 (t0) REVERT: b 121 GLU cc_start: 0.8289 (pt0) cc_final: 0.8053 (tm-30) REVERT: c 41 MET cc_start: 0.8721 (mmp) cc_final: 0.8353 (mmp) REVERT: c 200 TYR cc_start: 0.7233 (m-80) cc_final: 0.6929 (m-10) REVERT: c 303 MET cc_start: 0.8858 (mmm) cc_final: 0.8583 (mpp) REVERT: d 1 MET cc_start: 0.3380 (ttt) cc_final: 0.2867 (ptm) REVERT: d 75 MET cc_start: 0.3974 (tpt) cc_final: 0.3237 (tpt) REVERT: d 206 MET cc_start: 0.6799 (ptm) cc_final: 0.6597 (ptm) REVERT: f 112 MET cc_start: 0.0794 (ptt) cc_final: -0.1119 (mmp) REVERT: f 122 ILE cc_start: 0.1669 (tp) cc_final: 0.0972 (mt) REVERT: f 135 MET cc_start: -0.0489 (pmm) cc_final: -0.2871 (ttt) REVERT: f 162 MET cc_start: 0.3823 (mmp) cc_final: 0.2981 (tpp) REVERT: f 384 MET cc_start: 0.2347 (mmm) cc_final: 0.1885 (mtm) REVERT: f 446 ASN cc_start: 0.4049 (t0) cc_final: 0.3742 (m110) REVERT: f 570 MET cc_start: 0.6872 (ptm) cc_final: 0.5114 (tpp) REVERT: f 572 MET cc_start: 0.2240 (tpt) cc_final: 0.1355 (mmm) REVERT: f 629 MET cc_start: 0.0936 (ptp) cc_final: -0.0061 (mmt) outliers start: 6 outliers final: 0 residues processed: 1359 average time/residue: 0.7135 time to fit residues: 1679.6556 Evaluate side-chains 1010 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1010 time to evaluate : 6.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 789 optimal weight: 20.0000 chunk 538 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 706 optimal weight: 30.0000 chunk 391 optimal weight: 20.0000 chunk 809 optimal weight: 7.9990 chunk 655 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 484 optimal weight: 7.9990 chunk 851 optimal weight: 9.9990 chunk 239 optimal weight: 6.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 238 HIS ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 HIS ** M 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 HIS ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 157 ASN ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 162 GLN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 GLN ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN F 258 GLN ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 177 ASN ** V 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 400 HIS V 473 GLN W 84 ASN ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 361 HIS ** X 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 251 HIS Y 258 GLN Z 44 GLN ** Z 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 ASN Z 157 HIS Z 256 GLN a 86 GLN ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 227 ASN ** a 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 273 GLN a 345 GLN c 44 HIS ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 HIS ** c 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 6 GLN f 114 ASN f 293 ASN ** f 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.6396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 79128 Z= 0.315 Angle : 0.887 14.597 106985 Z= 0.459 Chirality : 0.048 0.329 12177 Planarity : 0.006 0.099 13802 Dihedral : 6.723 83.848 10988 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 28.53 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.52 % Favored : 93.06 % Rotamer: Outliers : 0.08 % Allowed : 4.43 % Favored : 95.48 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 6.55 % Cis-general : 2.01 % Twisted Proline : 0.28 % Twisted General : 0.03 % 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: -1.94 (0.08), residues: 9841 helix: -1.01 (0.07), residues: 4703 sheet: -0.62 (0.15), residues: 1055 loop : -1.66 (0.09), residues: 4083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP P 154 HIS 0.025 0.002 HIS Z 196 PHE 0.034 0.003 PHE C 175 TYR 0.058 0.003 TYR L 24 ARG 0.049 0.001 ARG E 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1241 time to evaluate : 5.958 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: G 61 LEU cc_start: 0.7671 (tt) cc_final: 0.7375 (tt) REVERT: G 80 MET cc_start: 0.8350 (mmp) cc_final: 0.8127 (mmp) REVERT: G 95 ARG cc_start: 0.8590 (mtt-85) cc_final: 0.8351 (mmt90) REVERT: G 100 ASN cc_start: 0.8571 (m-40) cc_final: 0.8310 (m110) REVERT: G 115 CYS cc_start: 0.7993 (m) cc_final: 0.7777 (m) REVERT: G 171 LYS cc_start: 0.8112 (mmtp) cc_final: 0.7871 (mptt) REVERT: H 165 LYS cc_start: 0.8252 (mttt) cc_final: 0.7992 (mtmm) REVERT: H 175 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8352 (tp30) REVERT: I 26 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8427 (mt-10) REVERT: I 89 GLU cc_start: 0.8772 (tp30) cc_final: 0.8360 (mm-30) REVERT: I 96 ARG cc_start: 0.9512 (ptp-170) cc_final: 0.9102 (mtp85) REVERT: I 100 GLN cc_start: 0.8829 (tt0) cc_final: 0.8466 (tp40) REVERT: I 101 TYR cc_start: 0.8675 (m-80) cc_final: 0.8274 (m-80) REVERT: I 243 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8259 (mp0) REVERT: J 24 GLU cc_start: 0.8438 (tt0) cc_final: 0.8161 (tt0) REVERT: K 29 GLU cc_start: 0.8945 (tp30) cc_final: 0.8641 (mt-10) REVERT: K 84 ASP cc_start: 0.8343 (m-30) cc_final: 0.8054 (m-30) REVERT: K 156 MET cc_start: 0.6357 (ppp) cc_final: 0.5973 (ppp) REVERT: L 27 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8023 (mt-10) REVERT: M 39 ILE cc_start: 0.8687 (mm) cc_final: 0.8452 (mm) REVERT: M 50 GLU cc_start: 0.7293 (tt0) cc_final: 0.6236 (tp30) REVERT: M 67 PHE cc_start: 0.6241 (t80) cc_final: 0.5922 (t80) REVERT: M 69 VAL cc_start: 0.6376 (t) cc_final: 0.5693 (p) REVERT: M 75 MET cc_start: 0.6802 (mmm) cc_final: 0.5976 (mmm) REVERT: M 136 MET cc_start: 0.6902 (mtt) cc_final: 0.6243 (mtp) REVERT: N 120 MET cc_start: 0.7515 (mmm) cc_final: 0.7019 (mmm) REVERT: N 162 LEU cc_start: 0.4866 (mt) cc_final: 0.4318 (tt) REVERT: O 48 THR cc_start: 0.7308 (m) cc_final: 0.6988 (t) REVERT: O 55 THR cc_start: 0.8599 (m) cc_final: 0.8363 (t) REVERT: O 84 LYS cc_start: 0.6759 (ptpt) cc_final: 0.6446 (tttp) REVERT: O 135 MET cc_start: 0.6097 (tpp) cc_final: 0.5613 (ttp) REVERT: P 14 MET cc_start: 0.5789 (tpp) cc_final: 0.5498 (tpp) REVERT: P 45 MET cc_start: 0.9045 (tpt) cc_final: 0.8648 (tpt) REVERT: P 69 PHE cc_start: 0.9200 (t80) cc_final: 0.8575 (t80) REVERT: P 88 MET cc_start: 0.9227 (tmm) cc_final: 0.8969 (tmm) REVERT: P 117 PHE cc_start: 0.7849 (p90) cc_final: 0.7630 (p90) REVERT: P 171 MET cc_start: 0.7728 (ttt) cc_final: 0.6758 (mmm) REVERT: Q 44 LEU cc_start: 0.8386 (mp) cc_final: 0.8089 (mp) REVERT: R 36 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8141 (tp30) REVERT: R 86 MET cc_start: 0.7174 (ptt) cc_final: 0.6904 (ppp) REVERT: S 36 HIS cc_start: 0.5660 (m-70) cc_final: 0.5148 (m-70) REVERT: S 163 HIS cc_start: 0.4898 (m-70) cc_final: 0.3846 (p-80) REVERT: S 206 GLU cc_start: 0.6721 (pt0) cc_final: 0.5541 (mp0) REVERT: T 50 MET cc_start: 0.7937 (ttp) cc_final: 0.6760 (ppp) REVERT: T 51 LEU cc_start: 0.8806 (tp) cc_final: 0.8572 (tp) REVERT: T 110 MET cc_start: 0.7813 (mpp) cc_final: 0.6944 (mpp) REVERT: T 211 ILE cc_start: 0.5813 (pt) cc_final: 0.5320 (tt) REVERT: T 214 MET cc_start: 0.1632 (mtt) cc_final: 0.0485 (ppp) REVERT: A 138 MET cc_start: 0.6197 (ttt) cc_final: 0.5940 (ttt) REVERT: A 225 CYS cc_start: 0.8935 (m) cc_final: 0.8504 (t) REVERT: A 249 TYR cc_start: 0.7868 (t80) cc_final: 0.7303 (t80) REVERT: A 285 PHE cc_start: 0.6858 (p90) cc_final: 0.6551 (p90) REVERT: A 299 MET cc_start: 0.9338 (tmm) cc_final: 0.9136 (tmm) REVERT: A 318 LEU cc_start: 0.8597 (tp) cc_final: 0.8307 (tp) REVERT: A 362 MET cc_start: 0.7651 (ttt) cc_final: 0.7261 (ttp) REVERT: A 430 MET cc_start: 0.7161 (ptp) cc_final: 0.6932 (ppp) REVERT: B 107 MET cc_start: 0.5148 (ptm) cc_final: 0.4146 (ppp) REVERT: B 109 VAL cc_start: 0.8309 (t) cc_final: 0.8031 (t) REVERT: B 141 LYS cc_start: 0.8381 (pttt) cc_final: 0.7895 (mttm) REVERT: B 155 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7775 (ttmm) REVERT: B 163 LEU cc_start: 0.8293 (mp) cc_final: 0.7708 (tp) REVERT: B 251 VAL cc_start: 0.7695 (t) cc_final: 0.7172 (m) REVERT: B 264 PRO cc_start: 0.6995 (Cg_endo) cc_final: 0.4954 (Cg_exo) REVERT: B 306 GLN cc_start: 0.8759 (tt0) cc_final: 0.8503 (tm-30) REVERT: B 311 GLU cc_start: 0.8147 (tp30) cc_final: 0.7596 (tt0) REVERT: B 349 ARG cc_start: 0.7486 (tpt170) cc_final: 0.6980 (mtt90) REVERT: B 385 MET cc_start: 0.8225 (ttt) cc_final: 0.7946 (mmt) REVERT: D 170 MET cc_start: 0.8069 (ptm) cc_final: 0.6925 (tpp) REVERT: D 179 GLU cc_start: 0.9077 (pt0) cc_final: 0.8653 (pt0) REVERT: D 240 LEU cc_start: 0.7649 (pp) cc_final: 0.7308 (pp) REVERT: D 283 ARG cc_start: 0.9128 (ttt-90) cc_final: 0.8510 (mtp180) REVERT: D 352 MET cc_start: 0.8105 (mtt) cc_final: 0.7802 (mmm) REVERT: D 381 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8679 (mt-10) REVERT: E 50 LEU cc_start: 0.7615 (mt) cc_final: 0.7248 (mt) REVERT: E 51 GLN cc_start: 0.7755 (mm-40) cc_final: 0.6823 (pp30) REVERT: E 69 PHE cc_start: 0.8024 (m-80) cc_final: 0.7580 (m-80) REVERT: E 114 GLU cc_start: 0.8227 (pt0) cc_final: 0.7765 (tp30) REVERT: E 242 ARG cc_start: 0.5432 (ptt-90) cc_final: 0.4619 (tpt90) REVERT: E 255 ARG cc_start: 0.9210 (ptp-170) cc_final: 0.8912 (ptp-170) REVERT: E 277 MET cc_start: 0.7553 (ptp) cc_final: 0.7223 (ptp) REVERT: E 327 ASP cc_start: 0.6610 (t70) cc_final: 0.5451 (m-30) REVERT: F 225 MET cc_start: 0.5264 (ttt) cc_final: 0.4923 (ptt) REVERT: F 235 LEU cc_start: 0.8006 (mp) cc_final: 0.7539 (tt) REVERT: F 260 PHE cc_start: 0.7240 (m-10) cc_final: 0.6893 (m-10) REVERT: F 288 LEU cc_start: 0.9027 (tp) cc_final: 0.8659 (mp) REVERT: F 430 LYS cc_start: 0.6321 (mtmm) cc_final: 0.5266 (tttp) REVERT: C 23 TYR cc_start: 0.6988 (t80) cc_final: 0.6099 (t80) REVERT: C 67 GLN cc_start: 0.6517 (tp-100) cc_final: 0.6155 (tm-30) REVERT: C 80 MET cc_start: 0.7155 (mpp) cc_final: 0.6946 (mpp) REVERT: C 145 ASP cc_start: 0.8669 (m-30) cc_final: 0.8140 (t70) REVERT: C 233 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6851 (pm20) REVERT: C 275 GLU cc_start: 0.8860 (pt0) cc_final: 0.8527 (mm-30) REVERT: C 351 MET cc_start: 0.8372 (tmm) cc_final: 0.8073 (tmm) REVERT: C 368 MET cc_start: 0.9035 (mmp) cc_final: 0.8366 (ptt) REVERT: C 372 ARG cc_start: 0.9269 (ttt-90) cc_final: 0.8583 (mtp85) REVERT: C 391 MET cc_start: 0.8274 (tmm) cc_final: 0.8042 (tmm) REVERT: U 87 LEU cc_start: 0.6698 (mp) cc_final: 0.6242 (tt) REVERT: U 128 GLN cc_start: 0.8891 (tp40) cc_final: 0.8292 (mm-40) REVERT: U 235 LYS cc_start: 0.7710 (mttt) cc_final: 0.7359 (mptt) REVERT: U 355 ASN cc_start: 0.8519 (m110) cc_final: 0.8139 (t0) REVERT: U 448 LEU cc_start: 0.8822 (tt) cc_final: 0.8401 (mm) REVERT: U 532 MET cc_start: 0.7736 (mtp) cc_final: 0.6804 (ttm) REVERT: U 548 LEU cc_start: 0.8013 (mt) cc_final: 0.7604 (mt) REVERT: U 693 LEU cc_start: 0.8966 (mm) cc_final: 0.8648 (tp) REVERT: U 770 TRP cc_start: 0.5382 (m-90) cc_final: 0.4846 (m-10) REVERT: U 901 GLN cc_start: 0.8336 (mt0) cc_final: 0.8074 (mp10) REVERT: V 444 ASP cc_start: 0.8606 (m-30) cc_final: 0.8260 (t0) REVERT: V 489 MET cc_start: 0.8701 (mmp) cc_final: 0.8211 (ttp) REVERT: W 130 MET cc_start: 0.8020 (mmp) cc_final: 0.7559 (tmm) REVERT: W 188 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8794 (mt-10) REVERT: W 308 LEU cc_start: 0.8641 (tp) cc_final: 0.7996 (mt) REVERT: W 375 MET cc_start: 0.8952 (tpt) cc_final: 0.8292 (ptm) REVERT: W 428 TRP cc_start: 0.8763 (m100) cc_final: 0.8484 (m100) REVERT: W 436 MET cc_start: 0.8844 (mmm) cc_final: 0.8609 (ttp) REVERT: W 451 MET cc_start: 0.6694 (mmt) cc_final: 0.5781 (ttm) REVERT: X 211 ASP cc_start: 0.7694 (m-30) cc_final: 0.7467 (m-30) REVERT: X 234 GLU cc_start: 0.8454 (tp30) cc_final: 0.8193 (tt0) REVERT: X 282 ARG cc_start: 0.7419 (mmm-85) cc_final: 0.7043 (mmm160) REVERT: Y 32 ARG cc_start: 0.6850 (tpt90) cc_final: 0.5379 (ptp-170) REVERT: Y 34 ASP cc_start: 0.8600 (p0) cc_final: 0.8320 (p0) REVERT: Y 38 ARG cc_start: 0.8788 (mtm-85) cc_final: 0.8291 (ppt90) REVERT: Y 42 MET cc_start: 0.7615 (ptt) cc_final: 0.7314 (ptt) REVERT: Y 55 GLU cc_start: 0.7104 (mp0) cc_final: 0.6416 (pt0) REVERT: Y 73 MET cc_start: 0.7615 (mtp) cc_final: 0.6668 (mmm) REVERT: Y 77 ASN cc_start: 0.7878 (t0) cc_final: 0.7548 (m-40) REVERT: Y 102 ASP cc_start: 0.9206 (t0) cc_final: 0.8962 (t0) REVERT: Y 105 MET cc_start: 0.7817 (ptp) cc_final: 0.6271 (ptp) REVERT: Y 124 PHE cc_start: 0.8039 (m-10) cc_final: 0.7581 (m-80) REVERT: Y 257 ARG cc_start: 0.7152 (ttp-170) cc_final: 0.6353 (tmm160) REVERT: Z 75 LEU cc_start: 0.8592 (tt) cc_final: 0.8125 (mp) REVERT: Z 78 MET cc_start: 0.8323 (tpt) cc_final: 0.7985 (tpp) REVERT: Z 81 MET cc_start: 0.8631 (mmp) cc_final: 0.8374 (mmm) REVERT: Z 165 GLU cc_start: 0.7345 (pp20) cc_final: 0.6918 (pm20) REVERT: Z 176 LEU cc_start: 0.8589 (pp) cc_final: 0.8230 (mt) REVERT: Z 221 PRO cc_start: 0.7618 (Cg_exo) cc_final: 0.6991 (Cg_endo) REVERT: Z 247 LYS cc_start: 0.8400 (mptt) cc_final: 0.8188 (mtmm) REVERT: Z 257 MET cc_start: 0.7288 (tpt) cc_final: 0.6958 (mmm) REVERT: a 121 LEU cc_start: 0.8558 (mp) cc_final: 0.8067 (tt) REVERT: a 124 ASN cc_start: 0.7005 (m-40) cc_final: 0.6426 (t0) REVERT: a 127 ASP cc_start: 0.7339 (m-30) cc_final: 0.7137 (m-30) REVERT: a 312 MET cc_start: 0.8604 (mmt) cc_final: 0.8309 (mmt) REVERT: b 14 GLU cc_start: 0.7658 (pt0) cc_final: 0.7428 (tm-30) REVERT: b 52 ILE cc_start: 0.8024 (pt) cc_final: 0.7520 (tp) REVERT: b 57 ASP cc_start: 0.7741 (t0) cc_final: 0.7249 (t0) REVERT: b 59 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6343 (mm-30) REVERT: b 121 GLU cc_start: 0.8291 (pt0) cc_final: 0.8052 (tm-30) REVERT: c 41 MET cc_start: 0.8634 (mmp) cc_final: 0.8303 (mmp) REVERT: c 57 MET cc_start: 0.7494 (mmt) cc_final: 0.7048 (mmt) REVERT: c 200 TYR cc_start: 0.7282 (m-80) cc_final: 0.6987 (m-10) REVERT: c 207 TYR cc_start: 0.7136 (m-80) cc_final: 0.6862 (m-80) REVERT: c 303 MET cc_start: 0.8893 (mmm) cc_final: 0.8642 (mpp) REVERT: d 1 MET cc_start: 0.3570 (ttt) cc_final: 0.2543 (ptm) REVERT: d 206 MET cc_start: 0.6818 (ptm) cc_final: 0.6494 (ptm) REVERT: f 112 MET cc_start: 0.1074 (ptt) cc_final: -0.1006 (mmp) REVERT: f 135 MET cc_start: -0.0268 (pmm) cc_final: -0.2720 (ttt) REVERT: f 162 MET cc_start: 0.4065 (mmp) cc_final: 0.3583 (tpp) REVERT: f 384 MET cc_start: 0.2247 (mmm) cc_final: 0.1789 (mtm) REVERT: f 446 ASN cc_start: 0.4165 (t0) cc_final: 0.3699 (m110) REVERT: f 570 MET cc_start: 0.6870 (ptm) cc_final: 0.5084 (mmt) REVERT: f 572 MET cc_start: 0.2246 (tpt) cc_final: 0.1489 (mmm) outliers start: 7 outliers final: 1 residues processed: 1245 average time/residue: 0.7125 time to fit residues: 1540.0198 Evaluate side-chains 896 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 895 time to evaluate : 6.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 319 optimal weight: 20.0000 chunk 853 optimal weight: 10.0000 chunk 187 optimal weight: 30.0000 chunk 556 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 chunk 949 optimal weight: 20.0000 chunk 787 optimal weight: 0.0470 chunk 439 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 313 optimal weight: 8.9990 chunk 498 optimal weight: 20.0000 overall best weight: 7.0088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 HIS ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 72 ASN ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 188 HIS Q 55 GLN ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82 ASN ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 162 GLN A 433 ASN ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS F 130 GLN ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 ASN F 436 GLN C 36 ASN C 241 HIS ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 115 ASN U 145 HIS ** U 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN U 880 ASN ** V 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 106 GLN W 361 HIS W 430 GLN X 182 ASN ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 273 GLN a 290 GLN b 30 GLN ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 194 HIS ** c 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 102 ASN d 116 HIS f 293 ASN ** f 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.7141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 79128 Z= 0.270 Angle : 0.833 15.316 106985 Z= 0.431 Chirality : 0.047 0.308 12177 Planarity : 0.006 0.105 13802 Dihedral : 6.676 80.400 10988 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 26.77 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.31 % Favored : 93.28 % Rotamer: Outliers : 0.08 % Allowed : 3.21 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.55 % Cis-general : 2.01 % Twisted Proline : 0.57 % Twisted General : 0.03 % 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: -1.87 (0.08), residues: 9841 helix: -0.86 (0.07), residues: 4657 sheet: -0.68 (0.15), residues: 1071 loop : -1.73 (0.09), residues: 4113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP Y 286 HIS 0.020 0.002 HIS Z 196 PHE 0.050 0.002 PHE C 175 TYR 0.026 0.002 TYR f 395 ARG 0.011 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1197 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1190 time to evaluate : 6.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 78 CYS cc_start: 0.5178 (p) cc_final: 0.1434 (p) REVERT: G 95 ARG cc_start: 0.8573 (mtt-85) cc_final: 0.8238 (mmt90) REVERT: G 100 ASN cc_start: 0.8727 (m-40) cc_final: 0.8433 (m110) REVERT: H 79 MET cc_start: 0.8481 (pmm) cc_final: 0.8270 (pmm) REVERT: H 165 LYS cc_start: 0.8242 (mttt) cc_final: 0.7993 (mtmm) REVERT: H 175 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8436 (tp30) REVERT: I 26 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8461 (mt-10) REVERT: I 89 GLU cc_start: 0.8767 (tp30) cc_final: 0.8343 (mm-30) REVERT: I 96 ARG cc_start: 0.9516 (ptp-170) cc_final: 0.9164 (mtp85) REVERT: I 99 LEU cc_start: 0.8275 (tp) cc_final: 0.8043 (tp) REVERT: I 100 GLN cc_start: 0.8853 (tt0) cc_final: 0.8300 (tp40) REVERT: I 243 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8228 (mp0) REVERT: J 24 GLU cc_start: 0.8434 (tt0) cc_final: 0.8176 (tt0) REVERT: J 82 ILE cc_start: 0.9141 (mm) cc_final: 0.8771 (tp) REVERT: J 86 ARG cc_start: 0.7362 (tpp-160) cc_final: 0.7097 (mmp80) REVERT: K 26 TYR cc_start: 0.8025 (m-10) cc_final: 0.7729 (m-10) REVERT: K 29 GLU cc_start: 0.8932 (tp30) cc_final: 0.8618 (mt-10) REVERT: K 66 LYS cc_start: 0.7243 (tptt) cc_final: 0.6927 (tptt) REVERT: K 84 ASP cc_start: 0.8491 (m-30) cc_final: 0.8198 (m-30) REVERT: K 156 MET cc_start: 0.6992 (ppp) cc_final: 0.6589 (ppp) REVERT: L 178 GLU cc_start: 0.8757 (pt0) cc_final: 0.8509 (mm-30) REVERT: L 181 GLU cc_start: 0.7998 (mp0) cc_final: 0.7353 (pm20) REVERT: M 50 GLU cc_start: 0.7215 (tt0) cc_final: 0.6484 (tp30) REVERT: M 67 PHE cc_start: 0.6342 (t80) cc_final: 0.5885 (t80) REVERT: M 75 MET cc_start: 0.7101 (mmm) cc_final: 0.6103 (mmm) REVERT: M 136 MET cc_start: 0.7140 (mtt) cc_final: 0.6709 (mtt) REVERT: M 240 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8372 (mmtm) REVERT: N 119 MET cc_start: 0.0826 (ptp) cc_final: 0.0455 (ptp) REVERT: N 162 LEU cc_start: 0.5245 (mt) cc_final: 0.4631 (tt) REVERT: O 48 THR cc_start: 0.7489 (m) cc_final: 0.7215 (t) REVERT: O 54 MET cc_start: 0.8173 (mpp) cc_final: 0.7956 (mpp) REVERT: O 55 THR cc_start: 0.8652 (m) cc_final: 0.8407 (t) REVERT: O 127 MET cc_start: 0.4322 (mmm) cc_final: 0.4120 (mmt) REVERT: P 66 ARG cc_start: 0.8505 (mmt-90) cc_final: 0.7910 (mmt-90) REVERT: P 69 PHE cc_start: 0.9179 (t80) cc_final: 0.8534 (t80) REVERT: P 88 MET cc_start: 0.9271 (tmm) cc_final: 0.9018 (tmm) REVERT: P 171 MET cc_start: 0.7470 (ttt) cc_final: 0.6792 (mmm) REVERT: Q 44 LEU cc_start: 0.8446 (mp) cc_final: 0.8205 (mp) REVERT: R 36 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8216 (tp30) REVERT: S 36 HIS cc_start: 0.5804 (m-70) cc_final: 0.5250 (m-70) REVERT: S 206 GLU cc_start: 0.6732 (pt0) cc_final: 0.5518 (mp0) REVERT: T 50 MET cc_start: 0.7949 (ttp) cc_final: 0.6942 (tmm) REVERT: T 110 MET cc_start: 0.7855 (mpp) cc_final: 0.7062 (mpp) REVERT: T 214 MET cc_start: 0.2286 (mtt) cc_final: 0.1152 (ppp) REVERT: A 225 CYS cc_start: 0.9002 (m) cc_final: 0.8620 (t) REVERT: A 249 TYR cc_start: 0.7751 (t80) cc_final: 0.7337 (t80) REVERT: A 285 PHE cc_start: 0.6719 (p90) cc_final: 0.6426 (p90) REVERT: A 300 LEU cc_start: 0.9147 (mt) cc_final: 0.8901 (mt) REVERT: A 318 LEU cc_start: 0.8642 (tp) cc_final: 0.8327 (tp) REVERT: A 362 MET cc_start: 0.7592 (ttt) cc_final: 0.6723 (tmm) REVERT: A 366 ARG cc_start: 0.8845 (mtt90) cc_final: 0.7979 (tmm160) REVERT: B 107 MET cc_start: 0.5293 (ptm) cc_final: 0.4346 (ppp) REVERT: B 109 VAL cc_start: 0.8436 (t) cc_final: 0.8162 (t) REVERT: B 162 VAL cc_start: 0.4918 (t) cc_final: 0.4380 (t) REVERT: B 163 LEU cc_start: 0.8397 (mp) cc_final: 0.7672 (tp) REVERT: B 237 LYS cc_start: 0.9068 (mttt) cc_final: 0.8862 (mttt) REVERT: B 306 GLN cc_start: 0.8777 (tt0) cc_final: 0.8518 (tm-30) REVERT: D 64 GLU cc_start: 0.9202 (pp20) cc_final: 0.8885 (pp20) REVERT: D 170 MET cc_start: 0.8077 (ptm) cc_final: 0.6859 (tpp) REVERT: D 179 GLU cc_start: 0.9129 (pt0) cc_final: 0.8702 (pt0) REVERT: D 240 LEU cc_start: 0.7692 (pp) cc_final: 0.7367 (pp) REVERT: D 283 ARG cc_start: 0.9112 (ttt-90) cc_final: 0.8635 (mtp180) REVERT: D 381 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8740 (mt-10) REVERT: E 50 LEU cc_start: 0.7742 (mt) cc_final: 0.7331 (mt) REVERT: E 51 GLN cc_start: 0.7795 (mm-40) cc_final: 0.6904 (pp30) REVERT: E 69 PHE cc_start: 0.7760 (m-80) cc_final: 0.7452 (m-80) REVERT: E 110 TYR cc_start: 0.8059 (p90) cc_final: 0.7791 (p90) REVERT: E 114 GLU cc_start: 0.8219 (pt0) cc_final: 0.7717 (tp30) REVERT: E 218 MET cc_start: 0.8430 (mmp) cc_final: 0.8209 (mmm) REVERT: E 255 ARG cc_start: 0.9175 (ptp-170) cc_final: 0.8933 (ptp-170) REVERT: E 279 THR cc_start: 0.7446 (p) cc_final: 0.7024 (t) REVERT: E 327 ASP cc_start: 0.6555 (t70) cc_final: 0.5362 (m-30) REVERT: F 225 MET cc_start: 0.5382 (ttt) cc_final: 0.5023 (ptt) REVERT: F 235 LEU cc_start: 0.8079 (mp) cc_final: 0.7717 (tp) REVERT: F 260 PHE cc_start: 0.7383 (m-10) cc_final: 0.7149 (m-10) REVERT: F 288 LEU cc_start: 0.9173 (tp) cc_final: 0.8811 (mp) REVERT: F 430 LYS cc_start: 0.6450 (mtmm) cc_final: 0.5233 (tttp) REVERT: C 23 TYR cc_start: 0.7197 (t80) cc_final: 0.6343 (t80) REVERT: C 67 GLN cc_start: 0.6615 (tp-100) cc_final: 0.6289 (tm-30) REVERT: C 80 MET cc_start: 0.7179 (mpp) cc_final: 0.6975 (mpp) REVERT: C 139 MET cc_start: 0.8103 (mmp) cc_final: 0.7751 (tpt) REVERT: C 145 ASP cc_start: 0.8632 (m-30) cc_final: 0.8111 (t70) REVERT: C 233 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6890 (pm20) REVERT: C 275 GLU cc_start: 0.8898 (pt0) cc_final: 0.8553 (mm-30) REVERT: C 368 MET cc_start: 0.9078 (mmp) cc_final: 0.8435 (ptt) REVERT: C 369 TYR cc_start: 0.8520 (m-10) cc_final: 0.8223 (m-80) REVERT: C 372 ARG cc_start: 0.9257 (ttt-90) cc_final: 0.8551 (mtp85) REVERT: C 391 MET cc_start: 0.8326 (tmm) cc_final: 0.8089 (tmm) REVERT: U 87 LEU cc_start: 0.6953 (mp) cc_final: 0.6273 (tt) REVERT: U 128 GLN cc_start: 0.8925 (tp40) cc_final: 0.8406 (mm-40) REVERT: U 235 LYS cc_start: 0.7635 (mttt) cc_final: 0.7404 (mmmm) REVERT: U 355 ASN cc_start: 0.8590 (m110) cc_final: 0.8103 (t0) REVERT: U 448 LEU cc_start: 0.8745 (tt) cc_final: 0.8235 (mm) REVERT: U 510 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7314 (pm20) REVERT: U 548 LEU cc_start: 0.8026 (mt) cc_final: 0.7743 (mt) REVERT: U 654 MET cc_start: 0.8927 (mmp) cc_final: 0.8610 (mtp) REVERT: U 693 LEU cc_start: 0.8911 (mm) cc_final: 0.8645 (tp) REVERT: U 709 PHE cc_start: 0.8564 (m-80) cc_final: 0.8332 (m-80) REVERT: U 880 ASN cc_start: 0.6786 (OUTLIER) cc_final: 0.5448 (t0) REVERT: U 894 MET cc_start: 0.5031 (ptm) cc_final: 0.4710 (ptm) REVERT: U 901 GLN cc_start: 0.8266 (mt0) cc_final: 0.7426 (pp30) REVERT: V 444 ASP cc_start: 0.8591 (m-30) cc_final: 0.8325 (t0) REVERT: V 489 MET cc_start: 0.8785 (mmp) cc_final: 0.8333 (tpt) REVERT: W 130 MET cc_start: 0.8142 (mmp) cc_final: 0.7613 (tmm) REVERT: W 188 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8876 (mt-10) REVERT: W 308 LEU cc_start: 0.8635 (tp) cc_final: 0.8138 (mt) REVERT: W 361 HIS cc_start: 0.8247 (t-90) cc_final: 0.7990 (t-170) REVERT: W 375 MET cc_start: 0.8947 (tpt) cc_final: 0.8191 (ptm) REVERT: W 428 TRP cc_start: 0.8782 (m100) cc_final: 0.8479 (m100) REVERT: W 436 MET cc_start: 0.8834 (mmm) cc_final: 0.8590 (ttp) REVERT: W 451 MET cc_start: 0.6701 (mmt) cc_final: 0.5890 (ttm) REVERT: X 211 ASP cc_start: 0.7708 (m-30) cc_final: 0.7462 (m-30) REVERT: X 234 GLU cc_start: 0.8480 (tp30) cc_final: 0.8212 (tt0) REVERT: X 277 LEU cc_start: 0.7313 (pt) cc_final: 0.7034 (pt) REVERT: X 278 ARG cc_start: 0.7781 (tpt90) cc_final: 0.6893 (mmm160) REVERT: Y 32 ARG cc_start: 0.6782 (mmm160) cc_final: 0.5754 (ptp-170) REVERT: Y 34 ASP cc_start: 0.8497 (p0) cc_final: 0.8174 (p0) REVERT: Y 38 ARG cc_start: 0.8810 (mtm-85) cc_final: 0.8365 (ppt90) REVERT: Y 55 GLU cc_start: 0.7151 (mp0) cc_final: 0.6465 (pt0) REVERT: Y 73 MET cc_start: 0.7649 (mtp) cc_final: 0.6870 (mmt) REVERT: Y 77 ASN cc_start: 0.7907 (t0) cc_final: 0.7574 (m-40) REVERT: Y 124 PHE cc_start: 0.7918 (m-10) cc_final: 0.7597 (m-80) REVERT: Y 188 CYS cc_start: 0.8432 (m) cc_final: 0.7885 (p) REVERT: Y 228 MET cc_start: 0.7182 (ptm) cc_final: 0.6974 (ptm) REVERT: Y 257 ARG cc_start: 0.6956 (ttp-170) cc_final: 0.6117 (tmm160) REVERT: Z 75 LEU cc_start: 0.8651 (tt) cc_final: 0.8183 (mp) REVERT: Z 78 MET cc_start: 0.8218 (tpt) cc_final: 0.7893 (tpp) REVERT: Z 176 LEU cc_start: 0.8570 (pp) cc_final: 0.8112 (mt) REVERT: Z 196 HIS cc_start: 0.8227 (p90) cc_final: 0.8008 (p90) REVERT: Z 221 PRO cc_start: 0.7648 (Cg_exo) cc_final: 0.7116 (Cg_endo) REVERT: Z 244 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8461 (mt-10) REVERT: Z 247 LYS cc_start: 0.8487 (mptt) cc_final: 0.8224 (mtmm) REVERT: Z 257 MET cc_start: 0.7843 (tpt) cc_final: 0.7524 (mmm) REVERT: a 22 TRP cc_start: 0.7539 (t-100) cc_final: 0.7327 (t-100) REVERT: a 121 LEU cc_start: 0.8438 (mp) cc_final: 0.8036 (tt) REVERT: a 124 ASN cc_start: 0.7298 (m-40) cc_final: 0.6913 (t0) REVERT: a 127 ASP cc_start: 0.7244 (m-30) cc_final: 0.7038 (m-30) REVERT: a 312 MET cc_start: 0.8611 (mmt) cc_final: 0.8306 (mmt) REVERT: b 14 GLU cc_start: 0.7601 (pt0) cc_final: 0.7347 (tm-30) REVERT: b 57 ASP cc_start: 0.7848 (t0) cc_final: 0.7372 (t0) REVERT: b 59 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6155 (mm-30) REVERT: b 121 GLU cc_start: 0.8306 (pt0) cc_final: 0.8068 (tm-30) REVERT: c 41 MET cc_start: 0.8476 (mmp) cc_final: 0.8200 (mmp) REVERT: c 200 TYR cc_start: 0.7493 (m-80) cc_final: 0.7157 (m-10) REVERT: c 207 TYR cc_start: 0.7187 (m-80) cc_final: 0.6893 (m-80) REVERT: c 303 MET cc_start: 0.8896 (mmm) cc_final: 0.8683 (mpp) REVERT: d 1 MET cc_start: 0.3398 (ttt) cc_final: 0.2093 (ptm) REVERT: d 9 TRP cc_start: 0.7101 (t60) cc_final: 0.6883 (t60) REVERT: d 53 ASP cc_start: 0.7683 (m-30) cc_final: 0.7412 (p0) REVERT: d 54 ILE cc_start: 0.5773 (pt) cc_final: 0.4459 (pt) REVERT: d 206 MET cc_start: 0.6916 (ptm) cc_final: 0.6609 (ptm) REVERT: f 112 MET cc_start: 0.0520 (ptt) cc_final: -0.0436 (mmp) REVERT: f 135 MET cc_start: -0.0087 (pmm) cc_final: -0.2428 (ttt) REVERT: f 162 MET cc_start: 0.4040 (mmp) cc_final: 0.3615 (tpp) REVERT: f 384 MET cc_start: 0.1997 (mmm) cc_final: 0.1655 (mtm) REVERT: f 570 MET cc_start: 0.6839 (ptm) cc_final: 0.4934 (mmt) REVERT: f 572 MET cc_start: 0.2632 (tpt) cc_final: 0.1574 (tpt) outliers start: 7 outliers final: 0 residues processed: 1195 average time/residue: 0.6617 time to fit residues: 1368.8203 Evaluate side-chains 887 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 886 time to evaluate : 6.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 915 optimal weight: 40.0000 chunk 106 optimal weight: 20.0000 chunk 540 optimal weight: 6.9990 chunk 693 optimal weight: 5.9990 chunk 537 optimal weight: 3.9990 chunk 798 optimal weight: 6.9990 chunk 530 optimal weight: 30.0000 chunk 945 optimal weight: 40.0000 chunk 591 optimal weight: 20.0000 chunk 576 optimal weight: 30.0000 chunk 436 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN N 66 HIS ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 162 GLN ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 HIS B 157 HIS ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 ASN ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 GLN ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 HIS ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 115 ASN U 145 HIS ** U 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN ** U 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 106 GLN ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 72 HIS ** Z 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 273 GLN a 290 GLN b 29 GLN ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 298 GLN ** d 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 HIS ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 293 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.7799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 79128 Z= 0.259 Angle : 0.843 13.607 106985 Z= 0.433 Chirality : 0.047 0.308 12177 Planarity : 0.006 0.100 13802 Dihedral : 6.770 84.973 10988 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 27.65 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.99 % Favored : 92.60 % Rotamer: Outliers : 0.04 % Allowed : 2.06 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.55 % Cis-general : 2.01 % Twisted Proline : 0.57 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.08), residues: 9841 helix: -0.82 (0.07), residues: 4659 sheet: -0.74 (0.16), residues: 1053 loop : -1.74 (0.09), residues: 4129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP U 35 HIS 0.019 0.002 HIS Z 196 PHE 0.043 0.002 PHE f 431 TYR 0.045 0.002 TYR Z 211 ARG 0.023 0.001 ARG Z 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1157 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1154 time to evaluate : 6.566 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: G 37 LEU cc_start: 0.8676 (tp) cc_final: 0.8105 (tt) REVERT: G 78 CYS cc_start: 0.5045 (p) cc_final: 0.4583 (p) REVERT: G 80 MET cc_start: 0.8289 (mmp) cc_final: 0.7821 (mmp) REVERT: G 100 ASN cc_start: 0.8807 (m-40) cc_final: 0.8527 (m110) REVERT: G 125 TYR cc_start: 0.8773 (m-10) cc_final: 0.8457 (m-80) REVERT: G 138 MET cc_start: 0.8576 (tmm) cc_final: 0.8341 (tmm) REVERT: G 171 LYS cc_start: 0.8284 (mmtp) cc_final: 0.7938 (mppt) REVERT: H 79 MET cc_start: 0.8542 (pmm) cc_final: 0.8141 (pmm) REVERT: H 165 LYS cc_start: 0.8296 (mttt) cc_final: 0.8075 (mtmm) REVERT: H 175 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8372 (tp30) REVERT: I 26 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8448 (mt-10) REVERT: I 89 GLU cc_start: 0.8769 (tp30) cc_final: 0.8352 (mm-30) REVERT: I 96 ARG cc_start: 0.9529 (ptp-170) cc_final: 0.9223 (mtp85) REVERT: I 107 CYS cc_start: 0.9064 (t) cc_final: 0.8687 (p) REVERT: I 136 TYR cc_start: 0.8484 (m-10) cc_final: 0.8088 (m-80) REVERT: I 243 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8202 (mt-10) REVERT: I 246 LYS cc_start: 0.8622 (tptt) cc_final: 0.8231 (mmtt) REVERT: J 13 ASP cc_start: 0.8164 (p0) cc_final: 0.7719 (t0) REVERT: J 62 ILE cc_start: 0.7733 (pt) cc_final: 0.7383 (pt) REVERT: J 82 ILE cc_start: 0.9176 (mm) cc_final: 0.8853 (tp) REVERT: J 86 ARG cc_start: 0.7634 (tpp-160) cc_final: 0.7245 (mmp80) REVERT: K 29 GLU cc_start: 0.8930 (tp30) cc_final: 0.8577 (mt-10) REVERT: K 66 LYS cc_start: 0.7417 (tptt) cc_final: 0.7038 (tptt) REVERT: K 84 ASP cc_start: 0.8708 (m-30) cc_final: 0.8336 (m-30) REVERT: K 156 MET cc_start: 0.7066 (ppp) cc_final: 0.6791 (ppp) REVERT: L 26 MET cc_start: 0.7667 (mtp) cc_final: 0.7456 (mtt) REVERT: L 178 GLU cc_start: 0.8738 (pt0) cc_final: 0.8325 (mm-30) REVERT: L 181 GLU cc_start: 0.7818 (mp0) cc_final: 0.7332 (pm20) REVERT: M 50 GLU cc_start: 0.7257 (tt0) cc_final: 0.6510 (tp30) REVERT: M 67 PHE cc_start: 0.6308 (t80) cc_final: 0.5851 (t80) REVERT: M 75 MET cc_start: 0.7241 (mmm) cc_final: 0.6181 (mmm) REVERT: M 136 MET cc_start: 0.7357 (mtt) cc_final: 0.7088 (mtt) REVERT: M 183 GLU cc_start: 0.8774 (mp0) cc_final: 0.8566 (mp0) REVERT: M 198 TYR cc_start: 0.6656 (t80) cc_final: 0.6435 (t80) REVERT: N 95 MET cc_start: 0.3234 (ptm) cc_final: 0.2988 (ptm) REVERT: N 119 MET cc_start: 0.0948 (ptp) cc_final: 0.0246 (ptp) REVERT: N 162 LEU cc_start: 0.5341 (mt) cc_final: 0.4796 (tt) REVERT: O 48 THR cc_start: 0.7573 (m) cc_final: 0.7321 (t) REVERT: O 54 MET cc_start: 0.8397 (mpp) cc_final: 0.8171 (mpp) REVERT: O 55 THR cc_start: 0.8803 (m) cc_final: 0.8556 (t) REVERT: O 84 LYS cc_start: 0.7469 (mtmt) cc_final: 0.6636 (tttm) REVERT: O 127 MET cc_start: 0.4472 (mmm) cc_final: 0.4245 (mmt) REVERT: P 66 ARG cc_start: 0.8535 (mmt-90) cc_final: 0.8034 (mmt-90) REVERT: P 69 PHE cc_start: 0.9197 (t80) cc_final: 0.8591 (t80) REVERT: P 82 ILE cc_start: 0.6412 (tt) cc_final: 0.5850 (tt) REVERT: P 88 MET cc_start: 0.9266 (tmm) cc_final: 0.8978 (tmm) REVERT: P 171 MET cc_start: 0.7392 (ttt) cc_final: 0.6581 (mmm) REVERT: Q 44 LEU cc_start: 0.8562 (mp) cc_final: 0.8335 (mp) REVERT: Q 137 PHE cc_start: 0.7696 (m-80) cc_final: 0.7490 (t80) REVERT: R 36 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8345 (mm-30) REVERT: S 36 HIS cc_start: 0.5874 (m-70) cc_final: 0.5428 (m-70) REVERT: S 104 TYR cc_start: 0.6067 (m-80) cc_final: 0.5850 (m-80) REVERT: S 206 GLU cc_start: 0.6738 (pt0) cc_final: 0.5503 (mp0) REVERT: T 50 MET cc_start: 0.8034 (ttp) cc_final: 0.6753 (ppp) REVERT: T 110 MET cc_start: 0.7739 (mpp) cc_final: 0.6927 (mpp) REVERT: T 214 MET cc_start: 0.2424 (mtt) cc_final: 0.1256 (ppp) REVERT: A 138 MET cc_start: 0.8879 (mpp) cc_final: 0.8435 (ptm) REVERT: A 225 CYS cc_start: 0.9054 (m) cc_final: 0.8670 (t) REVERT: A 249 TYR cc_start: 0.7775 (t80) cc_final: 0.7223 (t80) REVERT: A 252 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7176 (mm-30) REVERT: A 285 PHE cc_start: 0.6772 (p90) cc_final: 0.6343 (p90) REVERT: A 318 LEU cc_start: 0.8641 (tp) cc_final: 0.8324 (tp) REVERT: A 362 MET cc_start: 0.7578 (ttt) cc_final: 0.6712 (tmm) REVERT: A 366 ARG cc_start: 0.8908 (mtt90) cc_final: 0.8020 (tmm160) REVERT: B 107 MET cc_start: 0.5565 (ptm) cc_final: 0.4611 (ppp) REVERT: B 141 LYS cc_start: 0.8435 (pttt) cc_final: 0.8045 (mttt) REVERT: B 163 LEU cc_start: 0.8385 (mp) cc_final: 0.7721 (tp) REVERT: B 390 LEU cc_start: 0.6024 (tp) cc_final: 0.5824 (tp) REVERT: D 64 GLU cc_start: 0.9223 (pp20) cc_final: 0.8938 (pp20) REVERT: D 170 MET cc_start: 0.8015 (ptm) cc_final: 0.6946 (tpp) REVERT: D 179 GLU cc_start: 0.9113 (pt0) cc_final: 0.8726 (pt0) REVERT: D 381 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8803 (mt-10) REVERT: E 50 LEU cc_start: 0.7840 (mt) cc_final: 0.7398 (mt) REVERT: E 51 GLN cc_start: 0.7691 (mm-40) cc_final: 0.6760 (pp30) REVERT: E 69 PHE cc_start: 0.7786 (m-80) cc_final: 0.7459 (m-80) REVERT: E 110 TYR cc_start: 0.8083 (p90) cc_final: 0.7803 (p90) REVERT: E 114 GLU cc_start: 0.8295 (pt0) cc_final: 0.7764 (tp30) REVERT: E 251 ARG cc_start: 0.6852 (tpt90) cc_final: 0.6537 (tpt170) REVERT: E 255 ARG cc_start: 0.9246 (ptp-170) cc_final: 0.8706 (ptt-90) REVERT: E 279 THR cc_start: 0.7770 (p) cc_final: 0.7482 (t) REVERT: E 327 ASP cc_start: 0.6607 (t70) cc_final: 0.5554 (p0) REVERT: E 353 PHE cc_start: 0.8950 (t80) cc_final: 0.8710 (t80) REVERT: F 235 LEU cc_start: 0.8148 (mp) cc_final: 0.7811 (tp) REVERT: F 260 PHE cc_start: 0.7467 (m-10) cc_final: 0.7198 (m-10) REVERT: F 373 MET cc_start: 0.8198 (mmp) cc_final: 0.7905 (mmm) REVERT: F 430 LYS cc_start: 0.6330 (mtmm) cc_final: 0.5198 (tttp) REVERT: C 23 TYR cc_start: 0.7234 (t80) cc_final: 0.6478 (t80) REVERT: C 67 GLN cc_start: 0.6522 (tp-100) cc_final: 0.6222 (tm-30) REVERT: C 138 MET cc_start: 0.7512 (tpt) cc_final: 0.7058 (tpt) REVERT: C 139 MET cc_start: 0.8082 (mmp) cc_final: 0.6790 (tpp) REVERT: C 142 LYS cc_start: 0.7619 (tptt) cc_final: 0.6998 (ptmm) REVERT: C 145 ASP cc_start: 0.8635 (m-30) cc_final: 0.8147 (t70) REVERT: C 233 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6889 (pm20) REVERT: C 275 GLU cc_start: 0.8906 (pt0) cc_final: 0.8589 (mm-30) REVERT: C 368 MET cc_start: 0.9003 (mmp) cc_final: 0.8427 (ptt) REVERT: C 369 TYR cc_start: 0.8524 (m-10) cc_final: 0.8187 (m-80) REVERT: C 372 ARG cc_start: 0.9220 (ttt-90) cc_final: 0.8567 (mtp85) REVERT: C 391 MET cc_start: 0.8353 (tmm) cc_final: 0.8139 (tmm) REVERT: U 76 GLU cc_start: 0.8436 (tt0) cc_final: 0.8088 (tm-30) REVERT: U 87 LEU cc_start: 0.7080 (mp) cc_final: 0.6409 (tt) REVERT: U 128 GLN cc_start: 0.8925 (tp40) cc_final: 0.8476 (mm-40) REVERT: U 355 ASN cc_start: 0.8637 (m110) cc_final: 0.8022 (t0) REVERT: U 448 LEU cc_start: 0.8714 (tt) cc_final: 0.8276 (mm) REVERT: U 532 MET cc_start: 0.7912 (mtm) cc_final: 0.7694 (mtt) REVERT: U 548 LEU cc_start: 0.8175 (mt) cc_final: 0.7834 (mt) REVERT: U 693 LEU cc_start: 0.8994 (mm) cc_final: 0.8691 (tp) REVERT: U 709 PHE cc_start: 0.8638 (m-80) cc_final: 0.8363 (m-80) REVERT: U 770 TRP cc_start: 0.5406 (m-90) cc_final: 0.5169 (m-10) REVERT: V 90 GLU cc_start: 0.6472 (mp0) cc_final: 0.6034 (mp0) REVERT: V 444 ASP cc_start: 0.8611 (m-30) cc_final: 0.8383 (t0) REVERT: V 489 MET cc_start: 0.8859 (mmp) cc_final: 0.8323 (tpt) REVERT: W 88 MET cc_start: 0.2609 (mtm) cc_final: 0.2284 (mpp) REVERT: W 130 MET cc_start: 0.8175 (mmp) cc_final: 0.7578 (tmm) REVERT: W 305 LEU cc_start: 0.8883 (tt) cc_final: 0.8656 (tp) REVERT: W 308 LEU cc_start: 0.8664 (tp) cc_final: 0.7968 (mt) REVERT: W 378 MET cc_start: 0.8454 (mtt) cc_final: 0.8058 (mmm) REVERT: W 428 TRP cc_start: 0.8780 (m100) cc_final: 0.8473 (m100) REVERT: W 451 MET cc_start: 0.6716 (mmt) cc_final: 0.6428 (tpp) REVERT: X 69 LEU cc_start: 0.7836 (tp) cc_final: 0.7530 (mt) REVERT: X 278 ARG cc_start: 0.7731 (tpt90) cc_final: 0.6811 (ptm160) REVERT: X 380 GLN cc_start: 0.8748 (tt0) cc_final: 0.8147 (pm20) REVERT: X 410 VAL cc_start: 0.7875 (t) cc_final: 0.7494 (p) REVERT: Y 38 ARG cc_start: 0.8863 (mtm-85) cc_final: 0.8336 (ppt90) REVERT: Y 55 GLU cc_start: 0.7150 (mp0) cc_final: 0.6527 (pt0) REVERT: Y 73 MET cc_start: 0.7742 (mtp) cc_final: 0.6950 (mmt) REVERT: Y 77 ASN cc_start: 0.7830 (t0) cc_final: 0.7503 (m-40) REVERT: Y 102 ASP cc_start: 0.9066 (t0) cc_final: 0.8664 (t0) REVERT: Y 124 PHE cc_start: 0.8012 (m-10) cc_final: 0.7669 (m-80) REVERT: Y 188 CYS cc_start: 0.8473 (m) cc_final: 0.7979 (p) REVERT: Y 228 MET cc_start: 0.7321 (ptm) cc_final: 0.7100 (ptm) REVERT: Z 75 LEU cc_start: 0.8702 (tt) cc_final: 0.8237 (mp) REVERT: Z 176 LEU cc_start: 0.8678 (pp) cc_final: 0.8337 (mt) REVERT: Z 196 HIS cc_start: 0.8081 (p90) cc_final: 0.7849 (p90) REVERT: Z 247 LYS cc_start: 0.8578 (mptt) cc_final: 0.8291 (mtmm) REVERT: Z 279 LYS cc_start: 0.7053 (mtpt) cc_final: 0.6121 (mmmt) REVERT: a 22 TRP cc_start: 0.7506 (t-100) cc_final: 0.7274 (t-100) REVERT: a 121 LEU cc_start: 0.8418 (mp) cc_final: 0.8012 (tt) REVERT: a 124 ASN cc_start: 0.7466 (m-40) cc_final: 0.6972 (t0) REVERT: b 7 MET cc_start: 0.7823 (mtp) cc_final: 0.6703 (tpp) REVERT: b 14 GLU cc_start: 0.7654 (pt0) cc_final: 0.7364 (tm-30) REVERT: b 57 ASP cc_start: 0.7921 (t0) cc_final: 0.7565 (t0) REVERT: b 59 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6078 (mm-30) REVERT: b 121 GLU cc_start: 0.8345 (pt0) cc_final: 0.8117 (tm-30) REVERT: c 41 MET cc_start: 0.8498 (mmp) cc_final: 0.8100 (mmp) REVERT: c 200 TYR cc_start: 0.7591 (m-80) cc_final: 0.7154 (m-10) REVERT: c 303 MET cc_start: 0.8885 (mmm) cc_final: 0.8681 (mpp) REVERT: d 1 MET cc_start: 0.3305 (ttt) cc_final: 0.2137 (ptm) REVERT: d 9 TRP cc_start: 0.7063 (t60) cc_final: 0.6800 (t60) REVERT: d 53 ASP cc_start: 0.7642 (m-30) cc_final: 0.7435 (p0) REVERT: d 54 ILE cc_start: 0.5924 (pt) cc_final: 0.4631 (pt) REVERT: d 206 MET cc_start: 0.7018 (ptm) cc_final: 0.6723 (ptm) REVERT: f 112 MET cc_start: 0.0497 (ptt) cc_final: -0.0713 (mmp) REVERT: f 135 MET cc_start: -0.0066 (pmm) cc_final: -0.2482 (ttt) REVERT: f 162 MET cc_start: 0.4081 (mmp) cc_final: 0.3714 (tpp) REVERT: f 384 MET cc_start: 0.1963 (mmm) cc_final: 0.0930 (tpt) REVERT: f 570 MET cc_start: 0.6763 (ptm) cc_final: 0.4822 (mmt) REVERT: f 572 MET cc_start: 0.2366 (tpt) cc_final: 0.1341 (tpt) REVERT: f 683 VAL cc_start: 0.2938 (p) cc_final: 0.2628 (p) outliers start: 3 outliers final: 0 residues processed: 1156 average time/residue: 0.6445 time to fit residues: 1289.5498 Evaluate side-chains 872 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 872 time to evaluate : 6.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 584 optimal weight: 7.9990 chunk 377 optimal weight: 5.9990 chunk 564 optimal weight: 20.0000 chunk 284 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 183 optimal weight: 40.0000 chunk 601 optimal weight: 20.0000 chunk 644 optimal weight: 20.0000 chunk 467 optimal weight: 0.0970 chunk 88 optimal weight: 5.9990 chunk 743 optimal weight: 8.9990 overall best weight: 5.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 GLN ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 29 GLN ** T 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 162 GLN ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN C 40 GLN ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 115 ASN U 218 GLN ** U 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN ** U 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 329 HIS ** V 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 459 GLN ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 106 GLN ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 102 HIS ** Z 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 264 ASN a 273 GLN ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 237 HIS ** c 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 293 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.8188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 79128 Z= 0.248 Angle : 0.818 17.091 106985 Z= 0.420 Chirality : 0.047 0.300 12177 Planarity : 0.005 0.132 13802 Dihedral : 6.703 88.295 10988 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 26.59 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.76 % Favored : 92.82 % Rotamer: Outliers : 0.04 % Allowed : 1.73 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.55 % Cis-general : 2.01 % Twisted Proline : 0.57 % Twisted General : 0.04 % 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: -1.78 (0.08), residues: 9841 helix: -0.72 (0.07), residues: 4664 sheet: -0.84 (0.16), residues: 1042 loop : -1.71 (0.10), residues: 4135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP Y 286 HIS 0.017 0.001 HIS c 183 PHE 0.045 0.002 PHE C 175 TYR 0.023 0.002 TYR f 395 ARG 0.011 0.001 ARG U 616 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1139 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1136 time to evaluate : 6.576 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: G 37 LEU cc_start: 0.8716 (tp) cc_final: 0.8278 (tt) REVERT: G 61 LEU cc_start: 0.7568 (tt) cc_final: 0.7302 (tt) REVERT: G 78 CYS cc_start: 0.5912 (p) cc_final: 0.4291 (p) REVERT: G 80 MET cc_start: 0.8369 (mmp) cc_final: 0.8111 (mmp) REVERT: G 100 ASN cc_start: 0.8853 (m-40) cc_final: 0.8546 (m110) REVERT: G 125 TYR cc_start: 0.8676 (m-10) cc_final: 0.8354 (m-80) REVERT: H 79 MET cc_start: 0.8571 (pmm) cc_final: 0.7977 (tpt) REVERT: H 175 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8365 (tp30) REVERT: I 26 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8455 (mt-10) REVERT: I 89 GLU cc_start: 0.8778 (tp30) cc_final: 0.8347 (mm-30) REVERT: I 96 ARG cc_start: 0.9541 (ptp-170) cc_final: 0.9253 (mtp85) REVERT: I 136 TYR cc_start: 0.8460 (m-10) cc_final: 0.8225 (m-80) REVERT: I 212 GLU cc_start: 0.8099 (tt0) cc_final: 0.7871 (pt0) REVERT: I 243 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8265 (mt-10) REVERT: I 246 LYS cc_start: 0.8642 (tptt) cc_final: 0.8216 (mmtt) REVERT: J 62 ILE cc_start: 0.7779 (pt) cc_final: 0.7424 (pt) REVERT: J 82 ILE cc_start: 0.9216 (mm) cc_final: 0.8928 (tp) REVERT: J 86 ARG cc_start: 0.7704 (tpp-160) cc_final: 0.7384 (mmp80) REVERT: K 66 LYS cc_start: 0.7493 (tptt) cc_final: 0.7013 (tptt) REVERT: K 78 MET cc_start: 0.8303 (pmm) cc_final: 0.8075 (pmm) REVERT: K 84 ASP cc_start: 0.8885 (m-30) cc_final: 0.8499 (m-30) REVERT: L 26 MET cc_start: 0.7770 (mtp) cc_final: 0.7548 (mtt) REVERT: L 181 GLU cc_start: 0.7723 (mp0) cc_final: 0.7458 (pm20) REVERT: M 50 GLU cc_start: 0.7208 (tt0) cc_final: 0.6471 (tp30) REVERT: M 67 PHE cc_start: 0.6341 (t80) cc_final: 0.5975 (t80) REVERT: M 75 MET cc_start: 0.7306 (mmm) cc_final: 0.6261 (mmm) REVERT: M 183 GLU cc_start: 0.8816 (mp0) cc_final: 0.8589 (mp0) REVERT: N 95 MET cc_start: 0.3218 (ptm) cc_final: 0.2888 (ptm) REVERT: N 162 LEU cc_start: 0.5427 (mt) cc_final: 0.4873 (tt) REVERT: O 54 MET cc_start: 0.8511 (mpp) cc_final: 0.8276 (mpp) REVERT: O 55 THR cc_start: 0.8914 (m) cc_final: 0.8700 (t) REVERT: O 148 GLU cc_start: 0.8501 (pt0) cc_final: 0.8109 (pm20) REVERT: P 66 ARG cc_start: 0.8556 (mmt-90) cc_final: 0.8091 (mmt-90) REVERT: P 69 PHE cc_start: 0.9211 (t80) cc_final: 0.8599 (t80) REVERT: P 88 MET cc_start: 0.9302 (tmm) cc_final: 0.9018 (tmm) REVERT: P 117 PHE cc_start: 0.8048 (p90) cc_final: 0.7790 (p90) REVERT: P 171 MET cc_start: 0.7471 (ttt) cc_final: 0.6574 (mmm) REVERT: P 204 MET cc_start: -0.2055 (tmm) cc_final: -0.2562 (tpt) REVERT: R 36 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8293 (mm-30) REVERT: S 36 HIS cc_start: 0.6046 (m-70) cc_final: 0.5578 (m-70) REVERT: S 110 ILE cc_start: 0.8354 (pt) cc_final: 0.8104 (pt) REVERT: T 5 MET cc_start: 0.4185 (mmm) cc_final: 0.3513 (mmm) REVERT: T 50 MET cc_start: 0.8128 (ttp) cc_final: 0.6840 (ppp) REVERT: T 110 MET cc_start: 0.7667 (mpp) cc_final: 0.6917 (mpp) REVERT: T 214 MET cc_start: 0.2471 (mtt) cc_final: 0.1391 (ppp) REVERT: A 225 CYS cc_start: 0.9068 (m) cc_final: 0.8685 (t) REVERT: A 249 TYR cc_start: 0.7816 (t80) cc_final: 0.7274 (t80) REVERT: A 252 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7272 (mm-30) REVERT: A 255 ARG cc_start: 0.8951 (mmp80) cc_final: 0.8688 (mpt180) REVERT: A 366 ARG cc_start: 0.8881 (mtt90) cc_final: 0.7998 (tmm160) REVERT: B 107 MET cc_start: 0.5754 (ptm) cc_final: 0.5490 (ptp) REVERT: B 141 LYS cc_start: 0.8444 (pttt) cc_final: 0.7988 (tttt) REVERT: B 163 LEU cc_start: 0.8373 (mp) cc_final: 0.7702 (tp) REVERT: D 64 GLU cc_start: 0.9231 (pp20) cc_final: 0.8933 (pp20) REVERT: D 170 MET cc_start: 0.8013 (ptm) cc_final: 0.7125 (tpp) REVERT: D 381 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8826 (mt-10) REVERT: E 69 PHE cc_start: 0.7736 (m-80) cc_final: 0.7418 (m-80) REVERT: E 110 TYR cc_start: 0.7833 (p90) cc_final: 0.7534 (p90) REVERT: E 114 GLU cc_start: 0.8196 (pt0) cc_final: 0.7697 (tp30) REVERT: E 251 ARG cc_start: 0.6792 (tpt90) cc_final: 0.6517 (tpt170) REVERT: E 255 ARG cc_start: 0.9227 (ptp-170) cc_final: 0.8717 (ptt-90) REVERT: E 279 THR cc_start: 0.7591 (p) cc_final: 0.7369 (t) REVERT: E 327 ASP cc_start: 0.6597 (t70) cc_final: 0.5493 (p0) REVERT: F 235 LEU cc_start: 0.8287 (mp) cc_final: 0.7916 (tp) REVERT: F 258 GLN cc_start: 0.3559 (mt0) cc_final: 0.3224 (mt0) REVERT: F 260 PHE cc_start: 0.7411 (m-10) cc_final: 0.7129 (m-10) REVERT: F 430 LYS cc_start: 0.6584 (mtmm) cc_final: 0.5431 (tttp) REVERT: C 23 TYR cc_start: 0.7360 (t80) cc_final: 0.6726 (t80) REVERT: C 24 TYR cc_start: 0.8203 (m-80) cc_final: 0.7842 (m-80) REVERT: C 67 GLN cc_start: 0.6591 (tp-100) cc_final: 0.6294 (tm-30) REVERT: C 80 MET cc_start: 0.7060 (mpp) cc_final: 0.6765 (mpp) REVERT: C 139 MET cc_start: 0.8101 (mmp) cc_final: 0.7190 (mmm) REVERT: C 142 LYS cc_start: 0.7635 (tptt) cc_final: 0.7135 (pttp) REVERT: C 145 ASP cc_start: 0.8562 (m-30) cc_final: 0.8090 (t70) REVERT: C 233 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6898 (pm20) REVERT: C 275 GLU cc_start: 0.8940 (pt0) cc_final: 0.8692 (mm-30) REVERT: C 368 MET cc_start: 0.8992 (mmp) cc_final: 0.8425 (ptt) REVERT: C 369 TYR cc_start: 0.8573 (m-10) cc_final: 0.8212 (m-80) REVERT: C 372 ARG cc_start: 0.9224 (ttt-90) cc_final: 0.8572 (mtp85) REVERT: U 76 GLU cc_start: 0.8421 (tt0) cc_final: 0.8026 (tm-30) REVERT: U 87 LEU cc_start: 0.7145 (mp) cc_final: 0.6408 (tt) REVERT: U 128 GLN cc_start: 0.8905 (tp40) cc_final: 0.8491 (mm-40) REVERT: U 188 MET cc_start: 0.3694 (tpp) cc_final: 0.3456 (tpp) REVERT: U 355 ASN cc_start: 0.8611 (m110) cc_final: 0.7993 (t0) REVERT: U 448 LEU cc_start: 0.8664 (tt) cc_final: 0.8218 (mm) REVERT: U 532 MET cc_start: 0.7886 (mtm) cc_final: 0.7669 (mtt) REVERT: U 654 MET cc_start: 0.9059 (mmp) cc_final: 0.8856 (mtp) REVERT: U 693 LEU cc_start: 0.9025 (mm) cc_final: 0.8753 (tp) REVERT: U 775 LEU cc_start: 0.7789 (mt) cc_final: 0.7107 (pp) REVERT: V 180 ARG cc_start: 0.8852 (mmt-90) cc_final: 0.8561 (mmt-90) REVERT: V 444 ASP cc_start: 0.8608 (m-30) cc_final: 0.8389 (t0) REVERT: V 489 MET cc_start: 0.8864 (mmp) cc_final: 0.8390 (tpt) REVERT: W 1 MET cc_start: 0.4832 (mmm) cc_final: 0.4579 (mmm) REVERT: W 130 MET cc_start: 0.8214 (mmp) cc_final: 0.7610 (tmm) REVERT: W 305 LEU cc_start: 0.8878 (tt) cc_final: 0.8634 (tp) REVERT: W 308 LEU cc_start: 0.8611 (tp) cc_final: 0.7959 (mt) REVERT: W 312 MET cc_start: 0.4704 (tpt) cc_final: 0.4172 (tpt) REVERT: W 428 TRP cc_start: 0.8799 (m100) cc_final: 0.8484 (m100) REVERT: W 451 MET cc_start: 0.6788 (mmt) cc_final: 0.6577 (tpp) REVERT: X 69 LEU cc_start: 0.7842 (tp) cc_final: 0.7542 (mt) REVERT: X 278 ARG cc_start: 0.7700 (tpt90) cc_final: 0.6782 (ptm-80) REVERT: X 380 GLN cc_start: 0.8654 (tt0) cc_final: 0.8110 (pm20) REVERT: Y 38 ARG cc_start: 0.8882 (mtm-85) cc_final: 0.8349 (ppt90) REVERT: Y 55 GLU cc_start: 0.7129 (mp0) cc_final: 0.6520 (pt0) REVERT: Y 73 MET cc_start: 0.7743 (mtp) cc_final: 0.7011 (mmt) REVERT: Y 77 ASN cc_start: 0.7828 (t0) cc_final: 0.7520 (m-40) REVERT: Y 102 ASP cc_start: 0.8961 (t0) cc_final: 0.8705 (t0) REVERT: Y 105 MET cc_start: 0.7499 (ptp) cc_final: 0.6912 (ptp) REVERT: Y 124 PHE cc_start: 0.7966 (m-10) cc_final: 0.7585 (m-80) REVERT: Y 188 CYS cc_start: 0.8490 (m) cc_final: 0.8007 (p) REVERT: Y 228 MET cc_start: 0.7383 (ptm) cc_final: 0.7090 (ptm) REVERT: Z 75 LEU cc_start: 0.8722 (tt) cc_final: 0.8303 (mt) REVERT: Z 78 MET cc_start: 0.8277 (tpt) cc_final: 0.8025 (tpp) REVERT: Z 172 VAL cc_start: 0.8599 (t) cc_final: 0.8292 (m) REVERT: Z 176 LEU cc_start: 0.8657 (pp) cc_final: 0.8324 (mt) REVERT: Z 196 HIS cc_start: 0.8078 (p90) cc_final: 0.7786 (p90) REVERT: Z 247 LYS cc_start: 0.8587 (mptt) cc_final: 0.8345 (mtmm) REVERT: Z 250 TYR cc_start: 0.8108 (p90) cc_final: 0.7627 (p90) REVERT: Z 279 LYS cc_start: 0.7070 (mtpt) cc_final: 0.6196 (mmmt) REVERT: a 22 TRP cc_start: 0.7432 (t-100) cc_final: 0.7190 (t-100) REVERT: a 121 LEU cc_start: 0.8351 (mp) cc_final: 0.7927 (tt) REVERT: a 124 ASN cc_start: 0.7575 (m-40) cc_final: 0.7070 (t0) REVERT: a 155 PHE cc_start: 0.8705 (t80) cc_final: 0.8367 (t80) REVERT: a 312 MET cc_start: 0.8645 (mmt) cc_final: 0.8315 (mmt) REVERT: b 7 MET cc_start: 0.7886 (mtp) cc_final: 0.6751 (tpp) REVERT: b 14 GLU cc_start: 0.7643 (pt0) cc_final: 0.7396 (tm-30) REVERT: b 57 ASP cc_start: 0.7923 (t0) cc_final: 0.7571 (t0) REVERT: b 59 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6147 (mm-30) REVERT: b 121 GLU cc_start: 0.8339 (pt0) cc_final: 0.8112 (tm-30) REVERT: c 41 MET cc_start: 0.8500 (mmp) cc_final: 0.8085 (mmp) REVERT: c 200 TYR cc_start: 0.7579 (m-80) cc_final: 0.7112 (m-10) REVERT: d 1 MET cc_start: 0.3443 (ttt) cc_final: 0.2266 (ptm) REVERT: d 9 TRP cc_start: 0.6964 (t60) cc_final: 0.6542 (t60) REVERT: d 53 ASP cc_start: 0.7628 (m-30) cc_final: 0.7399 (p0) REVERT: d 54 ILE cc_start: 0.5994 (pt) cc_final: 0.4721 (pt) REVERT: d 206 MET cc_start: 0.7103 (ptm) cc_final: 0.6814 (ptm) REVERT: d 252 GLN cc_start: 0.8678 (mt0) cc_final: 0.8452 (mt0) REVERT: f 112 MET cc_start: 0.0002 (ptt) cc_final: -0.1111 (mmp) REVERT: f 135 MET cc_start: -0.0138 (pmm) cc_final: -0.2366 (ttt) REVERT: f 162 MET cc_start: 0.4140 (mmp) cc_final: 0.3827 (tpp) REVERT: f 353 MET cc_start: 0.3048 (mtt) cc_final: 0.2679 (mtt) REVERT: f 384 MET cc_start: 0.1554 (mmm) cc_final: 0.0873 (tpt) REVERT: f 570 MET cc_start: 0.6765 (ptm) cc_final: 0.4805 (mmt) REVERT: f 572 MET cc_start: 0.2417 (tpt) cc_final: 0.1618 (tpt) outliers start: 3 outliers final: 0 residues processed: 1137 average time/residue: 0.6801 time to fit residues: 1340.1626 Evaluate side-chains 863 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 863 time to evaluate : 6.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 860 optimal weight: 20.0000 chunk 905 optimal weight: 6.9990 chunk 826 optimal weight: 6.9990 chunk 881 optimal weight: 4.9990 chunk 530 optimal weight: 30.0000 chunk 383 optimal weight: 9.9990 chunk 691 optimal weight: 9.9990 chunk 270 optimal weight: 20.0000 chunk 796 optimal weight: 8.9990 chunk 833 optimal weight: 0.4980 chunk 878 optimal weight: 8.9990 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 HIS ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 162 GLN ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 ASN ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 GLN ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN C 64 GLN ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN ** V 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 488 ASN ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 106 GLN ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 ASN ** Z 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 243 GLN ** Z 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 273 GLN ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 298 GLN ** d 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 102 ASN d 228 GLN f 293 ASN f 455 HIS ** f 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.8665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 79128 Z= 0.248 Angle : 0.842 15.949 106985 Z= 0.431 Chirality : 0.047 0.489 12177 Planarity : 0.006 0.103 13802 Dihedral : 6.789 87.725 10988 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 26.96 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.12 % Favored : 92.42 % Rotamer: Outliers : 0.02 % Allowed : 0.96 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.55 % Cis-general : 2.01 % Twisted Proline : 0.28 % Twisted General : 0.04 % 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: -1.78 (0.08), residues: 9841 helix: -0.70 (0.07), residues: 4645 sheet: -0.84 (0.16), residues: 1025 loop : -1.74 (0.10), residues: 4171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP Y 286 HIS 0.017 0.001 HIS Z 196 PHE 0.053 0.002 PHE S 101 TYR 0.028 0.002 TYR f 395 ARG 0.015 0.001 ARG D 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1102 time to evaluate : 6.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 37 LEU cc_start: 0.8714 (tp) cc_final: 0.7892 (tt) REVERT: G 61 LEU cc_start: 0.7455 (tt) cc_final: 0.7165 (tt) REVERT: G 70 PHE cc_start: 0.6232 (t80) cc_final: 0.5958 (t80) REVERT: G 78 CYS cc_start: 0.5416 (p) cc_final: 0.4381 (p) REVERT: G 80 MET cc_start: 0.8441 (mmp) cc_final: 0.8241 (mmp) REVERT: G 100 ASN cc_start: 0.8829 (m-40) cc_final: 0.8511 (m110) REVERT: G 125 TYR cc_start: 0.8657 (m-10) cc_final: 0.8316 (m-80) REVERT: G 171 LYS cc_start: 0.8402 (mmtp) cc_final: 0.8082 (mptt) REVERT: G 208 ILE cc_start: 0.6831 (mm) cc_final: 0.6614 (mm) REVERT: H 79 MET cc_start: 0.8628 (pmm) cc_final: 0.8139 (pmm) REVERT: H 165 LYS cc_start: 0.6117 (pttm) cc_final: 0.5626 (mtmm) REVERT: H 175 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8333 (tp30) REVERT: I 26 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8460 (mt-10) REVERT: I 89 GLU cc_start: 0.8851 (tp30) cc_final: 0.8439 (mm-30) REVERT: I 96 ARG cc_start: 0.9554 (ptp-170) cc_final: 0.9316 (ptp-110) REVERT: I 151 ASP cc_start: 0.8396 (t0) cc_final: 0.8083 (t0) REVERT: I 212 GLU cc_start: 0.8169 (tt0) cc_final: 0.7910 (pt0) REVERT: I 243 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8182 (mt-10) REVERT: I 246 LYS cc_start: 0.8629 (tptt) cc_final: 0.8178 (mmtt) REVERT: J 62 ILE cc_start: 0.7755 (pt) cc_final: 0.7371 (pt) REVERT: J 82 ILE cc_start: 0.9264 (mm) cc_final: 0.9019 (tp) REVERT: K 29 GLU cc_start: 0.9006 (tp30) cc_final: 0.8641 (mt-10) REVERT: K 66 LYS cc_start: 0.7375 (tptt) cc_final: 0.6941 (tptt) REVERT: K 78 MET cc_start: 0.8336 (pmm) cc_final: 0.8051 (pmm) REVERT: K 84 ASP cc_start: 0.9032 (m-30) cc_final: 0.8491 (p0) REVERT: L 26 MET cc_start: 0.7824 (mtp) cc_final: 0.7605 (mtt) REVERT: L 181 GLU cc_start: 0.7827 (mp0) cc_final: 0.7545 (pm20) REVERT: M 50 GLU cc_start: 0.7178 (tt0) cc_final: 0.6443 (tp30) REVERT: M 67 PHE cc_start: 0.6333 (t80) cc_final: 0.5971 (t80) REVERT: M 75 MET cc_start: 0.7354 (mmm) cc_final: 0.6223 (mmm) REVERT: M 183 GLU cc_start: 0.8826 (mp0) cc_final: 0.8586 (mp0) REVERT: N 95 MET cc_start: 0.3607 (ptm) cc_final: 0.3243 (ptm) REVERT: N 162 LEU cc_start: 0.5689 (mt) cc_final: 0.5127 (tt) REVERT: O 54 MET cc_start: 0.8606 (mpp) cc_final: 0.8377 (mpp) REVERT: O 55 THR cc_start: 0.9025 (m) cc_final: 0.8793 (t) REVERT: O 148 GLU cc_start: 0.8497 (pt0) cc_final: 0.8114 (pm20) REVERT: P 45 MET cc_start: 0.8995 (tpt) cc_final: 0.8734 (tpt) REVERT: P 66 ARG cc_start: 0.8537 (mmt-90) cc_final: 0.8154 (mmt-90) REVERT: P 69 PHE cc_start: 0.9222 (t80) cc_final: 0.8709 (t80) REVERT: P 88 MET cc_start: 0.9315 (tmm) cc_final: 0.9048 (tmm) REVERT: P 117 PHE cc_start: 0.8061 (p90) cc_final: 0.7794 (p90) REVERT: P 171 MET cc_start: 0.7435 (ttt) cc_final: 0.6669 (mmm) REVERT: P 204 MET cc_start: -0.2591 (tmm) cc_final: -0.3193 (tpt) REVERT: R 36 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8493 (mm-30) REVERT: S 36 HIS cc_start: 0.6122 (m-70) cc_final: 0.5512 (m-70) REVERT: S 48 ASP cc_start: 0.8653 (m-30) cc_final: 0.8146 (p0) REVERT: S 110 ILE cc_start: 0.8419 (pt) cc_final: 0.8200 (pt) REVERT: T 5 MET cc_start: 0.4605 (mmm) cc_final: 0.4116 (mmm) REVERT: T 50 MET cc_start: 0.8110 (ttp) cc_final: 0.7903 (ttp) REVERT: T 110 MET cc_start: 0.7621 (mpp) cc_final: 0.6876 (mpp) REVERT: T 173 MET cc_start: 0.6770 (tpp) cc_final: 0.6424 (ttt) REVERT: T 214 MET cc_start: 0.2534 (mtt) cc_final: 0.1514 (ppp) REVERT: A 225 CYS cc_start: 0.9096 (m) cc_final: 0.8728 (t) REVERT: A 249 TYR cc_start: 0.7776 (t80) cc_final: 0.7192 (t80) REVERT: A 252 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7362 (mm-30) REVERT: A 362 MET cc_start: 0.7206 (tmm) cc_final: 0.6734 (tmm) REVERT: A 366 ARG cc_start: 0.8905 (mtt90) cc_final: 0.8037 (tmm160) REVERT: B 107 MET cc_start: 0.5708 (ptm) cc_final: 0.5346 (ppp) REVERT: B 141 LYS cc_start: 0.8501 (pttt) cc_final: 0.8060 (tttt) REVERT: B 163 LEU cc_start: 0.8645 (mp) cc_final: 0.7761 (tp) REVERT: D 64 GLU cc_start: 0.9226 (pp20) cc_final: 0.8909 (pp20) REVERT: D 170 MET cc_start: 0.7800 (ptm) cc_final: 0.6858 (tpp) REVERT: D 179 GLU cc_start: 0.9200 (pt0) cc_final: 0.8991 (pt0) REVERT: D 381 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8843 (mt-10) REVERT: E 69 PHE cc_start: 0.7778 (m-80) cc_final: 0.7465 (m-80) REVERT: E 110 TYR cc_start: 0.7828 (p90) cc_final: 0.7528 (p90) REVERT: E 114 GLU cc_start: 0.8330 (pt0) cc_final: 0.7754 (tp30) REVERT: E 170 CYS cc_start: 0.8715 (m) cc_final: 0.8496 (t) REVERT: E 251 ARG cc_start: 0.6856 (tpt90) cc_final: 0.6568 (tpt170) REVERT: E 255 ARG cc_start: 0.9235 (ptp-170) cc_final: 0.8755 (ptt-90) REVERT: E 279 THR cc_start: 0.7900 (p) cc_final: 0.7691 (t) REVERT: E 327 ASP cc_start: 0.6523 (t70) cc_final: 0.5528 (m-30) REVERT: F 235 LEU cc_start: 0.8333 (mp) cc_final: 0.7938 (tp) REVERT: F 260 PHE cc_start: 0.7472 (m-10) cc_final: 0.7203 (m-10) REVERT: F 430 LYS cc_start: 0.6697 (mtmm) cc_final: 0.5531 (tttp) REVERT: C 23 TYR cc_start: 0.7489 (t80) cc_final: 0.6888 (t80) REVERT: C 24 TYR cc_start: 0.8232 (m-80) cc_final: 0.7768 (m-80) REVERT: C 67 GLN cc_start: 0.6434 (tp-100) cc_final: 0.6131 (tm-30) REVERT: C 80 MET cc_start: 0.7136 (mpp) cc_final: 0.6855 (mpp) REVERT: C 104 ASP cc_start: 0.8524 (t0) cc_final: 0.8055 (p0) REVERT: C 138 MET cc_start: 0.7517 (tpt) cc_final: 0.7156 (tpt) REVERT: C 139 MET cc_start: 0.8110 (mmp) cc_final: 0.6817 (mmm) REVERT: C 142 LYS cc_start: 0.7637 (tptt) cc_final: 0.7042 (ptmm) REVERT: C 145 ASP cc_start: 0.8562 (m-30) cc_final: 0.8115 (t70) REVERT: C 233 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6824 (pm20) REVERT: C 275 GLU cc_start: 0.8957 (pt0) cc_final: 0.8734 (mm-30) REVERT: C 368 MET cc_start: 0.8985 (mmp) cc_final: 0.8428 (ptt) REVERT: C 369 TYR cc_start: 0.8571 (m-10) cc_final: 0.8233 (m-80) REVERT: C 372 ARG cc_start: 0.9222 (ttt-90) cc_final: 0.8584 (mtp85) REVERT: U 71 LEU cc_start: 0.8443 (pp) cc_final: 0.8069 (mt) REVERT: U 76 GLU cc_start: 0.8412 (tt0) cc_final: 0.8047 (tm-30) REVERT: U 87 LEU cc_start: 0.7416 (mp) cc_final: 0.6599 (tt) REVERT: U 128 GLN cc_start: 0.8855 (tp40) cc_final: 0.8468 (mm-40) REVERT: U 188 MET cc_start: 0.3863 (tpp) cc_final: 0.3623 (tpp) REVERT: U 355 ASN cc_start: 0.8726 (m110) cc_final: 0.8119 (t0) REVERT: U 448 LEU cc_start: 0.8664 (tt) cc_final: 0.8230 (mm) REVERT: U 532 MET cc_start: 0.7882 (mtm) cc_final: 0.7110 (ttm) REVERT: U 626 LEU cc_start: 0.8599 (mm) cc_final: 0.8366 (mt) REVERT: U 775 LEU cc_start: 0.8065 (mt) cc_final: 0.7346 (pp) REVERT: V 269 LYS cc_start: 0.9284 (mtmt) cc_final: 0.8703 (tppt) REVERT: V 309 MET cc_start: 0.5541 (tpt) cc_final: 0.5306 (tpt) REVERT: V 409 MET cc_start: 0.9047 (ttt) cc_final: 0.8663 (tpt) REVERT: V 489 MET cc_start: 0.8859 (mmp) cc_final: 0.8405 (tpt) REVERT: W 1 MET cc_start: 0.4914 (mmm) cc_final: 0.4654 (mmm) REVERT: W 130 MET cc_start: 0.8220 (mmp) cc_final: 0.7623 (tmm) REVERT: W 305 LEU cc_start: 0.8837 (tt) cc_final: 0.8566 (tp) REVERT: W 308 LEU cc_start: 0.8642 (tp) cc_final: 0.8019 (mt) REVERT: W 312 MET cc_start: 0.4648 (tpt) cc_final: 0.3615 (tpt) REVERT: W 366 MET cc_start: 0.7525 (mtp) cc_final: 0.7296 (mtp) REVERT: W 378 MET cc_start: 0.8100 (mmm) cc_final: 0.7465 (mmm) REVERT: W 428 TRP cc_start: 0.8766 (m100) cc_final: 0.8423 (m100) REVERT: W 451 MET cc_start: 0.6774 (mmt) cc_final: 0.6561 (tpp) REVERT: X 69 LEU cc_start: 0.7855 (tp) cc_final: 0.7555 (mt) REVERT: X 175 LYS cc_start: 0.6900 (tttt) cc_final: 0.6639 (mttm) REVERT: X 278 ARG cc_start: 0.7671 (tpt90) cc_final: 0.6722 (ptm-80) REVERT: X 380 GLN cc_start: 0.8718 (tt0) cc_final: 0.8088 (pm20) REVERT: Y 38 ARG cc_start: 0.8898 (mtm-85) cc_final: 0.8362 (ppt90) REVERT: Y 55 GLU cc_start: 0.7131 (mp0) cc_final: 0.6522 (pt0) REVERT: Y 73 MET cc_start: 0.7759 (mtp) cc_final: 0.6946 (mmm) REVERT: Y 77 ASN cc_start: 0.7812 (t0) cc_final: 0.7497 (m-40) REVERT: Y 102 ASP cc_start: 0.8964 (t0) cc_final: 0.8704 (t0) REVERT: Y 105 MET cc_start: 0.7549 (ptp) cc_final: 0.6979 (ptp) REVERT: Y 124 PHE cc_start: 0.8005 (m-10) cc_final: 0.7623 (m-80) REVERT: Y 188 CYS cc_start: 0.8507 (m) cc_final: 0.7993 (p) REVERT: Y 319 MET cc_start: 0.7390 (mmm) cc_final: 0.7064 (mmp) REVERT: Y 364 TRP cc_start: 0.8403 (t-100) cc_final: 0.8187 (t-100) REVERT: Z 54 PHE cc_start: 0.7815 (p90) cc_final: 0.7521 (p90) REVERT: Z 75 LEU cc_start: 0.8741 (tt) cc_final: 0.8286 (mp) REVERT: Z 78 MET cc_start: 0.8350 (tpt) cc_final: 0.7532 (tpp) REVERT: Z 82 PHE cc_start: 0.8991 (m-10) cc_final: 0.8710 (m-80) REVERT: Z 172 VAL cc_start: 0.8668 (t) cc_final: 0.8365 (m) REVERT: Z 176 LEU cc_start: 0.8710 (pp) cc_final: 0.8399 (mt) REVERT: Z 196 HIS cc_start: 0.8029 (p90) cc_final: 0.7701 (p90) REVERT: Z 279 LYS cc_start: 0.7077 (mtpt) cc_final: 0.6251 (mmmt) REVERT: a 22 TRP cc_start: 0.7420 (t-100) cc_final: 0.7139 (t-100) REVERT: a 121 LEU cc_start: 0.8255 (mp) cc_final: 0.7829 (tt) REVERT: a 124 ASN cc_start: 0.7623 (m-40) cc_final: 0.7093 (t0) REVERT: a 155 PHE cc_start: 0.8794 (t80) cc_final: 0.8443 (t80) REVERT: a 312 MET cc_start: 0.8630 (mmt) cc_final: 0.8300 (mmt) REVERT: b 7 MET cc_start: 0.7950 (mtp) cc_final: 0.6784 (tpp) REVERT: b 14 GLU cc_start: 0.7722 (pt0) cc_final: 0.7462 (tm-30) REVERT: b 57 ASP cc_start: 0.7913 (t0) cc_final: 0.7587 (t70) REVERT: b 59 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6069 (mm-30) REVERT: b 121 GLU cc_start: 0.8375 (pt0) cc_final: 0.8144 (tm-30) REVERT: c 130 GLN cc_start: 0.8881 (tp40) cc_final: 0.8380 (tm-30) REVERT: c 200 TYR cc_start: 0.7497 (m-80) cc_final: 0.7057 (m-10) REVERT: c 265 MET cc_start: 0.8763 (tpt) cc_final: 0.8562 (tpt) REVERT: d 1 MET cc_start: 0.3501 (ttt) cc_final: 0.2274 (ptm) REVERT: d 9 TRP cc_start: 0.6957 (t60) cc_final: 0.6492 (t60) REVERT: d 53 ASP cc_start: 0.7653 (m-30) cc_final: 0.7447 (p0) REVERT: d 54 ILE cc_start: 0.6165 (pt) cc_final: 0.4911 (pt) REVERT: d 75 MET cc_start: 0.6148 (tpt) cc_final: 0.5932 (tpp) REVERT: d 206 MET cc_start: 0.7326 (ptm) cc_final: 0.7078 (ptm) REVERT: e 1 MET cc_start: 0.4828 (ttt) cc_final: 0.4330 (tpt) REVERT: f 112 MET cc_start: -0.0324 (ptt) cc_final: -0.1373 (mmp) REVERT: f 135 MET cc_start: -0.0138 (pmm) cc_final: -0.2395 (ttt) REVERT: f 162 MET cc_start: 0.4358 (mmp) cc_final: 0.4013 (tpp) REVERT: f 384 MET cc_start: 0.1600 (mmm) cc_final: 0.1068 (tpt) REVERT: f 570 MET cc_start: 0.6807 (ptm) cc_final: 0.4752 (mmt) REVERT: f 572 MET cc_start: 0.2341 (tpt) cc_final: 0.1555 (tpt) REVERT: f 629 MET cc_start: 0.1802 (ptp) cc_final: 0.0242 (tpp) REVERT: f 683 VAL cc_start: 0.2774 (p) cc_final: 0.2314 (p) outliers start: 2 outliers final: 0 residues processed: 1102 average time/residue: 0.6606 time to fit residues: 1263.6456 Evaluate side-chains 858 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 858 time to evaluate : 6.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 578 optimal weight: 1.9990 chunk 931 optimal weight: 7.9990 chunk 568 optimal weight: 7.9990 chunk 442 optimal weight: 5.9990 chunk 647 optimal weight: 0.8980 chunk 977 optimal weight: 20.0000 chunk 899 optimal weight: 20.0000 chunk 778 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 601 optimal weight: 20.0000 chunk 477 optimal weight: 8.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 HIS ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 109 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 162 GLN ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 HIS ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 ASN ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 GLN ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 145 HIS U 345 ASN ** U 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN ** U 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 106 GLN ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 ASN ** Z 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 273 GLN b 29 GLN ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 237 HIS ** c 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 102 ASN f 293 ASN ** f 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.8938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 79128 Z= 0.227 Angle : 0.826 15.594 106985 Z= 0.421 Chirality : 0.047 0.541 12177 Planarity : 0.005 0.109 13802 Dihedral : 6.662 84.977 10988 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 25.80 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.72 % Favored : 92.85 % Rotamer: Outliers : 0.02 % Allowed : 0.44 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.55 % Cis-general : 2.01 % Twisted Proline : 0.57 % Twisted General : 0.04 % 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 (0.08), residues: 9841 helix: -0.63 (0.07), residues: 4633 sheet: -0.87 (0.16), residues: 1074 loop : -1.74 (0.10), residues: 4134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP Y 286 HIS 0.018 0.001 HIS Z 196 PHE 0.047 0.002 PHE C 175 TYR 0.029 0.002 TYR V 258 ARG 0.008 0.001 ARG A 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19682 Ramachandran restraints generated. 9841 Oldfield, 0 Emsley, 9841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1091 time to evaluate : 6.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 37 LEU cc_start: 0.8741 (tp) cc_final: 0.7949 (tt) REVERT: G 61 LEU cc_start: 0.7485 (tt) cc_final: 0.7166 (tt) REVERT: G 70 PHE cc_start: 0.6069 (t80) cc_final: 0.5865 (t80) REVERT: G 78 CYS cc_start: 0.5511 (p) cc_final: 0.4581 (p) REVERT: G 80 MET cc_start: 0.8463 (mmp) cc_final: 0.8230 (mmp) REVERT: G 100 ASN cc_start: 0.8865 (m-40) cc_final: 0.8554 (m110) REVERT: G 125 TYR cc_start: 0.8620 (m-10) cc_final: 0.8264 (m-80) REVERT: G 164 LYS cc_start: 0.5706 (mtmm) cc_final: 0.5034 (tppt) REVERT: G 171 LYS cc_start: 0.8400 (mmtp) cc_final: 0.8186 (mptt) REVERT: G 208 ILE cc_start: 0.6866 (mm) cc_final: 0.6437 (mm) REVERT: G 209 ASP cc_start: 0.6981 (m-30) cc_final: 0.6580 (t0) REVERT: H 79 MET cc_start: 0.8646 (pmm) cc_final: 0.8147 (pmm) REVERT: H 175 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8373 (tp30) REVERT: I 26 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8485 (mt-10) REVERT: I 72 MET cc_start: 0.8323 (mtt) cc_final: 0.7569 (mtt) REVERT: I 89 GLU cc_start: 0.8856 (tp30) cc_final: 0.8436 (mm-30) REVERT: I 96 ARG cc_start: 0.9543 (ptp-170) cc_final: 0.9302 (ptp-110) REVERT: I 212 GLU cc_start: 0.8207 (tt0) cc_final: 0.7944 (pt0) REVERT: I 243 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8219 (mt-10) REVERT: I 246 LYS cc_start: 0.8589 (tptt) cc_final: 0.8120 (mmtt) REVERT: K 29 GLU cc_start: 0.9013 (tp30) cc_final: 0.8604 (mt-10) REVERT: K 84 ASP cc_start: 0.9021 (m-30) cc_final: 0.8468 (p0) REVERT: K 107 MET cc_start: 0.5567 (ttt) cc_final: 0.5299 (tpp) REVERT: L 26 MET cc_start: 0.7870 (mtp) cc_final: 0.7596 (mtp) REVERT: L 181 GLU cc_start: 0.7890 (mp0) cc_final: 0.7244 (mp0) REVERT: M 50 GLU cc_start: 0.7330 (tt0) cc_final: 0.6553 (tp30) REVERT: M 67 PHE cc_start: 0.6287 (t80) cc_final: 0.5937 (t80) REVERT: M 75 MET cc_start: 0.7343 (mmm) cc_final: 0.6256 (mmm) REVERT: M 180 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7737 (mm-40) REVERT: N 4 MET cc_start: 0.8687 (mmp) cc_final: 0.8420 (mmm) REVERT: N 94 LEU cc_start: 0.8342 (mt) cc_final: 0.8090 (mm) REVERT: N 95 MET cc_start: 0.3542 (ptm) cc_final: 0.3332 (ptm) REVERT: N 120 MET cc_start: 0.7632 (mmt) cc_final: 0.6902 (mpp) REVERT: N 162 LEU cc_start: 0.5704 (mt) cc_final: 0.5197 (tt) REVERT: O 54 MET cc_start: 0.8730 (mpp) cc_final: 0.8521 (mpp) REVERT: O 55 THR cc_start: 0.9023 (m) cc_final: 0.8774 (t) REVERT: O 148 GLU cc_start: 0.8536 (pt0) cc_final: 0.8147 (pm20) REVERT: P 66 ARG cc_start: 0.8558 (mmt-90) cc_final: 0.8158 (mmt-90) REVERT: P 69 PHE cc_start: 0.9185 (t80) cc_final: 0.8705 (t80) REVERT: P 88 MET cc_start: 0.9304 (tmm) cc_final: 0.9055 (tmm) REVERT: P 117 PHE cc_start: 0.8107 (p90) cc_final: 0.7809 (p90) REVERT: P 171 MET cc_start: 0.7534 (ttt) cc_final: 0.6766 (mmm) REVERT: P 204 MET cc_start: -0.3017 (tmm) cc_final: -0.3837 (tpt) REVERT: Q 35 MET cc_start: 0.6941 (tpp) cc_final: 0.5389 (tmm) REVERT: R 36 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8454 (mm-30) REVERT: S 36 HIS cc_start: 0.6221 (m-70) cc_final: 0.5767 (m90) REVERT: S 48 ASP cc_start: 0.8670 (m-30) cc_final: 0.8171 (p0) REVERT: S 109 ILE cc_start: 0.6065 (mm) cc_final: 0.5810 (mm) REVERT: S 110 ILE cc_start: 0.8416 (pt) cc_final: 0.8211 (pt) REVERT: T 5 MET cc_start: 0.5150 (mmm) cc_final: 0.4802 (mmm) REVERT: T 110 MET cc_start: 0.7655 (mpp) cc_final: 0.6910 (mpp) REVERT: T 214 MET cc_start: 0.2672 (mtt) cc_final: 0.1613 (ptt) REVERT: A 225 CYS cc_start: 0.9126 (m) cc_final: 0.8789 (t) REVERT: A 249 TYR cc_start: 0.7829 (t80) cc_final: 0.7263 (t80) REVERT: A 252 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7370 (mm-30) REVERT: A 362 MET cc_start: 0.7180 (tmm) cc_final: 0.6667 (tmm) REVERT: B 107 MET cc_start: 0.5505 (ptm) cc_final: 0.5247 (ppp) REVERT: B 141 LYS cc_start: 0.8488 (pttt) cc_final: 0.8078 (tttt) REVERT: B 163 LEU cc_start: 0.8744 (mp) cc_final: 0.7848 (tp) REVERT: D 64 GLU cc_start: 0.9224 (pp20) cc_final: 0.8905 (pp20) REVERT: D 170 MET cc_start: 0.7791 (ptm) cc_final: 0.6896 (tpp) REVERT: D 179 GLU cc_start: 0.9197 (pt0) cc_final: 0.8956 (pt0) REVERT: E 69 PHE cc_start: 0.7809 (m-80) cc_final: 0.7393 (m-80) REVERT: E 110 TYR cc_start: 0.7715 (p90) cc_final: 0.7461 (p90) REVERT: E 114 GLU cc_start: 0.8210 (pt0) cc_final: 0.7682 (tp30) REVERT: E 327 ASP cc_start: 0.6483 (t70) cc_final: 0.5539 (p0) REVERT: E 353 PHE cc_start: 0.9017 (t80) cc_final: 0.8759 (t80) REVERT: F 223 VAL cc_start: 0.7407 (t) cc_final: 0.6605 (t) REVERT: F 224 LEU cc_start: 0.8354 (tp) cc_final: 0.7704 (tp) REVERT: F 260 PHE cc_start: 0.7451 (m-10) cc_final: 0.7165 (m-10) REVERT: F 373 MET cc_start: 0.8319 (mmp) cc_final: 0.7973 (mmp) REVERT: F 430 LYS cc_start: 0.6729 (mtmm) cc_final: 0.5589 (tttp) REVERT: C 23 TYR cc_start: 0.7481 (t80) cc_final: 0.6956 (t80) REVERT: C 24 TYR cc_start: 0.8277 (m-80) cc_final: 0.7809 (m-80) REVERT: C 80 MET cc_start: 0.7084 (mpp) cc_final: 0.6799 (mpp) REVERT: C 139 MET cc_start: 0.8114 (mmp) cc_final: 0.7115 (mmm) REVERT: C 142 LYS cc_start: 0.7668 (tptt) cc_final: 0.7178 (pttp) REVERT: C 145 ASP cc_start: 0.8519 (m-30) cc_final: 0.8059 (t70) REVERT: C 233 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6904 (pm20) REVERT: C 275 GLU cc_start: 0.8961 (pt0) cc_final: 0.8744 (mm-30) REVERT: C 314 LYS cc_start: 0.8086 (tppp) cc_final: 0.7871 (ptmt) REVERT: C 368 MET cc_start: 0.8975 (mmp) cc_final: 0.8451 (ptt) REVERT: C 369 TYR cc_start: 0.8512 (m-10) cc_final: 0.8269 (m-80) REVERT: C 372 ARG cc_start: 0.9201 (ttt-90) cc_final: 0.8553 (mtp180) REVERT: U 76 GLU cc_start: 0.8341 (tt0) cc_final: 0.7957 (tm-30) REVERT: U 128 GLN cc_start: 0.8874 (tp40) cc_final: 0.8479 (mm-40) REVERT: U 188 MET cc_start: 0.3739 (tpp) cc_final: 0.3458 (tpp) REVERT: U 355 ASN cc_start: 0.8747 (m110) cc_final: 0.8138 (t0) REVERT: U 448 LEU cc_start: 0.8612 (tt) cc_final: 0.8166 (mm) REVERT: U 556 MET cc_start: 0.7192 (tpp) cc_final: 0.6990 (tpp) REVERT: U 775 LEU cc_start: 0.8021 (mt) cc_final: 0.7291 (pp) REVERT: V 269 LYS cc_start: 0.9255 (mtmt) cc_final: 0.8718 (tppt) REVERT: V 309 MET cc_start: 0.5571 (tpt) cc_final: 0.5344 (tpt) REVERT: V 409 MET cc_start: 0.9062 (ttt) cc_final: 0.8671 (tpt) REVERT: V 489 MET cc_start: 0.8850 (mmp) cc_final: 0.8408 (tpt) REVERT: W 1 MET cc_start: 0.4776 (mmm) cc_final: 0.4498 (mmm) REVERT: W 130 MET cc_start: 0.8189 (mmp) cc_final: 0.7625 (tmm) REVERT: W 305 LEU cc_start: 0.8818 (tt) cc_final: 0.8542 (tp) REVERT: W 308 LEU cc_start: 0.8677 (tp) cc_final: 0.8052 (mt) REVERT: W 312 MET cc_start: 0.4780 (tpt) cc_final: 0.3779 (tpt) REVERT: W 378 MET cc_start: 0.8187 (mmm) cc_final: 0.7861 (mmm) REVERT: W 428 TRP cc_start: 0.8719 (m100) cc_final: 0.8374 (m100) REVERT: X 69 LEU cc_start: 0.7846 (tp) cc_final: 0.7556 (mt) REVERT: X 175 LYS cc_start: 0.6884 (tttt) cc_final: 0.6627 (mttm) REVERT: X 225 TRP cc_start: 0.6076 (m100) cc_final: 0.5867 (m100) REVERT: X 260 MET cc_start: 0.7924 (mpp) cc_final: 0.7540 (mpp) REVERT: X 278 ARG cc_start: 0.7661 (tpt90) cc_final: 0.6708 (ptm-80) REVERT: X 380 GLN cc_start: 0.8646 (tt0) cc_final: 0.8059 (pm20) REVERT: Y 38 ARG cc_start: 0.8894 (mtm-85) cc_final: 0.8360 (ppt90) REVERT: Y 55 GLU cc_start: 0.7068 (mp0) cc_final: 0.6429 (pt0) REVERT: Y 73 MET cc_start: 0.7746 (mtp) cc_final: 0.6965 (mmm) REVERT: Y 77 ASN cc_start: 0.7768 (t0) cc_final: 0.7480 (m-40) REVERT: Y 102 ASP cc_start: 0.8946 (t0) cc_final: 0.8679 (t0) REVERT: Y 105 MET cc_start: 0.7601 (ptp) cc_final: 0.7016 (ptp) REVERT: Y 124 PHE cc_start: 0.7921 (m-10) cc_final: 0.7531 (m-80) REVERT: Y 157 ILE cc_start: 0.7210 (pt) cc_final: 0.6878 (tp) REVERT: Y 188 CYS cc_start: 0.8547 (m) cc_final: 0.8075 (p) REVERT: Y 228 MET cc_start: 0.7600 (ptm) cc_final: 0.6942 (ptm) REVERT: Y 299 MET cc_start: 0.7553 (mmm) cc_final: 0.7098 (mmm) REVERT: Y 364 TRP cc_start: 0.8352 (t-100) cc_final: 0.8100 (t-100) REVERT: Z 54 PHE cc_start: 0.7861 (p90) cc_final: 0.7515 (p90) REVERT: Z 75 LEU cc_start: 0.8735 (tt) cc_final: 0.8336 (mt) REVERT: Z 78 MET cc_start: 0.8340 (tpt) cc_final: 0.7525 (tpp) REVERT: Z 82 PHE cc_start: 0.9029 (m-10) cc_final: 0.8784 (m-80) REVERT: Z 172 VAL cc_start: 0.8652 (t) cc_final: 0.8349 (m) REVERT: Z 176 LEU cc_start: 0.8709 (pp) cc_final: 0.8388 (mt) REVERT: Z 196 HIS cc_start: 0.8000 (p90) cc_final: 0.7665 (p90) REVERT: Z 279 LYS cc_start: 0.7166 (mtpt) cc_final: 0.6368 (mmmt) REVERT: a 22 TRP cc_start: 0.7437 (t-100) cc_final: 0.7146 (t-100) REVERT: a 87 MET cc_start: 0.3423 (mtt) cc_final: 0.3128 (mmm) REVERT: a 121 LEU cc_start: 0.8220 (mp) cc_final: 0.7803 (tt) REVERT: a 124 ASN cc_start: 0.7484 (m-40) cc_final: 0.6881 (t0) REVERT: a 155 PHE cc_start: 0.8821 (t80) cc_final: 0.8479 (t80) REVERT: a 312 MET cc_start: 0.8648 (mmt) cc_final: 0.8322 (mmt) REVERT: b 7 MET cc_start: 0.7913 (mtp) cc_final: 0.6818 (tpp) REVERT: b 14 GLU cc_start: 0.7651 (pt0) cc_final: 0.7357 (tm-30) REVERT: b 57 ASP cc_start: 0.7905 (t0) cc_final: 0.7567 (t70) REVERT: b 59 GLU cc_start: 0.6747 (mt-10) cc_final: 0.6015 (mm-30) REVERT: b 121 GLU cc_start: 0.8373 (pt0) cc_final: 0.8138 (tm-30) REVERT: b 145 GLU cc_start: 0.5405 (pm20) cc_final: 0.5092 (pm20) REVERT: c 130 GLN cc_start: 0.8883 (tp40) cc_final: 0.8376 (tm-30) REVERT: c 200 TYR cc_start: 0.7497 (m-80) cc_final: 0.7012 (m-10) REVERT: c 234 TYR cc_start: 0.6827 (m-80) cc_final: 0.6623 (m-80) REVERT: c 265 MET cc_start: 0.8770 (tpt) cc_final: 0.8402 (tpt) REVERT: d 9 TRP cc_start: 0.6895 (t60) cc_final: 0.6461 (t60) REVERT: d 54 ILE cc_start: 0.6337 (pt) cc_final: 0.5080 (pt) REVERT: d 206 MET cc_start: 0.7388 (ptm) cc_final: 0.7160 (ptm) REVERT: e 1 MET cc_start: 0.4900 (ttt) cc_final: 0.4423 (tpt) REVERT: f 112 MET cc_start: -0.0421 (ptt) cc_final: -0.1535 (mmp) REVERT: f 135 MET cc_start: -0.0096 (pmm) cc_final: -0.2177 (ttt) REVERT: f 162 MET cc_start: 0.4252 (mmp) cc_final: 0.3201 (mmm) REVERT: f 353 MET cc_start: 0.3517 (mtt) cc_final: 0.3112 (mtt) REVERT: f 570 MET cc_start: 0.6614 (ptm) cc_final: 0.4497 (mmt) REVERT: f 572 MET cc_start: 0.1923 (tpt) cc_final: 0.1191 (tpt) REVERT: f 629 MET cc_start: 0.1619 (ptp) cc_final: 0.0082 (tpp) outliers start: 2 outliers final: 0 residues processed: 1091 average time/residue: 0.6636 time to fit residues: 1266.5951 Evaluate side-chains 854 residues out of total 8514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 854 time to evaluate : 6.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 618 optimal weight: 0.2980 chunk 829 optimal weight: 8.9990 chunk 238 optimal weight: 40.0000 chunk 717 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 chunk 216 optimal weight: 0.8980 chunk 779 optimal weight: 5.9990 chunk 326 optimal weight: 30.0000 chunk 800 optimal weight: 8.9990 chunk 98 optimal weight: 30.0000 chunk 143 optimal weight: 30.0000 overall best weight: 3.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 63 HIS ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 HIS N 154 GLN O 109 HIS ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 65 GLN ** T 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 162 GLN ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 HIS ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 ASN ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 145 HIS ** U 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN ** U 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 232 HIS ** V 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 106 GLN W 361 HIS ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 ASN ** Z 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 273 GLN b 29 GLN ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 298 GLN ** d 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 293 ASN ** f 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.070959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.059256 restraints weight = 666593.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.060251 restraints weight = 464336.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.061002 restraints weight = 344916.632| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.9104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 79128 Z= 0.212 Angle : 0.810 15.605 106985 Z= 0.412 Chirality : 0.046 0.421 12177 Planarity : 0.005 0.105 13802 Dihedral : 6.564 82.829 10988 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 24.60 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.80 % Favored : 92.76 % Rotamer: Outliers : 0.04 % Allowed : 0.42 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.55 % Cis-general : 2.01 % Twisted Proline : 0.57 % Twisted General : 0.04 % 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: -1.66 (0.08), residues: 9841 helix: -0.55 (0.07), residues: 4634 sheet: -0.87 (0.16), residues: 1060 loop : -1.72 (0.10), residues: 4147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP Y 286 HIS 0.019 0.001 HIS Z 196 PHE 0.040 0.002 PHE C 175 TYR 0.030 0.002 TYR B 295 ARG 0.013 0.001 ARG V 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23519.34 seconds wall clock time: 410 minutes 15.45 seconds (24615.45 seconds total)