Starting phenix.real_space_refine on Wed Mar 20 13:19:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qy7_14209/03_2024/7qy7_14209_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qy7_14209/03_2024/7qy7_14209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qy7_14209/03_2024/7qy7_14209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qy7_14209/03_2024/7qy7_14209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qy7_14209/03_2024/7qy7_14209_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qy7_14209/03_2024/7qy7_14209_updated.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 15 5.49 5 S 581 5.16 5 C 63095 2.51 5 N 17177 2.21 5 O 19042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 196": "NH1" <-> "NH2" Residue "a ARG 226": "NH1" <-> "NH2" Residue "a ARG 270": "NH1" <-> "NH2" Residue "a ARG 284": "NH1" <-> "NH2" Residue "b ARG 70": "NH1" <-> "NH2" Residue "c ARG 68": "NH1" <-> "NH2" Residue "c PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 104": "NH1" <-> "NH2" Residue "d ARG 52": "NH1" <-> "NH2" Residue "d ARG 65": "NH1" <-> "NH2" Residue "d ARG 111": "NH1" <-> "NH2" Residue "d ARG 175": "NH1" <-> "NH2" Residue "e ARG 57": "NH1" <-> "NH2" Residue "f TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 140": "NH1" <-> "NH2" Residue "U ARG 159": "NH1" <-> "NH2" Residue "U ARG 194": "NH1" <-> "NH2" Residue "U TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 306": "NH1" <-> "NH2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ARG 355": "NH1" <-> "NH2" Residue "V ARG 397": "NH1" <-> "NH2" Residue "W ARG 8": "NH1" <-> "NH2" Residue "W ARG 12": "NH1" <-> "NH2" Residue "W ARG 55": "NH1" <-> "NH2" Residue "W ARG 182": "NH1" <-> "NH2" Residue "W ARG 357": "NH1" <-> "NH2" Residue "W ARG 364": "NH1" <-> "NH2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 137": "NH1" <-> "NH2" Residue "Y ARG 176": "NH1" <-> "NH2" Residue "Y ARG 177": "NH1" <-> "NH2" Residue "Y ARG 179": "NH1" <-> "NH2" Residue "Y ARG 267": "NH1" <-> "NH2" Residue "Y ARG 297": "NH1" <-> "NH2" Residue "Y ARG 300": "NH1" <-> "NH2" Residue "Y ARG 312": "NH1" <-> "NH2" Residue "Y ARG 342": "NH1" <-> "NH2" Residue "Y ARG 358": "NH1" <-> "NH2" Residue "Z ARG 267": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B ASP 320": "OD1" <-> "OD2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "D ARG 342": "NH1" <-> "NH2" Residue "D GLU 411": "OE1" <-> "OE2" Residue "D TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 251": "NH1" <-> "NH2" Residue "E ARG 255": "NH1" <-> "NH2" Residue "E ARG 291": "NH1" <-> "NH2" Residue "F ARG 238": "NH1" <-> "NH2" Residue "F ARG 269": "NH1" <-> "NH2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F ARG 334": "NH1" <-> "NH2" Residue "F ARG 364": "NH1" <-> "NH2" Residue "G GLU 19": "OE1" <-> "OE2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "I ARG 249": "NH1" <-> "NH2" Residue "K ARG 10": "NH1" <-> "NH2" Residue "K ARG 20": "NH1" <-> "NH2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "L ARG 157": "NH1" <-> "NH2" Residue "L ARG 239": "NH1" <-> "NH2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M ARG 187": "NH1" <-> "NH2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N ARG 91": "NH1" <-> "NH2" Residue "O ARG 201": "NH1" <-> "NH2" Residue "P ARG 66": "NH1" <-> "NH2" Residue "P PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 173": "NH1" <-> "NH2" Residue "T PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "i ARG 249": "NH1" <-> "NH2" Residue "k ARG 10": "NH1" <-> "NH2" Residue "k ARG 20": "NH1" <-> "NH2" Residue "k GLU 232": "OE1" <-> "OE2" Residue "l ARG 96": "NH1" <-> "NH2" Residue "l ARG 157": "NH1" <-> "NH2" Residue "l ARG 239": "NH1" <-> "NH2" Residue "m ARG 19": "NH1" <-> "NH2" Residue "m ARG 187": "NH1" <-> "NH2" Residue "m ARG 232": "NH1" <-> "NH2" Residue "n ARG 45": "NH1" <-> "NH2" Residue "o ARG 201": "NH1" <-> "NH2" Residue "p ARG 66": "NH1" <-> "NH2" Residue "q PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 173": "NH1" <-> "NH2" Residue "t PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 99911 Number of models: 1 Model: "" Number of chains: 51 Chain: "a" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2995 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain: "b" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1458 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain: "c" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2187 Classifications: {'peptide': 278} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 267} Chain breaks: 1 Chain: "d" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2116 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 245} Chain: "e" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 334 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain breaks: 1 Chain: "f" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5319 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 25, 'TRANS': 663} Chain breaks: 9 Chain: "U" Number of atoms: 6287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6287 Classifications: {'peptide': 806} Link IDs: {'PTRANS': 26, 'TRANS': 779} Chain breaks: 3 Chain: "V" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3799 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 20, 'TRANS': 451} Chain: "W" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3703 Classifications: {'peptide': 456} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 447} Chain: "X" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1905 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain: "Y" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3115 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 370} Chain: "Z" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "A" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2672 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2706 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2850 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 3021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3021 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 17, 'TRANS': 360} Chain breaks: 1 Chain: "E" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2860 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 18, 'TRANS': 356} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "F" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2859 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1820 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'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: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1688 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "I" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1895 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 242} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1704 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "K" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1850 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "M" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1856 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1430 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "O" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1643 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1585 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1570 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1548 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1667 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 207} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1826 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "h" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1708 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "i" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1912 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "j" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1704 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "k" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1722 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "l" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1850 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "m" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1856 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "n" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1430 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "o" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1643 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "p" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1585 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "q" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1570 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "r" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1548 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "s" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1667 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 207} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'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: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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} Residues with excluded nonbonded symmetry interactions: 11 residue: pdb=" N ILE b 90 " occ=0.79 ... (6 atoms not shown) pdb=" CD1 ILE b 90 " occ=0.79 residue: pdb=" N SER b 115 " occ=0.80 ... (4 atoms not shown) pdb=" OG SER b 115 " occ=0.80 residue: pdb=" N ILE b 140 " occ=0.60 ... (6 atoms not shown) pdb=" CD1 ILE b 140 " occ=0.60 residue: pdb=" N VAL b 173 " occ=0.49 ... (5 atoms not shown) pdb=" CG2 VAL b 173 " occ=0.49 residue: pdb=" N GLY b 191 " occ=0.88 ... (2 atoms not shown) pdb=" O GLY b 191 " occ=0.88 residue: pdb=" N ILE d 63 " occ=0.67 ... (6 atoms not shown) pdb=" CD1 ILE d 63 " occ=0.67 residue: pdb=" N SER d 70 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER d 70 " occ=0.00 residue: pdb=" N MET d 95 " occ=0.99 ... (6 atoms not shown) pdb=" CE MET d 95 " occ=0.99 residue: pdb=" N ALA X 359 " occ=0.98 ... (3 atoms not shown) pdb=" CB ALA X 359 " occ=0.98 residue: pdb=" N GLN X 380 " occ=0.83 ... (7 atoms not shown) pdb=" NE2 GLN X 380 " occ=0.83 residue: pdb=" N GLY Z 30 " occ=0.40 ... (2 atoms not shown) pdb=" O GLY Z 30 " occ=0.40 Time building chain proxies: 38.42, per 1000 atoms: 0.38 Number of scatterers: 99911 At special positions: 0 Unit cell: (332.91, 201.39, 201.39, 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 581 16.00 P 15 15.00 O 19042 8.00 N 17177 7.00 C 63095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 186 " distance=2.02 Simple disulfide: pdb=" SG CYS m 41 " - pdb=" SG CYS m 186 " distance=2.02 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 Atom "HETATM99908 O5' ATP E 401 .*. O " rejected from bonding due to valence issues. Atom "HETATM99907 O4' ATP E 401 .*. O " rejected from bonding due to valence issues. Atom "HETATM99905 O3B ATP E 401 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 34.61 Conformation dependent library (CDL) restraints added in 13.7 seconds 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 24032 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 457 helices and 89 sheets defined 41.6% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.46 Creating SS restraints... Processing helix chain 'a' and resid 5 through 9 Processing helix chain 'a' and resid 18 through 20 No H-bonds generated for 'chain 'a' and resid 18 through 20' Processing helix chain 'a' and resid 22 through 31 removed outlier: 4.474A pdb=" N GLU a 27 " --> pdb=" O HIS a 23 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR a 29 " --> pdb=" O LEU a 25 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR a 30 " --> pdb=" O GLU a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 35 through 46 Processing helix chain 'a' and resid 53 through 66 removed outlier: 5.331A pdb=" N LEU a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 87 removed outlier: 4.739A pdb=" N ARG a 85 " --> pdb=" O LEU a 81 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN a 86 " --> pdb=" O HIS a 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 91 through 103 removed outlier: 4.311A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 110 through 120 Processing helix chain 'a' and resid 122 through 124 No H-bonds generated for 'chain 'a' and resid 122 through 124' Processing helix chain 'a' and resid 131 through 141 removed outlier: 3.883A pdb=" N GLU a 139 " --> pdb=" O ILE a 135 " (cutoff:3.500A) Processing helix chain 'a' and resid 151 through 164 Processing helix chain 'a' and resid 171 through 182 Processing helix chain 'a' and resid 190 through 205 Processing helix chain 'a' and resid 220 through 228 removed outlier: 4.120A pdb=" N LEU a 225 " --> pdb=" O VAL a 221 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR a 228 " --> pdb=" O SER a 224 " (cutoff:3.500A) Processing helix chain 'a' and resid 233 through 238 Processing helix chain 'a' and resid 247 through 250 No H-bonds generated for 'chain 'a' and resid 247 through 250' Processing helix chain 'a' and resid 252 through 255 No H-bonds generated for 'chain 'a' and resid 252 through 255' Processing helix chain 'a' and resid 265 through 283 removed outlier: 3.795A pdb=" N GLN a 273 " --> pdb=" O LEU a 269 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET a 278 " --> pdb=" O LEU a 274 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 299 Processing helix chain 'a' and resid 304 through 317 removed outlier: 3.734A pdb=" N VAL a 307 " --> pdb=" O VAL a 304 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU a 308 " --> pdb=" O ASN a 305 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LYS a 313 " --> pdb=" O LEU a 310 " (cutoff:3.500A) Processing helix chain 'a' and resid 343 through 370 removed outlier: 5.838A pdb=" N LYS a 350 " --> pdb=" O ILE a 346 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASP a 351 " --> pdb=" O LYS a 347 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ARG a 352 " --> pdb=" O GLY a 348 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N PHE a 355 " --> pdb=" O ASP a 351 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 43 Processing helix chain 'b' and resid 69 through 75 Processing helix chain 'b' and resid 86 through 96 removed outlier: 4.091A pdb=" N ILE b 90 " --> pdb=" O PHE b 86 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 133 Processing helix chain 'b' and resid 152 through 158 Processing helix chain 'b' and resid 180 through 185 Processing helix chain 'c' and resid 35 through 46 Processing helix chain 'c' and resid 84 through 86 No H-bonds generated for 'chain 'c' and resid 84 through 86' Processing helix chain 'c' and resid 89 through 101 Processing helix chain 'c' and resid 126 through 134 removed outlier: 5.329A pdb=" N GLN c 131 " --> pdb=" O ILE c 127 " (cutoff:3.500A) Processing helix chain 'c' and resid 180 through 187 Proline residue: c 187 - end of helix Processing helix chain 'c' and resid 191 through 197 Processing helix chain 'c' and resid 211 through 224 removed outlier: 4.767A pdb=" N MET c 216 " --> pdb=" O LEU c 212 " (cutoff:3.500A) Processing helix chain 'c' and resid 247 through 258 Processing helix chain 'c' and resid 260 through 263 No H-bonds generated for 'chain 'c' and resid 260 through 263' Processing helix chain 'c' and resid 265 through 269 Processing helix chain 'c' and resid 288 through 308 removed outlier: 4.559A pdb=" N ASP c 305 " --> pdb=" O ALA c 301 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N THR c 306 " --> pdb=" O ALA c 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 3 through 6 Processing helix chain 'd' and resid 18 through 32 Processing helix chain 'd' and resid 46 through 64 Processing helix chain 'd' and resid 68 through 83 removed outlier: 3.628A pdb=" N TYR d 82 " --> pdb=" O LEU d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 109 removed outlier: 4.525A pdb=" N HIS d 96 " --> pdb=" O ALA d 93 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU d 98 " --> pdb=" O MET d 95 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU d 99 " --> pdb=" O HIS d 96 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN d 102 " --> pdb=" O LEU d 99 " (cutoff:3.500A) Processing helix chain 'd' and resid 114 through 121 Processing helix chain 'd' and resid 131 through 145 Proline residue: d 136 - end of helix Processing helix chain 'd' and resid 150 through 157 removed outlier: 3.777A pdb=" N GLY d 156 " --> pdb=" O PHE d 152 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN d 157 " --> pdb=" O LEU d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 180 removed outlier: 4.096A pdb=" N GLU d 177 " --> pdb=" O THR d 173 " (cutoff:3.500A) Processing helix chain 'd' and resid 191 through 196 Processing helix chain 'd' and resid 204 through 209 Processing helix chain 'd' and resid 240 through 253 Processing helix chain 'e' and resid 5 through 8 removed outlier: 4.151A pdb=" N VAL e 8 " --> pdb=" O LYS e 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 5 through 8' Processing helix chain 'e' and resid 43 through 48 Processing helix chain 'e' and resid 60 through 63 No H-bonds generated for 'chain 'e' and resid 60 through 63' Processing helix chain 'f' and resid 12 through 15 removed outlier: 3.553A pdb=" N GLN f 15 " --> pdb=" O GLN f 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 12 through 15' Processing helix chain 'f' and resid 20 through 35 Proline residue: f 28 - end of helix removed outlier: 4.112A pdb=" N ASP f 35 " --> pdb=" O LYS f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 43 through 48 removed outlier: 4.217A pdb=" N SER f 46 " --> pdb=" O GLN f 43 " (cutoff:3.500A) Processing helix chain 'f' and resid 50 through 52 No H-bonds generated for 'chain 'f' and resid 50 through 52' Processing helix chain 'f' and resid 72 through 83 Processing helix chain 'f' and resid 91 through 99 Proline residue: f 95 - end of helix Processing helix chain 'f' and resid 120 through 125 Processing helix chain 'f' and resid 129 through 144 Processing helix chain 'f' and resid 165 through 180 Processing helix chain 'f' and resid 186 through 192 removed outlier: 4.585A pdb=" N VAL f 192 " --> pdb=" O VAL f 188 " (cutoff:3.500A) Processing helix chain 'f' and resid 208 through 216 Processing helix chain 'f' and resid 222 through 238 Processing helix chain 'f' and resid 242 through 257 removed outlier: 3.693A pdb=" N SER f 246 " --> pdb=" O GLU f 242 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA f 247 " --> pdb=" O PRO f 243 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS f 251 " --> pdb=" O ALA f 247 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU f 253 " --> pdb=" O LEU f 249 " (cutoff:3.500A) Processing helix chain 'f' and resid 262 through 272 removed outlier: 4.142A pdb=" N LEU f 272 " --> pdb=" O ALA f 269 " (cutoff:3.500A) Processing helix chain 'f' and resid 276 through 287 Processing helix chain 'f' and resid 298 through 308 Processing helix chain 'f' and resid 313 through 323 Processing helix chain 'f' and resid 330 through 333 No H-bonds generated for 'chain 'f' and resid 330 through 333' Processing helix chain 'f' and resid 343 through 350 Processing helix chain 'f' and resid 370 through 381 removed outlier: 3.503A pdb=" N VAL f 381 " --> pdb=" O VAL f 377 " (cutoff:3.500A) Processing helix chain 'f' and resid 391 through 393 No H-bonds generated for 'chain 'f' and resid 391 through 393' Processing helix chain 'f' and resid 404 through 411 Processing helix chain 'f' and resid 413 through 416 No H-bonds generated for 'chain 'f' and resid 413 through 416' Processing helix chain 'f' and resid 422 through 429 removed outlier: 3.587A pdb=" N LEU f 426 " --> pdb=" O VAL f 422 " (cutoff:3.500A) Processing helix chain 'f' and resid 438 through 451 Processing helix chain 'f' and resid 460 through 463 No H-bonds generated for 'chain 'f' and resid 460 through 463' Processing helix chain 'f' and resid 473 through 488 removed outlier: 3.580A pdb=" N ILE f 482 " --> pdb=" O ARG f 478 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE f 483 " --> pdb=" O LEU f 479 " (cutoff:3.500A) Processing helix chain 'f' and resid 496 through 507 Proline residue: f 503 - end of helix Processing helix chain 'f' and resid 512 through 526 Processing helix chain 'f' and resid 536 through 543 Processing helix chain 'f' and resid 554 through 565 Proline residue: f 559 - end of helix Processing helix chain 'f' and resid 574 through 581 Processing helix chain 'f' and resid 588 through 598 Processing helix chain 'f' and resid 606 through 617 removed outlier: 4.232A pdb=" N SER f 617 " --> pdb=" O LEU f 613 " (cutoff:3.500A) Processing helix chain 'f' and resid 623 through 634 removed outlier: 5.068A pdb=" N LYS f 631 " --> pdb=" O GLU f 627 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LYS f 632 " --> pdb=" O ASP f 628 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLU f 633 " --> pdb=" O LYS f 629 " (cutoff:3.500A) Processing helix chain 'f' and resid 653 through 661 Processing helix chain 'f' and resid 669 through 679 removed outlier: 4.057A pdb=" N HIS f 677 " --> pdb=" O ARG f 673 " (cutoff:3.500A) Processing helix chain 'f' and resid 687 through 696 Proline residue: f 691 - end of helix Processing helix chain 'f' and resid 718 through 727 Processing helix chain 'f' and resid 740 through 753 Processing helix chain 'f' and resid 775 through 777 No H-bonds generated for 'chain 'f' and resid 775 through 777' Processing helix chain 'f' and resid 779 through 783 Processing helix chain 'f' and resid 791 through 795 Processing helix chain 'U' and resid 17 through 30 removed outlier: 3.746A pdb=" N PHE U 22 " --> pdb=" O GLN U 18 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA U 29 " --> pdb=" O HIS U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 40 removed outlier: 3.590A pdb=" N SER U 39 " --> pdb=" O TRP U 35 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU U 40 " --> pdb=" O ALA U 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 35 through 40' Processing helix chain 'U' and resid 42 through 50 Processing helix chain 'U' and resid 57 through 71 Processing helix chain 'U' and resid 75 through 82 Processing helix chain 'U' and resid 97 through 116 Processing helix chain 'U' and resid 134 through 142 removed outlier: 4.483A pdb=" N GLN U 139 " --> pdb=" O ASN U 135 " (cutoff:3.500A) Processing helix chain 'U' and resid 147 through 157 removed outlier: 3.795A pdb=" N ALA U 154 " --> pdb=" O ALA U 150 " (cutoff:3.500A) Processing helix chain 'U' and resid 162 through 165 No H-bonds generated for 'chain 'U' and resid 162 through 165' Processing helix chain 'U' and resid 174 through 186 removed outlier: 4.349A pdb=" N TYR U 179 " --> pdb=" O MET U 176 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N CYS U 184 " --> pdb=" O LEU U 181 " (cutoff:3.500A) Processing helix chain 'U' and resid 194 through 207 removed outlier: 4.175A pdb=" N VAL U 202 " --> pdb=" O LEU U 198 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS U 203 " --> pdb=" O ARG U 199 " (cutoff:3.500A) Processing helix chain 'U' and resid 214 through 219 Processing helix chain 'U' and resid 228 through 238 Processing helix chain 'U' and resid 246 through 255 Processing helix chain 'U' and resid 258 through 268 Processing helix chain 'U' and resid 321 through 330 removed outlier: 4.990A pdb=" N ILE U 326 " --> pdb=" O THR U 322 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU U 329 " --> pdb=" O MET U 325 " (cutoff:3.500A) Processing helix chain 'U' and resid 332 through 344 Processing helix chain 'U' and resid 350 through 359 removed outlier: 5.592A pdb=" N ALA U 359 " --> pdb=" O ASN U 355 " (cutoff:3.500A) Processing helix chain 'U' and resid 364 through 376 removed outlier: 4.625A pdb=" N VAL U 370 " --> pdb=" O HIS U 366 " (cutoff:3.500A) Processing helix chain 'U' and resid 402 through 411 removed outlier: 5.264A pdb=" N LEU U 408 " --> pdb=" O ALA U 404 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLY U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) Processing helix chain 'U' and resid 437 through 449 removed outlier: 4.423A pdb=" N GLY U 442 " --> pdb=" O GLN U 438 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU U 443 " --> pdb=" O GLU U 439 " (cutoff:3.500A) Processing helix chain 'U' and resid 456 through 464 Processing helix chain 'U' and resid 474 through 484 removed outlier: 5.458A pdb=" N LEU U 479 " --> pdb=" O HIS U 475 " (cutoff:3.500A) Processing helix chain 'U' and resid 492 through 501 removed outlier: 3.625A pdb=" N THR U 499 " --> pdb=" O ASP U 495 " (cutoff:3.500A) Processing helix chain 'U' and resid 506 through 520 removed outlier: 4.935A pdb=" N ALA U 511 " --> pdb=" O VAL U 507 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET U 520 " --> pdb=" O LEU U 516 " (cutoff:3.500A) Processing helix chain 'U' and resid 528 through 532 Processing helix chain 'U' and resid 535 through 538 No H-bonds generated for 'chain 'U' and resid 535 through 538' Processing helix chain 'U' and resid 544 through 554 Processing helix chain 'U' and resid 564 through 572 Processing helix chain 'U' and resid 576 through 589 Processing helix chain 'U' and resid 600 through 607 Processing helix chain 'U' and resid 612 through 624 removed outlier: 3.903A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) Processing helix chain 'U' and resid 632 through 642 removed outlier: 4.110A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU U 642 " --> pdb=" O SER U 638 " (cutoff:3.500A) Processing helix chain 'U' and resid 646 through 659 Processing helix chain 'U' and resid 667 through 675 Proline residue: U 674 - end of helix Processing helix chain 'U' and resid 681 through 694 Processing helix chain 'U' and resid 706 through 718 removed outlier: 4.048A pdb=" N SER U 714 " --> pdb=" O ARG U 710 " (cutoff:3.500A) Processing helix chain 'U' and resid 730 through 737 Processing helix chain 'U' and resid 757 through 765 Processing helix chain 'U' and resid 773 through 778 removed outlier: 3.505A pdb=" N PHE U 778 " --> pdb=" O LEU U 775 " (cutoff:3.500A) Processing helix chain 'U' and resid 808 through 811 Processing helix chain 'V' and resid 29 through 42 removed outlier: 3.564A pdb=" N MET V 37 " --> pdb=" O GLN V 33 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA V 42 " --> pdb=" O LYS V 38 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 49 Processing helix chain 'V' and resid 61 through 75 Processing helix chain 'V' and resid 89 through 93 Processing helix chain 'V' and resid 102 through 112 removed outlier: 3.925A pdb=" N SER V 105 " --> pdb=" O PRO V 102 " (cutoff:3.500A) Processing helix chain 'V' and resid 116 through 119 No H-bonds generated for 'chain 'V' and resid 116 through 119' Processing helix chain 'V' and resid 131 through 141 removed outlier: 4.410A pdb=" N GLU V 136 " --> pdb=" O LEU V 132 " (cutoff:3.500A) Proline residue: V 138 - end of helix Processing helix chain 'V' and resid 149 through 154 Processing helix chain 'V' and resid 160 through 162 No H-bonds generated for 'chain 'V' and resid 160 through 162' Processing helix chain 'V' and resid 172 through 190 Processing helix chain 'V' and resid 200 through 217 removed outlier: 5.203A pdb=" N LEU V 205 " --> pdb=" O ARG V 201 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS V 209 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR V 211 " --> pdb=" O ALA V 207 " (cutoff:3.500A) Processing helix chain 'V' and resid 227 through 237 Processing helix chain 'V' and resid 246 through 260 Processing helix chain 'V' and resid 267 through 271 Processing helix chain 'V' and resid 284 through 300 removed outlier: 3.561A pdb=" N LEU V 300 " --> pdb=" O LYS V 296 " (cutoff:3.500A) Processing helix chain 'V' and resid 303 through 314 Processing helix chain 'V' and resid 326 through 330 Processing helix chain 'V' and resid 332 through 337 removed outlier: 4.279A pdb=" N VAL V 335 " --> pdb=" O LEU V 332 " (cutoff:3.500A) Processing helix chain 'V' and resid 351 through 354 No H-bonds generated for 'chain 'V' and resid 351 through 354' Processing helix chain 'V' and resid 358 through 368 removed outlier: 3.728A pdb=" N LEU V 362 " --> pdb=" O MET V 358 " (cutoff:3.500A) Processing helix chain 'V' and resid 373 through 389 removed outlier: 3.748A pdb=" N LEU V 379 " --> pdb=" O PHE V 375 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU V 384 " --> pdb=" O ASP V 380 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS V 385 " --> pdb=" O GLN V 381 " (cutoff:3.500A) Processing helix chain 'V' and resid 393 through 396 No H-bonds generated for 'chain 'V' and resid 393 through 396' Processing helix chain 'V' and resid 398 through 413 Processing helix chain 'V' and resid 419 through 425 removed outlier: 3.607A pdb=" N LYS V 425 " --> pdb=" O ASP V 421 " (cutoff:3.500A) Processing helix chain 'V' and resid 431 through 444 Processing helix chain 'V' and resid 470 through 496 removed outlier: 3.638A pdb=" N HIS V 477 " --> pdb=" O GLN V 473 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE V 496 " --> pdb=" O LYS V 492 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 9 removed outlier: 3.868A pdb=" N ARG W 8 " --> pdb=" O GLY W 4 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 16 No H-bonds generated for 'chain 'W' and resid 14 through 16' Processing helix chain 'W' and resid 25 through 37 Proline residue: W 29 - end of helix Processing helix chain 'W' and resid 44 through 61 Processing helix chain 'W' and resid 70 through 85 Processing helix chain 'W' and resid 95 through 109 removed outlier: 3.889A pdb=" N GLN W 99 " --> pdb=" O SER W 95 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA W 100 " --> pdb=" O GLN W 96 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 133 removed outlier: 4.056A pdb=" N ARG W 129 " --> pdb=" O ILE W 125 " (cutoff:3.500A) Processing helix chain 'W' and resid 139 through 155 removed outlier: 4.222A pdb=" N GLN W 155 " --> pdb=" O THR W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 159 through 166 Processing helix chain 'W' and resid 183 through 186 No H-bonds generated for 'chain 'W' and resid 183 through 186' Processing helix chain 'W' and resid 191 through 194 No H-bonds generated for 'chain 'W' and resid 191 through 194' Processing helix chain 'W' and resid 199 through 207 Processing helix chain 'W' and resid 223 through 234 removed outlier: 4.589A pdb=" N ASN W 228 " --> pdb=" O LEU W 224 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU W 229 " --> pdb=" O LYS W 225 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASP W 234 " --> pdb=" O MET W 230 " (cutoff:3.500A) Processing helix chain 'W' and resid 262 through 269 Processing helix chain 'W' and resid 281 through 289 removed outlier: 3.712A pdb=" N ASP W 285 " --> pdb=" O ASN W 281 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU W 286 " --> pdb=" O GLU W 282 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N HIS W 288 " --> pdb=" O SER W 284 " (cutoff:3.500A) Processing helix chain 'W' and resid 300 through 309 Processing helix chain 'W' and resid 312 through 314 No H-bonds generated for 'chain 'W' and resid 312 through 314' Processing helix chain 'W' and resid 317 through 323 Processing helix chain 'W' and resid 335 through 340 Processing helix chain 'W' and resid 347 through 369 removed outlier: 5.500A pdb=" N LYS W 368 " --> pdb=" O ARG W 364 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TYR W 369 " --> pdb=" O ILE W 365 " (cutoff:3.500A) Processing helix chain 'W' and resid 376 through 381 Processing helix chain 'W' and resid 387 through 399 Processing helix chain 'W' and resid 424 through 454 removed outlier: 3.849A pdb=" N SER W 429 " --> pdb=" O ASN W 426 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN W 430 " --> pdb=" O ASP W 427 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS W 431 " --> pdb=" O TRP W 428 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU W 432 " --> pdb=" O SER W 429 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN W 433 " --> pdb=" O GLN W 430 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER W 434 " --> pdb=" O LYS W 431 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU W 435 " --> pdb=" O LEU W 432 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET W 436 " --> pdb=" O ASN W 433 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS W 441 " --> pdb=" O LEU W 438 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR W 442 " --> pdb=" O VAL W 439 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE W 446 " --> pdb=" O THR W 443 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS W 448 " --> pdb=" O LEU W 445 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU W 449 " --> pdb=" O ILE W 446 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU W 450 " --> pdb=" O ALA W 447 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS W 453 " --> pdb=" O GLU W 450 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN W 454 " --> pdb=" O MET W 451 " (cutoff:3.500A) Processing helix chain 'X' and resid 185 through 195 removed outlier: 3.878A pdb=" N THR X 195 " --> pdb=" O THR X 191 " (cutoff:3.500A) Processing helix chain 'X' and resid 204 through 220 removed outlier: 3.906A pdb=" N HIS X 218 " --> pdb=" O SER X 214 " (cutoff:3.500A) Processing helix chain 'X' and resid 227 through 238 removed outlier: 3.821A pdb=" N GLU X 237 " --> pdb=" O TYR X 233 " (cutoff:3.500A) Processing helix chain 'X' and resid 244 through 248 Processing helix chain 'X' and resid 252 through 259 Processing helix chain 'X' and resid 266 through 269 No H-bonds generated for 'chain 'X' and resid 266 through 269' Processing helix chain 'X' and resid 283 through 293 removed outlier: 3.937A pdb=" N CYS X 289 " --> pdb=" O GLU X 285 " (cutoff:3.500A) Processing helix chain 'X' and resid 302 through 305 No H-bonds generated for 'chain 'X' and resid 302 through 305' 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 324 through 338 removed outlier: 4.895A pdb=" N GLU X 332 " --> pdb=" O ASP X 328 " (cutoff:3.500A) Processing helix chain 'X' and resid 347 through 352 Processing helix chain 'X' and resid 361 through 370 Processing helix chain 'X' and resid 394 through 421 removed outlier: 3.796A pdb=" N ALA X 399 " --> pdb=" O LYS X 395 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR X 415 " --> pdb=" O VAL X 411 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN X 416 " --> pdb=" O ASP X 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 14 through 27 Processing helix chain 'Y' and resid 35 through 45 Processing helix chain 'Y' and resid 51 through 58 removed outlier: 4.530A pdb=" N ALA Y 56 " --> pdb=" O PRO Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 91 removed outlier: 4.328A pdb=" N MET Y 73 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU Y 89 " --> pdb=" O ASP Y 85 " (cutoff:3.500A) Processing helix chain 'Y' and resid 99 through 114 removed outlier: 3.761A pdb=" N LYS Y 107 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) Processing helix chain 'Y' and resid 117 through 121 Processing helix chain 'Y' and resid 135 through 150 removed outlier: 4.808A pdb=" N ILE Y 140 " --> pdb=" O HIS Y 136 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE Y 147 " --> pdb=" O TYR Y 143 " (cutoff:3.500A) Processing helix chain 'Y' and resid 155 through 166 removed outlier: 3.984A pdb=" N THR Y 161 " --> pdb=" O ILE Y 157 " (cutoff:3.500A) Processing helix chain 'Y' and resid 174 through 190 Processing helix chain 'Y' and resid 194 through 200 Processing helix chain 'Y' and resid 216 through 227 removed outlier: 3.947A pdb=" N VAL Y 226 " --> pdb=" O TYR Y 222 " (cutoff:3.500A) Processing helix chain 'Y' and resid 233 through 240 Processing helix chain 'Y' and resid 247 through 251 Processing helix chain 'Y' and resid 254 through 265 Processing helix chain 'Y' and resid 269 through 283 Processing helix chain 'Y' and resid 292 through 310 removed outlier: 4.434A pdb=" N VAL Y 296 " --> pdb=" O ARG Y 293 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG Y 297 " --> pdb=" O TYR Y 294 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER Y 305 " --> pdb=" O HIS Y 302 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN Y 306 " --> pdb=" O ALA Y 303 " (cutoff:3.500A) Processing helix chain 'Y' and resid 316 through 323 removed outlier: 3.931A 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 368 through 386 removed outlier: 4.339A pdb=" N LEU Y 375 " --> pdb=" O LYS Y 371 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU Y 377 " --> pdb=" O GLY Y 373 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL Y 386 " --> pdb=" O LYS Y 382 " (cutoff:3.500A) Processing helix chain 'Z' and resid 13 through 29 removed outlier: 3.713A pdb=" N GLY Z 27 " --> pdb=" O PHE Z 23 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS Z 28 " --> pdb=" O ASN Z 24 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 85 removed outlier: 3.867A pdb=" N ASN Z 77 " --> pdb=" O ASP Z 73 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N MET Z 78 " --> pdb=" O TYR Z 74 " (cutoff:3.500A) Processing helix chain 'Z' and resid 105 through 113 removed outlier: 3.999A pdb=" N MET Z 112 " --> pdb=" O ILE Z 108 " (cutoff:3.500A) Processing helix chain 'Z' and resid 169 through 172 No H-bonds generated for 'chain 'Z' and resid 169 through 172' Processing helix chain 'Z' and resid 188 through 216 removed outlier: 4.089A pdb=" N SER Z 203 " --> pdb=" O LYS Z 199 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL Z 215 " --> pdb=" O TYR Z 211 " (cutoff:3.500A) Processing helix chain 'Z' and resid 220 through 222 No H-bonds generated for 'chain 'Z' and resid 220 through 222' Processing helix chain 'Z' and resid 227 through 236 removed outlier: 4.173A pdb=" N VAL Z 233 " --> pdb=" O GLN Z 229 " (cutoff:3.500A) Processing helix chain 'Z' and resid 246 through 289 removed outlier: 3.857A pdb=" N TYR Z 250 " --> pdb=" O LYS Z 247 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU Z 251 " --> pdb=" O ALA Z 248 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN Z 256 " --> pdb=" O THR Z 253 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N MET Z 257 " --> pdb=" O ASN Z 254 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL Z 259 " --> pdb=" O GLN Z 256 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL Z 260 " --> pdb=" O MET Z 257 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU Z 262 " --> pdb=" O VAL Z 259 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA Z 263 " --> pdb=" O VAL Z 260 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU Z 265 " --> pdb=" O LEU Z 262 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE Z 266 " --> pdb=" O ALA Z 263 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG Z 267 " --> pdb=" O SER Z 264 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN Z 274 " --> pdb=" O ALA Z 271 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU Z 275 " --> pdb=" O LEU Z 272 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE Z 276 " --> pdb=" O HIS Z 273 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN Z 277 " --> pdb=" O ASN Z 274 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN Z 278 " --> pdb=" O LEU Z 275 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA Z 281 " --> pdb=" O ASN Z 278 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP Z 284 " --> pdb=" O ALA Z 281 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS Z 287 " --> pdb=" O ASP Z 284 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS Z 288 " --> pdb=" O ALA Z 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 90 removed outlier: 3.607A pdb=" N GLN A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.820A pdb=" N ALA A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 245 Processing helix chain 'A' and resid 252 through 261 Processing helix chain 'A' and resid 277 through 280 No H-bonds generated for 'chain 'A' and resid 277 through 280' Processing helix chain 'A' and resid 294 through 306 Processing helix chain 'A' and resid 349 through 360 Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 382 through 398 Processing helix chain 'A' and resid 406 through 416 Processing helix chain 'B' and resid 92 through 102 Processing helix chain 'B' and resid 141 through 143 No H-bonds generated for 'chain 'B' and resid 141 through 143' Processing helix chain 'B' and resid 171 through 174 No H-bonds generated for 'chain 'B' and resid 171 through 174' Processing helix chain 'B' and resid 193 through 206 removed outlier: 4.580A pdb=" N LEU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Proline residue: B 204 - end of helix Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 232 through 241 Processing helix chain 'B' and resid 252 through 255 removed outlier: 4.185A pdb=" N LEU B 255 " --> pdb=" O GLY B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 255' Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 305 through 317 removed outlier: 4.021A pdb=" N ASP B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 342 No H-bonds generated for 'chain 'B' and resid 339 through 342' Processing helix chain 'B' and resid 358 through 368 removed outlier: 4.480A pdb=" N ARG B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 364 " --> pdb=" O THR B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 386 removed outlier: 3.517A pdb=" N ILE B 384 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET B 385 " --> pdb=" O ASP B 382 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA B 386 " --> pdb=" O LEU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 409 removed outlier: 4.506A pdb=" N GLY B 403 " --> pdb=" O CYS B 399 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU B 409 " --> pdb=" O MET B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 426 Processing helix chain 'C' and resid 29 through 68 removed outlier: 3.889A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LYS C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N SER C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLN C 40 " --> pdb=" O ASN C 36 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN C 41 " --> pdb=" O ASP C 37 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLN C 64 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.900A pdb=" N LEU C 137 " --> 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 164 Processing helix chain 'C' and resid 166 through 170 Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 197 through 207 removed outlier: 4.305A pdb=" N HIS C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR C 207 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 240 removed outlier: 3.616A pdb=" N ARG C 239 " --> pdb=" O VAL C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 280 Processing helix chain 'C' and resid 322 through 334 Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 358 through 372 Processing helix chain 'C' and resid 380 through 390 Processing helix chain 'D' and resid 46 through 79 removed outlier: 3.598A pdb=" N GLU D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N PHE D 53 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 171 through 186 removed outlier: 4.627A pdb=" N LEU D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Proline residue: D 184 - end of helix Processing helix chain 'D' and resid 190 through 193 No H-bonds generated for 'chain 'D' and resid 190 through 193' Processing helix chain 'D' and resid 212 through 222 removed outlier: 4.514A pdb=" N ALA D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 257 Processing helix chain 'D' and resid 284 through 296 removed outlier: 4.226A pdb=" N LEU D 290 " --> pdb=" O ARG D 287 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU D 293 " --> pdb=" O LEU D 290 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN D 294 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN D 295 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 350 removed outlier: 3.552A pdb=" N SER D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 388 removed outlier: 3.728A pdb=" N GLU D 381 " --> pdb=" O ILE D 378 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER D 382 " --> pdb=" O CYS D 379 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY D 383 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET D 384 " --> pdb=" O GLU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 403 Processing helix chain 'E' and resid 17 through 49 removed outlier: 4.145A pdb=" N ARG E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 123 No H-bonds generated for 'chain 'E' and resid 120 through 123' Processing helix chain 'E' and resid 139 through 149 Processing helix chain 'E' and resid 151 through 154 No H-bonds generated for 'chain 'E' and resid 151 through 154' Processing helix chain 'E' and resid 157 through 162 Processing helix chain 'E' and resid 180 through 190 Processing helix chain 'E' and resid 209 through 224 Processing helix chain 'E' and resid 235 through 237 No H-bonds generated for 'chain 'E' and resid 235 through 237' Processing helix chain 'E' and resid 251 through 263 Processing helix chain 'E' and resid 306 through 315 Processing helix chain 'E' and resid 328 through 334 Processing helix chain 'E' and resid 340 through 358 removed outlier: 4.967A pdb=" N ALA E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 380 removed outlier: 3.528A pdb=" N MET E 368 " --> pdb=" O GLU E 365 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL E 374 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA E 375 " --> pdb=" O ARG E 372 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP E 376 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS E 378 " --> pdb=" O ALA E 375 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS E 379 " --> pdb=" O ASP E 376 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 62 Processing helix chain 'F' and resid 64 through 67 No H-bonds generated for 'chain 'F' and resid 64 through 67' Processing helix chain 'F' and resid 69 through 84 removed outlier: 3.793A pdb=" N LYS F 74 " --> pdb=" O LYS F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 207 removed outlier: 5.156A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) Proline residue: F 205 - end of helix Processing helix chain 'F' and resid 210 through 213 No H-bonds generated for 'chain 'F' and resid 210 through 213' Processing helix chain 'F' and resid 235 through 242 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 269 through 272 No H-bonds generated for 'chain 'F' and resid 269 through 272' 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 306 through 317 removed outlier: 3.810A pdb=" N LEU F 311 " --> pdb=" O ARG F 308 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU F 312 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU F 314 " --> pdb=" O LEU F 311 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN F 316 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU F 317 " --> pdb=" O LEU F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 342 No H-bonds generated for 'chain 'F' and resid 340 through 342' Processing helix chain 'F' and resid 360 through 369 Processing helix chain 'F' and resid 381 through 387 Processing helix chain 'F' and resid 393 through 409 Processing helix chain 'F' and resid 417 through 423 Processing helix chain 'F' and resid 426 through 428 No H-bonds generated for 'chain 'F' and resid 426 through 428' Processing helix chain 'G' and resid 8 through 11 Processing helix chain 'G' and resid 23 through 28 Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 84 through 105 Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 173 through 182 Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 232 through 242 Processing helix chain 'H' and resid 20 through 30 Processing helix chain 'H' and resid 80 through 101 removed outlier: 3.931A pdb=" N VAL H 85 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 123 Processing helix chain 'H' and resid 167 through 177 Processing helix chain 'H' and resid 184 through 195 Processing helix chain 'H' and resid 223 through 229 Processing helix chain 'I' and resid 19 through 28 removed outlier: 3.763A pdb=" N TYR I 23 " --> pdb=" O TYR I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 101 Processing helix chain 'I' and resid 109 through 123 removed outlier: 3.761A pdb=" N TYR I 121 " --> pdb=" O ILE I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 177 removed outlier: 4.866A pdb=" N ALA I 170 " --> pdb=" O ASN I 166 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ALA I 171 " --> pdb=" O ASN I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 199 Processing helix chain 'I' and resid 208 through 210 No H-bonds generated for 'chain 'I' and resid 208 through 210' Processing helix chain 'I' and resid 231 through 250 removed outlier: 4.674A pdb=" N GLU I 250 " --> pdb=" O LYS I 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 removed outlier: 3.974A pdb=" N ALA J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 97 Processing helix chain 'J' and resid 104 through 120 Processing helix chain 'J' and resid 138 through 140 No H-bonds generated for 'chain 'J' and resid 138 through 140' Processing helix chain 'J' and resid 165 through 173 Processing helix chain 'J' and resid 184 through 196 Processing helix chain 'J' and resid 224 through 239 Processing helix chain 'K' and resid 24 through 32 removed outlier: 4.009A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 103 Processing helix chain 'K' and resid 109 through 120 removed outlier: 4.466A pdb=" N LEU K 119 " --> pdb=" O ALA K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 184 Processing helix chain 'K' and resid 191 through 205 Processing helix chain 'K' and resid 233 through 240 Processing helix chain 'L' and resid 21 through 30 Processing helix chain 'L' and resid 79 through 98 Processing helix chain 'L' and resid 105 through 117 Processing helix chain 'L' and resid 165 through 175 Processing helix chain 'L' and resid 184 through 195 Processing helix chain 'L' and resid 229 through 233 Processing helix chain 'M' and resid 21 through 31 removed outlier: 3.622A pdb=" N LYS M 28 " --> pdb=" O GLU M 24 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA M 29 " --> pdb=" O TYR M 25 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 102 Processing helix chain 'M' and resid 108 through 124 Processing helix chain 'M' and resid 169 through 176 removed outlier: 5.000A pdb=" N GLU M 175 " --> pdb=" O ALA M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 199 removed outlier: 4.103A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (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 89 Processing helix chain 'N' and resid 130 through 142 removed outlier: 3.923A pdb=" N SER N 133 " --> pdb=" O SER N 130 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR N 134 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE N 135 " --> pdb=" O SER N 132 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL N 139 " --> pdb=" O TYR N 136 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASP N 140 " --> pdb=" O GLY N 137 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR N 142 " --> pdb=" O VAL N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 166 Processing helix chain 'O' and resid 49 through 70 Processing helix chain 'O' and resid 76 through 89 Processing helix chain 'O' and resid 129 through 141 removed outlier: 4.437A pdb=" N LEU O 132 " --> pdb=" O SER O 129 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE O 138 " --> pdb=" O MET O 135 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU O 139 " --> pdb=" O ALA O 136 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP O 140 " --> pdb=" O VAL O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 148 through 164 Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 57 through 77 Processing helix chain 'P' and resid 84 through 98 removed outlier: 3.728A pdb=" N LYS P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 144 through 153 Processing helix chain 'P' and resid 160 through 177 Processing helix chain 'Q' and resid 50 through 70 removed outlier: 3.834A pdb=" N VAL Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 92 Processing helix chain 'Q' and resid 134 through 145 removed outlier: 3.712A pdb=" N PHE Q 137 " --> pdb=" O TYR Q 134 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR Q 139 " --> pdb=" O ALA Q 136 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER Q 141 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU Q 143 " --> pdb=" O LEU Q 140 " (cutoff:3.500A) Processing helix chain 'Q' and resid 153 through 167 Processing helix chain 'R' and resid 49 through 70 Processing helix chain 'R' and resid 76 through 90 removed outlier: 3.760A pdb=" N GLN R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 141 removed outlier: 4.558A pdb=" N VAL R 133 " --> pdb=" O SER R 130 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL R 138 " --> pdb=" O ALA R 135 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET R 139 " --> pdb=" O TYR R 136 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP R 140 " --> pdb=" O GLY R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 166 Processing helix chain 'R' and resid 192 through 199 Processing helix chain 'S' and resid 58 through 79 Processing helix chain 'S' and resid 85 through 99 removed outlier: 3.670A pdb=" N ARG S 99 " --> pdb=" O ILE S 95 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 152 Processing helix chain 'S' and resid 168 through 183 Processing helix chain 'T' and resid 57 through 77 Processing helix chain 'T' and resid 85 through 102 removed outlier: 3.503A pdb=" N LYS T 102 " --> pdb=" O SER T 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 146 through 156 Processing helix chain 'T' and resid 162 through 179 Processing helix chain 'T' and resid 210 through 213 Processing helix chain 'g' and resid 9 through 11 No H-bonds generated for 'chain 'g' and resid 9 through 11' Processing helix chain 'g' and resid 23 through 28 Processing helix chain 'g' and resid 64 through 66 No H-bonds generated for 'chain 'g' and resid 64 through 66' Processing helix chain 'g' and resid 84 through 105 Processing helix chain 'g' and resid 111 through 127 Processing helix chain 'g' and resid 173 through 182 Processing helix chain 'g' and resid 193 through 205 Processing helix chain 'g' and resid 232 through 242 Processing helix chain 'h' and resid 20 through 30 Processing helix chain 'h' and resid 80 through 101 removed outlier: 3.931A pdb=" N VAL h 85 " --> pdb=" O PRO h 81 " (cutoff:3.500A) Processing helix chain 'h' and resid 107 through 123 Processing helix chain 'h' and resid 167 through 177 Processing helix chain 'h' and resid 184 through 195 Processing helix chain 'h' and resid 223 through 229 Processing helix chain 'i' and resid 19 through 28 removed outlier: 3.762A pdb=" N TYR i 23 " --> pdb=" O TYR i 19 " (cutoff:3.500A) Processing helix chain 'i' and resid 80 through 101 Processing helix chain 'i' and resid 109 through 122 removed outlier: 3.730A pdb=" N TYR i 121 " --> pdb=" O ILE i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 166 through 177 removed outlier: 4.866A pdb=" N ALA i 170 " --> pdb=" O ASN i 166 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ALA i 171 " --> pdb=" O ASN i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 186 through 199 Processing helix chain 'i' and resid 208 through 210 No H-bonds generated for 'chain 'i' and resid 208 through 210' Processing helix chain 'i' and resid 231 through 250 removed outlier: 4.673A pdb=" N GLU i 250 " --> pdb=" O LYS i 246 " (cutoff:3.500A) Processing helix chain 'j' and resid 17 through 27 removed outlier: 3.975A pdb=" N ALA j 25 " --> pdb=" O TYR j 21 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL j 26 " --> pdb=" O ALA j 22 " (cutoff:3.500A) Processing helix chain 'j' and resid 78 through 97 Processing helix chain 'j' and resid 104 through 120 Processing helix chain 'j' and resid 138 through 140 No H-bonds generated for 'chain 'j' and resid 138 through 140' Processing helix chain 'j' and resid 165 through 173 Processing helix chain 'j' and resid 184 through 196 Processing helix chain 'j' and resid 224 through 239 Processing helix chain 'k' and resid 24 through 32 removed outlier: 4.009A pdb=" N LYS k 32 " --> pdb=" O ILE k 28 " (cutoff:3.500A) Processing helix chain 'k' and resid 83 through 103 Processing helix chain 'k' and resid 109 through 120 removed outlier: 4.466A pdb=" N LEU k 119 " --> pdb=" O ALA k 115 " (cutoff:3.500A) Processing helix chain 'k' and resid 174 through 184 Processing helix chain 'k' and resid 191 through 205 Processing helix chain 'k' and resid 233 through 240 Processing helix chain 'l' and resid 21 through 30 Processing helix chain 'l' and resid 79 through 98 Processing helix chain 'l' and resid 105 through 117 Processing helix chain 'l' and resid 165 through 175 Processing helix chain 'l' and resid 184 through 195 Processing helix chain 'l' and resid 229 through 233 Processing helix chain 'm' and resid 21 through 31 removed outlier: 3.623A pdb=" N LYS m 28 " --> pdb=" O GLU m 24 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA m 29 " --> pdb=" O TYR m 25 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL m 30 " --> pdb=" O ALA m 26 " (cutoff:3.500A) Processing helix chain 'm' and resid 81 through 102 Processing helix chain 'm' and resid 108 through 124 Processing helix chain 'm' and resid 169 through 176 removed outlier: 5.000A pdb=" N GLU m 175 " --> pdb=" O ALA m 171 " (cutoff:3.500A) Processing helix chain 'm' and resid 186 through 199 removed outlier: 4.103A pdb=" N LYS m 191 " --> pdb=" O ARG m 187 " (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 89 Processing helix chain 'n' and resid 130 through 142 removed outlier: 3.923A pdb=" N SER n 133 " --> pdb=" O SER n 130 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR n 134 " --> pdb=" O GLY n 131 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE n 135 " --> pdb=" O SER n 132 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL n 139 " --> pdb=" O TYR n 136 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASP n 140 " --> pdb=" O GLY n 137 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR n 142 " --> pdb=" O VAL n 139 " (cutoff:3.500A) Processing helix chain 'n' and resid 149 through 166 Processing helix chain 'o' and resid 49 through 70 Processing helix chain 'o' and resid 76 through 89 Processing helix chain 'o' and resid 129 through 141 removed outlier: 4.437A pdb=" N LEU o 132 " --> pdb=" O SER o 129 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE o 138 " --> pdb=" O MET o 135 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU o 139 " --> pdb=" O ALA o 136 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP o 140 " --> pdb=" O VAL o 137 " (cutoff:3.500A) Processing helix chain 'o' and resid 148 through 164 Processing helix chain 'p' and resid 4 through 6 No H-bonds generated for 'chain 'p' and resid 4 through 6' Processing helix chain 'p' and resid 57 through 77 Processing helix chain 'p' and resid 84 through 98 removed outlier: 3.728A pdb=" N LYS p 98 " --> pdb=" O LEU p 94 " (cutoff:3.500A) Processing helix chain 'p' and resid 144 through 153 Processing helix chain 'p' and resid 160 through 177 Processing helix chain 'q' and resid 50 through 70 removed outlier: 3.835A pdb=" N VAL q 54 " --> pdb=" O ALA q 50 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN q 55 " --> pdb=" O GLY q 51 " (cutoff:3.500A) Processing helix chain 'q' and resid 77 through 92 Processing helix chain 'q' and resid 134 through 145 removed outlier: 3.712A pdb=" N PHE q 137 " --> pdb=" O TYR q 134 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR q 139 " --> pdb=" O ALA q 136 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER q 141 " --> pdb=" O LEU q 138 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU q 143 " --> pdb=" O LEU q 140 " (cutoff:3.500A) Processing helix chain 'q' and resid 153 through 167 Processing helix chain 'r' and resid 49 through 70 Processing helix chain 'r' and resid 76 through 90 removed outlier: 3.759A pdb=" N GLN r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR r 90 " --> pdb=" O MET r 86 " (cutoff:3.500A) Processing helix chain 'r' and resid 130 through 141 removed outlier: 4.558A pdb=" N VAL r 133 " --> pdb=" O SER r 130 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL r 138 " --> pdb=" O ALA r 135 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET r 139 " --> pdb=" O TYR r 136 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP r 140 " --> pdb=" O GLY r 137 " (cutoff:3.500A) Processing helix chain 'r' and resid 149 through 166 Processing helix chain 'r' and resid 192 through 199 Processing helix chain 's' and resid 58 through 79 Processing helix chain 's' and resid 85 through 99 removed outlier: 3.670A pdb=" N ARG s 99 " --> pdb=" O ILE s 95 " (cutoff:3.500A) Processing helix chain 's' and resid 146 through 152 Processing helix chain 's' and resid 168 through 183 Processing helix chain 't' and resid 57 through 77 Processing helix chain 't' and resid 85 through 102 removed outlier: 3.503A pdb=" N LYS t 102 " --> pdb=" O SER t 98 " (cutoff:3.500A) Processing helix chain 't' and resid 146 through 156 Processing helix chain 't' and resid 162 through 179 Processing helix chain 't' and resid 210 through 213 Processing sheet with id= A, first strand: chain 'a' and resid 290 through 292 Processing sheet with id= B, first strand: chain 'b' and resid 4 through 9 removed outlier: 6.399A pdb=" N LYS b 106 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N MET b 7 " --> pdb=" O LYS b 106 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ARG b 108 " --> pdb=" O MET b 7 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N CYS b 9 " --> pdb=" O ARG b 108 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE b 110 " --> pdb=" O CYS b 9 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ASN b 137 " --> pdb=" O ILE b 109 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N ALA b 111 " --> pdb=" O ASN b 137 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ASP b 139 " --> pdb=" O ALA b 111 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N VAL b 113 " --> pdb=" O ASP b 139 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE b 141 " --> pdb=" O VAL b 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'c' and resid 205 through 207 removed outlier: 6.033A pdb=" N VAL c 31 " --> pdb=" O ASN c 206 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL c 67 " --> pdb=" O TYR c 32 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE c 70 " --> pdb=" O LEU c 58 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU c 58 " --> pdb=" O ILE c 70 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'c' and resid 142 through 144 removed outlier: 3.560A pdb=" N PHE c 160 " --> pdb=" O ALA c 142 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'd' and resid 216 through 218 Processing sheet with id= F, first strand: chain 'U' and resid 788 through 790 removed outlier: 6.855A pdb=" N GLY U 910 " --> pdb=" O ILE U 789 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'Z' and resid 53 through 55 Processing sheet with id= H, first strand: chain 'A' and resid 112 through 114 Processing sheet with id= I, first strand: chain 'A' and resid 213 through 215 removed outlier: 7.937A pdb=" N LEU A 214 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N MET A 319 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N CYS A 270 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LEU A 318 " --> pdb=" O CYS A 270 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE A 272 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ALA A 320 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHE A 274 " --> pdb=" O ALA A 320 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 139 through 142 removed outlier: 4.820A pdb=" N ARG A 139 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 153 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE A 151 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 107 through 111 Processing sheet with id= L, first strand: chain 'B' and resid 120 through 122 Processing sheet with id= M, first strand: chain 'B' and resid 349 through 351 removed outlier: 7.535A pdb=" N VAL B 327 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N LEU B 224 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N MET B 329 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU B 248 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ASP B 285 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL B 250 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 73 through 75 removed outlier: 4.146A pdb=" N ARG C 113 " --> pdb=" O LEU C 127 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 188 through 190 removed outlier: 6.632A pdb=" N ILE C 315 " --> pdb=" O TYR C 189 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.885A pdb=" N ASP D 141 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE D 102 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 202 through 204 Processing sheet with id= R, first strand: chain 'D' and resid 228 through 231 Processing sheet with id= S, first strand: chain 'E' and resid 78 through 81 removed outlier: 6.160A pdb=" N LYS E 72 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL E 60 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 297 through 301 removed outlier: 4.015A pdb=" N ARG E 297 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N MET E 275 " --> pdb=" O CYS E 170 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU E 172 " --> pdb=" O MET E 275 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N MET E 277 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N GLY E 174 " --> pdb=" O MET E 277 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 90 through 92 Processing sheet with id= V, first strand: chain 'F' and resid 122 through 125 Processing sheet with id= W, first strand: chain 'F' and resid 350 through 354 removed outlier: 6.541A pdb=" N ILE F 283 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ALA F 331 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE F 285 " --> pdb=" O ALA F 331 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 166 through 169 Processing sheet with id= Y, first strand: chain 'G' and resid 69 through 71 Processing sheet with id= Z, first strand: chain 'H' and resid 160 through 163 removed outlier: 4.015A pdb=" N MET H 163 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER H 35 " --> pdb=" O MET H 163 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 155 through 157 removed outlier: 3.729A pdb=" N ARG H 143 " --> pdb=" O ASN H 140 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU H 74 " --> pdb=" O PRO H 67 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 43 through 48 Processing sheet with id= AC, first strand: chain 'I' and resid 135 through 138 removed outlier: 3.508A pdb=" N GLY I 138 " --> pdb=" O GLN I 146 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 158 through 160 Processing sheet with id= AE, first strand: chain 'J' and resid 69 through 72 removed outlier: 3.653A pdb=" N VAL J 134 " --> pdb=" O CYS J 70 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU J 144 " --> pdb=" O TRP J 156 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 167 through 169 removed outlier: 3.641A pdb=" N VAL K 50 " --> pdb=" O GLU K 216 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU K 216 " --> pdb=" O VAL K 50 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'K' and resid 75 through 77 Processing sheet with id= AH, first strand: chain 'L' and resid 158 through 161 removed outlier: 3.576A pdb=" N ILE L 212 " --> pdb=" O TYR L 224 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 154 through 156 removed outlier: 4.207A pdb=" N ILE L 144 " --> pdb=" O CYS L 156 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP L 138 " --> pdb=" O GLY L 141 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE L 72 " --> pdb=" O HIS L 65 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N HIS L 65 " --> pdb=" O ILE L 72 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 162 through 165 removed outlier: 3.948A pdb=" N GLY M 44 " --> pdb=" O CYS M 41 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 49 through 51 Processing sheet with id= AL, first strand: chain 'M' and resid 135 through 140 removed outlier: 4.565A pdb=" N LEU M 148 " --> pdb=" O TYR M 160 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= AN, first strand: chain 'N' and resid 34 through 36 removed outlier: 4.206A pdb=" N VAL N 111 " --> pdb=" O GLN N 123 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'N' and resid 20 through 22 removed outlier: 6.024A pdb=" N THR N 22 " --> pdb=" O ILE N 26 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE N 26 " --> pdb=" O THR N 22 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'O' and resid 124 through 128 Processing sheet with id= AQ, first strand: chain 'O' and resid 34 through 36 Processing sheet with id= AR, first strand: chain 'O' and resid 20 through 22 removed outlier: 6.129A pdb=" N GLU O 22 " --> pdb=" O VAL O 26 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL O 26 " --> pdb=" O GLU O 22 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'P' and resid 136 through 140 removed outlier: 6.340A pdb=" N ALA P 10 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL P 185 " --> pdb=" O LEU P 200 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'P' and resid 42 through 44 removed outlier: 3.773A pdb=" N ALA P 54 " --> pdb=" O GLU P 106 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Q' and resid 4 through 8 removed outlier: 4.385A pdb=" N VAL Q 180 " --> pdb=" O LEU Q 191 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Q' and resid 43 through 48 Processing sheet with id= AW, first strand: chain 'R' and resid 125 through 129 removed outlier: 5.631A pdb=" N HIS R 178 " --> pdb=" O ARG R 186 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG R 186 " --> pdb=" O HIS R 178 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'R' and resid 41 through 43 Processing sheet with id= AY, first strand: chain 'R' and resid 20 through 22 removed outlier: 5.601A pdb=" N ALA R 22 " --> pdb=" O ILE R 26 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE R 26 " --> pdb=" O ALA R 22 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'S' and resid 135 through 139 Processing sheet with id= BA, first strand: chain 'S' and resid 130 through 133 removed outlier: 3.667A pdb=" N GLN S 131 " --> pdb=" O SER S 123 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL S 121 " --> pdb=" O ASP S 133 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN S 108 " --> pdb=" O PHE S 124 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR S 50 " --> pdb=" O THR S 47 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE S 52 " --> pdb=" O LYS S 45 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYS S 45 " --> pdb=" O ILE S 52 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N CYS S 54 " --> pdb=" O CYS S 43 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N CYS S 43 " --> pdb=" O CYS S 54 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'S' and resid 29 through 31 removed outlier: 6.207A pdb=" N GLU S 31 " --> pdb=" O ILE S 35 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE S 35 " --> pdb=" O GLU S 31 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'T' and resid 136 through 138 Processing sheet with id= BD, first strand: chain 'T' and resid 49 through 55 Processing sheet with id= BE, first strand: chain 'g' and resid 166 through 169 Processing sheet with id= BF, first strand: chain 'g' and resid 69 through 71 Processing sheet with id= BG, first strand: chain 'h' and resid 36 through 39 Processing sheet with id= BH, first strand: chain 'h' and resid 155 through 157 removed outlier: 3.729A pdb=" N ARG h 143 " --> pdb=" O ASN h 140 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU h 74 " --> pdb=" O PRO h 67 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'i' and resid 43 through 48 Processing sheet with id= BJ, first strand: chain 'i' and resid 135 through 138 removed outlier: 3.507A pdb=" N GLY i 138 " --> pdb=" O GLN i 146 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'j' and resid 158 through 160 Processing sheet with id= BL, first strand: chain 'j' and resid 69 through 72 removed outlier: 3.654A pdb=" N VAL j 134 " --> pdb=" O CYS j 70 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU j 144 " --> pdb=" O TRP j 156 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'k' and resid 167 through 169 removed outlier: 3.640A pdb=" N VAL k 50 " --> pdb=" O GLU k 216 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU k 216 " --> pdb=" O VAL k 50 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'k' and resid 75 through 77 Processing sheet with id= BO, first strand: chain 'l' and resid 158 through 161 removed outlier: 3.575A pdb=" N ILE l 212 " --> pdb=" O TYR l 224 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'l' and resid 154 through 156 removed outlier: 4.206A pdb=" N ILE l 144 " --> pdb=" O CYS l 156 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE l 72 " --> pdb=" O HIS l 65 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N HIS l 65 " --> pdb=" O ILE l 72 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'm' and resid 162 through 165 removed outlier: 3.948A pdb=" N GLY m 44 " --> pdb=" O CYS m 41 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'm' and resid 49 through 51 Processing sheet with id= BS, first strand: chain 'm' and resid 135 through 140 removed outlier: 4.564A pdb=" N LEU m 148 " --> pdb=" O TYR m 160 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'n' and resid 3 through 7 Processing sheet with id= BU, first strand: chain 'n' and resid 34 through 36 removed outlier: 4.207A pdb=" N VAL n 111 " --> pdb=" O GLN n 123 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'n' and resid 20 through 22 removed outlier: 6.023A pdb=" N THR n 22 " --> pdb=" O ILE n 26 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE n 26 " --> pdb=" O THR n 22 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'o' and resid 124 through 128 Processing sheet with id= BX, first strand: chain 'o' and resid 34 through 36 Processing sheet with id= BY, first strand: chain 'o' and resid 20 through 22 removed outlier: 6.129A pdb=" N GLU o 22 " --> pdb=" O VAL o 26 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL o 26 " --> pdb=" O GLU o 22 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'p' and resid 136 through 140 removed outlier: 6.339A pdb=" N ALA p 10 " --> pdb=" O ASP p 25 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL p 185 " --> pdb=" O LEU p 200 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'p' and resid 42 through 44 removed outlier: 3.772A pdb=" N ALA p 54 " --> pdb=" O GLU p 106 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'q' and resid 4 through 8 removed outlier: 4.385A pdb=" N VAL q 180 " --> pdb=" O LEU q 191 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'q' and resid 43 through 48 Processing sheet with id= CD, first strand: chain 'r' and resid 125 through 129 removed outlier: 5.631A pdb=" N HIS r 178 " --> pdb=" O ARG r 186 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ARG r 186 " --> pdb=" O HIS r 178 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'r' and resid 41 through 43 Processing sheet with id= CF, first strand: chain 'r' and resid 20 through 22 removed outlier: 5.602A pdb=" N ALA r 22 " --> pdb=" O ILE r 26 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE r 26 " --> pdb=" O ALA r 22 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 's' and resid 135 through 139 removed outlier: 6.082A pdb=" N THR s 11 " --> pdb=" O ASP s 26 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP s 26 " --> pdb=" O THR s 11 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 's' and resid 130 through 133 removed outlier: 3.667A pdb=" N GLN s 131 " --> pdb=" O SER s 123 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL s 121 " --> pdb=" O ASP s 133 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN s 108 " --> pdb=" O PHE s 124 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR s 50 " --> pdb=" O THR s 47 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE s 52 " --> pdb=" O LYS s 45 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYS s 45 " --> pdb=" O ILE s 52 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N CYS s 54 " --> pdb=" O CYS s 43 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N CYS s 43 " --> pdb=" O CYS s 54 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 's' and resid 29 through 31 removed outlier: 6.207A pdb=" N GLU s 31 " --> pdb=" O ILE s 35 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE s 35 " --> pdb=" O GLU s 31 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 't' and resid 136 through 138 Processing sheet with id= CK, first strand: chain 't' and resid 49 through 55 4103 hydrogen bonds defined for protein. 11445 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: 42.40 Time building geometry restraints manager: 37.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 33714 1.36 - 1.51: 29355 1.51 - 1.65: 37589 1.65 - 1.80: 698 1.80 - 1.95: 270 Bond restraints: 101626 Sorted by residual: bond pdb=" O1G ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 1.491 1.946 -0.455 2.00e-02 2.50e+03 5.18e+02 bond pdb=" O1G ATP D 502 " pdb=" PG ATP D 502 " ideal model delta sigma weight residual 1.491 1.946 -0.455 2.00e-02 2.50e+03 5.17e+02 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.83e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.42e+01 bond pdb=" C5 ATP B 501 " pdb=" C6 ATP B 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.35e+01 ... (remaining 101621 not shown) Histogram of bond angle deviations from ideal: 95.21 - 103.44: 1188 103.44 - 111.67: 45208 111.67 - 119.89: 45046 119.89 - 128.12: 45359 128.12 - 136.35: 669 Bond angle restraints: 137470 Sorted by residual: angle pdb=" PB ATP D 502 " pdb=" O3B ATP D 502 " pdb=" PG ATP D 502 " ideal model delta sigma weight residual 139.87 113.47 26.40 1.00e+00 1.00e+00 6.97e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 114.22 25.65 1.00e+00 1.00e+00 6.58e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 113.68 23.15 1.00e+00 1.00e+00 5.36e+02 angle pdb=" PA ATP E 401 " pdb=" O3A ATP E 401 " pdb=" PB ATP E 401 " ideal model delta sigma weight residual 136.83 113.70 23.13 1.00e+00 1.00e+00 5.35e+02 angle pdb=" PA ATP D 502 " pdb=" O3A ATP D 502 " pdb=" PB ATP D 502 " ideal model delta sigma weight residual 136.83 113.86 22.97 1.00e+00 1.00e+00 5.28e+02 ... (remaining 137465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 58426 17.98 - 35.96: 2720 35.96 - 53.94: 567 53.94 - 71.91: 117 71.91 - 89.89: 67 Dihedral angle restraints: 61897 sinusoidal: 24558 harmonic: 37339 Sorted by residual: dihedral pdb=" N ASP D 318 " pdb=" C ASP D 318 " pdb=" CA ASP D 318 " pdb=" CB ASP D 318 " ideal model delta harmonic sigma weight residual 122.80 150.29 -27.49 0 2.50e+00 1.60e-01 1.21e+02 dihedral pdb=" C ASP D 318 " pdb=" N ASP D 318 " pdb=" CA ASP D 318 " pdb=" CB ASP D 318 " ideal model delta harmonic sigma weight residual -122.60 -148.07 25.47 0 2.50e+00 1.60e-01 1.04e+02 dihedral pdb=" CA GLU D 146 " pdb=" C GLU D 146 " pdb=" N ALA D 147 " pdb=" CA ALA D 147 " ideal model delta harmonic sigma weight residual -180.00 -150.02 -29.98 0 5.00e+00 4.00e-02 3.59e+01 ... (remaining 61894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.218: 15542 0.218 - 0.436: 105 0.436 - 0.654: 5 0.654 - 0.872: 0 0.872 - 1.090: 1 Chirality restraints: 15653 Sorted by residual: chirality pdb=" CA ASP D 318 " pdb=" N ASP D 318 " pdb=" C ASP D 318 " pdb=" CB ASP D 318 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.97e+01 chirality pdb=" CB ILE V 466 " pdb=" CA ILE V 466 " pdb=" CG1 ILE V 466 " pdb=" CG2 ILE V 466 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.56 2.00e-01 2.50e+01 7.74e+00 chirality pdb=" CA PHE D 299 " pdb=" N PHE D 299 " pdb=" C PHE D 299 " pdb=" CB PHE D 299 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.40e+00 ... (remaining 15650 not shown) Planarity restraints: 17764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 415 " -0.026 2.00e-02 2.50e+03 5.52e-02 3.04e+01 pdb=" C GLU D 415 " 0.095 2.00e-02 2.50e+03 pdb=" O GLU D 415 " -0.038 2.00e-02 2.50e+03 pdb=" N PHE D 416 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN V 193 " -0.026 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C GLN V 193 " 0.092 2.00e-02 2.50e+03 pdb=" O GLN V 193 " -0.035 2.00e-02 2.50e+03 pdb=" N LYS V 194 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 338 " 0.023 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" C ARG D 338 " -0.083 2.00e-02 2.50e+03 pdb=" O ARG D 338 " 0.032 2.00e-02 2.50e+03 pdb=" N ARG D 339 " 0.027 2.00e-02 2.50e+03 ... (remaining 17761 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.79: 66 1.79 - 2.57: 1636 2.57 - 3.35: 132821 3.35 - 4.12: 255789 4.12 - 4.90: 445809 Nonbonded interactions: 836121 Sorted by model distance: nonbonded pdb=" N SER c 150 " pdb=" NZ LYS c 154 " model vdw 1.015 3.200 nonbonded pdb=" N ASP E 250 " pdb=" OE1 GLU F 299 " model vdw 1.056 2.520 nonbonded pdb=" CE2 TYR J 3 " pdb=" NH2 ARG K 10 " model vdw 1.143 3.420 nonbonded pdb=" O ALA X 311 " pdb=" CD ARG X 314 " model vdw 1.179 3.440 nonbonded pdb=" CA ALA X 311 " pdb=" NH1 ARG X 314 " model vdw 1.200 3.550 ... (remaining 836116 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'G' selection = (chain 'g' and resid 6 through 244) } ncs_group { reference = chain 'H' selection = (chain 'h' and resid 5 through 234) } ncs_group { reference = chain 'I' selection = (chain 'i' and resid 4 through 251) } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = (chain 'K' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 241)) selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'O' selection = chain 'o' } ncs_group { reference = chain 'P' selection = chain 'p' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'R' selection = chain 'r' } ncs_group { reference = chain 'S' selection = chain 's' } ncs_group { reference = chain 'T' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 11.270 Check model and map are aligned: 1.080 Set scattering table: 0.710 Process input model: 213.550 Find NCS groups from input model: 6.200 Set up NCS constraints: 0.980 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 238.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.455 101626 Z= 0.467 Angle : 1.208 26.396 137470 Z= 0.699 Chirality : 0.064 1.090 15653 Planarity : 0.008 0.092 17764 Dihedral : 11.956 89.892 37859 Min Nonbonded Distance : 1.015 Molprobity Statistics. All-atom Clashscore : 21.97 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.27 % Favored : 88.89 % Rotamer: Outliers : 1.70 % Allowed : 3.77 % Favored : 94.53 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.06), residues: 12733 helix: -3.12 (0.05), residues: 5446 sheet: -2.07 (0.12), residues: 1670 loop : -3.24 (0.07), residues: 5617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP k 100 HIS 0.020 0.003 HIS l 190 PHE 0.043 0.004 PHE U 728 TYR 0.051 0.003 TYR Y 54 ARG 0.018 0.001 ARG U 616 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1780 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1600 time to evaluate : 9.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 87 MET cc_start: 0.5318 (mtp) cc_final: 0.4958 (mtp) REVERT: a 124 ASN cc_start: 0.9023 (m110) cc_final: 0.8637 (t0) REVERT: a 312 MET cc_start: 0.8474 (mtm) cc_final: 0.8233 (mtp) REVERT: b 1 MET cc_start: 0.0791 (mmt) cc_final: -0.1897 (ppp) REVERT: b 7 MET cc_start: 0.3300 (tpt) cc_final: 0.3053 (tpp) REVERT: b 86 PHE cc_start: 0.7436 (t80) cc_final: 0.6571 (t80) REVERT: b 90 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8736 (pt) REVERT: c 72 VAL cc_start: 0.8017 (t) cc_final: 0.7165 (p) REVERT: c 75 MET cc_start: 0.4271 (mmm) cc_final: 0.3841 (mmm) REVERT: c 95 MET cc_start: 0.9010 (tpt) cc_final: 0.8806 (tmm) REVERT: c 98 MET cc_start: 0.8696 (mtt) cc_final: 0.3661 (mtt) REVERT: c 160 PHE cc_start: 0.8868 (m-80) cc_final: 0.8516 (m-80) REVERT: c 194 HIS cc_start: 0.9047 (t70) cc_final: 0.8688 (t-170) REVERT: c 197 ASN cc_start: 0.8793 (t0) cc_final: 0.8512 (m-40) REVERT: c 216 MET cc_start: 0.8726 (ptm) cc_final: 0.8448 (ptp) REVERT: c 226 MET cc_start: 0.9121 (tpp) cc_final: 0.8373 (tmm) REVERT: c 289 ASP cc_start: 0.9163 (m-30) cc_final: 0.8945 (p0) REVERT: d 1 MET cc_start: 0.4569 (ttt) cc_final: 0.4175 (tpp) REVERT: d 67 ASP cc_start: 0.8560 (t0) cc_final: 0.8307 (t0) REVERT: d 162 SER cc_start: 0.8544 (OUTLIER) cc_final: 0.8150 (t) REVERT: e 55 GLN cc_start: 0.1384 (OUTLIER) cc_final: 0.1081 (tm-30) REVERT: f 33 ARG cc_start: 0.7080 (mpt90) cc_final: 0.6504 (tpt90) REVERT: f 88 SER cc_start: 0.3748 (OUTLIER) cc_final: 0.3147 (t) REVERT: f 477 MET cc_start: 0.6860 (ttm) cc_final: 0.6596 (ttp) REVERT: f 512 MET cc_start: 0.5849 (tpt) cc_final: 0.4591 (tpt) REVERT: f 557 TRP cc_start: 0.7644 (m-10) cc_final: 0.7226 (m-10) REVERT: U 206 MET cc_start: 0.6687 (mmp) cc_final: 0.6482 (mmp) REVERT: U 355 ASN cc_start: 0.7787 (m110) cc_final: 0.7332 (t0) REVERT: U 456 ASP cc_start: 0.9661 (t0) cc_final: 0.9413 (p0) REVERT: U 470 ASN cc_start: 0.8458 (m-40) cc_final: 0.8072 (t0) REVERT: U 583 MET cc_start: 0.8943 (mmm) cc_final: 0.8674 (mmm) REVERT: U 675 MET cc_start: 0.9326 (mmm) cc_final: 0.9122 (tpp) REVERT: U 725 MET cc_start: 0.8579 (ttm) cc_final: 0.8188 (tpp) REVERT: U 761 VAL cc_start: 0.8999 (t) cc_final: 0.7990 (t) REVERT: U 770 TRP cc_start: 0.6105 (m-90) cc_final: 0.5809 (m-10) REVERT: U 797 MET cc_start: 0.7617 (ptp) cc_final: 0.7358 (mpp) REVERT: U 913 ILE cc_start: 0.2569 (OUTLIER) cc_final: 0.2270 (mt) REVERT: V 100 MET cc_start: 0.6140 (mtp) cc_final: 0.5869 (mtt) REVERT: V 175 MET cc_start: 0.7172 (mtt) cc_final: 0.6700 (mtt) REVERT: V 358 MET cc_start: 0.8887 (mmm) cc_final: 0.8654 (mtt) REVERT: V 448 GLU cc_start: 0.6068 (OUTLIER) cc_final: 0.4859 (pm20) REVERT: W 16 MET cc_start: -0.0118 (mmt) cc_final: -0.0636 (mmp) REVERT: W 88 MET cc_start: 0.3972 (mtm) cc_final: 0.3430 (mtt) REVERT: W 137 TYR cc_start: 0.7619 (t80) cc_final: 0.6987 (t80) REVERT: W 312 MET cc_start: 0.4631 (ttt) cc_final: 0.4402 (tpt) REVERT: W 313 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.5994 (mm-30) REVERT: W 418 PRO cc_start: 0.9376 (Cg_exo) cc_final: 0.9119 (Cg_endo) REVERT: X 225 TRP cc_start: 0.6533 (t-100) cc_final: 0.5013 (m100) REVERT: X 253 TYR cc_start: 0.8923 (m-80) cc_final: 0.8471 (m-80) REVERT: X 254 MET cc_start: 0.7798 (ptp) cc_final: 0.6837 (ttt) REVERT: X 395 LYS cc_start: 0.8941 (ttpp) cc_final: 0.8714 (mmpt) REVERT: X 401 LEU cc_start: 0.9594 (mt) cc_final: 0.9150 (pp) REVERT: Y 368 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8878 (tp30) REVERT: Y 369 THR cc_start: 0.9100 (p) cc_final: 0.8868 (t) REVERT: Y 372 LYS cc_start: 0.9638 (mmmt) cc_final: 0.9107 (mtmt) REVERT: Z 7 GLN cc_start: 0.9377 (tt0) cc_final: 0.9170 (tp-100) REVERT: Z 68 TRP cc_start: 0.5917 (p-90) cc_final: 0.5545 (p-90) REVERT: Z 225 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6770 (pm20) REVERT: A 325 ASP cc_start: 0.7816 (t0) cc_final: 0.7587 (p0) REVERT: A 362 MET cc_start: 0.7799 (ptm) cc_final: 0.7510 (ptt) REVERT: A 389 CYS cc_start: 0.9278 (m) cc_final: 0.7502 (m) REVERT: A 423 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.7121 (p90) REVERT: B 385 MET cc_start: 0.8579 (tmt) cc_final: 0.7797 (ptm) REVERT: C 87 VAL cc_start: 0.9736 (t) cc_final: 0.9362 (p) REVERT: C 94 LYS cc_start: 0.8613 (mtmm) cc_final: 0.8379 (mmmt) REVERT: C 95 PHE cc_start: 0.8905 (m-80) cc_final: 0.8682 (m-80) REVERT: C 130 LYS cc_start: 0.8675 (mmpt) cc_final: 0.8189 (mttt) REVERT: C 221 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7841 (mt0) REVERT: C 237 MET cc_start: 0.6875 (ptm) cc_final: 0.6138 (ptm) REVERT: C 377 HIS cc_start: 0.8524 (m90) cc_final: 0.8299 (p-80) REVERT: D 59 GLU cc_start: 0.9592 (tt0) cc_final: 0.9327 (tm-30) REVERT: D 170 MET cc_start: 0.7482 (ttm) cc_final: 0.7138 (tpp) REVERT: D 296 MET cc_start: 0.9098 (tpt) cc_final: 0.8641 (tmm) REVERT: D 333 PHE cc_start: 0.8918 (m-10) cc_final: 0.8414 (m-80) REVERT: D 409 LYS cc_start: 0.3902 (OUTLIER) cc_final: 0.3170 (mmmt) REVERT: E 258 MET cc_start: 0.9575 (mtm) cc_final: 0.9321 (mtp) REVERT: E 262 ASN cc_start: 0.9627 (t0) cc_final: 0.8886 (p0) REVERT: E 302 ASP cc_start: 0.9387 (m-30) cc_final: 0.8976 (t70) REVERT: E 336 ASP cc_start: 0.8458 (t0) cc_final: 0.8126 (p0) REVERT: F 259 MET cc_start: -0.3088 (ttt) cc_final: -0.3562 (ptp) REVERT: F 405 MET cc_start: 0.8810 (mtm) cc_final: 0.8536 (mtt) REVERT: F 432 LYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6223 (tttt) REVERT: G 209 ASP cc_start: 0.8001 (m-30) cc_final: 0.7583 (t0) REVERT: H 46 LEU cc_start: 0.9518 (mt) cc_final: 0.9314 (mp) REVERT: H 64 LYS cc_start: 0.8207 (mmtp) cc_final: 0.7806 (mttt) REVERT: H 197 GLU cc_start: 0.9364 (tp30) cc_final: 0.9044 (tt0) REVERT: I 99 LEU cc_start: 0.9489 (tp) cc_final: 0.9231 (tp) REVERT: I 166 ASN cc_start: 0.9015 (t0) cc_final: 0.8390 (p0) REVERT: J 66 ASP cc_start: 0.8125 (t0) cc_final: 0.7675 (p0) REVERT: K 52 LYS cc_start: 0.8853 (mttp) cc_final: 0.8454 (mmtm) REVERT: K 65 GLU cc_start: 0.9192 (pm20) cc_final: 0.8562 (tp30) REVERT: K 142 LEU cc_start: 0.8619 (mt) cc_final: 0.8273 (mm) REVERT: K 206 MET cc_start: 0.8907 (ptp) cc_final: 0.8349 (ptt) REVERT: L 132 LEU cc_start: 0.9372 (mt) cc_final: 0.9060 (tp) REVERT: L 228 ASP cc_start: 0.9139 (m-30) cc_final: 0.8732 (t0) REVERT: M 181 MET cc_start: 0.8743 (ptp) cc_final: 0.8345 (ptp) REVERT: M 241 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8150 (tt0) REVERT: N 32 ASP cc_start: 0.9251 (m-30) cc_final: 0.8572 (t0) REVERT: N 84 LYS cc_start: 0.9519 (ttpp) cc_final: 0.8929 (ttpp) REVERT: N 85 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8527 (mt-10) REVERT: N 92 GLU cc_start: 0.9451 (OUTLIER) cc_final: 0.9185 (mp0) REVERT: N 179 ILE cc_start: 0.9559 (mt) cc_final: 0.9312 (mt) REVERT: O 22 GLU cc_start: 0.8963 (tt0) cc_final: 0.8654 (mm-30) REVERT: O 64 GLU cc_start: 0.9434 (tt0) cc_final: 0.9161 (mt-10) REVERT: O 194 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8917 (mmtm) REVERT: P 12 MET cc_start: 0.9108 (ttm) cc_final: 0.8784 (mtp) REVERT: P 39 PHE cc_start: 0.8811 (t80) cc_final: 0.8156 (t80) REVERT: P 90 MET cc_start: 0.9197 (ttm) cc_final: 0.8613 (mmp) REVERT: P 117 PHE cc_start: 0.8013 (p90) cc_final: 0.7134 (p90) REVERT: P 118 LYS cc_start: 0.9504 (ttmm) cc_final: 0.9238 (mmmt) REVERT: P 171 MET cc_start: 0.9702 (mmm) cc_final: 0.9204 (mmm) REVERT: Q 4 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8098 (pp) REVERT: Q 69 MET cc_start: 0.8673 (mmm) cc_final: 0.8269 (mmt) REVERT: Q 75 LEU cc_start: 0.9187 (mt) cc_final: 0.8749 (tp) REVERT: Q 124 LEU cc_start: 0.7768 (mt) cc_final: 0.7556 (mt) REVERT: R 54 PHE cc_start: 0.9442 (t80) cc_final: 0.9240 (t80) REVERT: R 139 MET cc_start: 0.9443 (ttp) cc_final: 0.9094 (tmm) REVERT: S 48 ASP cc_start: 0.8805 (m-30) cc_final: 0.8439 (p0) REVERT: S 91 MET cc_start: 0.9043 (ttp) cc_final: 0.8608 (tpt) REVERT: S 96 LEU cc_start: 0.9655 (mt) cc_final: 0.9446 (tp) REVERT: S 144 MET cc_start: 0.9339 (mtt) cc_final: 0.8870 (mmm) REVERT: T 60 PHE cc_start: 0.9334 (t80) cc_final: 0.8921 (t80) REVERT: T 108 ASN cc_start: 0.8339 (m110) cc_final: 0.7869 (m-40) REVERT: T 127 MET cc_start: 0.8366 (ttp) cc_final: 0.8041 (tmm) REVERT: T 173 MET cc_start: 0.9554 (mmm) cc_final: 0.9226 (ptp) REVERT: g 80 MET cc_start: 0.5779 (mmm) cc_final: 0.5210 (mmm) REVERT: g 103 TYR cc_start: 0.9506 (t80) cc_final: 0.9282 (t80) REVERT: g 134 LEU cc_start: 0.9525 (mt) cc_final: 0.9231 (pp) REVERT: g 202 LEU cc_start: 0.9774 (tt) cc_final: 0.9521 (pp) REVERT: h 8 PHE cc_start: 0.5402 (OUTLIER) cc_final: 0.4659 (m-10) REVERT: h 113 ARG cc_start: 0.8975 (mtt-85) cc_final: 0.8772 (mmt90) REVERT: h 206 ASP cc_start: 0.8590 (m-30) cc_final: 0.7926 (p0) REVERT: i 44 LEU cc_start: 0.8752 (pp) cc_final: 0.8147 (tp) REVERT: i 172 VAL cc_start: 0.9328 (t) cc_final: 0.8813 (t) REVERT: j 43 LEU cc_start: 0.9842 (pp) cc_final: 0.9455 (mp) REVERT: j 71 MET cc_start: 0.9158 (mmp) cc_final: 0.8937 (mmp) REVERT: k 66 LYS cc_start: 0.8999 (mmtt) cc_final: 0.8643 (mmtt) REVERT: k 78 MET cc_start: 0.8919 (ptp) cc_final: 0.8193 (ppp) REVERT: l 6 TYR cc_start: 0.8123 (p90) cc_final: 0.7777 (p90) REVERT: l 27 GLU cc_start: 0.9707 (mm-30) cc_final: 0.9470 (mt-10) REVERT: l 195 LEU cc_start: 0.9394 (mp) cc_final: 0.9189 (mp) REVERT: m 75 MET cc_start: 0.9416 (mtp) cc_final: 0.8699 (mtp) REVERT: m 135 PHE cc_start: 0.9369 (p90) cc_final: 0.9154 (p90) REVERT: m 187 ARG cc_start: 0.9313 (ttp-110) cc_final: 0.8942 (tpp-160) REVERT: n 4 MET cc_start: 0.9225 (ttt) cc_final: 0.8993 (tmm) REVERT: n 57 ASP cc_start: 0.9591 (m-30) cc_final: 0.9254 (m-30) REVERT: n 63 LEU cc_start: 0.9146 (tp) cc_final: 0.8609 (tt) REVERT: n 87 CYS cc_start: 0.9635 (m) cc_final: 0.9299 (t) REVERT: o 54 MET cc_start: 0.9527 (mmm) cc_final: 0.9166 (mmm) REVERT: o 127 MET cc_start: 0.9049 (mmm) cc_final: 0.7881 (mtt) REVERT: p 14 MET cc_start: 0.9379 (ttm) cc_final: 0.9127 (ttp) REVERT: p 45 MET cc_start: 0.9416 (mmm) cc_final: 0.9197 (mmm) REVERT: p 50 TYR cc_start: 0.8469 (m-10) cc_final: 0.8241 (m-10) REVERT: p 75 GLU cc_start: 0.9334 (mt-10) cc_final: 0.9072 (mm-30) REVERT: p 82 ILE cc_start: 0.8252 (tt) cc_final: 0.7862 (tt) REVERT: p 96 TYR cc_start: 0.9541 (t80) cc_final: 0.9290 (t80) REVERT: p 126 LEU cc_start: 0.8564 (pp) cc_final: 0.8103 (mt) REVERT: p 144 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8848 (mt-10) REVERT: q 24 ASN cc_start: 0.8642 (t0) cc_final: 0.8252 (p0) REVERT: q 35 MET cc_start: 0.8180 (mtt) cc_final: 0.7979 (mtt) REVERT: s 74 MET cc_start: 0.9559 (mtp) cc_final: 0.9271 (mtp) REVERT: t 26 MET cc_start: 0.8172 (mtp) cc_final: 0.7759 (mtt) REVERT: t 51 LEU cc_start: 0.9647 (tp) cc_final: 0.9409 (tp) REVERT: t 72 ILE cc_start: 0.9771 (mt) cc_final: 0.9562 (mt) REVERT: t 112 ILE cc_start: 0.9479 (mt) cc_final: 0.8681 (tp) outliers start: 180 outliers final: 82 residues processed: 1770 average time/residue: 1.0016 time to fit residues: 2982.6166 Evaluate side-chains 945 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 849 time to evaluate : 8.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1267 random chunks: chunk 1069 optimal weight: 8.9990 chunk 960 optimal weight: 20.0000 chunk 532 optimal weight: 5.9990 chunk 328 optimal weight: 8.9990 chunk 647 optimal weight: 8.9990 chunk 513 optimal weight: 6.9990 chunk 993 optimal weight: 7.9990 chunk 384 optimal weight: 7.9990 chunk 603 optimal weight: 5.9990 chunk 739 optimal weight: 30.0000 chunk 1150 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 241 ASN ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 GLN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 199 HIS c 221 HIS c 256 ASN c 287 HIS c 295 ASN ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 15 GLN f 51 GLN f 102 HIS f 329 ASN f 387 GLN f 405 HIS ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 473 ASN f 475 ASN f 747 GLN U 89 ASN U 247 GLN U 389 ASN U 421 GLN U 500 ASN U 541 HIS U 596 ASN ** U 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 721 HIS U 880 ASN V 260 HIS V 459 GLN ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 84 ASN W 86 ASN ** W 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 362 ASN ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 440 ASN X 296 ASN X 334 ASN ** X 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 367 GLN ** Z 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN C 270 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 HIS ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 HIS D 135 HIS ** D 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 HIS ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 HIS E 339 ASN F 214 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 GLN L 86 ASN ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 HIS N 28 ASN N 66 HIS O 62 ASN P 169 GLN ** Q 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN Q 101 ASN ** Q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS T 65 GLN T 213 HIS ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 112 GLN ** i 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 120 GLN ** j 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 215 GLN ** k 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 101 ASN m 110 HIS n 28 ASN ** n 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 HIS n 154 GLN o 62 ASN p 169 GLN q 27 GLN ** q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 101 ASN ** q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 186 ASN r 10 HIS r 119 ASN ** r 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 160 ASN t 213 HIS Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 101626 Z= 0.319 Angle : 0.817 16.567 137470 Z= 0.432 Chirality : 0.046 0.400 15653 Planarity : 0.006 0.086 17764 Dihedral : 7.960 89.540 14167 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 26.04 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.60 % Favored : 90.20 % Rotamer: Outliers : 0.14 % Allowed : 3.14 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.30 (0.07), residues: 12733 helix: -1.61 (0.06), residues: 5546 sheet: -1.58 (0.12), residues: 1661 loop : -2.97 (0.08), residues: 5526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 103 HIS 0.012 0.002 HIS k 186 PHE 0.037 0.002 PHE B 271 TYR 0.025 0.002 TYR a 156 ARG 0.017 0.001 ARG N 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1005 time to evaluate : 9.801 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: a 87 MET cc_start: 0.5487 (mtp) cc_final: 0.4989 (ttp) REVERT: a 312 MET cc_start: 0.8699 (mtm) cc_final: 0.8128 (mpp) REVERT: b 1 MET cc_start: 0.1120 (mmt) cc_final: -0.1457 (ppp) REVERT: b 86 PHE cc_start: 0.7627 (t80) cc_final: 0.6856 (t80) REVERT: b 163 LYS cc_start: 0.7387 (mmtt) cc_final: 0.6957 (ptpp) REVERT: c 54 MET cc_start: 0.8073 (pmm) cc_final: 0.7601 (pmm) REVERT: c 75 MET cc_start: 0.4386 (mmm) cc_final: 0.4135 (mmm) REVERT: c 160 PHE cc_start: 0.8942 (m-80) cc_final: 0.8658 (m-80) REVERT: c 197 ASN cc_start: 0.9045 (t0) cc_final: 0.8706 (m-40) REVERT: c 216 MET cc_start: 0.8838 (ptm) cc_final: 0.8602 (ptp) REVERT: c 226 MET cc_start: 0.9107 (tpp) cc_final: 0.8471 (tmm) REVERT: c 256 ASN cc_start: 0.9368 (m110) cc_final: 0.8803 (p0) REVERT: d 1 MET cc_start: 0.5836 (ttt) cc_final: 0.4879 (tpp) REVERT: d 67 ASP cc_start: 0.8634 (t0) cc_final: 0.8430 (t0) REVERT: f 33 ARG cc_start: 0.7239 (mpt90) cc_final: 0.6409 (tpt90) REVERT: f 185 LEU cc_start: 0.3871 (mt) cc_final: 0.3388 (pt) REVERT: f 370 MET cc_start: 0.6517 (mmt) cc_final: 0.5799 (mmp) REVERT: f 512 MET cc_start: 0.6306 (tpt) cc_final: 0.5762 (tpt) REVERT: f 557 TRP cc_start: 0.7795 (m-10) cc_final: 0.7391 (m100) REVERT: U 206 MET cc_start: 0.6897 (mmp) cc_final: 0.6547 (mmp) REVERT: U 351 MET cc_start: 0.8361 (ptp) cc_final: 0.8055 (ptp) REVERT: U 355 ASN cc_start: 0.7767 (m110) cc_final: 0.7220 (t0) REVERT: U 423 MET cc_start: 0.8365 (mmp) cc_final: 0.8029 (mmp) REVERT: U 456 ASP cc_start: 0.9423 (t0) cc_final: 0.9176 (p0) REVERT: U 470 ASN cc_start: 0.8697 (m-40) cc_final: 0.8232 (t0) REVERT: U 556 MET cc_start: 0.7911 (mmt) cc_final: 0.7640 (mmm) REVERT: U 560 MET cc_start: 0.8419 (mmt) cc_final: 0.7794 (mmm) REVERT: U 583 MET cc_start: 0.8847 (mmm) cc_final: 0.8612 (mmm) REVERT: U 654 MET cc_start: 0.9215 (mmp) cc_final: 0.8919 (mmm) REVERT: U 797 MET cc_start: 0.7741 (ptp) cc_final: 0.7441 (mpp) REVERT: U 885 MET cc_start: 0.5764 (mmt) cc_final: 0.5541 (mpp) REVERT: V 139 MET cc_start: 0.7868 (ptt) cc_final: 0.7595 (ppp) REVERT: V 142 GLU cc_start: 0.8848 (pt0) cc_final: 0.8645 (pm20) REVERT: V 255 LEU cc_start: 0.9477 (mp) cc_final: 0.9136 (pp) REVERT: V 358 MET cc_start: 0.9062 (mmm) cc_final: 0.8784 (mtt) REVERT: X 253 TYR cc_start: 0.8949 (m-80) cc_final: 0.8654 (m-80) REVERT: X 254 MET cc_start: 0.7696 (ptp) cc_final: 0.7449 (ttt) REVERT: X 257 CYS cc_start: 0.7733 (t) cc_final: 0.7353 (t) REVERT: X 260 MET cc_start: 0.4054 (tmm) cc_final: 0.3726 (tmm) REVERT: X 374 PHE cc_start: 0.9081 (t80) cc_final: 0.8448 (t80) REVERT: X 395 LYS cc_start: 0.8846 (ttpp) cc_final: 0.8634 (mmpt) REVERT: X 401 LEU cc_start: 0.9689 (mt) cc_final: 0.9471 (pp) REVERT: Y 40 GLU cc_start: 0.8672 (tt0) cc_final: 0.8161 (mt-10) REVERT: Y 364 TRP cc_start: 0.9439 (m-90) cc_final: 0.9226 (m-90) REVERT: Z 78 MET cc_start: 0.9146 (tpp) cc_final: 0.8158 (mtt) REVERT: A 256 MET cc_start: 0.8693 (mmp) cc_final: 0.8208 (mmp) REVERT: A 299 MET cc_start: 0.7781 (ptp) cc_final: 0.7541 (ptp) REVERT: A 325 ASP cc_start: 0.7933 (t0) cc_final: 0.7701 (p0) REVERT: A 389 CYS cc_start: 0.9120 (m) cc_final: 0.8824 (m) REVERT: B 405 MET cc_start: 0.7765 (mmp) cc_final: 0.7295 (mmp) REVERT: C 57 ARG cc_start: 0.9444 (ttt180) cc_final: 0.8684 (ttp-170) REVERT: C 87 VAL cc_start: 0.9674 (t) cc_final: 0.9398 (p) REVERT: C 221 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7763 (mt0) REVERT: C 377 HIS cc_start: 0.8502 (m-70) cc_final: 0.8211 (p-80) REVERT: D 59 GLU cc_start: 0.9603 (tt0) cc_final: 0.9331 (tm-30) REVERT: D 187 HIS cc_start: 0.9498 (m-70) cc_final: 0.9228 (m-70) REVERT: D 296 MET cc_start: 0.9326 (tpt) cc_final: 0.8836 (tmm) REVERT: D 333 PHE cc_start: 0.8735 (m-10) cc_final: 0.8485 (m-10) REVERT: D 416 PHE cc_start: 0.6695 (t80) cc_final: 0.6410 (t80) REVERT: E 302 ASP cc_start: 0.9386 (m-30) cc_final: 0.8895 (t70) REVERT: E 336 ASP cc_start: 0.8615 (t0) cc_final: 0.8355 (m-30) REVERT: E 382 SER cc_start: 0.4195 (p) cc_final: 0.3776 (t) REVERT: G 125 TYR cc_start: 0.9440 (m-80) cc_final: 0.8844 (m-80) REVERT: G 138 MET cc_start: 0.9500 (ttm) cc_final: 0.9174 (ttt) REVERT: G 209 ASP cc_start: 0.7931 (m-30) cc_final: 0.7631 (t0) REVERT: H 38 ILE cc_start: 0.9037 (mm) cc_final: 0.8786 (tp) REVERT: H 121 TYR cc_start: 0.8246 (m-80) cc_final: 0.7918 (m-80) REVERT: H 197 GLU cc_start: 0.9456 (tp30) cc_final: 0.9228 (tt0) REVERT: I 72 MET cc_start: 0.7471 (mmp) cc_final: 0.7165 (mmm) REVERT: I 99 LEU cc_start: 0.9577 (tp) cc_final: 0.9322 (tp) REVERT: I 130 PHE cc_start: 0.8726 (m-10) cc_final: 0.8449 (m-10) REVERT: I 166 ASN cc_start: 0.8995 (t0) cc_final: 0.8348 (p0) REVERT: J 66 ASP cc_start: 0.8465 (t0) cc_final: 0.7844 (p0) REVERT: J 132 LEU cc_start: 0.9512 (tt) cc_final: 0.8855 (mm) REVERT: J 159 ASN cc_start: 0.7835 (t0) cc_final: 0.7122 (t0) REVERT: K 65 GLU cc_start: 0.9240 (pm20) cc_final: 0.8788 (tp30) REVERT: K 156 MET cc_start: 0.9265 (ptm) cc_final: 0.8971 (ppp) REVERT: K 206 MET cc_start: 0.8312 (ptp) cc_final: 0.8049 (ptt) REVERT: L 88 MET cc_start: 0.9730 (ttp) cc_final: 0.9381 (ttp) REVERT: L 132 LEU cc_start: 0.9415 (mt) cc_final: 0.9073 (tp) REVERT: L 176 MET cc_start: 0.8688 (ptp) cc_final: 0.8380 (ptp) REVERT: L 228 ASP cc_start: 0.9027 (m-30) cc_final: 0.8730 (t0) REVERT: M 181 MET cc_start: 0.8621 (ptp) cc_final: 0.8040 (pmm) REVERT: N 32 ASP cc_start: 0.9237 (m-30) cc_final: 0.8707 (t0) REVERT: N 86 MET cc_start: 0.9699 (tpp) cc_final: 0.9497 (tpp) REVERT: N 120 MET cc_start: 0.9215 (ptm) cc_final: 0.8785 (tpp) REVERT: O 64 GLU cc_start: 0.9423 (tt0) cc_final: 0.9154 (mt-10) REVERT: O 86 MET cc_start: 0.8819 (tmm) cc_final: 0.8568 (tmm) REVERT: O 194 LYS cc_start: 0.9185 (mmmm) cc_final: 0.8956 (mmtm) REVERT: P 12 MET cc_start: 0.9348 (ttm) cc_final: 0.8874 (mtp) REVERT: P 39 PHE cc_start: 0.8863 (t80) cc_final: 0.8281 (t80) REVERT: P 88 MET cc_start: 0.9089 (ptp) cc_final: 0.8407 (ptt) REVERT: P 90 MET cc_start: 0.9333 (ttm) cc_final: 0.8567 (mmp) REVERT: P 117 PHE cc_start: 0.7768 (p90) cc_final: 0.7562 (p90) REVERT: P 171 MET cc_start: 0.9723 (mmm) cc_final: 0.9167 (mmm) REVERT: Q 69 MET cc_start: 0.9087 (mmm) cc_final: 0.8678 (mmt) REVERT: Q 124 LEU cc_start: 0.7774 (mt) cc_final: 0.7541 (mt) REVERT: R 139 MET cc_start: 0.9344 (ttp) cc_final: 0.9096 (tmm) REVERT: S 48 ASP cc_start: 0.8787 (m-30) cc_final: 0.8366 (p0) REVERT: S 83 MET cc_start: 0.8138 (mtp) cc_final: 0.7810 (ttm) REVERT: S 91 MET cc_start: 0.9069 (ttp) cc_final: 0.8787 (ttp) REVERT: S 144 MET cc_start: 0.9432 (mtt) cc_final: 0.8815 (mmm) REVERT: T 50 MET cc_start: 0.9176 (tpt) cc_final: 0.8770 (tpp) REVERT: T 173 MET cc_start: 0.9618 (mmm) cc_final: 0.9282 (ptp) REVERT: g 125 TYR cc_start: 0.9091 (m-80) cc_final: 0.8671 (m-80) REVERT: g 134 LEU cc_start: 0.9607 (mt) cc_final: 0.9231 (pp) REVERT: g 202 LEU cc_start: 0.9684 (tt) cc_final: 0.9367 (mp) REVERT: h 130 PHE cc_start: 0.7920 (m-80) cc_final: 0.6956 (m-10) REVERT: i 174 MET cc_start: 0.9030 (ttt) cc_final: 0.8812 (ttt) REVERT: j 20 GLU cc_start: 0.9657 (mp0) cc_final: 0.9445 (pm20) REVERT: j 43 LEU cc_start: 0.9845 (pp) cc_final: 0.9430 (mp) REVERT: k 66 LYS cc_start: 0.8884 (mmtt) cc_final: 0.8214 (mmtt) REVERT: k 107 MET cc_start: 0.7434 (mtp) cc_final: 0.7175 (mtt) REVERT: l 26 MET cc_start: 0.8471 (mmt) cc_final: 0.7871 (mmt) REVERT: l 86 ASN cc_start: 0.9413 (m-40) cc_final: 0.9181 (m-40) REVERT: l 88 MET cc_start: 0.9625 (ttp) cc_final: 0.9268 (ttp) REVERT: l 159 MET cc_start: 0.9164 (tmm) cc_final: 0.8716 (tmm) REVERT: l 195 LEU cc_start: 0.9561 (mp) cc_final: 0.9346 (mp) REVERT: m 75 MET cc_start: 0.9495 (mtp) cc_final: 0.9012 (mtp) REVERT: n 87 CYS cc_start: 0.9708 (m) cc_final: 0.9212 (p) REVERT: n 95 MET cc_start: 0.9061 (mpp) cc_final: 0.8764 (mpp) REVERT: n 120 MET cc_start: 0.8836 (ppp) cc_final: 0.8248 (ppp) REVERT: o 54 MET cc_start: 0.9574 (mmm) cc_final: 0.9219 (mmp) REVERT: o 86 MET cc_start: 0.9826 (mmp) cc_final: 0.9575 (mmm) REVERT: o 98 LEU cc_start: 0.9718 (mp) cc_final: 0.9440 (mm) REVERT: o 127 MET cc_start: 0.9106 (mmm) cc_final: 0.8086 (mtt) REVERT: p 96 TYR cc_start: 0.9562 (t80) cc_final: 0.9220 (t80) REVERT: p 117 PHE cc_start: 0.7549 (p90) cc_final: 0.7315 (p90) REVERT: p 136 PHE cc_start: 0.8613 (p90) cc_final: 0.7903 (p90) REVERT: p 149 MET cc_start: 0.9478 (mmm) cc_final: 0.9069 (mmm) REVERT: p 171 MET cc_start: 0.9543 (mmm) cc_final: 0.9247 (mmm) REVERT: p 176 ASP cc_start: 0.8844 (m-30) cc_final: 0.8640 (m-30) REVERT: p 204 MET cc_start: 0.9178 (mmm) cc_final: 0.8971 (mmp) REVERT: q 35 MET cc_start: 0.8304 (mtt) cc_final: 0.7960 (mtt) REVERT: q 38 MET cc_start: 0.9440 (mmp) cc_final: 0.8782 (mmm) REVERT: r 44 THR cc_start: 0.7621 (p) cc_final: 0.6270 (p) REVERT: r 56 GLU cc_start: 0.9334 (mt-10) cc_final: 0.8979 (mt-10) REVERT: r 100 MET cc_start: 0.8935 (mtm) cc_final: 0.8538 (mtt) REVERT: s 74 MET cc_start: 0.9532 (mtp) cc_final: 0.9273 (mtp) REVERT: t 70 MET cc_start: 0.9786 (mmp) cc_final: 0.9567 (mmm) REVERT: t 112 ILE cc_start: 0.9521 (mt) cc_final: 0.8744 (tt) REVERT: t 126 ASP cc_start: 0.9593 (t0) cc_final: 0.9364 (t0) REVERT: t 214 MET cc_start: 0.8658 (mpp) cc_final: 0.8213 (mpp) outliers start: 15 outliers final: 3 residues processed: 1018 average time/residue: 0.9592 time to fit residues: 1677.5671 Evaluate side-chains 732 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 729 time to evaluate : 9.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1267 random chunks: chunk 639 optimal weight: 0.4980 chunk 357 optimal weight: 6.9990 chunk 957 optimal weight: 0.9990 chunk 783 optimal weight: 0.0370 chunk 317 optimal weight: 10.0000 chunk 1152 optimal weight: 10.0000 chunk 1245 optimal weight: 10.0000 chunk 1026 optimal weight: 0.9980 chunk 1143 optimal weight: 8.9990 chunk 392 optimal weight: 9.9990 chunk 924 optimal weight: 9.9990 overall best weight: 1.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 46 GLN a 124 ASN ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 290 GLN b 79 GLN b 158 ASN ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 HIS ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 51 GLN f 102 HIS ** f 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN U 647 HIS U 677 ASN U 698 GLN U 768 GLN ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 292 GLN X 405 GLN Y 363 ASN Y 365 GLN Z 24 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 109 ASN ** Z 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 HIS ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 HIS E 121 ASN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 263 GLN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 GLN L 152 ASN ** M 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN Q 168 GLN ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 ASN T 2 GLN ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 88 ASN i 102 GLN ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 215 GLN ** k 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 152 ASN ** n 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 173 ASN q 65 GLN ** q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 101626 Z= 0.190 Angle : 0.696 18.344 137470 Z= 0.360 Chirality : 0.045 0.330 15653 Planarity : 0.005 0.079 17764 Dihedral : 7.376 89.286 14167 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.02 % Favored : 90.77 % Rotamer: Outliers : 0.08 % Allowed : 3.29 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.66 (0.07), residues: 12733 helix: -0.96 (0.07), residues: 5557 sheet: -1.35 (0.12), residues: 1667 loop : -2.74 (0.08), residues: 5509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP W 80 HIS 0.010 0.001 HIS Z 196 PHE 0.031 0.002 PHE k 22 TYR 0.024 0.001 TYR c 255 ARG 0.015 0.001 ARG l 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 973 time to evaluate : 8.973 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: a 87 MET cc_start: 0.5403 (mtp) cc_final: 0.5001 (ttp) REVERT: a 124 ASN cc_start: 0.9053 (m110) cc_final: 0.8806 (t0) REVERT: b 1 MET cc_start: 0.1196 (mmt) cc_final: -0.1383 (ppp) REVERT: b 7 MET cc_start: 0.3213 (tpt) cc_final: 0.2987 (tpp) REVERT: b 86 PHE cc_start: 0.7926 (t80) cc_final: 0.7109 (t80) REVERT: b 163 LYS cc_start: 0.7309 (mmtt) cc_final: 0.6855 (ptpp) REVERT: c 54 MET cc_start: 0.7850 (pmm) cc_final: 0.7398 (pmm) REVERT: c 57 MET cc_start: 0.8657 (mtm) cc_final: 0.8448 (mtp) REVERT: c 75 MET cc_start: 0.4315 (mmm) cc_final: 0.3965 (mmm) REVERT: c 160 PHE cc_start: 0.8859 (m-80) cc_final: 0.8658 (m-80) REVERT: c 197 ASN cc_start: 0.8972 (t0) cc_final: 0.8639 (m-40) REVERT: c 216 MET cc_start: 0.8768 (ptm) cc_final: 0.8496 (ptp) REVERT: c 224 SER cc_start: 0.7533 (t) cc_final: 0.7170 (m) REVERT: c 226 MET cc_start: 0.9134 (tpp) cc_final: 0.8283 (tmm) REVERT: c 305 ASP cc_start: 0.8318 (p0) cc_final: 0.8091 (p0) REVERT: d 1 MET cc_start: 0.5486 (ttt) cc_final: 0.4655 (tpp) REVERT: d 67 ASP cc_start: 0.8360 (t0) cc_final: 0.8126 (t0) REVERT: e 67 MET cc_start: 0.0811 (ptt) cc_final: 0.0576 (ptt) REVERT: f 33 ARG cc_start: 0.7100 (mpt90) cc_final: 0.6260 (tpt90) REVERT: f 275 MET cc_start: 0.7588 (pmm) cc_final: 0.5810 (tpt) REVERT: f 303 VAL cc_start: 0.5802 (t) cc_final: 0.5510 (p) REVERT: f 370 MET cc_start: 0.6707 (mmt) cc_final: 0.6194 (mmp) REVERT: f 512 MET cc_start: 0.6176 (tpt) cc_final: 0.5680 (tpt) REVERT: f 557 TRP cc_start: 0.7736 (m-10) cc_final: 0.7223 (m100) REVERT: U 206 MET cc_start: 0.6477 (mmp) cc_final: 0.6103 (mmp) REVERT: U 351 MET cc_start: 0.8223 (ptp) cc_final: 0.7931 (ptp) REVERT: U 355 ASN cc_start: 0.7730 (m110) cc_final: 0.7182 (t0) REVERT: U 423 MET cc_start: 0.8195 (mmp) cc_final: 0.7773 (tpt) REVERT: U 456 ASP cc_start: 0.9359 (t0) cc_final: 0.9092 (p0) REVERT: U 556 MET cc_start: 0.7816 (mmt) cc_final: 0.7388 (mmm) REVERT: U 560 MET cc_start: 0.8107 (mmt) cc_final: 0.7231 (mmm) REVERT: U 583 MET cc_start: 0.8711 (mmm) cc_final: 0.8458 (mmm) REVERT: U 654 MET cc_start: 0.9267 (mmp) cc_final: 0.8957 (mmm) REVERT: U 675 MET cc_start: 0.9291 (tpt) cc_final: 0.8880 (tpp) REVERT: U 797 MET cc_start: 0.7788 (ptp) cc_final: 0.7431 (mpp) REVERT: U 885 MET cc_start: 0.7345 (mmt) cc_final: 0.6862 (mtt) REVERT: V 139 MET cc_start: 0.7921 (ptt) cc_final: 0.7684 (ppp) REVERT: V 255 LEU cc_start: 0.9479 (mp) cc_final: 0.9132 (pp) REVERT: V 358 MET cc_start: 0.8991 (mmm) cc_final: 0.8653 (mtm) REVERT: W 190 MET cc_start: 0.8314 (ttp) cc_final: 0.7774 (tpp) REVERT: W 312 MET cc_start: 0.5595 (tpp) cc_final: 0.5286 (tpp) REVERT: W 428 TRP cc_start: 0.9024 (m100) cc_final: 0.8009 (m100) REVERT: X 201 TYR cc_start: 0.6852 (p90) cc_final: 0.6571 (p90) REVERT: X 253 TYR cc_start: 0.9077 (m-80) cc_final: 0.8565 (m-80) REVERT: X 254 MET cc_start: 0.7683 (ptp) cc_final: 0.7461 (ttt) REVERT: X 374 PHE cc_start: 0.9159 (t80) cc_final: 0.8486 (t80) REVERT: X 401 LEU cc_start: 0.9625 (mt) cc_final: 0.9413 (pp) REVERT: Y 40 GLU cc_start: 0.8402 (tt0) cc_final: 0.8173 (mt-10) REVERT: Z 247 LYS cc_start: 0.8881 (pttm) cc_final: 0.8356 (tptp) REVERT: Z 269 VAL cc_start: 0.9632 (t) cc_final: 0.9388 (t) REVERT: Z 273 HIS cc_start: 0.8743 (m170) cc_final: 0.8471 (m170) REVERT: A 256 MET cc_start: 0.8730 (mmp) cc_final: 0.8299 (mmp) REVERT: A 299 MET cc_start: 0.7763 (ptp) cc_final: 0.7507 (ptp) REVERT: A 319 MET cc_start: 0.7585 (ppp) cc_final: 0.7004 (ppp) REVERT: A 325 ASP cc_start: 0.7872 (t0) cc_final: 0.7666 (p0) REVERT: A 389 CYS cc_start: 0.9125 (m) cc_final: 0.8760 (m) REVERT: B 405 MET cc_start: 0.7720 (mmp) cc_final: 0.7133 (mmp) REVERT: C 86 LEU cc_start: 0.9040 (tt) cc_final: 0.8672 (tt) REVERT: C 221 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7614 (mt0) REVERT: C 279 GLN cc_start: 0.8952 (tt0) cc_final: 0.8603 (mm-40) REVERT: C 368 MET cc_start: 0.9193 (mtt) cc_final: 0.8888 (mtt) REVERT: C 377 HIS cc_start: 0.8477 (m-70) cc_final: 0.8147 (p-80) REVERT: C 399 MET cc_start: 0.7118 (mmt) cc_final: 0.6886 (mmp) REVERT: D 59 GLU cc_start: 0.9603 (tt0) cc_final: 0.9262 (tm-30) REVERT: D 264 ILE cc_start: 0.9541 (mt) cc_final: 0.9152 (mt) REVERT: D 296 MET cc_start: 0.9352 (tpt) cc_final: 0.8878 (tmm) REVERT: D 304 ASN cc_start: 0.9394 (t0) cc_final: 0.8906 (m-40) REVERT: D 333 PHE cc_start: 0.8984 (m-10) cc_final: 0.8769 (m-80) REVERT: E 302 ASP cc_start: 0.9347 (m-30) cc_final: 0.8769 (t70) REVERT: E 336 ASP cc_start: 0.8592 (t0) cc_final: 0.8380 (m-30) REVERT: E 382 SER cc_start: 0.4159 (p) cc_final: 0.3804 (t) REVERT: G 113 MET cc_start: 0.6384 (mmt) cc_final: 0.5978 (mmt) REVERT: G 125 TYR cc_start: 0.9403 (m-80) cc_final: 0.8807 (m-80) REVERT: G 209 ASP cc_start: 0.7821 (m-30) cc_final: 0.7537 (t0) REVERT: H 38 ILE cc_start: 0.8950 (mm) cc_final: 0.8631 (tp) REVERT: H 121 TYR cc_start: 0.8272 (m-80) cc_final: 0.7860 (m-80) REVERT: H 197 GLU cc_start: 0.9371 (tp30) cc_final: 0.9064 (tt0) REVERT: I 72 MET cc_start: 0.6947 (mmp) cc_final: 0.6545 (mmp) REVERT: I 99 LEU cc_start: 0.9546 (tp) cc_final: 0.9274 (tp) REVERT: I 163 CYS cc_start: 0.8569 (p) cc_final: 0.7981 (t) REVERT: I 166 ASN cc_start: 0.8969 (t0) cc_final: 0.8421 (p0) REVERT: J 132 LEU cc_start: 0.9498 (tt) cc_final: 0.8934 (mm) REVERT: J 159 ASN cc_start: 0.7659 (t0) cc_final: 0.7190 (t0) REVERT: K 65 GLU cc_start: 0.9241 (pm20) cc_final: 0.8726 (tp30) REVERT: K 137 PHE cc_start: 0.8797 (m-80) cc_final: 0.8482 (m-80) REVERT: K 156 MET cc_start: 0.9281 (ptm) cc_final: 0.8932 (ppp) REVERT: K 206 MET cc_start: 0.8339 (ptp) cc_final: 0.8036 (ptt) REVERT: L 88 MET cc_start: 0.9736 (ttp) cc_final: 0.9375 (ptt) REVERT: L 132 LEU cc_start: 0.9423 (mt) cc_final: 0.9133 (tp) REVERT: L 176 MET cc_start: 0.8665 (ptp) cc_final: 0.8218 (ptm) REVERT: L 228 ASP cc_start: 0.9156 (m-30) cc_final: 0.8689 (t0) REVERT: M 75 MET cc_start: 0.8896 (mmm) cc_final: 0.8579 (mmm) REVERT: M 135 PHE cc_start: 0.9246 (p90) cc_final: 0.8626 (p90) REVERT: M 181 MET cc_start: 0.8639 (ptp) cc_final: 0.7940 (ptp) REVERT: N 32 ASP cc_start: 0.9186 (m-30) cc_final: 0.8609 (t0) REVERT: N 95 MET cc_start: 0.8175 (mpp) cc_final: 0.7621 (mpp) REVERT: N 116 MET cc_start: 0.8902 (mpp) cc_final: 0.8578 (mmp) REVERT: N 119 MET cc_start: 0.8238 (pmm) cc_final: 0.7559 (pmm) REVERT: N 120 MET cc_start: 0.8865 (ptm) cc_final: 0.8661 (pmm) REVERT: O 64 GLU cc_start: 0.9410 (tt0) cc_final: 0.9194 (mm-30) REVERT: O 86 MET cc_start: 0.8842 (tmm) cc_final: 0.8469 (tmm) REVERT: O 194 LYS cc_start: 0.9163 (mmmm) cc_final: 0.8933 (mmtm) REVERT: P 39 PHE cc_start: 0.8843 (t80) cc_final: 0.8304 (t80) REVERT: P 88 MET cc_start: 0.9111 (ptp) cc_final: 0.8717 (ptp) REVERT: P 144 GLU cc_start: 0.8765 (mp0) cc_final: 0.7785 (mt-10) REVERT: P 171 MET cc_start: 0.9649 (mmm) cc_final: 0.9102 (mmm) REVERT: Q 69 MET cc_start: 0.9077 (mmm) cc_final: 0.8609 (tpt) REVERT: Q 124 LEU cc_start: 0.7739 (mt) cc_final: 0.7501 (mt) REVERT: R 37 ILE cc_start: 0.8237 (mm) cc_final: 0.8010 (mm) REVERT: R 54 PHE cc_start: 0.9561 (t80) cc_final: 0.9360 (t80) REVERT: R 139 MET cc_start: 0.9313 (ttp) cc_final: 0.9059 (tmm) REVERT: S 48 ASP cc_start: 0.8860 (m-30) cc_final: 0.8380 (p0) REVERT: S 91 MET cc_start: 0.9185 (ttp) cc_final: 0.8756 (tpt) REVERT: S 144 MET cc_start: 0.9454 (mtt) cc_final: 0.8809 (mmm) REVERT: T 127 MET cc_start: 0.8367 (ttm) cc_final: 0.7711 (ttt) REVERT: T 173 MET cc_start: 0.9627 (mmm) cc_final: 0.9268 (mtm) REVERT: g 125 TYR cc_start: 0.9053 (m-80) cc_final: 0.8547 (m-80) REVERT: g 134 LEU cc_start: 0.9661 (mt) cc_final: 0.9201 (pp) REVERT: g 179 LEU cc_start: 0.9519 (mt) cc_final: 0.9182 (pp) REVERT: g 202 LEU cc_start: 0.9728 (tt) cc_final: 0.9366 (mm) REVERT: h 130 PHE cc_start: 0.7569 (m-80) cc_final: 0.6791 (m-10) REVERT: i 44 LEU cc_start: 0.9110 (pp) cc_final: 0.8650 (tp) REVERT: j 20 GLU cc_start: 0.9651 (mp0) cc_final: 0.9435 (pm20) REVERT: j 43 LEU cc_start: 0.9821 (pp) cc_final: 0.9361 (mp) REVERT: k 66 LYS cc_start: 0.8340 (mmtt) cc_final: 0.7994 (mtmt) REVERT: k 89 ILE cc_start: 0.9278 (mt) cc_final: 0.9054 (mt) REVERT: k 107 MET cc_start: 0.7388 (mtp) cc_final: 0.7136 (mtt) REVERT: k 143 PHE cc_start: 0.8764 (m-80) cc_final: 0.8477 (m-10) REVERT: l 26 MET cc_start: 0.8486 (mmt) cc_final: 0.8152 (mmt) REVERT: l 61 LYS cc_start: 0.9297 (pttm) cc_final: 0.9045 (ttpp) REVERT: l 86 ASN cc_start: 0.9381 (m-40) cc_final: 0.9104 (m110) REVERT: l 159 MET cc_start: 0.9136 (tmm) cc_final: 0.8891 (tmm) REVERT: m 47 PHE cc_start: 0.9192 (m-10) cc_final: 0.8989 (m-10) REVERT: m 75 MET cc_start: 0.9355 (mtp) cc_final: 0.8827 (mtp) REVERT: n 57 ASP cc_start: 0.9498 (m-30) cc_final: 0.9294 (m-30) REVERT: n 87 CYS cc_start: 0.9668 (m) cc_final: 0.9109 (p) REVERT: n 119 MET cc_start: 0.8362 (ppp) cc_final: 0.8127 (ppp) REVERT: o 54 MET cc_start: 0.9584 (mmm) cc_final: 0.9189 (mmp) REVERT: o 86 MET cc_start: 0.9793 (mmp) cc_final: 0.9538 (mmm) REVERT: o 98 LEU cc_start: 0.9749 (mp) cc_final: 0.9452 (mm) REVERT: o 127 MET cc_start: 0.9099 (mmm) cc_final: 0.8054 (mtt) REVERT: p 14 MET cc_start: 0.8755 (ttp) cc_final: 0.7959 (ptm) REVERT: p 45 MET cc_start: 0.9462 (mmp) cc_final: 0.9187 (mmm) REVERT: p 75 GLU cc_start: 0.9255 (mt-10) cc_final: 0.8979 (mm-30) REVERT: p 82 ILE cc_start: 0.8642 (tt) cc_final: 0.8412 (tt) REVERT: p 96 TYR cc_start: 0.9544 (t80) cc_final: 0.9177 (t80) REVERT: q 38 MET cc_start: 0.9275 (mmp) cc_final: 0.8761 (mmm) REVERT: q 69 MET cc_start: 0.9271 (tpt) cc_final: 0.8840 (tpp) REVERT: r 44 THR cc_start: 0.7798 (p) cc_final: 0.7001 (p) REVERT: r 56 GLU cc_start: 0.9259 (mt-10) cc_final: 0.8999 (mt-10) REVERT: r 100 MET cc_start: 0.8962 (mtm) cc_final: 0.8520 (mtt) REVERT: s 74 MET cc_start: 0.9565 (mtp) cc_final: 0.9332 (mtp) REVERT: s 91 MET cc_start: 0.9412 (ppp) cc_final: 0.9155 (ppp) REVERT: s 144 MET cc_start: 0.8793 (mtm) cc_final: 0.7562 (mtm) REVERT: t 70 MET cc_start: 0.9797 (mmp) cc_final: 0.9410 (mtp) REVERT: t 112 ILE cc_start: 0.9541 (mt) cc_final: 0.8780 (tt) REVERT: t 127 MET cc_start: 0.7984 (mtp) cc_final: 0.7726 (mtp) REVERT: t 214 MET cc_start: 0.8777 (mpp) cc_final: 0.8322 (mpp) outliers start: 9 outliers final: 4 residues processed: 980 average time/residue: 0.9062 time to fit residues: 1531.1366 Evaluate side-chains 740 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 736 time to evaluate : 8.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1267 random chunks: chunk 1138 optimal weight: 4.9990 chunk 866 optimal weight: 10.0000 chunk 598 optimal weight: 6.9990 chunk 127 optimal weight: 40.0000 chunk 550 optimal weight: 3.9990 chunk 773 optimal weight: 10.0000 chunk 1156 optimal weight: 20.0000 chunk 1224 optimal weight: 5.9990 chunk 604 optimal weight: 10.0000 chunk 1096 optimal weight: 4.9990 chunk 330 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 372 HIS ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 169 HIS ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 254 ASN ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 51 GLN ** f 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN ** U 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 880 ASN ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 306 GLN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 254 ASN ** Z 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS I 142 HIS ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 GLN ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 101 ASN Q 65 GLN Q 87 ASN ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 GLN ** T 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 90 GLN h 71 HIS ** h 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 8 ASN ** n 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 85 ASN s 131 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 101626 Z= 0.258 Angle : 0.719 17.401 137470 Z= 0.376 Chirality : 0.045 0.371 15653 Planarity : 0.005 0.076 17764 Dihedral : 7.157 88.550 14167 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.71 % Favored : 90.11 % Rotamer: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.32 (0.07), residues: 12733 helix: -0.59 (0.07), residues: 5546 sheet: -1.16 (0.12), residues: 1653 loop : -2.66 (0.08), residues: 5534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 104 HIS 0.010 0.001 HIS j 154 PHE 0.032 0.002 PHE C 223 TYR 0.051 0.002 TYR U 437 ARG 0.026 0.001 ARG m 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 849 time to evaluate : 9.033 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: a 87 MET cc_start: 0.5643 (mtp) cc_final: 0.5246 (ttp) REVERT: a 312 MET cc_start: 0.8780 (mtm) cc_final: 0.8541 (mtp) REVERT: b 1 MET cc_start: 0.1227 (mmt) cc_final: -0.1251 (ppp) REVERT: b 86 PHE cc_start: 0.8018 (t80) cc_final: 0.7189 (t80) REVERT: b 107 MET cc_start: 0.6768 (ttm) cc_final: 0.6451 (ttm) REVERT: c 51 MET cc_start: 0.7266 (ppp) cc_final: 0.7012 (tmm) REVERT: c 54 MET cc_start: 0.7959 (pmm) cc_final: 0.7323 (pmm) REVERT: c 75 MET cc_start: 0.4164 (mmm) cc_final: 0.3834 (mmm) REVERT: c 216 MET cc_start: 0.8745 (ptm) cc_final: 0.8441 (ptp) REVERT: c 224 SER cc_start: 0.7307 (t) cc_final: 0.6984 (m) REVERT: c 226 MET cc_start: 0.9127 (tpp) cc_final: 0.8469 (tmm) REVERT: d 1 MET cc_start: 0.5173 (ttt) cc_final: 0.4774 (tpp) REVERT: d 67 ASP cc_start: 0.8348 (t0) cc_final: 0.8136 (t0) REVERT: e 67 MET cc_start: 0.1231 (ptt) cc_final: 0.0859 (ppp) REVERT: f 33 ARG cc_start: 0.6976 (mpt90) cc_final: 0.6045 (tpt90) REVERT: f 185 LEU cc_start: 0.4598 (mt) cc_final: 0.3911 (pt) REVERT: f 275 MET cc_start: 0.7650 (pmm) cc_final: 0.6088 (tpt) REVERT: f 303 VAL cc_start: 0.5524 (t) cc_final: 0.5231 (p) REVERT: f 512 MET cc_start: 0.6437 (tpt) cc_final: 0.5875 (tpt) REVERT: f 557 TRP cc_start: 0.7801 (m-10) cc_final: 0.7407 (m100) REVERT: U 106 ASP cc_start: 0.9213 (t0) cc_final: 0.8914 (m-30) REVERT: U 206 MET cc_start: 0.6631 (mmp) cc_final: 0.6275 (mmp) REVERT: U 423 MET cc_start: 0.8313 (mmp) cc_final: 0.7995 (mmp) REVERT: U 456 ASP cc_start: 0.9399 (t0) cc_final: 0.9149 (p0) REVERT: U 532 MET cc_start: 0.9138 (ptm) cc_final: 0.8405 (tmm) REVERT: U 556 MET cc_start: 0.7861 (mmt) cc_final: 0.7517 (mmm) REVERT: U 583 MET cc_start: 0.8738 (mmm) cc_final: 0.8526 (mmm) REVERT: U 654 MET cc_start: 0.9176 (mmp) cc_final: 0.8851 (mmm) REVERT: U 675 MET cc_start: 0.9380 (tpt) cc_final: 0.9058 (tpp) REVERT: U 695 MET cc_start: 0.9395 (ttm) cc_final: 0.9111 (ptt) REVERT: U 797 MET cc_start: 0.7824 (ptp) cc_final: 0.7350 (mpp) REVERT: U 885 MET cc_start: 0.7631 (mmt) cc_final: 0.6955 (mtt) REVERT: V 139 MET cc_start: 0.7840 (ptt) cc_final: 0.7631 (ppp) REVERT: V 255 LEU cc_start: 0.9534 (mp) cc_final: 0.9169 (pp) REVERT: V 358 MET cc_start: 0.9158 (mmm) cc_final: 0.8834 (mtt) REVERT: W 190 MET cc_start: 0.8458 (ttp) cc_final: 0.7914 (tpp) REVERT: W 312 MET cc_start: 0.5738 (tpp) cc_final: 0.5366 (tpp) REVERT: W 428 TRP cc_start: 0.9014 (m100) cc_final: 0.8084 (m100) REVERT: X 253 TYR cc_start: 0.9208 (m-80) cc_final: 0.8753 (m-80) REVERT: X 374 PHE cc_start: 0.9213 (t80) cc_final: 0.8482 (t80) REVERT: X 401 LEU cc_start: 0.9576 (mt) cc_final: 0.9360 (pp) REVERT: Y 40 GLU cc_start: 0.8289 (tt0) cc_final: 0.8063 (mt-10) REVERT: Z 78 MET cc_start: 0.9238 (mmp) cc_final: 0.8760 (mmm) REVERT: Z 247 LYS cc_start: 0.9028 (pttm) cc_final: 0.8426 (tptp) REVERT: Z 269 VAL cc_start: 0.9633 (t) cc_final: 0.9392 (t) REVERT: Z 273 HIS cc_start: 0.8882 (m170) cc_final: 0.8596 (m170) REVERT: A 256 MET cc_start: 0.8775 (mmp) cc_final: 0.8327 (mmp) REVERT: A 299 MET cc_start: 0.7859 (ptp) cc_final: 0.7560 (ptp) REVERT: A 319 MET cc_start: 0.7871 (ppp) cc_final: 0.7669 (ppp) REVERT: A 430 MET cc_start: 0.6970 (tpt) cc_final: 0.6150 (tpp) REVERT: B 405 MET cc_start: 0.7933 (mmp) cc_final: 0.7476 (mmp) REVERT: C 89 VAL cc_start: 0.9647 (t) cc_final: 0.9348 (t) REVERT: C 139 MET cc_start: 0.9132 (tmm) cc_final: 0.8441 (ptp) REVERT: C 221 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7797 (mt0) REVERT: C 368 MET cc_start: 0.9262 (mtt) cc_final: 0.8960 (mtt) REVERT: C 377 HIS cc_start: 0.8506 (m-70) cc_final: 0.8178 (p-80) REVERT: C 399 MET cc_start: 0.7203 (mmt) cc_final: 0.6855 (mmt) REVERT: D 59 GLU cc_start: 0.9610 (tt0) cc_final: 0.9307 (tm-30) REVERT: D 214 MET cc_start: 0.7705 (ptp) cc_final: 0.7434 (ptp) REVERT: D 296 MET cc_start: 0.9283 (tpt) cc_final: 0.8864 (tmm) REVERT: D 304 ASN cc_start: 0.9495 (t0) cc_final: 0.9105 (t0) REVERT: E 302 ASP cc_start: 0.9312 (m-30) cc_final: 0.8748 (t70) REVERT: E 336 ASP cc_start: 0.8647 (t0) cc_final: 0.8408 (m-30) REVERT: E 382 SER cc_start: 0.4178 (p) cc_final: 0.3793 (t) REVERT: G 209 ASP cc_start: 0.7975 (m-30) cc_final: 0.7674 (t0) REVERT: H 121 TYR cc_start: 0.8483 (m-80) cc_final: 0.8086 (m-80) REVERT: I 35 LEU cc_start: 0.9341 (pt) cc_final: 0.8961 (mt) REVERT: I 72 MET cc_start: 0.7330 (mmp) cc_final: 0.6982 (mmp) REVERT: I 163 CYS cc_start: 0.8567 (p) cc_final: 0.8012 (t) REVERT: I 166 ASN cc_start: 0.8838 (t0) cc_final: 0.8267 (p0) REVERT: J 132 LEU cc_start: 0.9505 (tt) cc_final: 0.8819 (mm) REVERT: J 159 ASN cc_start: 0.8065 (t0) cc_final: 0.7428 (t0) REVERT: K 65 GLU cc_start: 0.9284 (pm20) cc_final: 0.8819 (tp30) REVERT: K 156 MET cc_start: 0.9384 (ptm) cc_final: 0.8972 (ppp) REVERT: K 206 MET cc_start: 0.8447 (ptp) cc_final: 0.8214 (ptt) REVERT: L 88 MET cc_start: 0.9762 (ttp) cc_final: 0.9440 (ptt) REVERT: L 132 LEU cc_start: 0.9469 (mt) cc_final: 0.9169 (tp) REVERT: L 176 MET cc_start: 0.8722 (ptp) cc_final: 0.8317 (ptm) REVERT: L 228 ASP cc_start: 0.9055 (m-30) cc_final: 0.8643 (t0) REVERT: M 51 LYS cc_start: 0.9241 (tmmt) cc_final: 0.9032 (ttmt) REVERT: M 75 MET cc_start: 0.9039 (mmm) cc_final: 0.8796 (mmm) REVERT: M 181 MET cc_start: 0.8721 (ptp) cc_final: 0.8157 (ptp) REVERT: N 32 ASP cc_start: 0.9195 (m-30) cc_final: 0.8682 (t70) REVERT: N 86 MET cc_start: 0.9749 (tpp) cc_final: 0.9541 (tpp) REVERT: N 116 MET cc_start: 0.8837 (mpp) cc_final: 0.8630 (mpp) REVERT: N 119 MET cc_start: 0.8344 (pmm) cc_final: 0.7518 (pmm) REVERT: O 86 MET cc_start: 0.8901 (tmm) cc_final: 0.8663 (tmm) REVERT: O 194 LYS cc_start: 0.9194 (mmmm) cc_final: 0.8952 (mmtm) REVERT: P 14 MET cc_start: 0.8167 (ptm) cc_final: 0.7957 (ptt) REVERT: P 39 PHE cc_start: 0.8956 (t80) cc_final: 0.8391 (t80) REVERT: P 88 MET cc_start: 0.9231 (ptp) cc_final: 0.8910 (ptt) REVERT: P 144 GLU cc_start: 0.8860 (mp0) cc_final: 0.7817 (mt-10) REVERT: P 171 MET cc_start: 0.9755 (mmm) cc_final: 0.9434 (mmm) REVERT: Q 38 MET cc_start: 0.9597 (mmp) cc_final: 0.9386 (mmm) REVERT: Q 69 MET cc_start: 0.9289 (mmm) cc_final: 0.8860 (mmt) REVERT: Q 124 LEU cc_start: 0.7764 (mt) cc_final: 0.7544 (mt) REVERT: R 139 MET cc_start: 0.9326 (ttp) cc_final: 0.8929 (tmm) REVERT: S 48 ASP cc_start: 0.9047 (m-30) cc_final: 0.8459 (p0) REVERT: S 69 GLU cc_start: 0.9590 (pt0) cc_final: 0.9320 (pp20) REVERT: S 144 MET cc_start: 0.9479 (mtt) cc_final: 0.8729 (mmm) REVERT: T 26 MET cc_start: 0.7318 (mtm) cc_final: 0.7069 (mpp) REVERT: T 127 MET cc_start: 0.8562 (ttm) cc_final: 0.8161 (ttt) REVERT: T 173 MET cc_start: 0.9648 (mmm) cc_final: 0.9296 (mtm) REVERT: g 113 MET cc_start: 0.9546 (mmp) cc_final: 0.9333 (mmm) REVERT: g 134 LEU cc_start: 0.9671 (mt) cc_final: 0.9317 (pp) REVERT: g 202 LEU cc_start: 0.9741 (tt) cc_final: 0.9412 (mm) REVERT: h 130 PHE cc_start: 0.7808 (m-80) cc_final: 0.7079 (m-80) REVERT: i 174 MET cc_start: 0.9037 (ttt) cc_final: 0.8631 (ttt) REVERT: j 20 GLU cc_start: 0.9662 (mp0) cc_final: 0.9439 (pm20) REVERT: j 43 LEU cc_start: 0.9831 (pp) cc_final: 0.9368 (mp) REVERT: k 66 LYS cc_start: 0.8362 (mmtt) cc_final: 0.7994 (mttp) REVERT: k 107 MET cc_start: 0.7685 (mtp) cc_final: 0.7359 (mtt) REVERT: m 75 MET cc_start: 0.9390 (mtp) cc_final: 0.8773 (mtp) REVERT: m 135 PHE cc_start: 0.9261 (p90) cc_final: 0.8927 (p90) REVERT: m 150 MET cc_start: 0.9269 (tpt) cc_final: 0.8809 (ppp) REVERT: n 85 GLU cc_start: 0.9514 (mm-30) cc_final: 0.9267 (mp0) REVERT: n 87 CYS cc_start: 0.9718 (m) cc_final: 0.9242 (p) REVERT: n 119 MET cc_start: 0.8497 (ppp) cc_final: 0.8192 (ppp) REVERT: o 54 MET cc_start: 0.9541 (mmm) cc_final: 0.9214 (mmp) REVERT: o 86 MET cc_start: 0.9814 (mmp) cc_final: 0.9561 (mmm) REVERT: o 98 LEU cc_start: 0.9743 (mp) cc_final: 0.9495 (mm) REVERT: o 127 MET cc_start: 0.9097 (mmm) cc_final: 0.8123 (mtt) REVERT: o 157 GLU cc_start: 0.9482 (mm-30) cc_final: 0.9277 (mm-30) REVERT: p 45 MET cc_start: 0.9337 (mmp) cc_final: 0.9104 (mmm) REVERT: p 75 GLU cc_start: 0.9355 (mt-10) cc_final: 0.8924 (mm-30) REVERT: p 96 TYR cc_start: 0.9562 (t80) cc_final: 0.9156 (t80) REVERT: p 144 GLU cc_start: 0.8894 (mt-10) cc_final: 0.7859 (mt-10) REVERT: p 149 MET cc_start: 0.9433 (mmm) cc_final: 0.9112 (mtp) REVERT: p 171 MET cc_start: 0.9539 (mmm) cc_final: 0.9272 (mmm) REVERT: q 38 MET cc_start: 0.9276 (mmp) cc_final: 0.8771 (mmm) REVERT: q 69 MET cc_start: 0.9295 (tpt) cc_final: 0.8948 (tpt) REVERT: q 124 LEU cc_start: 0.8944 (mt) cc_final: 0.8457 (mt) REVERT: r 100 MET cc_start: 0.9050 (mtm) cc_final: 0.8559 (mtt) REVERT: s 74 MET cc_start: 0.9524 (mtp) cc_final: 0.9296 (mtp) REVERT: s 144 MET cc_start: 0.9033 (mtm) cc_final: 0.8370 (mtp) REVERT: t 26 MET cc_start: 0.7115 (mpp) cc_final: 0.6839 (mpp) REVERT: t 43 MET cc_start: 0.8716 (tpt) cc_final: 0.8489 (tmm) REVERT: t 59 ASP cc_start: 0.9124 (m-30) cc_final: 0.8918 (m-30) REVERT: t 112 ILE cc_start: 0.9515 (mt) cc_final: 0.8783 (tt) REVERT: t 214 MET cc_start: 0.8752 (mpp) cc_final: 0.8216 (mpp) outliers start: 9 outliers final: 5 residues processed: 857 average time/residue: 0.8963 time to fit residues: 1333.2375 Evaluate side-chains 678 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 673 time to evaluate : 8.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1267 random chunks: chunk 1019 optimal weight: 5.9990 chunk 695 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 911 optimal weight: 20.0000 chunk 505 optimal weight: 8.9990 chunk 1045 optimal weight: 20.0000 chunk 846 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 625 optimal weight: 2.9990 chunk 1099 optimal weight: 20.0000 chunk 309 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 40 GLN ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 76 HIS b 79 GLN b 161 ASN c 30 GLN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 128 ASN ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN U 463 ASN U 491 GLN U 777 HIS U 805 ASN ** U 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 361 HIS ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 426 ASN ** W 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 254 ASN ** Z 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 69 GLN ** T 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 71 HIS h 102 GLN ** h 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 215 GLN ** k 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 101 ASN ** n 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 186 ASN ** t 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 101626 Z= 0.283 Angle : 0.741 15.705 137470 Z= 0.388 Chirality : 0.045 0.384 15653 Planarity : 0.005 0.074 17764 Dihedral : 7.125 84.166 14167 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 27.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.88 % Favored : 89.95 % Rotamer: Outliers : 0.05 % Allowed : 3.26 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.16 (0.07), residues: 12733 helix: -0.43 (0.07), residues: 5568 sheet: -1.17 (0.12), residues: 1674 loop : -2.59 (0.08), residues: 5491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP Y 364 HIS 0.011 0.002 HIS Z 196 PHE 0.030 0.002 PHE C 223 TYR 0.022 0.002 TYR L 137 ARG 0.022 0.001 ARG l 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 806 time to evaluate : 9.122 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: a 312 MET cc_start: 0.8822 (mtm) cc_final: 0.8503 (mtp) REVERT: a 363 MET cc_start: 0.9189 (mtm) cc_final: 0.8615 (mtt) REVERT: b 1 MET cc_start: 0.2361 (mmt) cc_final: 0.0276 (ppp) REVERT: b 86 PHE cc_start: 0.8041 (t80) cc_final: 0.7278 (t80) REVERT: c 54 MET cc_start: 0.7834 (pmm) cc_final: 0.7128 (pmm) REVERT: c 224 SER cc_start: 0.7498 (t) cc_final: 0.7063 (m) REVERT: c 226 MET cc_start: 0.9255 (tpp) cc_final: 0.8787 (tmm) REVERT: d 1 MET cc_start: 0.6406 (ttt) cc_final: 0.5502 (tpp) REVERT: f 33 ARG cc_start: 0.6894 (mpt90) cc_final: 0.5772 (tpt90) REVERT: f 275 MET cc_start: 0.7433 (pmm) cc_final: 0.6006 (tpt) REVERT: f 512 MET cc_start: 0.6595 (tpt) cc_final: 0.5604 (tpt) REVERT: f 781 TYR cc_start: 0.8707 (p90) cc_final: 0.8503 (p90) REVERT: U 206 MET cc_start: 0.7277 (mmp) cc_final: 0.6888 (mmp) REVERT: U 351 MET cc_start: 0.8368 (pmm) cc_final: 0.8139 (pmm) REVERT: U 520 MET cc_start: 0.6890 (mmm) cc_final: 0.6664 (mtt) REVERT: U 532 MET cc_start: 0.9195 (ptm) cc_final: 0.8831 (ptm) REVERT: U 556 MET cc_start: 0.7714 (mmt) cc_final: 0.7460 (mmm) REVERT: U 560 MET cc_start: 0.7886 (mmt) cc_final: 0.7381 (mmm) REVERT: U 654 MET cc_start: 0.9301 (mmp) cc_final: 0.8953 (mmm) REVERT: U 675 MET cc_start: 0.9485 (tpp) cc_final: 0.9170 (tpp) REVERT: U 725 MET cc_start: 0.8680 (mmp) cc_final: 0.8350 (tpp) REVERT: U 770 TRP cc_start: 0.6883 (m-90) cc_final: 0.5830 (m-90) REVERT: U 885 MET cc_start: 0.7752 (mmt) cc_final: 0.6922 (mtt) REVERT: W 190 MET cc_start: 0.8633 (ttm) cc_final: 0.8140 (tpp) REVERT: W 312 MET cc_start: 0.5607 (tpp) cc_final: 0.5106 (tpp) REVERT: W 315 MET cc_start: 0.3281 (ppp) cc_final: 0.2560 (ppp) REVERT: W 329 ARG cc_start: 0.7165 (mpp-170) cc_final: 0.6741 (mmt180) REVERT: W 428 TRP cc_start: 0.9030 (m100) cc_final: 0.8053 (m100) REVERT: W 437 SER cc_start: 0.9555 (t) cc_final: 0.9348 (m) REVERT: X 253 TYR cc_start: 0.9190 (m-80) cc_final: 0.8686 (m-80) REVERT: X 374 PHE cc_start: 0.9076 (t80) cc_final: 0.8256 (t80) REVERT: X 401 LEU cc_start: 0.9569 (mt) cc_final: 0.9336 (pp) REVERT: Y 214 MET cc_start: 0.7467 (ptt) cc_final: 0.7179 (ptp) REVERT: Z 78 MET cc_start: 0.9096 (mmp) cc_final: 0.8599 (mmm) REVERT: A 256 MET cc_start: 0.8917 (mmp) cc_final: 0.8479 (mmp) REVERT: A 299 MET cc_start: 0.7966 (ptp) cc_final: 0.7610 (ptp) REVERT: A 319 MET cc_start: 0.7936 (ppp) cc_final: 0.7680 (ppp) REVERT: A 430 MET cc_start: 0.6867 (tpt) cc_final: 0.5968 (tpp) REVERT: A 432 TYR cc_start: 0.7677 (m-10) cc_final: 0.7058 (m-80) REVERT: B 412 MET cc_start: 0.7995 (tpp) cc_final: 0.7737 (tpp) REVERT: C 221 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7739 (tt0) REVERT: C 335 LYS cc_start: 0.8998 (mttt) cc_final: 0.8471 (ttpp) REVERT: C 368 MET cc_start: 0.9315 (mtt) cc_final: 0.9019 (mtt) REVERT: C 377 HIS cc_start: 0.8512 (m-70) cc_final: 0.8190 (p-80) REVERT: D 59 GLU cc_start: 0.9616 (tt0) cc_final: 0.9336 (tm-30) REVERT: D 214 MET cc_start: 0.7721 (ptp) cc_final: 0.7359 (ptp) REVERT: D 296 MET cc_start: 0.9085 (tpt) cc_final: 0.8774 (tmm) REVERT: D 304 ASN cc_start: 0.9570 (t0) cc_final: 0.9338 (t0) REVERT: E 336 ASP cc_start: 0.8671 (t0) cc_final: 0.8440 (m-30) REVERT: G 33 ASN cc_start: 0.9384 (m-40) cc_final: 0.9164 (t0) REVERT: G 209 ASP cc_start: 0.7906 (m-30) cc_final: 0.7666 (t0) REVERT: H 38 ILE cc_start: 0.9046 (mm) cc_final: 0.8773 (tp) REVERT: H 121 TYR cc_start: 0.8808 (m-80) cc_final: 0.8391 (m-80) REVERT: I 35 LEU cc_start: 0.9226 (pt) cc_final: 0.8947 (mt) REVERT: I 45 LEU cc_start: 0.9261 (mm) cc_final: 0.8643 (tt) REVERT: I 163 CYS cc_start: 0.8383 (p) cc_final: 0.7850 (t) REVERT: I 166 ASN cc_start: 0.8891 (t0) cc_final: 0.8309 (p0) REVERT: J 132 LEU cc_start: 0.9555 (tt) cc_final: 0.8980 (mm) REVERT: J 159 ASN cc_start: 0.7446 (t0) cc_final: 0.6632 (t0) REVERT: K 65 GLU cc_start: 0.9372 (pm20) cc_final: 0.8851 (tm-30) REVERT: K 156 MET cc_start: 0.9515 (ptm) cc_final: 0.9229 (ppp) REVERT: K 206 MET cc_start: 0.8446 (ptp) cc_final: 0.8180 (ptt) REVERT: L 26 MET cc_start: 0.9056 (mmt) cc_final: 0.8759 (mmt) REVERT: L 132 LEU cc_start: 0.9404 (mt) cc_final: 0.9124 (tp) REVERT: L 176 MET cc_start: 0.8644 (ptp) cc_final: 0.8256 (ptm) REVERT: L 228 ASP cc_start: 0.9054 (m-30) cc_final: 0.8664 (t0) REVERT: M 75 MET cc_start: 0.9139 (mmm) cc_final: 0.8689 (mmm) REVERT: M 135 PHE cc_start: 0.9360 (p90) cc_final: 0.8856 (p90) REVERT: M 136 MET cc_start: 0.8294 (mtt) cc_final: 0.7958 (mtt) REVERT: M 181 MET cc_start: 0.8802 (ptp) cc_final: 0.8265 (ptp) REVERT: N 32 ASP cc_start: 0.9205 (m-30) cc_final: 0.8670 (t0) REVERT: N 86 MET cc_start: 0.9773 (tpp) cc_final: 0.9558 (tpp) REVERT: N 119 MET cc_start: 0.8700 (pmm) cc_final: 0.8009 (pmm) REVERT: N 147 MET cc_start: 0.8115 (mmp) cc_final: 0.7411 (mmm) REVERT: O 86 MET cc_start: 0.9113 (tmm) cc_final: 0.8728 (tmm) REVERT: O 194 LYS cc_start: 0.9219 (mmmm) cc_final: 0.8952 (mmtm) REVERT: P 14 MET cc_start: 0.8163 (ptm) cc_final: 0.7950 (ptt) REVERT: P 39 PHE cc_start: 0.9011 (t80) cc_final: 0.8448 (t80) REVERT: P 88 MET cc_start: 0.9240 (ptp) cc_final: 0.8886 (ptt) REVERT: Q 69 MET cc_start: 0.9413 (mmm) cc_final: 0.9038 (mmt) REVERT: Q 124 LEU cc_start: 0.7853 (mt) cc_final: 0.7504 (mt) REVERT: R 139 MET cc_start: 0.9228 (ttp) cc_final: 0.8830 (tmm) REVERT: S 2 PHE cc_start: 0.7803 (p90) cc_final: 0.5552 (p90) REVERT: S 48 ASP cc_start: 0.9197 (m-30) cc_final: 0.8515 (p0) REVERT: S 83 MET cc_start: 0.8472 (ptm) cc_final: 0.8143 (ptm) REVERT: S 91 MET cc_start: 0.9552 (ttm) cc_final: 0.9203 (mmm) REVERT: S 144 MET cc_start: 0.9576 (mtt) cc_final: 0.8828 (mmm) REVERT: T 127 MET cc_start: 0.8675 (ttm) cc_final: 0.8300 (ttt) REVERT: g 125 TYR cc_start: 0.9080 (m-80) cc_final: 0.8682 (m-80) REVERT: g 134 LEU cc_start: 0.9617 (mt) cc_final: 0.9097 (pp) REVERT: j 20 GLU cc_start: 0.9658 (mp0) cc_final: 0.9448 (pm20) REVERT: j 178 ASP cc_start: 0.9395 (p0) cc_final: 0.9045 (t0) REVERT: k 107 MET cc_start: 0.7811 (mtp) cc_final: 0.7547 (mtt) REVERT: l 26 MET cc_start: 0.8620 (mmt) cc_final: 0.7988 (mmt) REVERT: m 75 MET cc_start: 0.9293 (mtp) cc_final: 0.8776 (mtp) REVERT: m 135 PHE cc_start: 0.9269 (p90) cc_final: 0.8972 (p90) REVERT: m 150 MET cc_start: 0.9394 (tpt) cc_final: 0.8870 (ppp) REVERT: n 85 GLU cc_start: 0.9589 (mm-30) cc_final: 0.9340 (mp0) REVERT: n 86 MET cc_start: 0.9677 (mmm) cc_final: 0.9391 (mmm) REVERT: n 87 CYS cc_start: 0.9705 (m) cc_final: 0.9262 (p) REVERT: n 119 MET cc_start: 0.8790 (ppp) cc_final: 0.8453 (ppp) REVERT: o 54 MET cc_start: 0.9537 (mmm) cc_final: 0.9249 (mmp) REVERT: o 82 MET cc_start: 0.9593 (mtp) cc_final: 0.9389 (mtp) REVERT: o 86 MET cc_start: 0.9795 (mmp) cc_final: 0.9512 (mmm) REVERT: o 127 MET cc_start: 0.9085 (mmm) cc_final: 0.7897 (mtp) REVERT: o 157 GLU cc_start: 0.9487 (mm-30) cc_final: 0.9275 (mm-30) REVERT: p 14 MET cc_start: 0.8868 (ttp) cc_final: 0.8321 (ptm) REVERT: p 75 GLU cc_start: 0.9476 (mt-10) cc_final: 0.8901 (mm-30) REVERT: p 96 TYR cc_start: 0.9492 (t80) cc_final: 0.9149 (t80) REVERT: p 149 MET cc_start: 0.9503 (mmm) cc_final: 0.9246 (mmm) REVERT: p 171 MET cc_start: 0.9565 (mmm) cc_final: 0.9285 (mmm) REVERT: q 38 MET cc_start: 0.9341 (mmp) cc_final: 0.8997 (mmm) REVERT: q 124 LEU cc_start: 0.9106 (mt) cc_final: 0.8554 (mt) REVERT: q 158 GLU cc_start: 0.9697 (mt-10) cc_final: 0.9357 (tm-30) REVERT: r 86 MET cc_start: 0.9771 (tpt) cc_final: 0.9536 (tpt) REVERT: s 74 MET cc_start: 0.9437 (mtp) cc_final: 0.9207 (mtp) REVERT: s 83 MET cc_start: 0.7705 (ptm) cc_final: 0.7226 (ptm) REVERT: s 91 MET cc_start: 0.9479 (ppp) cc_final: 0.9259 (ppp) REVERT: t 70 MET cc_start: 0.9787 (mmp) cc_final: 0.9392 (mtp) REVERT: t 96 MET cc_start: 0.9781 (mmp) cc_final: 0.9436 (mmm) REVERT: t 112 ILE cc_start: 0.9471 (mt) cc_final: 0.8756 (tt) REVERT: t 214 MET cc_start: 0.8832 (mpp) cc_final: 0.8511 (mpp) outliers start: 5 outliers final: 3 residues processed: 811 average time/residue: 0.8976 time to fit residues: 1266.7431 Evaluate side-chains 654 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 651 time to evaluate : 9.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1267 random chunks: chunk 412 optimal weight: 5.9990 chunk 1102 optimal weight: 6.9990 chunk 242 optimal weight: 0.9980 chunk 719 optimal weight: 8.9990 chunk 302 optimal weight: 20.0000 chunk 1225 optimal weight: 9.9990 chunk 1017 optimal weight: 2.9990 chunk 567 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 405 optimal weight: 10.0000 chunk 643 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 HIS ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 389 ASN U 421 GLN U 880 ASN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 329 HIS ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 456 GLN ** X 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 405 GLN X 416 ASN ** Y 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 254 ASN ** Z 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 HIS C 50 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS I 20 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 GLN ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 GLN ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 HIS g 90 GLN h 71 HIS ** h 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 215 GLN k 98 ASN ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 101626 Z= 0.201 Angle : 0.673 14.496 137470 Z= 0.347 Chirality : 0.044 0.328 15653 Planarity : 0.005 0.095 17764 Dihedral : 6.885 87.959 14167 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 22.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.13 % Favored : 90.72 % Rotamer: Outliers : 0.08 % Allowed : 2.00 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.84 (0.07), residues: 12733 helix: -0.13 (0.07), residues: 5577 sheet: -1.04 (0.12), residues: 1702 loop : -2.45 (0.08), residues: 5454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP Y 364 HIS 0.011 0.001 HIS Z 196 PHE 0.037 0.002 PHE k 22 TYR 0.032 0.002 TYR L 137 ARG 0.013 0.000 ARG X 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 806 time to evaluate : 9.250 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: a 312 MET cc_start: 0.8766 (mtm) cc_final: 0.8535 (mtp) REVERT: a 363 MET cc_start: 0.8932 (mtm) cc_final: 0.8655 (mtt) REVERT: b 1 MET cc_start: 0.1985 (mmt) cc_final: -0.0279 (ppp) REVERT: b 86 PHE cc_start: 0.7964 (t80) cc_final: 0.7261 (t80) REVERT: b 107 MET cc_start: 0.6722 (ttm) cc_final: 0.6429 (mpp) REVERT: c 41 MET cc_start: 0.8838 (mmp) cc_final: 0.8495 (mmm) REVERT: c 54 MET cc_start: 0.7876 (pmm) cc_final: 0.7399 (pmm) REVERT: c 75 MET cc_start: 0.3709 (mmm) cc_final: 0.3088 (mmm) REVERT: c 160 PHE cc_start: 0.9008 (m-80) cc_final: 0.8791 (m-80) REVERT: c 224 SER cc_start: 0.7627 (t) cc_final: 0.7133 (m) REVERT: c 226 MET cc_start: 0.9269 (tpp) cc_final: 0.8795 (tmm) REVERT: d 1 MET cc_start: 0.6437 (ttt) cc_final: 0.5620 (tpp) REVERT: f 33 ARG cc_start: 0.6597 (mpt90) cc_final: 0.5526 (tpt90) REVERT: f 185 LEU cc_start: 0.4068 (mt) cc_final: 0.3237 (pt) REVERT: f 275 MET cc_start: 0.7484 (pmm) cc_final: 0.6118 (tpt) REVERT: f 512 MET cc_start: 0.6564 (tpt) cc_final: 0.5467 (tpt) REVERT: U 206 MET cc_start: 0.7296 (mmp) cc_final: 0.6917 (mmp) REVERT: U 532 MET cc_start: 0.9139 (ptm) cc_final: 0.8787 (ptm) REVERT: U 556 MET cc_start: 0.7754 (mmt) cc_final: 0.7432 (mmm) REVERT: U 560 MET cc_start: 0.8052 (mmt) cc_final: 0.7498 (mmm) REVERT: U 654 MET cc_start: 0.9207 (mmp) cc_final: 0.8876 (mmm) REVERT: U 770 TRP cc_start: 0.7100 (m-90) cc_final: 0.6603 (m-90) REVERT: U 885 MET cc_start: 0.7665 (mmt) cc_final: 0.6991 (mtt) REVERT: W 190 MET cc_start: 0.8577 (ttm) cc_final: 0.8107 (tpp) REVERT: W 312 MET cc_start: 0.5216 (tpp) cc_final: 0.4735 (tpt) REVERT: W 329 ARG cc_start: 0.7211 (mpp-170) cc_final: 0.6724 (mmt180) REVERT: W 428 TRP cc_start: 0.8956 (m100) cc_final: 0.7858 (m100) REVERT: W 437 SER cc_start: 0.9454 (t) cc_final: 0.9236 (m) REVERT: X 212 MET cc_start: 0.8704 (mmp) cc_final: 0.8297 (mmp) REVERT: X 374 PHE cc_start: 0.9218 (t80) cc_final: 0.8499 (t80) REVERT: X 397 TYR cc_start: 0.9193 (m-80) cc_final: 0.8951 (m-10) REVERT: Y 214 MET cc_start: 0.7571 (ptt) cc_final: 0.7319 (ptp) REVERT: Z 78 MET cc_start: 0.9040 (mmp) cc_final: 0.8588 (mmm) REVERT: A 85 GLN cc_start: 0.8922 (pm20) cc_final: 0.8717 (pm20) REVERT: A 256 MET cc_start: 0.8916 (mmp) cc_final: 0.8463 (mmp) REVERT: A 299 MET cc_start: 0.7948 (ptp) cc_final: 0.7574 (ptp) REVERT: A 319 MET cc_start: 0.7818 (ppp) cc_final: 0.7613 (ppp) REVERT: A 430 MET cc_start: 0.6626 (tpt) cc_final: 0.5745 (tpp) REVERT: A 432 TYR cc_start: 0.7601 (m-10) cc_final: 0.7007 (m-80) REVERT: B 405 MET cc_start: 0.8352 (mmp) cc_final: 0.7989 (mmp) REVERT: B 412 MET cc_start: 0.7883 (tpp) cc_final: 0.7549 (tpp) REVERT: C 221 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7697 (mt0) REVERT: C 368 MET cc_start: 0.9336 (mtt) cc_final: 0.9015 (mtm) REVERT: C 377 HIS cc_start: 0.8526 (m-70) cc_final: 0.8192 (p-80) REVERT: D 59 GLU cc_start: 0.9654 (tt0) cc_final: 0.9316 (tm-30) REVERT: D 214 MET cc_start: 0.7601 (ptp) cc_final: 0.7210 (ptp) REVERT: D 296 MET cc_start: 0.9105 (tpt) cc_final: 0.8768 (tmm) REVERT: D 304 ASN cc_start: 0.9574 (t0) cc_final: 0.9258 (t0) REVERT: E 220 ASN cc_start: 0.9514 (t0) cc_final: 0.9165 (t0) REVERT: E 258 MET cc_start: 0.9247 (ptp) cc_final: 0.8972 (ptp) REVERT: E 262 ASN cc_start: 0.9720 (t0) cc_final: 0.9012 (p0) REVERT: E 336 ASP cc_start: 0.8677 (t0) cc_final: 0.8474 (m-30) REVERT: E 382 SER cc_start: 0.3668 (p) cc_final: 0.3333 (t) REVERT: G 209 ASP cc_start: 0.7933 (m-30) cc_final: 0.7663 (t0) REVERT: H 38 ILE cc_start: 0.9055 (mm) cc_final: 0.8760 (tp) REVERT: I 35 LEU cc_start: 0.9265 (pt) cc_final: 0.8828 (mt) REVERT: I 45 LEU cc_start: 0.9256 (mm) cc_final: 0.8561 (tt) REVERT: I 163 CYS cc_start: 0.8396 (p) cc_final: 0.7686 (t) REVERT: I 166 ASN cc_start: 0.8930 (t0) cc_final: 0.8365 (p0) REVERT: J 132 LEU cc_start: 0.9442 (tt) cc_final: 0.8884 (mm) REVERT: J 159 ASN cc_start: 0.7192 (t0) cc_final: 0.6303 (t0) REVERT: K 65 GLU cc_start: 0.9375 (pm20) cc_final: 0.8981 (mp0) REVERT: L 88 MET cc_start: 0.9789 (ttp) cc_final: 0.9400 (ptt) REVERT: L 132 LEU cc_start: 0.9400 (mt) cc_final: 0.9146 (tp) REVERT: L 176 MET cc_start: 0.8561 (ptp) cc_final: 0.8126 (ptm) REVERT: L 228 ASP cc_start: 0.9066 (m-30) cc_final: 0.8692 (t0) REVERT: M 75 MET cc_start: 0.9242 (mmm) cc_final: 0.8748 (mmm) REVERT: M 135 PHE cc_start: 0.9357 (p90) cc_final: 0.8847 (p90) REVERT: M 136 MET cc_start: 0.8451 (mtt) cc_final: 0.8244 (mtt) REVERT: M 181 MET cc_start: 0.8719 (ptp) cc_final: 0.8098 (ptp) REVERT: N 32 ASP cc_start: 0.9130 (m-30) cc_final: 0.8621 (t70) REVERT: N 86 MET cc_start: 0.9752 (tpp) cc_final: 0.9516 (tpp) REVERT: N 95 MET cc_start: 0.8729 (mpp) cc_final: 0.8010 (mpp) REVERT: N 116 MET cc_start: 0.8786 (mpp) cc_final: 0.8485 (mmp) REVERT: N 119 MET cc_start: 0.8564 (pmm) cc_final: 0.7902 (pmm) REVERT: O 86 MET cc_start: 0.9055 (tmm) cc_final: 0.8709 (tmm) REVERT: O 157 GLU cc_start: 0.9269 (mp0) cc_final: 0.9068 (mp0) REVERT: O 194 LYS cc_start: 0.9208 (mmmm) cc_final: 0.8942 (mmtm) REVERT: P 39 PHE cc_start: 0.9008 (t80) cc_final: 0.8442 (t80) REVERT: P 88 MET cc_start: 0.9217 (ptp) cc_final: 0.8896 (ptt) REVERT: P 146 MET cc_start: 0.8654 (ptp) cc_final: 0.8361 (ptt) REVERT: Q 69 MET cc_start: 0.9411 (mmm) cc_final: 0.9026 (mmt) REVERT: Q 124 LEU cc_start: 0.7878 (mt) cc_final: 0.7612 (mt) REVERT: R 45 MET cc_start: 0.9768 (ppp) cc_final: 0.9490 (ppp) REVERT: R 139 MET cc_start: 0.9183 (ttp) cc_final: 0.8779 (tmm) REVERT: S 48 ASP cc_start: 0.9224 (m-30) cc_final: 0.8537 (p0) REVERT: S 83 MET cc_start: 0.8814 (ptm) cc_final: 0.7522 (ptm) REVERT: S 144 MET cc_start: 0.9589 (mtt) cc_final: 0.8835 (mmm) REVERT: T 43 MET cc_start: 0.9338 (tmm) cc_final: 0.9128 (tmm) REVERT: T 102 LYS cc_start: 0.9497 (ptpp) cc_final: 0.9193 (pttm) REVERT: T 127 MET cc_start: 0.8596 (ttm) cc_final: 0.8370 (ttt) REVERT: T 173 MET cc_start: 0.9644 (mmm) cc_final: 0.9298 (mtm) REVERT: g 96 TYR cc_start: 0.9394 (t80) cc_final: 0.9149 (t80) REVERT: g 125 TYR cc_start: 0.9128 (m-80) cc_final: 0.8713 (m-80) REVERT: g 134 LEU cc_start: 0.9613 (mt) cc_final: 0.9110 (pp) REVERT: g 202 LEU cc_start: 0.9735 (tt) cc_final: 0.9419 (mm) REVERT: i 175 LEU cc_start: 0.9027 (pp) cc_final: 0.8802 (pp) REVERT: j 43 LEU cc_start: 0.9844 (pp) cc_final: 0.9512 (tt) REVERT: j 178 ASP cc_start: 0.9237 (p0) cc_final: 0.8814 (t0) REVERT: k 107 MET cc_start: 0.7823 (mtp) cc_final: 0.7612 (mtt) REVERT: k 143 PHE cc_start: 0.9028 (m-80) cc_final: 0.8792 (m-80) REVERT: l 26 MET cc_start: 0.8636 (mmt) cc_final: 0.8009 (mmt) REVERT: l 159 MET cc_start: 0.9046 (tmm) cc_final: 0.8679 (tmm) REVERT: m 75 MET cc_start: 0.9264 (mtp) cc_final: 0.8756 (mtp) REVERT: m 135 PHE cc_start: 0.9307 (p90) cc_final: 0.9042 (p90) REVERT: m 150 MET cc_start: 0.9428 (tpt) cc_final: 0.8988 (ppp) REVERT: n 85 GLU cc_start: 0.9576 (mm-30) cc_final: 0.9303 (mp0) REVERT: n 86 MET cc_start: 0.9689 (mmm) cc_final: 0.9381 (mmm) REVERT: n 87 CYS cc_start: 0.9705 (m) cc_final: 0.9497 (t) REVERT: n 119 MET cc_start: 0.8811 (ppp) cc_final: 0.8488 (ppp) REVERT: n 120 MET cc_start: 0.8640 (ppp) cc_final: 0.7896 (ppp) REVERT: o 54 MET cc_start: 0.9557 (mmm) cc_final: 0.9210 (mmp) REVERT: o 82 MET cc_start: 0.9566 (mtp) cc_final: 0.9346 (mtp) REVERT: o 86 MET cc_start: 0.9785 (mmp) cc_final: 0.9454 (mmm) REVERT: o 127 MET cc_start: 0.9086 (mmm) cc_final: 0.8129 (mtt) REVERT: o 157 GLU cc_start: 0.9464 (mm-30) cc_final: 0.9247 (mm-30) REVERT: p 12 MET cc_start: 0.9528 (tpp) cc_final: 0.9292 (tpt) REVERT: p 14 MET cc_start: 0.9105 (ttp) cc_final: 0.8824 (ttp) REVERT: p 75 GLU cc_start: 0.9456 (mt-10) cc_final: 0.8852 (mm-30) REVERT: p 96 TYR cc_start: 0.9428 (t80) cc_final: 0.9074 (t80) REVERT: p 149 MET cc_start: 0.9487 (mmm) cc_final: 0.9255 (mmp) REVERT: p 157 ASN cc_start: 0.9483 (t0) cc_final: 0.9181 (t0) REVERT: p 171 MET cc_start: 0.9596 (mmm) cc_final: 0.9336 (mmm) REVERT: q 28 MET cc_start: 0.8690 (mpp) cc_final: 0.8264 (mpp) REVERT: q 38 MET cc_start: 0.9325 (mmp) cc_final: 0.8882 (mmm) REVERT: q 124 LEU cc_start: 0.9240 (mt) cc_final: 0.8851 (mt) REVERT: r 86 MET cc_start: 0.9755 (tpt) cc_final: 0.9529 (tpp) REVERT: r 89 GLN cc_start: 0.9603 (tm-30) cc_final: 0.9351 (tm-30) REVERT: r 93 MET cc_start: 0.7629 (mtp) cc_final: 0.7300 (mtp) REVERT: r 100 MET cc_start: 0.8927 (mtm) cc_final: 0.8566 (mtt) REVERT: s 74 MET cc_start: 0.9509 (mtp) cc_final: 0.9290 (mtp) REVERT: s 91 MET cc_start: 0.9479 (ppp) cc_final: 0.9243 (ppp) REVERT: s 144 MET cc_start: 0.9158 (mtp) cc_final: 0.8788 (mtp) REVERT: t 59 ASP cc_start: 0.9291 (m-30) cc_final: 0.9056 (m-30) REVERT: t 70 MET cc_start: 0.9792 (mmp) cc_final: 0.9321 (mtp) REVERT: t 96 MET cc_start: 0.9776 (mmp) cc_final: 0.9506 (mmm) REVERT: t 112 ILE cc_start: 0.9504 (mt) cc_final: 0.8783 (tt) REVERT: t 144 TYR cc_start: 0.9261 (m-80) cc_final: 0.8992 (m-80) REVERT: t 214 MET cc_start: 0.8817 (mpp) cc_final: 0.8456 (mpp) outliers start: 8 outliers final: 3 residues processed: 814 average time/residue: 0.8903 time to fit residues: 1271.5681 Evaluate side-chains 643 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 640 time to evaluate : 9.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1267 random chunks: chunk 1181 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 698 optimal weight: 8.9990 chunk 895 optimal weight: 10.0000 chunk 693 optimal weight: 20.0000 chunk 1031 optimal weight: 10.0000 chunk 684 optimal weight: 8.9990 chunk 1221 optimal weight: 20.0000 chunk 764 optimal weight: 7.9990 chunk 744 optimal weight: 9.9990 chunk 563 optimal weight: 10.0000 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 290 GLN ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 79 GLN ** b 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 149 GLN ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 15 GLN f 224 ASN ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 389 ASN U 421 GLN U 768 GLN U 880 ASN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 84 ASN ** W 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 405 GLN ** Y 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 HIS ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 GLN ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 GLN ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 GLN ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 GLN g 90 GLN h 71 HIS ** h 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 167 ASN ** i 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 215 GLN ** k 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 79 ASN ** t 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 101626 Z= 0.272 Angle : 0.715 15.209 137470 Z= 0.373 Chirality : 0.045 0.329 15653 Planarity : 0.005 0.086 17764 Dihedral : 6.947 89.869 14167 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 27.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.14 % Favored : 89.70 % Rotamer: Outliers : 0.08 % Allowed : 1.93 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.07), residues: 12733 helix: -0.15 (0.07), residues: 5562 sheet: -1.01 (0.12), residues: 1670 loop : -2.47 (0.08), residues: 5501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP Y 364 HIS 0.012 0.001 HIS X 322 PHE 0.038 0.002 PHE U 728 TYR 0.043 0.002 TYR M 238 ARG 0.008 0.001 ARG c 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 753 time to evaluate : 10.378 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: a 312 MET cc_start: 0.8732 (mtm) cc_final: 0.8439 (mtp) REVERT: a 349 MET cc_start: 0.7951 (ppp) cc_final: 0.7462 (ppp) REVERT: a 363 MET cc_start: 0.8939 (mtm) cc_final: 0.8611 (mtt) REVERT: b 1 MET cc_start: 0.2063 (mmt) cc_final: -0.0133 (ppp) REVERT: b 86 PHE cc_start: 0.7977 (t80) cc_final: 0.7262 (t80) REVERT: c 54 MET cc_start: 0.7914 (pmm) cc_final: 0.6964 (pmm) REVERT: c 75 MET cc_start: 0.4588 (mmm) cc_final: 0.4183 (mmm) REVERT: c 120 CYS cc_start: 0.8327 (p) cc_final: 0.8041 (p) REVERT: c 224 SER cc_start: 0.7233 (t) cc_final: 0.6337 (m) REVERT: c 226 MET cc_start: 0.9296 (tpp) cc_final: 0.8812 (tmm) REVERT: d 1 MET cc_start: 0.6868 (ttt) cc_final: 0.5939 (tpp) REVERT: f 33 ARG cc_start: 0.6759 (mpt90) cc_final: 0.6012 (tpt90) REVERT: f 275 MET cc_start: 0.7575 (pmm) cc_final: 0.6169 (tpt) REVERT: f 370 MET cc_start: 0.6440 (mmp) cc_final: 0.5744 (mmp) REVERT: f 512 MET cc_start: 0.6667 (tpt) cc_final: 0.5988 (tpt) REVERT: f 557 TRP cc_start: 0.8069 (m-10) cc_final: 0.7531 (m100) REVERT: U 206 MET cc_start: 0.7126 (mmp) cc_final: 0.6728 (mmp) REVERT: U 532 MET cc_start: 0.9119 (ptm) cc_final: 0.8773 (ptm) REVERT: U 556 MET cc_start: 0.7700 (mmt) cc_final: 0.7386 (mmm) REVERT: U 560 MET cc_start: 0.8168 (mmt) cc_final: 0.7590 (mmm) REVERT: U 654 MET cc_start: 0.9249 (mmp) cc_final: 0.8922 (mmm) REVERT: U 766 PHE cc_start: 0.9070 (t80) cc_final: 0.8738 (t80) REVERT: U 885 MET cc_start: 0.7770 (mmt) cc_final: 0.6895 (mtt) REVERT: W 190 MET cc_start: 0.8630 (ttm) cc_final: 0.8133 (tpp) REVERT: W 230 MET cc_start: 0.7763 (mmp) cc_final: 0.7538 (mmp) REVERT: W 312 MET cc_start: 0.5470 (tpp) cc_final: 0.4869 (tpt) REVERT: W 329 ARG cc_start: 0.7145 (mpp-170) cc_final: 0.6720 (mmt180) REVERT: W 428 TRP cc_start: 0.9037 (m100) cc_final: 0.7966 (m100) REVERT: W 437 SER cc_start: 0.9436 (t) cc_final: 0.9195 (m) REVERT: X 212 MET cc_start: 0.8707 (mmp) cc_final: 0.8219 (mmp) REVERT: X 374 PHE cc_start: 0.9099 (t80) cc_final: 0.8347 (t80) REVERT: X 397 TYR cc_start: 0.9194 (m-80) cc_final: 0.8913 (m-10) REVERT: Y 364 TRP cc_start: 0.9375 (m-90) cc_final: 0.9157 (m-90) REVERT: Z 7 GLN cc_start: 0.9155 (tp-100) cc_final: 0.8904 (tp-100) REVERT: Z 47 VAL cc_start: 0.7810 (p) cc_final: 0.7574 (t) REVERT: Z 78 MET cc_start: 0.9076 (mmp) cc_final: 0.8627 (mmm) REVERT: Z 273 HIS cc_start: 0.9147 (m90) cc_final: 0.8936 (m170) REVERT: A 256 MET cc_start: 0.8927 (mmp) cc_final: 0.8449 (mmp) REVERT: A 299 MET cc_start: 0.8026 (ptp) cc_final: 0.7738 (ptp) REVERT: A 319 MET cc_start: 0.7912 (ppp) cc_final: 0.7678 (ppp) REVERT: A 430 MET cc_start: 0.6594 (tpt) cc_final: 0.5950 (tpp) REVERT: A 432 TYR cc_start: 0.7662 (m-10) cc_final: 0.7075 (m-80) REVERT: B 405 MET cc_start: 0.8397 (mmp) cc_final: 0.7953 (mmp) REVERT: B 412 MET cc_start: 0.7866 (tpp) cc_final: 0.7492 (tpp) REVERT: C 221 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7684 (tt0) REVERT: C 368 MET cc_start: 0.9340 (mtt) cc_final: 0.8942 (mtt) REVERT: C 377 HIS cc_start: 0.8525 (m-70) cc_final: 0.8181 (p-80) REVERT: D 59 GLU cc_start: 0.9656 (tt0) cc_final: 0.9360 (tm-30) REVERT: D 214 MET cc_start: 0.7543 (ptp) cc_final: 0.7125 (ptp) REVERT: D 296 MET cc_start: 0.8995 (tpt) cc_final: 0.8664 (tmm) REVERT: D 304 ASN cc_start: 0.9603 (t0) cc_final: 0.9218 (m-40) REVERT: E 336 ASP cc_start: 0.8701 (t0) cc_final: 0.8470 (m-30) REVERT: E 382 SER cc_start: 0.3678 (p) cc_final: 0.3341 (t) REVERT: G 209 ASP cc_start: 0.7858 (m-30) cc_final: 0.7566 (t0) REVERT: H 38 ILE cc_start: 0.8976 (mm) cc_final: 0.8649 (tp) REVERT: I 45 LEU cc_start: 0.9204 (mm) cc_final: 0.8477 (tt) REVERT: I 163 CYS cc_start: 0.8240 (p) cc_final: 0.7669 (t) REVERT: I 166 ASN cc_start: 0.8990 (t0) cc_final: 0.8442 (p0) REVERT: J 66 ASP cc_start: 0.8493 (t0) cc_final: 0.8112 (p0) REVERT: J 132 LEU cc_start: 0.9435 (tt) cc_final: 0.9224 (mm) REVERT: J 159 ASN cc_start: 0.7168 (t0) cc_final: 0.6218 (t0) REVERT: K 65 GLU cc_start: 0.9394 (pm20) cc_final: 0.9083 (mp0) REVERT: K 107 MET cc_start: 0.8858 (ptp) cc_final: 0.8265 (ptp) REVERT: K 156 MET cc_start: 0.9379 (ppp) cc_final: 0.9033 (ppp) REVERT: L 132 LEU cc_start: 0.9377 (mt) cc_final: 0.9107 (tp) REVERT: M 75 MET cc_start: 0.9268 (mmm) cc_final: 0.8989 (mmm) REVERT: M 181 MET cc_start: 0.8756 (ptp) cc_final: 0.8241 (ptp) REVERT: N 32 ASP cc_start: 0.9165 (m-30) cc_final: 0.8670 (t0) REVERT: N 86 MET cc_start: 0.9735 (tpp) cc_final: 0.9513 (tpp) REVERT: N 95 MET cc_start: 0.8895 (mpp) cc_final: 0.8631 (mpp) REVERT: N 116 MET cc_start: 0.8779 (mpp) cc_final: 0.8490 (mmp) REVERT: N 119 MET cc_start: 0.8564 (pmm) cc_final: 0.7962 (pmm) REVERT: O 86 MET cc_start: 0.9092 (tmm) cc_final: 0.8792 (tmm) REVERT: O 93 TYR cc_start: 0.9240 (m-80) cc_final: 0.8915 (m-80) REVERT: P 14 MET cc_start: 0.7440 (ptt) cc_final: 0.6902 (pmm) REVERT: P 39 PHE cc_start: 0.9039 (t80) cc_final: 0.8493 (t80) REVERT: Q 69 MET cc_start: 0.9470 (mmm) cc_final: 0.9093 (mmt) REVERT: Q 124 LEU cc_start: 0.7769 (mt) cc_final: 0.7379 (mt) REVERT: R 45 MET cc_start: 0.9523 (ppp) cc_final: 0.9268 (ppp) REVERT: R 139 MET cc_start: 0.9204 (ttp) cc_final: 0.8816 (tmm) REVERT: S 48 ASP cc_start: 0.9294 (m-30) cc_final: 0.8653 (p0) REVERT: S 83 MET cc_start: 0.8738 (ptm) cc_final: 0.7659 (ptm) REVERT: S 144 MET cc_start: 0.9621 (mtt) cc_final: 0.8922 (mmm) REVERT: T 127 MET cc_start: 0.8748 (ttm) cc_final: 0.8393 (ttt) REVERT: T 160 LEU cc_start: 0.9382 (mt) cc_final: 0.9099 (tp) REVERT: T 173 MET cc_start: 0.9629 (mmm) cc_final: 0.9311 (mtm) REVERT: g 96 TYR cc_start: 0.9396 (t80) cc_final: 0.9165 (t80) REVERT: g 125 TYR cc_start: 0.9133 (m-80) cc_final: 0.8732 (m-80) REVERT: g 134 LEU cc_start: 0.9601 (mt) cc_final: 0.9096 (pp) REVERT: i 175 LEU cc_start: 0.9147 (pp) cc_final: 0.8907 (pp) REVERT: j 43 LEU cc_start: 0.9854 (pp) cc_final: 0.9408 (mp) REVERT: l 159 MET cc_start: 0.9086 (tmm) cc_final: 0.8773 (tmm) REVERT: m 75 MET cc_start: 0.9271 (mtp) cc_final: 0.8949 (mtp) REVERT: m 150 MET cc_start: 0.9471 (tpt) cc_final: 0.8959 (ppp) REVERT: n 85 GLU cc_start: 0.9576 (mm-30) cc_final: 0.9232 (mt-10) REVERT: n 86 MET cc_start: 0.9712 (mmm) cc_final: 0.9442 (mmm) REVERT: n 87 CYS cc_start: 0.9716 (m) cc_final: 0.9508 (t) REVERT: n 119 MET cc_start: 0.8778 (ppp) cc_final: 0.8407 (ppp) REVERT: n 120 MET cc_start: 0.8670 (ppp) cc_final: 0.7984 (ppp) REVERT: o 54 MET cc_start: 0.9535 (mmm) cc_final: 0.9268 (mmp) REVERT: o 127 MET cc_start: 0.9094 (mmm) cc_final: 0.8139 (mtt) REVERT: o 157 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9247 (mm-30) REVERT: p 75 GLU cc_start: 0.9484 (mt-10) cc_final: 0.8905 (mm-30) REVERT: p 149 MET cc_start: 0.9525 (mmm) cc_final: 0.9222 (mmm) REVERT: p 157 ASN cc_start: 0.9506 (t0) cc_final: 0.9188 (t0) REVERT: p 171 MET cc_start: 0.9602 (mmm) cc_final: 0.9400 (mmm) REVERT: q 1 MET cc_start: 0.9546 (tpt) cc_final: 0.9237 (tpp) REVERT: q 28 MET cc_start: 0.8714 (mpp) cc_final: 0.8427 (mpp) REVERT: q 38 MET cc_start: 0.9335 (mmp) cc_final: 0.9007 (mmm) REVERT: q 58 GLU cc_start: 0.9347 (mp0) cc_final: 0.8860 (mp0) REVERT: q 69 MET cc_start: 0.9110 (tpp) cc_final: 0.8775 (tpp) REVERT: q 124 LEU cc_start: 0.9110 (mt) cc_final: 0.8629 (mt) REVERT: r 86 MET cc_start: 0.9742 (tpt) cc_final: 0.9498 (tpp) REVERT: r 89 GLN cc_start: 0.9592 (tm-30) cc_final: 0.9366 (tm-30) REVERT: r 93 MET cc_start: 0.7679 (mtp) cc_final: 0.7353 (mtp) REVERT: r 100 MET cc_start: 0.8979 (mtm) cc_final: 0.8698 (mtt) REVERT: s 74 MET cc_start: 0.9515 (mtp) cc_final: 0.9308 (mtp) REVERT: s 144 MET cc_start: 0.9101 (mtp) cc_final: 0.8687 (mtp) REVERT: t 70 MET cc_start: 0.9794 (mmp) cc_final: 0.9570 (mmm) REVERT: t 96 MET cc_start: 0.9801 (mmp) cc_final: 0.9332 (mmm) REVERT: t 112 ILE cc_start: 0.9493 (mt) cc_final: 0.8784 (tt) REVERT: t 144 TYR cc_start: 0.9318 (m-80) cc_final: 0.9011 (m-80) REVERT: t 214 MET cc_start: 0.8722 (mpp) cc_final: 0.8328 (mpp) outliers start: 8 outliers final: 3 residues processed: 760 average time/residue: 0.8860 time to fit residues: 1183.3141 Evaluate side-chains 627 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 624 time to evaluate : 9.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1267 random chunks: chunk 755 optimal weight: 7.9990 chunk 487 optimal weight: 9.9990 chunk 729 optimal weight: 0.9990 chunk 367 optimal weight: 2.9990 chunk 239 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 chunk 776 optimal weight: 7.9990 chunk 831 optimal weight: 6.9990 chunk 603 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 959 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 79 GLN ** b 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 HIS ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 15 GLN ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 389 ASN U 421 GLN U 880 ASN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 84 ASN ** W 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 440 ASN ** X 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 405 GLN ** Y 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 254 ASN ** Z 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 GLN ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 90 GLN ** h 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 215 GLN ** k 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 101626 Z= 0.180 Angle : 0.667 16.196 137470 Z= 0.341 Chirality : 0.044 0.319 15653 Planarity : 0.005 0.084 17764 Dihedral : 6.763 89.008 14167 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 21.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.06 % Favored : 90.80 % Rotamer: Outliers : 0.06 % Allowed : 1.05 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.59 (0.07), residues: 12733 helix: 0.10 (0.07), residues: 5573 sheet: -0.88 (0.12), residues: 1691 loop : -2.35 (0.08), residues: 5469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Y 364 HIS 0.011 0.001 HIS Z 196 PHE 0.036 0.001 PHE U 728 TYR 0.028 0.001 TYR c 255 ARG 0.017 0.000 ARG f 785 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 785 time to evaluate : 9.216 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: a 312 MET cc_start: 0.8704 (mtm) cc_final: 0.8430 (mtp) REVERT: a 349 MET cc_start: 0.7843 (ppp) cc_final: 0.7198 (ppp) REVERT: a 363 MET cc_start: 0.8848 (mtm) cc_final: 0.8573 (mtt) REVERT: b 1 MET cc_start: 0.2081 (mmt) cc_final: -0.0218 (ppp) REVERT: b 86 PHE cc_start: 0.7923 (t80) cc_final: 0.7442 (t80) REVERT: c 54 MET cc_start: 0.7789 (pmm) cc_final: 0.6924 (pmm) REVERT: c 75 MET cc_start: 0.4460 (mmm) cc_final: 0.4037 (mmm) REVERT: c 226 MET cc_start: 0.9404 (tpp) cc_final: 0.8891 (tmm) REVERT: c 292 MET cc_start: 0.9336 (mmp) cc_final: 0.9134 (mmm) REVERT: d 1 MET cc_start: 0.6655 (ttt) cc_final: 0.5726 (tpp) REVERT: f 33 ARG cc_start: 0.6921 (mpt90) cc_final: 0.6175 (tpt90) REVERT: f 275 MET cc_start: 0.7532 (pmm) cc_final: 0.6160 (tpt) REVERT: U 206 MET cc_start: 0.7109 (mmp) cc_final: 0.6709 (mmp) REVERT: U 532 MET cc_start: 0.9077 (ptm) cc_final: 0.8717 (ptm) REVERT: U 556 MET cc_start: 0.7677 (mmt) cc_final: 0.7358 (mmm) REVERT: U 560 MET cc_start: 0.7802 (mmt) cc_final: 0.7263 (mmm) REVERT: U 654 MET cc_start: 0.9240 (mmp) cc_final: 0.8914 (mmm) REVERT: U 675 MET cc_start: 0.9473 (tpt) cc_final: 0.9272 (tpp) REVERT: U 885 MET cc_start: 0.7780 (mmt) cc_final: 0.6875 (mtt) REVERT: W 190 MET cc_start: 0.8576 (ttm) cc_final: 0.8072 (tpp) REVERT: W 312 MET cc_start: 0.5131 (tpp) cc_final: 0.4582 (tpt) REVERT: W 428 TRP cc_start: 0.9017 (m100) cc_final: 0.7935 (m100) REVERT: W 437 SER cc_start: 0.9409 (t) cc_final: 0.9169 (m) REVERT: X 254 MET cc_start: 0.7314 (ttt) cc_final: 0.6753 (tpp) REVERT: X 374 PHE cc_start: 0.9188 (t80) cc_final: 0.8553 (t80) REVERT: X 397 TYR cc_start: 0.9208 (m-80) cc_final: 0.8901 (m-80) REVERT: Y 364 TRP cc_start: 0.9342 (m-90) cc_final: 0.9075 (m-90) REVERT: Z 7 GLN cc_start: 0.9078 (tp-100) cc_final: 0.8817 (tp-100) REVERT: Z 78 MET cc_start: 0.9037 (mmp) cc_final: 0.8593 (mmm) REVERT: A 256 MET cc_start: 0.8931 (mmp) cc_final: 0.8486 (mmp) REVERT: A 299 MET cc_start: 0.7965 (ptp) cc_final: 0.7697 (ptp) REVERT: A 319 MET cc_start: 0.7817 (ppp) cc_final: 0.7573 (ppp) REVERT: A 430 MET cc_start: 0.6665 (tpt) cc_final: 0.6053 (tpp) REVERT: A 432 TYR cc_start: 0.7645 (m-10) cc_final: 0.6995 (m-80) REVERT: B 405 MET cc_start: 0.8386 (mmp) cc_final: 0.8123 (mmp) REVERT: B 412 MET cc_start: 0.8019 (tpp) cc_final: 0.7689 (tpp) REVERT: C 221 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7756 (tt0) REVERT: C 273 MET cc_start: 0.9678 (tmm) cc_final: 0.9209 (mtp) REVERT: C 368 MET cc_start: 0.9362 (mtt) cc_final: 0.8977 (mtm) REVERT: C 377 HIS cc_start: 0.8511 (m-70) cc_final: 0.8173 (p-80) REVERT: D 59 GLU cc_start: 0.9649 (tt0) cc_final: 0.9348 (tm-30) REVERT: D 214 MET cc_start: 0.7402 (ptp) cc_final: 0.6957 (ptp) REVERT: D 296 MET cc_start: 0.9032 (tpt) cc_final: 0.8727 (tmm) REVERT: D 304 ASN cc_start: 0.9570 (t0) cc_final: 0.9074 (m-40) REVERT: E 258 MET cc_start: 0.9285 (ptp) cc_final: 0.8906 (ptp) REVERT: E 262 ASN cc_start: 0.9707 (t0) cc_final: 0.8877 (p0) REVERT: E 336 ASP cc_start: 0.8862 (t0) cc_final: 0.8628 (m-30) REVERT: E 382 SER cc_start: 0.3670 (p) cc_final: 0.3328 (t) REVERT: G 209 ASP cc_start: 0.7893 (m-30) cc_final: 0.7625 (t0) REVERT: I 45 LEU cc_start: 0.9202 (mm) cc_final: 0.8574 (tt) REVERT: I 166 ASN cc_start: 0.9013 (t0) cc_final: 0.8495 (p0) REVERT: J 66 ASP cc_start: 0.8465 (t0) cc_final: 0.8026 (p0) REVERT: J 132 LEU cc_start: 0.9396 (tt) cc_final: 0.8859 (mm) REVERT: J 159 ASN cc_start: 0.6861 (t0) cc_final: 0.6225 (t0) REVERT: K 65 GLU cc_start: 0.9361 (pm20) cc_final: 0.8986 (mp0) REVERT: K 107 MET cc_start: 0.8822 (ptp) cc_final: 0.8239 (ptp) REVERT: K 156 MET cc_start: 0.9401 (ppp) cc_final: 0.9170 (ppp) REVERT: L 26 MET cc_start: 0.9283 (mmt) cc_final: 0.8999 (mmt) REVERT: L 88 MET cc_start: 0.9803 (ttp) cc_final: 0.9399 (ptt) REVERT: L 132 LEU cc_start: 0.9379 (mt) cc_final: 0.9141 (tp) REVERT: L 176 MET cc_start: 0.9210 (ppp) cc_final: 0.8719 (ptp) REVERT: M 75 MET cc_start: 0.9296 (mmm) cc_final: 0.8875 (mmm) REVERT: M 135 PHE cc_start: 0.9510 (p90) cc_final: 0.9009 (p90) REVERT: M 181 MET cc_start: 0.8709 (ptp) cc_final: 0.8117 (ptp) REVERT: N 32 ASP cc_start: 0.9110 (m-30) cc_final: 0.8609 (t70) REVERT: N 86 MET cc_start: 0.9718 (tpp) cc_final: 0.9474 (tpp) REVERT: N 95 MET cc_start: 0.8867 (mpp) cc_final: 0.8538 (mmm) REVERT: N 116 MET cc_start: 0.8797 (mpp) cc_final: 0.8418 (mmp) REVERT: N 119 MET cc_start: 0.8322 (pmm) cc_final: 0.7700 (pmm) REVERT: O 80 ASN cc_start: 0.8539 (t0) cc_final: 0.8252 (t0) REVERT: O 86 MET cc_start: 0.9109 (tmm) cc_final: 0.8821 (ppp) REVERT: O 93 TYR cc_start: 0.9241 (m-80) cc_final: 0.8916 (m-80) REVERT: O 157 GLU cc_start: 0.9277 (mp0) cc_final: 0.9062 (mp0) REVERT: P 14 MET cc_start: 0.7480 (ptt) cc_final: 0.6888 (pmm) REVERT: P 39 PHE cc_start: 0.9026 (t80) cc_final: 0.8484 (t80) REVERT: P 135 ASP cc_start: 0.8616 (p0) cc_final: 0.8063 (p0) REVERT: P 146 MET cc_start: 0.8282 (ptp) cc_final: 0.7353 (ptt) REVERT: Q 69 MET cc_start: 0.9451 (mmm) cc_final: 0.9031 (mmt) REVERT: Q 124 LEU cc_start: 0.7910 (mt) cc_final: 0.7632 (mt) REVERT: R 37 ILE cc_start: 0.8498 (mm) cc_final: 0.7987 (mm) REVERT: R 45 MET cc_start: 0.9530 (ppp) cc_final: 0.9253 (ppp) REVERT: R 56 GLU cc_start: 0.9570 (mm-30) cc_final: 0.9161 (mt-10) REVERT: R 139 MET cc_start: 0.9173 (ttp) cc_final: 0.8758 (tmm) REVERT: S 48 ASP cc_start: 0.9358 (m-30) cc_final: 0.8729 (p0) REVERT: S 69 GLU cc_start: 0.9540 (pt0) cc_final: 0.9213 (pp20) REVERT: S 83 MET cc_start: 0.8640 (ptm) cc_final: 0.7393 (ptm) REVERT: S 91 MET cc_start: 0.9389 (mmp) cc_final: 0.8830 (mmm) REVERT: S 92 LEU cc_start: 0.9593 (tp) cc_final: 0.9392 (tp) REVERT: S 144 MET cc_start: 0.9556 (mtt) cc_final: 0.8856 (mmm) REVERT: T 43 MET cc_start: 0.9321 (tmm) cc_final: 0.9107 (tmm) REVERT: T 127 MET cc_start: 0.8695 (ttm) cc_final: 0.8219 (ttm) REVERT: T 160 LEU cc_start: 0.9414 (mt) cc_final: 0.9094 (tp) REVERT: T 172 CYS cc_start: 0.9412 (m) cc_final: 0.9166 (m) REVERT: T 173 MET cc_start: 0.9592 (mmm) cc_final: 0.9279 (mtm) REVERT: g 96 TYR cc_start: 0.9350 (t80) cc_final: 0.9112 (t80) REVERT: g 125 TYR cc_start: 0.9114 (m-80) cc_final: 0.8697 (m-80) REVERT: g 131 MET cc_start: 0.7935 (mmp) cc_final: 0.7634 (mmt) REVERT: g 134 LEU cc_start: 0.9552 (mt) cc_final: 0.8964 (pp) REVERT: g 202 LEU cc_start: 0.9724 (tt) cc_final: 0.9414 (mm) REVERT: i 175 LEU cc_start: 0.9132 (pp) cc_final: 0.8849 (pp) REVERT: j 43 LEU cc_start: 0.9843 (pp) cc_final: 0.9510 (tt) REVERT: j 178 ASP cc_start: 0.9344 (p0) cc_final: 0.9025 (t0) REVERT: k 78 MET cc_start: 0.7927 (ppp) cc_final: 0.7369 (ppp) REVERT: k 143 PHE cc_start: 0.9005 (m-80) cc_final: 0.8759 (m-80) REVERT: l 26 MET cc_start: 0.8644 (mmt) cc_final: 0.8015 (mmt) REVERT: l 159 MET cc_start: 0.9065 (tmm) cc_final: 0.8693 (tmm) REVERT: m 75 MET cc_start: 0.9233 (mtp) cc_final: 0.8825 (mtp) REVERT: n 86 MET cc_start: 0.9699 (mmm) cc_final: 0.9475 (mmm) REVERT: n 119 MET cc_start: 0.8894 (ppp) cc_final: 0.8566 (ppp) REVERT: n 120 MET cc_start: 0.8652 (ppp) cc_final: 0.7900 (ppp) REVERT: o 54 MET cc_start: 0.9554 (mmm) cc_final: 0.9227 (mmp) REVERT: o 82 MET cc_start: 0.9495 (mtp) cc_final: 0.9292 (mtp) REVERT: o 127 MET cc_start: 0.9108 (mmm) cc_final: 0.8123 (mtt) REVERT: o 157 GLU cc_start: 0.9454 (mm-30) cc_final: 0.9213 (mm-30) REVERT: p 14 MET cc_start: 0.9057 (ttp) cc_final: 0.8298 (ptm) REVERT: p 75 GLU cc_start: 0.9405 (mt-10) cc_final: 0.8767 (mm-30) REVERT: p 96 TYR cc_start: 0.9341 (t80) cc_final: 0.9050 (t80) REVERT: p 157 ASN cc_start: 0.9467 (t0) cc_final: 0.9119 (t0) REVERT: q 1 MET cc_start: 0.9559 (tpt) cc_final: 0.9343 (tpp) REVERT: q 28 MET cc_start: 0.8849 (mpp) cc_final: 0.8522 (mpp) REVERT: q 38 MET cc_start: 0.9404 (mmp) cc_final: 0.9058 (mmm) REVERT: q 58 GLU cc_start: 0.9429 (mp0) cc_final: 0.9208 (mp0) REVERT: q 69 MET cc_start: 0.9075 (tpp) cc_final: 0.8703 (tpp) REVERT: q 124 LEU cc_start: 0.9263 (mt) cc_final: 0.8902 (mt) REVERT: r 86 MET cc_start: 0.9751 (tpt) cc_final: 0.9504 (tpp) REVERT: r 89 GLN cc_start: 0.9595 (tm-30) cc_final: 0.9360 (tm-30) REVERT: r 93 MET cc_start: 0.7685 (mtp) cc_final: 0.7334 (mtp) REVERT: s 74 MET cc_start: 0.9496 (mtp) cc_final: 0.9295 (mtp) REVERT: s 91 MET cc_start: 0.9418 (ppp) cc_final: 0.9183 (ppp) REVERT: s 144 MET cc_start: 0.9051 (mtp) cc_final: 0.8719 (mtp) REVERT: t 59 ASP cc_start: 0.9331 (m-30) cc_final: 0.9124 (m-30) REVERT: t 70 MET cc_start: 0.9793 (mmp) cc_final: 0.9557 (mmm) REVERT: t 96 MET cc_start: 0.9786 (mmp) cc_final: 0.9500 (mmm) REVERT: t 112 ILE cc_start: 0.9522 (mt) cc_final: 0.8811 (tt) REVERT: t 144 TYR cc_start: 0.9194 (m-80) cc_final: 0.8889 (m-80) REVERT: t 214 MET cc_start: 0.8745 (mpp) cc_final: 0.8339 (mpp) outliers start: 6 outliers final: 3 residues processed: 791 average time/residue: 0.8741 time to fit residues: 1211.0277 Evaluate side-chains 636 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 633 time to evaluate : 8.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1267 random chunks: chunk 1110 optimal weight: 9.9990 chunk 1169 optimal weight: 5.9990 chunk 1067 optimal weight: 0.7980 chunk 1137 optimal weight: 0.7980 chunk 684 optimal weight: 9.9990 chunk 495 optimal weight: 40.0000 chunk 893 optimal weight: 20.0000 chunk 349 optimal weight: 10.0000 chunk 1028 optimal weight: 30.0000 chunk 1076 optimal weight: 4.9990 chunk 1134 optimal weight: 8.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 35 HIS ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 258 GLN ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 HIS f 15 GLN f 224 ASN ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN U 880 ASN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 257 ASN ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 84 ASN ** W 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 405 GLN ** Y 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 254 ASN ** Z 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS H 189 HIS ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 154 HIS ** k 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 101626 Z= 0.216 Angle : 0.683 13.691 137470 Z= 0.352 Chirality : 0.044 0.317 15653 Planarity : 0.005 0.080 17764 Dihedral : 6.726 89.657 14167 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 24.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.71 % Favored : 90.14 % Rotamer: Outliers : 0.05 % Allowed : 0.67 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.56 (0.07), residues: 12733 helix: 0.13 (0.07), residues: 5559 sheet: -0.86 (0.12), residues: 1688 loop : -2.34 (0.08), residues: 5486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP Y 364 HIS 0.008 0.001 HIS e 63 PHE 0.034 0.002 PHE k 22 TYR 0.021 0.002 TYR M 238 ARG 0.011 0.001 ARG Z 267 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 744 time to evaluate : 10.628 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: a 312 MET cc_start: 0.8732 (mtm) cc_final: 0.8447 (mtp) REVERT: a 349 MET cc_start: 0.7987 (ppp) cc_final: 0.7669 (ppp) REVERT: b 1 MET cc_start: 0.2129 (mmt) cc_final: -0.0251 (ppp) REVERT: b 107 MET cc_start: 0.8007 (mpp) cc_final: 0.7013 (ttt) REVERT: c 54 MET cc_start: 0.7889 (pmm) cc_final: 0.7010 (pmm) REVERT: c 75 MET cc_start: 0.4599 (mmm) cc_final: 0.3956 (mmm) REVERT: c 226 MET cc_start: 0.9414 (tpp) cc_final: 0.8893 (tmm) REVERT: d 1 MET cc_start: 0.6899 (ttt) cc_final: 0.5867 (tpp) REVERT: f 33 ARG cc_start: 0.6857 (mpt90) cc_final: 0.5978 (tpt90) REVERT: f 275 MET cc_start: 0.7577 (pmm) cc_final: 0.6176 (tpt) REVERT: U 206 MET cc_start: 0.7371 (mmp) cc_final: 0.6889 (mmp) REVERT: U 423 MET cc_start: 0.8213 (mmp) cc_final: 0.7809 (tpt) REVERT: U 532 MET cc_start: 0.9131 (ptm) cc_final: 0.8786 (ptm) REVERT: U 556 MET cc_start: 0.7680 (mmt) cc_final: 0.7325 (mmm) REVERT: U 560 MET cc_start: 0.7887 (mmt) cc_final: 0.7334 (mmm) REVERT: U 654 MET cc_start: 0.9284 (mmp) cc_final: 0.8959 (mmm) REVERT: U 766 PHE cc_start: 0.9089 (t80) cc_final: 0.8518 (t80) REVERT: U 885 MET cc_start: 0.7806 (mmt) cc_final: 0.6880 (mtt) REVERT: V 192 MET cc_start: 0.7775 (mmt) cc_final: 0.7564 (ttm) REVERT: W 190 MET cc_start: 0.8589 (ttm) cc_final: 0.8071 (tpp) REVERT: W 312 MET cc_start: 0.5337 (tpp) cc_final: 0.4690 (tpt) REVERT: W 428 TRP cc_start: 0.9098 (m100) cc_final: 0.8009 (m100) REVERT: W 437 SER cc_start: 0.9392 (t) cc_final: 0.9174 (m) REVERT: X 254 MET cc_start: 0.7431 (ttt) cc_final: 0.6865 (tpp) REVERT: X 374 PHE cc_start: 0.9105 (t80) cc_final: 0.8463 (t80) REVERT: X 397 TYR cc_start: 0.9149 (m-80) cc_final: 0.8926 (m-10) REVERT: X 401 LEU cc_start: 0.9646 (mt) cc_final: 0.9445 (pp) REVERT: Y 214 MET cc_start: 0.7211 (pmm) cc_final: 0.6998 (pmm) REVERT: Y 364 TRP cc_start: 0.9378 (m-90) cc_final: 0.9111 (m-90) REVERT: Z 7 GLN cc_start: 0.9025 (tp-100) cc_final: 0.8784 (tp-100) REVERT: Z 78 MET cc_start: 0.9022 (mmp) cc_final: 0.8581 (mmm) REVERT: A 256 MET cc_start: 0.8927 (mmp) cc_final: 0.8443 (mmp) REVERT: A 299 MET cc_start: 0.8027 (ptp) cc_final: 0.7738 (ptp) REVERT: A 319 MET cc_start: 0.7900 (ppp) cc_final: 0.7638 (ppp) REVERT: A 430 MET cc_start: 0.6654 (tpt) cc_final: 0.6014 (tpp) REVERT: A 432 TYR cc_start: 0.7575 (m-10) cc_final: 0.6969 (m-80) REVERT: B 405 MET cc_start: 0.8529 (mmp) cc_final: 0.8231 (mmp) REVERT: B 412 MET cc_start: 0.8058 (tpp) cc_final: 0.7708 (tpp) REVERT: C 221 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7774 (tt0) REVERT: C 230 MET cc_start: 0.9104 (pmm) cc_final: 0.8770 (pmm) REVERT: C 335 LYS cc_start: 0.9122 (mttt) cc_final: 0.8876 (ptmm) REVERT: C 368 MET cc_start: 0.9369 (mtt) cc_final: 0.8993 (mtt) REVERT: C 377 HIS cc_start: 0.8504 (m-70) cc_final: 0.8144 (p-80) REVERT: D 59 GLU cc_start: 0.9693 (tt0) cc_final: 0.9430 (tm-30) REVERT: D 214 MET cc_start: 0.7474 (ptp) cc_final: 0.7009 (ptp) REVERT: D 246 MET cc_start: 0.9242 (mtm) cc_final: 0.8838 (ptp) REVERT: D 296 MET cc_start: 0.8889 (tpt) cc_final: 0.8589 (tmm) REVERT: D 304 ASN cc_start: 0.9566 (t0) cc_final: 0.9069 (m-40) REVERT: E 336 ASP cc_start: 0.8694 (t0) cc_final: 0.8453 (m-30) REVERT: E 382 SER cc_start: 0.3449 (p) cc_final: 0.3103 (t) REVERT: F 432 LYS cc_start: 0.7159 (mmpt) cc_final: 0.6783 (tttt) REVERT: G 209 ASP cc_start: 0.7665 (m-30) cc_final: 0.7340 (t0) REVERT: I 25 MET cc_start: 0.8630 (mpp) cc_final: 0.8415 (mpp) REVERT: I 45 LEU cc_start: 0.9238 (mm) cc_final: 0.8548 (tp) REVERT: I 166 ASN cc_start: 0.9082 (t0) cc_final: 0.8580 (p0) REVERT: J 159 ASN cc_start: 0.6979 (t0) cc_final: 0.5882 (t0) REVERT: K 65 GLU cc_start: 0.9369 (pm20) cc_final: 0.9069 (mp0) REVERT: K 107 MET cc_start: 0.8848 (ptp) cc_final: 0.8253 (ptp) REVERT: K 156 MET cc_start: 0.9372 (ppp) cc_final: 0.9019 (ppp) REVERT: L 88 MET cc_start: 0.9805 (ttp) cc_final: 0.9396 (ptt) REVERT: L 132 LEU cc_start: 0.9367 (mt) cc_final: 0.9096 (tp) REVERT: M 75 MET cc_start: 0.9304 (mmm) cc_final: 0.8855 (mmm) REVERT: M 135 PHE cc_start: 0.9426 (p90) cc_final: 0.8960 (p90) REVERT: M 181 MET cc_start: 0.8722 (ptp) cc_final: 0.8174 (ptp) REVERT: N 32 ASP cc_start: 0.9092 (m-30) cc_final: 0.8679 (t0) REVERT: N 86 MET cc_start: 0.9704 (tpp) cc_final: 0.9475 (tpp) REVERT: N 95 MET cc_start: 0.8867 (mpp) cc_final: 0.8055 (mpp) REVERT: N 116 MET cc_start: 0.8797 (mpp) cc_final: 0.8458 (mmp) REVERT: N 119 MET cc_start: 0.8312 (pmm) cc_final: 0.7765 (pmm) REVERT: O 86 MET cc_start: 0.9126 (tmm) cc_final: 0.8805 (tmm) REVERT: O 93 TYR cc_start: 0.9261 (m-80) cc_final: 0.8723 (m-80) REVERT: P 14 MET cc_start: 0.7544 (ptt) cc_final: 0.7238 (ptt) REVERT: P 39 PHE cc_start: 0.9048 (t80) cc_final: 0.8484 (t80) REVERT: Q 69 MET cc_start: 0.9495 (mmm) cc_final: 0.9134 (mmt) REVERT: Q 124 LEU cc_start: 0.7927 (mt) cc_final: 0.7559 (mt) REVERT: R 45 MET cc_start: 0.9554 (ppp) cc_final: 0.9279 (ppp) REVERT: R 139 MET cc_start: 0.9184 (ttp) cc_final: 0.8787 (tmm) REVERT: S 48 ASP cc_start: 0.9354 (m-30) cc_final: 0.8738 (p0) REVERT: S 83 MET cc_start: 0.8463 (ptm) cc_final: 0.6831 (ptm) REVERT: S 91 MET cc_start: 0.9354 (mmp) cc_final: 0.8749 (mmm) REVERT: S 144 MET cc_start: 0.9618 (mtt) cc_final: 0.8900 (mmm) REVERT: T 127 MET cc_start: 0.8841 (ttm) cc_final: 0.7942 (ttm) REVERT: T 160 LEU cc_start: 0.9427 (mt) cc_final: 0.9124 (tp) REVERT: T 173 MET cc_start: 0.9632 (mmm) cc_final: 0.9338 (mtm) REVERT: g 96 TYR cc_start: 0.9387 (t80) cc_final: 0.9168 (t80) REVERT: g 125 TYR cc_start: 0.9155 (m-80) cc_final: 0.8749 (m-80) REVERT: g 134 LEU cc_start: 0.9582 (mt) cc_final: 0.8970 (pp) REVERT: g 202 LEU cc_start: 0.9719 (tt) cc_final: 0.9427 (mm) REVERT: i 175 LEU cc_start: 0.9178 (pp) cc_final: 0.8947 (pp) REVERT: j 43 LEU cc_start: 0.9845 (pp) cc_final: 0.9393 (mp) REVERT: k 78 MET cc_start: 0.7897 (ppp) cc_final: 0.7302 (ppp) REVERT: k 143 PHE cc_start: 0.9026 (m-80) cc_final: 0.8806 (m-80) REVERT: l 88 MET cc_start: 0.9721 (ptp) cc_final: 0.9518 (ptp) REVERT: l 159 MET cc_start: 0.9105 (tmm) cc_final: 0.8756 (tmm) REVERT: m 75 MET cc_start: 0.9265 (mtp) cc_final: 0.8942 (mtp) REVERT: n 119 MET cc_start: 0.8861 (ppp) cc_final: 0.8483 (ppp) REVERT: n 120 MET cc_start: 0.8648 (ppp) cc_final: 0.7941 (ppp) REVERT: o 54 MET cc_start: 0.9553 (mmm) cc_final: 0.9280 (mmp) REVERT: o 127 MET cc_start: 0.9105 (mmm) cc_final: 0.8118 (mtt) REVERT: o 157 GLU cc_start: 0.9474 (mm-30) cc_final: 0.9215 (mm-30) REVERT: p 75 GLU cc_start: 0.9492 (mt-10) cc_final: 0.8865 (mm-30) REVERT: p 157 ASN cc_start: 0.9489 (t0) cc_final: 0.9215 (t0) REVERT: q 1 MET cc_start: 0.9550 (tpt) cc_final: 0.9237 (tpp) REVERT: q 28 MET cc_start: 0.8876 (mpp) cc_final: 0.8565 (mpp) REVERT: q 38 MET cc_start: 0.9416 (mmp) cc_final: 0.8962 (mmm) REVERT: q 58 GLU cc_start: 0.9511 (mp0) cc_final: 0.9282 (mp0) REVERT: q 69 MET cc_start: 0.9122 (tpp) cc_final: 0.8739 (tpp) REVERT: q 124 LEU cc_start: 0.9130 (mt) cc_final: 0.8663 (mt) REVERT: r 86 MET cc_start: 0.9751 (tpt) cc_final: 0.9511 (tpp) REVERT: r 89 GLN cc_start: 0.9574 (tm-30) cc_final: 0.9344 (tm-30) REVERT: r 93 MET cc_start: 0.7671 (mtp) cc_final: 0.7327 (mtp) REVERT: r 139 MET cc_start: 0.9480 (tmm) cc_final: 0.9258 (tmm) REVERT: s 74 MET cc_start: 0.9495 (mtp) cc_final: 0.9288 (mtp) REVERT: s 144 MET cc_start: 0.9084 (mtp) cc_final: 0.8665 (mtp) REVERT: t 70 MET cc_start: 0.9799 (mmp) cc_final: 0.9575 (mmm) REVERT: t 96 MET cc_start: 0.9799 (mmp) cc_final: 0.9531 (mmm) REVERT: t 112 ILE cc_start: 0.9514 (mt) cc_final: 0.8708 (tt) REVERT: t 144 TYR cc_start: 0.9281 (m-80) cc_final: 0.8979 (m-80) REVERT: t 214 MET cc_start: 0.8690 (mpp) cc_final: 0.8308 (mpp) outliers start: 5 outliers final: 3 residues processed: 749 average time/residue: 0.8831 time to fit residues: 1160.8571 Evaluate side-chains 620 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 617 time to evaluate : 8.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1267 random chunks: chunk 747 optimal weight: 10.0000 chunk 1203 optimal weight: 0.8980 chunk 734 optimal weight: 8.9990 chunk 570 optimal weight: 7.9990 chunk 836 optimal weight: 6.9990 chunk 1262 optimal weight: 7.9990 chunk 1161 optimal weight: 20.0000 chunk 1005 optimal weight: 0.9990 chunk 104 optimal weight: 0.0570 chunk 776 optimal weight: 7.9990 chunk 616 optimal weight: 20.0000 overall best weight: 3.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 HIS ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN U 880 ASN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 257 ASN V 365 GLN ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 405 GLN ** Y 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 7 GLN ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 254 ASN ** Z 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 90 GLN ** h 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 146 GLN ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 101626 Z= 0.191 Angle : 0.668 13.450 137470 Z= 0.342 Chirality : 0.044 0.403 15653 Planarity : 0.005 0.081 17764 Dihedral : 6.670 89.008 14167 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.35 % Favored : 90.50 % Rotamer: Outliers : 0.05 % Allowed : 0.37 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.48 (0.08), residues: 12733 helix: 0.20 (0.07), residues: 5576 sheet: -0.74 (0.12), residues: 1675 loop : -2.34 (0.08), residues: 5482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Y 364 HIS 0.021 0.001 HIS U 70 PHE 0.033 0.001 PHE U 728 TYR 0.025 0.001 TYR m 125 ARG 0.011 0.000 ARG C 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25466 Ramachandran restraints generated. 12733 Oldfield, 0 Emsley, 12733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 755 time to evaluate : 9.226 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: a 312 MET cc_start: 0.8730 (mtm) cc_final: 0.8448 (mtp) REVERT: b 1 MET cc_start: 0.1842 (mmt) cc_final: -0.0640 (ppp) REVERT: c 54 MET cc_start: 0.7844 (pmm) cc_final: 0.7126 (pmm) REVERT: c 75 MET cc_start: 0.4551 (mmm) cc_final: 0.3898 (mmm) REVERT: c 226 MET cc_start: 0.9421 (tpp) cc_final: 0.8930 (tmm) REVERT: d 1 MET cc_start: 0.6985 (ttt) cc_final: 0.5891 (tpp) REVERT: f 275 MET cc_start: 0.7564 (pmm) cc_final: 0.6174 (tpt) REVERT: f 512 MET cc_start: 0.6496 (tpt) cc_final: 0.5410 (tpt) REVERT: U 206 MET cc_start: 0.7366 (mmp) cc_final: 0.6885 (mmp) REVERT: U 532 MET cc_start: 0.9088 (ptm) cc_final: 0.8736 (ptm) REVERT: U 556 MET cc_start: 0.7698 (mmt) cc_final: 0.7363 (mmm) REVERT: U 560 MET cc_start: 0.7712 (mmt) cc_final: 0.7242 (mmm) REVERT: U 654 MET cc_start: 0.9282 (mmp) cc_final: 0.8953 (mmm) REVERT: U 766 PHE cc_start: 0.9065 (t80) cc_final: 0.8509 (t80) REVERT: U 885 MET cc_start: 0.7814 (mmt) cc_final: 0.6868 (mtt) REVERT: V 175 MET cc_start: 0.7320 (mtt) cc_final: 0.5896 (mtt) REVERT: V 176 MET cc_start: 0.8908 (mmm) cc_final: 0.8701 (mmm) REVERT: V 192 MET cc_start: 0.7727 (mmt) cc_final: 0.7524 (ttt) REVERT: W 190 MET cc_start: 0.8614 (ttm) cc_final: 0.8089 (tpp) REVERT: W 312 MET cc_start: 0.5201 (tpp) cc_final: 0.4529 (tpt) REVERT: W 428 TRP cc_start: 0.9097 (m100) cc_final: 0.7970 (m100) REVERT: W 437 SER cc_start: 0.9401 (t) cc_final: 0.9194 (m) REVERT: X 253 TYR cc_start: 0.9404 (m-10) cc_final: 0.9136 (m-80) REVERT: X 254 MET cc_start: 0.7457 (ttt) cc_final: 0.6736 (tpp) REVERT: X 374 PHE cc_start: 0.8849 (t80) cc_final: 0.8149 (t80) REVERT: X 397 TYR cc_start: 0.9124 (m-80) cc_final: 0.8909 (m-10) REVERT: X 401 LEU cc_start: 0.9642 (mt) cc_final: 0.9438 (pp) REVERT: Y 214 MET cc_start: 0.6974 (pmm) cc_final: 0.6748 (pmm) REVERT: Y 364 TRP cc_start: 0.9349 (m-90) cc_final: 0.9079 (m-90) REVERT: Z 7 GLN cc_start: 0.8987 (tp40) cc_final: 0.8661 (tp-100) REVERT: Z 78 MET cc_start: 0.9003 (mmp) cc_final: 0.8567 (mmm) REVERT: A 256 MET cc_start: 0.8930 (mmp) cc_final: 0.8484 (mmp) REVERT: A 299 MET cc_start: 0.7990 (ptp) cc_final: 0.7726 (ptp) REVERT: A 319 MET cc_start: 0.7874 (ppp) cc_final: 0.7618 (ppp) REVERT: A 430 MET cc_start: 0.6643 (tpt) cc_final: 0.6010 (tpp) REVERT: A 432 TYR cc_start: 0.7572 (m-10) cc_final: 0.6962 (m-80) REVERT: B 405 MET cc_start: 0.8543 (mmp) cc_final: 0.8228 (mmp) REVERT: B 412 MET cc_start: 0.8054 (tpp) cc_final: 0.7715 (tpp) REVERT: C 221 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7775 (tt0) REVERT: C 273 MET cc_start: 0.9670 (tmm) cc_final: 0.9181 (mtp) REVERT: C 368 MET cc_start: 0.9341 (mtt) cc_final: 0.8941 (mtt) REVERT: C 377 HIS cc_start: 0.8515 (m-70) cc_final: 0.8192 (p-80) REVERT: D 59 GLU cc_start: 0.9667 (tt0) cc_final: 0.9409 (tm-30) REVERT: D 214 MET cc_start: 0.7402 (ptp) cc_final: 0.6971 (ptp) REVERT: D 246 MET cc_start: 0.9189 (mtm) cc_final: 0.8875 (mtp) REVERT: D 296 MET cc_start: 0.8958 (tpt) cc_final: 0.8684 (tmm) REVERT: D 302 ASN cc_start: 0.7716 (p0) cc_final: 0.7446 (m110) REVERT: D 304 ASN cc_start: 0.9562 (t0) cc_final: 0.9094 (m-40) REVERT: E 336 ASP cc_start: 0.8852 (t0) cc_final: 0.8611 (m-30) REVERT: E 382 SER cc_start: 0.3422 (p) cc_final: 0.3085 (t) REVERT: F 432 LYS cc_start: 0.7224 (mmpt) cc_final: 0.6773 (tttt) REVERT: G 125 TYR cc_start: 0.9585 (m-80) cc_final: 0.8994 (m-80) REVERT: G 209 ASP cc_start: 0.7659 (m-30) cc_final: 0.7352 (t0) REVERT: I 45 LEU cc_start: 0.9226 (mm) cc_final: 0.8530 (tp) REVERT: I 64 LYS cc_start: 0.9310 (mmtm) cc_final: 0.8985 (mtmt) REVERT: I 163 CYS cc_start: 0.8452 (p) cc_final: 0.7794 (t) REVERT: I 166 ASN cc_start: 0.9124 (t0) cc_final: 0.8672 (p0) REVERT: K 65 GLU cc_start: 0.9390 (pm20) cc_final: 0.9007 (mp0) REVERT: K 107 MET cc_start: 0.8842 (ptp) cc_final: 0.8257 (ptp) REVERT: K 156 MET cc_start: 0.9364 (ppp) cc_final: 0.9010 (ppp) REVERT: L 26 MET cc_start: 0.9234 (mmt) cc_final: 0.8927 (mmt) REVERT: L 88 MET cc_start: 0.9812 (ttp) cc_final: 0.9394 (ptt) REVERT: L 132 LEU cc_start: 0.9382 (mt) cc_final: 0.9135 (tp) REVERT: M 75 MET cc_start: 0.9311 (mmm) cc_final: 0.8951 (mmm) REVERT: M 135 PHE cc_start: 0.9553 (p90) cc_final: 0.9086 (p90) REVERT: M 181 MET cc_start: 0.8703 (ptp) cc_final: 0.8161 (ptp) REVERT: N 32 ASP cc_start: 0.9089 (m-30) cc_final: 0.8621 (t0) REVERT: N 86 MET cc_start: 0.9675 (tpp) cc_final: 0.9430 (tpp) REVERT: N 95 MET cc_start: 0.8925 (mpp) cc_final: 0.8497 (mmm) REVERT: N 116 MET cc_start: 0.8785 (mpp) cc_final: 0.8392 (mmp) REVERT: N 119 MET cc_start: 0.8251 (pmm) cc_final: 0.7690 (pmm) REVERT: O 86 MET cc_start: 0.9106 (tmm) cc_final: 0.8765 (ppp) REVERT: O 93 TYR cc_start: 0.9262 (m-80) cc_final: 0.8680 (m-80) REVERT: O 157 GLU cc_start: 0.9259 (mp0) cc_final: 0.9049 (mp0) REVERT: P 14 MET cc_start: 0.7460 (ptt) cc_final: 0.7177 (ptt) REVERT: P 39 PHE cc_start: 0.9051 (t80) cc_final: 0.8476 (t80) REVERT: Q 69 MET cc_start: 0.9500 (mmm) cc_final: 0.9140 (mmt) REVERT: Q 124 LEU cc_start: 0.7957 (mt) cc_final: 0.7568 (mt) REVERT: R 37 ILE cc_start: 0.8517 (mm) cc_final: 0.8004 (mm) REVERT: R 45 MET cc_start: 0.9549 (ppp) cc_final: 0.9267 (ppp) REVERT: R 56 GLU cc_start: 0.9576 (mm-30) cc_final: 0.9154 (mt-10) REVERT: R 139 MET cc_start: 0.9127 (ttp) cc_final: 0.8749 (ptm) REVERT: S 48 ASP cc_start: 0.9376 (m-30) cc_final: 0.8780 (p0) REVERT: S 83 MET cc_start: 0.8400 (ptm) cc_final: 0.6749 (ptm) REVERT: S 91 MET cc_start: 0.9333 (mmp) cc_final: 0.8739 (mmm) REVERT: S 92 LEU cc_start: 0.9645 (tp) cc_final: 0.9435 (tp) REVERT: S 144 MET cc_start: 0.9613 (mtt) cc_final: 0.8880 (mmm) REVERT: T 127 MET cc_start: 0.8839 (ttm) cc_final: 0.7925 (ttm) REVERT: T 160 LEU cc_start: 0.9446 (mt) cc_final: 0.9135 (tp) REVERT: T 173 MET cc_start: 0.9627 (mmm) cc_final: 0.9275 (mtm) REVERT: g 96 TYR cc_start: 0.9347 (t80) cc_final: 0.9129 (t80) REVERT: g 134 LEU cc_start: 0.9567 (mt) cc_final: 0.8610 (pp) REVERT: g 202 LEU cc_start: 0.9711 (tt) cc_final: 0.9414 (mm) REVERT: i 72 MET cc_start: 0.8735 (mmp) cc_final: 0.8494 (mmm) REVERT: i 175 LEU cc_start: 0.9141 (pp) cc_final: 0.8879 (pp) REVERT: j 43 LEU cc_start: 0.9849 (pp) cc_final: 0.9409 (mp) REVERT: k 78 MET cc_start: 0.7889 (ppp) cc_final: 0.7287 (ppp) REVERT: k 143 PHE cc_start: 0.8988 (m-80) cc_final: 0.8770 (m-80) REVERT: l 26 MET cc_start: 0.8703 (mmt) cc_final: 0.8061 (mmt) REVERT: l 159 MET cc_start: 0.8887 (tmm) cc_final: 0.8641 (tmm) REVERT: m 75 MET cc_start: 0.9183 (mtp) cc_final: 0.8846 (mtp) REVERT: m 150 MET cc_start: 0.9304 (tpt) cc_final: 0.8612 (ppp) REVERT: m 202 ASP cc_start: 0.8675 (p0) cc_final: 0.8315 (m-30) REVERT: n 119 MET cc_start: 0.8935 (ppp) cc_final: 0.8605 (ppp) REVERT: n 120 MET cc_start: 0.8665 (ppp) cc_final: 0.7954 (ppp) REVERT: o 54 MET cc_start: 0.9531 (mmm) cc_final: 0.9261 (mmp) REVERT: o 127 MET cc_start: 0.9105 (mmm) cc_final: 0.8117 (mtt) REVERT: o 157 GLU cc_start: 0.9457 (mm-30) cc_final: 0.9210 (mm-30) REVERT: p 33 GLN cc_start: 0.9029 (pp30) cc_final: 0.8819 (pp30) REVERT: p 157 ASN cc_start: 0.9517 (t0) cc_final: 0.9109 (t0) REVERT: q 1 MET cc_start: 0.9542 (tpt) cc_final: 0.9250 (tpp) REVERT: q 28 MET cc_start: 0.8890 (mpp) cc_final: 0.8571 (mpp) REVERT: q 38 MET cc_start: 0.9433 (mmp) cc_final: 0.9102 (mmm) REVERT: q 58 GLU cc_start: 0.9519 (mp0) cc_final: 0.9282 (mp0) REVERT: r 86 MET cc_start: 0.9750 (tpt) cc_final: 0.9507 (tpp) REVERT: r 89 GLN cc_start: 0.9585 (tm-30) cc_final: 0.9356 (tm-30) REVERT: r 93 MET cc_start: 0.7653 (mtp) cc_final: 0.7291 (mtp) REVERT: r 139 MET cc_start: 0.9514 (tmm) cc_final: 0.9312 (tmm) REVERT: s 83 MET cc_start: 0.7585 (ptm) cc_final: 0.7240 (tmm) REVERT: s 91 MET cc_start: 0.9440 (ppp) cc_final: 0.9224 (ppp) REVERT: s 144 MET cc_start: 0.9081 (mtp) cc_final: 0.8663 (mtp) REVERT: t 59 ASP cc_start: 0.9165 (m-30) cc_final: 0.8958 (m-30) REVERT: t 70 MET cc_start: 0.9800 (mmp) cc_final: 0.9577 (mmm) REVERT: t 96 MET cc_start: 0.9796 (mmp) cc_final: 0.9498 (mmm) REVERT: t 112 ILE cc_start: 0.9430 (mt) cc_final: 0.8829 (tt) REVERT: t 144 TYR cc_start: 0.9231 (m-80) cc_final: 0.8920 (m-80) REVERT: t 214 MET cc_start: 0.8667 (mpp) cc_final: 0.8294 (mpp) outliers start: 5 outliers final: 3 residues processed: 760 average time/residue: 0.8783 time to fit residues: 1171.3462 Evaluate side-chains 624 residues out of total 10969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 621 time to evaluate : 9.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1267 random chunks: chunk 798 optimal weight: 40.0000 chunk 1070 optimal weight: 20.0000 chunk 307 optimal weight: 1.9990 chunk 926 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 279 optimal weight: 0.8980 chunk 1006 optimal weight: 5.9990 chunk 421 optimal weight: 20.0000 chunk 1033 optimal weight: 40.0000 chunk 127 optimal weight: 30.0000 chunk 185 optimal weight: 8.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 79 GLN ** b 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 HIS ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 421 GLN U 880 ASN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 375 HIS X 405 GLN Y 306 GLN ** Y 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 254 ASN ** Z 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 215 GLN ** k 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.046321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.034528 restraints weight = 1089199.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.035531 restraints weight = 693078.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.036229 restraints weight = 487254.251| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 101626 Z= 0.237 Angle : 0.700 13.432 137470 Z= 0.362 Chirality : 0.045 0.404 15653 Planarity : 0.005 0.080 17764 Dihedral : 6.763 88.064 14167 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 25.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.17 % Favored : 89.70 % Rotamer: Outliers : 0.05 % Allowed : 0.29 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.52 (0.07), residues: 12733 helix: 0.16 (0.07), residues: 5549 sheet: -0.80 (0.12), residues: 1686 loop : -2.34 (0.08), residues: 5498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP j 156 HIS 0.011 0.001 HIS U 70 PHE 0.046 0.002 PHE D 333 TYR 0.034 0.002 TYR g 125 ARG 0.008 0.001 ARG g 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22851.22 seconds wall clock time: 405 minutes 53.76 seconds (24353.76 seconds total)