Starting phenix.real_space_refine on Fri Mar 22 16:20:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2u_38020/03_2024/8x2u_38020.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2u_38020/03_2024/8x2u_38020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2u_38020/03_2024/8x2u_38020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2u_38020/03_2024/8x2u_38020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2u_38020/03_2024/8x2u_38020.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2u_38020/03_2024/8x2u_38020.pdb" } resolution = 3.57 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= 0.015 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 21708 2.51 5 N 5746 2.21 5 O 6340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "E TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 13": "OE1" <-> "OE2" Residue "E GLU 29": "OE1" <-> "OE2" Residue "E PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E ASP 111": "OD1" <-> "OD2" Residue "E GLU 179": "OE1" <-> "OE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 181": "OE1" <-> "OE2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "G GLU 207": "OE1" <-> "OE2" Residue "G TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 249": "OD1" <-> "OD2" Residue "G GLU 252": "OE1" <-> "OE2" Residue "G TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 281": "OE1" <-> "OE2" Residue "G GLU 284": "OE1" <-> "OE2" Residue "G PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 322": "OE1" <-> "OE2" Residue "G ASP 331": "OD1" <-> "OD2" Residue "G GLU 332": "OE1" <-> "OE2" Residue "G TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 371": "OE1" <-> "OE2" Residue "G GLU 376": "OE1" <-> "OE2" Residue "G TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 479": "OE1" <-> "OE2" Residue "G GLU 522": "OE1" <-> "OE2" Residue "G GLU 523": "OE1" <-> "OE2" Residue "G GLU 537": "OE1" <-> "OE2" Residue "G PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 643": "OE1" <-> "OE2" Residue "G GLU 656": "OE1" <-> "OE2" Residue "G TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 669": "OE1" <-> "OE2" Residue "G TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 687": "OE1" <-> "OE2" Residue "H ASP 2": "OD1" <-> "OD2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 66": "OD1" <-> "OD2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "H ASP 145": "OD1" <-> "OD2" Residue "H PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 174": "OE1" <-> "OE2" Residue "H TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 42": "OD1" <-> "OD2" Residue "I TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 111": "OD1" <-> "OD2" Residue "I TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 151": "OE1" <-> "OE2" Residue "I TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 197": "OE1" <-> "OE2" Residue "I GLU 199": "OE1" <-> "OE2" Residue "J TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 332": "OE1" <-> "OE2" Residue "J GLU 369": "OE1" <-> "OE2" Residue "J PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 466": "OD1" <-> "OD2" Residue "J GLU 479": "OE1" <-> "OE2" Residue "J GLU 528": "OE1" <-> "OE2" Residue "J TYR 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 56": "OD1" <-> "OD2" Residue "c TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 90": "OE1" <-> "OE2" Residue "c TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 136": "OE1" <-> "OE2" Residue "c PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 218": "OE1" <-> "OE2" Residue "c TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 150": "OD1" <-> "OD2" Residue "K PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 276": "OE1" <-> "OE2" Residue "K PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 298": "OE1" <-> "OE2" Residue "M PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 111": "OD1" <-> "OD2" Residue "M PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 149": "OE1" <-> "OE2" Residue "N PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 151": "OE1" <-> "OE2" Residue "N TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 181": "OE1" <-> "OE2" Residue "N TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 195": "OE1" <-> "OE2" Residue "N GLU 196": "OE1" <-> "OE2" Residue "N GLU 198": "OE1" <-> "OE2" Residue "O GLU 207": "OE1" <-> "OE2" Residue "O ASP 241": "OD1" <-> "OD2" Residue "O ASP 249": "OD1" <-> "OD2" Residue "O GLU 252": "OE1" <-> "OE2" Residue "O ASP 257": "OD1" <-> "OD2" Residue "O GLU 281": "OE1" <-> "OE2" Residue "O PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 316": "OE1" <-> "OE2" Residue "O PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 322": "OE1" <-> "OE2" Residue "O GLU 332": "OE1" <-> "OE2" Residue "O PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 371": "OE1" <-> "OE2" Residue "O GLU 376": "OE1" <-> "OE2" Residue "O GLU 419": "OE1" <-> "OE2" Residue "O TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 479": "OE1" <-> "OE2" Residue "O TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 522": "OE1" <-> "OE2" Residue "O GLU 537": "OE1" <-> "OE2" Residue "O PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 643": "OE1" <-> "OE2" Residue "O GLU 656": "OE1" <-> "OE2" Residue "O GLU 669": "OE1" <-> "OE2" Residue "O TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 675": "OE1" <-> "OE2" Residue "O GLU 685": "OE1" <-> "OE2" Residue "O GLU 686": "OE1" <-> "OE2" Residue "P ASP 23": "OD1" <-> "OD2" Residue "P ASP 38": "OD1" <-> "OD2" Residue "P ASP 56": "OD1" <-> "OD2" Residue "P ASP 106": "OD1" <-> "OD2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P ASP 145": "OD1" <-> "OD2" Residue "P GLU 174": "OE1" <-> "OE2" Residue "P TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 267": "OE1" <-> "OE2" Residue "Q GLU 21": "OE1" <-> "OE2" Residue "Q TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 111": "OD1" <-> "OD2" Residue "Q TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 185": "OE1" <-> "OE2" Residue "Q GLU 195": "OE1" <-> "OE2" Residue "Q GLU 198": "OE1" <-> "OE2" Residue "Q GLU 199": "OE1" <-> "OE2" Residue "R TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 230": "OD1" <-> "OD2" Residue "R GLU 242": "OE1" <-> "OE2" Residue "R TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 281": "OE1" <-> "OE2" Residue "R GLU 316": "OE1" <-> "OE2" Residue "R TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 322": "OE1" <-> "OE2" Residue "R GLU 332": "OE1" <-> "OE2" Residue "R GLU 362": "OE1" <-> "OE2" Residue "R GLU 369": "OE1" <-> "OE2" Residue "R GLU 371": "OE1" <-> "OE2" Residue "R PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 419": "OE1" <-> "OE2" Residue "R TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 522": "OE1" <-> "OE2" Residue "R GLU 523": "OE1" <-> "OE2" Residue "R GLU 528": "OE1" <-> "OE2" Residue "R GLU 598": "OE1" <-> "OE2" Residue "R TYR 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 669": "OE1" <-> "OE2" Residue "R TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 685": "OE1" <-> "OE2" Residue "d ASP 23": "OD1" <-> "OD2" Residue "d ASP 38": "OD1" <-> "OD2" Residue "d ASP 56": "OD1" <-> "OD2" Residue "d TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 106": "OD1" <-> "OD2" Residue "d GLU 136": "OE1" <-> "OE2" Residue "d ASP 212": "OD1" <-> "OD2" Residue "d TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33922 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 369 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "B" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1489 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 16, 'TRANS': 161} Chain: "D" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 387 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 17, 'TRANS': 183} Chain: "F" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1514 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain: "G" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3099 Classifications: {'peptide': 387} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 30, 'TRANS': 352} Chain breaks: 5 Chain: "H" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1912 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 226} Chain breaks: 2 Chain: "I" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1514 Classifications: {'peptide': 185} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 178} Chain: "J" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3139 Classifications: {'peptide': 392} Link IDs: {'CIS': 3, 'PTRANS': 31, 'TRANS': 357} Chain breaks: 5 Chain: "c" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1926 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain breaks: 2 Chain: "C" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 369 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "K" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1489 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 16, 'TRANS': 162} Chain: "L" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 387 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "M" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 17, 'TRANS': 183} Chain: "N" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1514 Classifications: {'peptide': 185} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 179} Chain: "O" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3099 Classifications: {'peptide': 387} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 30, 'TRANS': 353} Chain breaks: 5 Chain: "P" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1912 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 225} Chain breaks: 2 Chain: "Q" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1514 Classifications: {'peptide': 185} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 178} Chain: "R" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3139 Classifications: {'peptide': 392} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 30, 'TRANS': 358} Chain breaks: 5 Chain: "d" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1926 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 225} Chain breaks: 2 Time building chain proxies: 16.44, per 1000 atoms: 0.48 Number of scatterers: 33922 At special positions: 0 Unit cell: (252.784, 181.902, 132.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 6340 8.00 N 5746 7.00 C 21708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.43 Conformation dependent library (CDL) restraints added in 5.5 seconds 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7764 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 50 sheets defined 31.7% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.96 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 4.157A pdb=" N LEU A 6 " --> pdb=" O ASP A 2 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 11 " --> pdb=" O LYS A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'A' and resid 28 through 45 Processing helix chain 'B' and resid 148 through 154 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 303 through 315 Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.619A pdb=" N GLY D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 330 removed outlier: 3.535A pdb=" N GLU D 329 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 38 removed outlier: 3.504A pdb=" N GLY E 38 " --> pdb=" O ILE E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 58 Processing helix chain 'E' and resid 67 through 76 removed outlier: 3.645A pdb=" N THR E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 98 Processing helix chain 'E' and resid 101 through 109 removed outlier: 3.650A pdb=" N GLU E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 118 Processing helix chain 'E' and resid 131 through 143 removed outlier: 3.739A pdb=" N PHE E 143 " --> pdb=" O ILE E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 164 Processing helix chain 'E' and resid 165 through 180 removed outlier: 4.005A pdb=" N GLN E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 195 removed outlier: 4.548A pdb=" N TRP E 187 " --> pdb=" O ASP E 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 219 removed outlier: 3.749A pdb=" N SER G 219 " --> pdb=" O ALA G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 242 Processing helix chain 'G' and resid 246 through 249 removed outlier: 3.857A pdb=" N ASP G 249 " --> pdb=" O ASP G 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 246 through 249' Processing helix chain 'G' and resid 250 through 260 removed outlier: 3.741A pdb=" N GLN G 256 " --> pdb=" O GLU G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 275 No H-bonds generated for 'chain 'G' and resid 273 through 275' Processing helix chain 'G' and resid 276 through 291 removed outlier: 4.551A pdb=" N ALA G 288 " --> pdb=" O GLU G 284 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU G 289 " --> pdb=" O THR G 285 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE G 290 " --> pdb=" O GLN G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 325 Processing helix chain 'G' and resid 328 through 347 removed outlier: 4.234A pdb=" N GLU G 332 " --> pdb=" O LEU G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 423 through 427 Processing helix chain 'G' and resid 447 through 452 Processing helix chain 'G' and resid 453 through 457 removed outlier: 3.925A pdb=" N LYS G 456 " --> pdb=" O THR G 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 495 removed outlier: 4.310A pdb=" N GLY G 493 " --> pdb=" O ARG G 489 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS G 495 " --> pdb=" O SER G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 533 through 538 removed outlier: 3.760A pdb=" N SER G 538 " --> pdb=" O ASP G 534 " (cutoff:3.500A) Processing helix chain 'G' and resid 595 through 600 removed outlier: 3.757A pdb=" N ASP G 599 " --> pdb=" O ILE G 596 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU G 600 " --> pdb=" O SER G 597 " (cutoff:3.500A) Processing helix chain 'G' and resid 673 through 677 removed outlier: 3.656A pdb=" N THR G 677 " --> pdb=" O PRO G 674 " (cutoff:3.500A) Processing helix chain 'G' and resid 683 through 692 removed outlier: 3.554A pdb=" N MET G 692 " --> pdb=" O GLN G 688 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 9 Processing helix chain 'H' and resid 9 through 14 Processing helix chain 'H' and resid 21 through 39 Processing helix chain 'H' and resid 89 through 96 removed outlier: 4.007A pdb=" N ILE H 96 " --> pdb=" O MET H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 99 No H-bonds generated for 'chain 'H' and resid 97 through 99' Processing helix chain 'H' and resid 136 through 151 Processing helix chain 'H' and resid 177 through 182 removed outlier: 4.220A pdb=" N ARG H 182 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 185 No H-bonds generated for 'chain 'H' and resid 183 through 185' Processing helix chain 'H' and resid 271 through 276 removed outlier: 3.649A pdb=" N MET H 275 " --> pdb=" O ASP H 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 218 Processing helix chain 'J' and resid 227 through 242 Processing helix chain 'J' and resid 249 through 261 removed outlier: 4.502A pdb=" N ASN J 253 " --> pdb=" O ASP J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 287 removed outlier: 3.979A pdb=" N GLU J 281 " --> pdb=" O LEU J 277 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 325 Processing helix chain 'J' and resid 328 through 347 removed outlier: 4.241A pdb=" N GLU J 332 " --> pdb=" O LEU J 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 447 through 452 Processing helix chain 'J' and resid 453 through 457 removed outlier: 4.007A pdb=" N LYS J 456 " --> pdb=" O THR J 453 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE J 457 " --> pdb=" O ALA J 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 453 through 457' Processing helix chain 'J' and resid 478 through 495 Processing helix chain 'J' and resid 531 through 538 removed outlier: 3.572A pdb=" N VAL J 536 " --> pdb=" O VAL J 532 " (cutoff:3.500A) Processing helix chain 'J' and resid 595 through 599 removed outlier: 3.663A pdb=" N GLU J 598 " --> pdb=" O PRO J 595 " (cutoff:3.500A) Processing helix chain 'J' and resid 673 through 678 Processing helix chain 'J' and resid 683 through 693 Processing helix chain 'c' and resid 2 through 6 removed outlier: 4.181A pdb=" N LEU c 6 " --> pdb=" O ALA c 3 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 15 Processing helix chain 'c' and resid 21 through 39 Processing helix chain 'c' and resid 89 through 96 Processing helix chain 'c' and resid 97 through 99 No H-bonds generated for 'chain 'c' and resid 97 through 99' Processing helix chain 'c' and resid 135 through 149 Processing helix chain 'c' and resid 177 through 182 removed outlier: 4.050A pdb=" N ARG c 182 " --> pdb=" O LEU c 178 " (cutoff:3.500A) Processing helix chain 'c' and resid 271 through 275 Processing helix chain 'C' and resid 2 through 10 removed outlier: 3.638A pdb=" N LEU C 6 " --> pdb=" O ASP C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 25 removed outlier: 4.060A pdb=" N THR C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 45 Processing helix chain 'K' and resid 147 through 154 Processing helix chain 'K' and resid 303 through 315 removed outlier: 3.545A pdb=" N LEU K 315 " --> pdb=" O ARG K 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 291 removed outlier: 3.555A pdb=" N GLY L 290 " --> pdb=" O ASP L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 330 removed outlier: 3.617A pdb=" N HIS L 330 " --> pdb=" O ASN L 326 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 25 No H-bonds generated for 'chain 'M' and resid 23 through 25' Processing helix chain 'M' and resid 26 through 38 removed outlier: 3.610A pdb=" N GLY M 38 " --> pdb=" O ILE M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 58 Processing helix chain 'M' and resid 67 through 76 removed outlier: 3.603A pdb=" N MET M 74 " --> pdb=" O LEU M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 98 Processing helix chain 'M' and resid 101 through 109 removed outlier: 4.467A pdb=" N GLU M 107 " --> pdb=" O LEU M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 118 Processing helix chain 'M' and resid 131 through 143 Processing helix chain 'M' and resid 154 through 165 removed outlier: 3.962A pdb=" N LYS M 158 " --> pdb=" O GLY M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 180 removed outlier: 4.424A pdb=" N GLN M 171 " --> pdb=" O PRO M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 195 removed outlier: 4.411A pdb=" N TRP M 187 " --> pdb=" O ASP M 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 207 through 217 Processing helix chain 'O' and resid 227 through 240 Processing helix chain 'O' and resid 244 through 249 removed outlier: 4.535A pdb=" N VAL O 248 " --> pdb=" O ALA O 245 " (cutoff:3.500A) Processing helix chain 'O' and resid 250 through 261 removed outlier: 3.881A pdb=" N GLN O 256 " --> pdb=" O GLU O 252 " (cutoff:3.500A) Processing helix chain 'O' and resid 273 through 275 No H-bonds generated for 'chain 'O' and resid 273 through 275' Processing helix chain 'O' and resid 276 through 286 removed outlier: 3.726A pdb=" N TYR O 280 " --> pdb=" O MET O 276 " (cutoff:3.500A) Processing helix chain 'O' and resid 287 through 291 removed outlier: 3.814A pdb=" N LEU O 291 " --> pdb=" O ALA O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 313 through 323 Processing helix chain 'O' and resid 329 through 347 Processing helix chain 'O' and resid 423 through 428 removed outlier: 3.622A pdb=" N ASN O 426 " --> pdb=" O THR O 423 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR O 428 " --> pdb=" O ALA O 425 " (cutoff:3.500A) Processing helix chain 'O' and resid 478 through 495 Processing helix chain 'O' and resid 531 through 538 removed outlier: 3.754A pdb=" N SER O 538 " --> pdb=" O ASP O 534 " (cutoff:3.500A) Processing helix chain 'O' and resid 595 through 599 removed outlier: 3.543A pdb=" N GLU O 598 " --> pdb=" O PRO O 595 " (cutoff:3.500A) Processing helix chain 'O' and resid 617 through 621 Processing helix chain 'O' and resid 673 through 677 removed outlier: 3.665A pdb=" N ILE O 676 " --> pdb=" O GLY O 673 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR O 677 " --> pdb=" O PRO O 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 673 through 677' Processing helix chain 'O' and resid 683 through 692 Processing helix chain 'P' and resid 3 through 8 removed outlier: 3.706A pdb=" N LEU P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 14 Processing helix chain 'P' and resid 21 through 39 Processing helix chain 'P' and resid 89 through 96 removed outlier: 3.763A pdb=" N ILE P 96 " --> pdb=" O MET P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 99 No H-bonds generated for 'chain 'P' and resid 97 through 99' Processing helix chain 'P' and resid 136 through 152 removed outlier: 3.596A pdb=" N ALA P 152 " --> pdb=" O ASP P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 182 removed outlier: 4.107A pdb=" N ARG P 182 " --> pdb=" O LEU P 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 185 No H-bonds generated for 'chain 'P' and resid 183 through 185' Processing helix chain 'P' and resid 216 through 220 removed outlier: 4.005A pdb=" N TYR P 219 " --> pdb=" O SER P 216 " (cutoff:3.500A) Processing helix chain 'P' and resid 232 through 235 Processing helix chain 'P' and resid 271 through 276 Processing helix chain 'Q' and resid 71 through 75 removed outlier: 3.598A pdb=" N ASN Q 74 " --> pdb=" O TYR Q 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 218 Processing helix chain 'R' and resid 227 through 243 Processing helix chain 'R' and resid 249 through 261 removed outlier: 4.631A pdb=" N ASN R 253 " --> pdb=" O ASP R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 287 removed outlier: 4.041A pdb=" N ILE R 282 " --> pdb=" O PRO R 278 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 291 Processing helix chain 'R' and resid 313 through 323 Processing helix chain 'R' and resid 328 through 347 removed outlier: 4.245A pdb=" N GLU R 332 " --> pdb=" O LEU R 328 " (cutoff:3.500A) Processing helix chain 'R' and resid 424 through 428 removed outlier: 4.571A pdb=" N TYR R 428 " --> pdb=" O ALA R 425 " (cutoff:3.500A) Processing helix chain 'R' and resid 447 through 451 Processing helix chain 'R' and resid 478 through 495 Processing helix chain 'R' and resid 531 through 538 Processing helix chain 'R' and resid 595 through 599 Processing helix chain 'R' and resid 683 through 693 Processing helix chain 'd' and resid 11 through 15 Processing helix chain 'd' and resid 21 through 39 removed outlier: 3.857A pdb=" N ARG d 37 " --> pdb=" O MET d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 89 through 97 Processing helix chain 'd' and resid 136 through 149 Processing helix chain 'd' and resid 177 through 182 removed outlier: 3.657A pdb=" N ARG d 182 " --> pdb=" O LEU d 178 " (cutoff:3.500A) Processing helix chain 'd' and resid 183 through 185 No H-bonds generated for 'chain 'd' and resid 183 through 185' Processing helix chain 'd' and resid 271 through 276 removed outlier: 3.772A pdb=" N MET d 275 " --> pdb=" O ASP d 271 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 142 through 147 removed outlier: 6.227A pdb=" N ARG B 142 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 214 " --> pdb=" O ARG B 142 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 218 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 155 through 160 Processing sheet with id=AA3, first strand: chain 'B' and resid 193 through 195 removed outlier: 3.709A pdb=" N THR B 195 " --> pdb=" O LYS E 201 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 223 through 226 removed outlier: 3.516A pdb=" N ASN B 229 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 230 " --> pdb=" O ASP B 289 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 245 through 250 Processing sheet with id=AA6, first strand: chain 'E' and resid 14 through 19 removed outlier: 4.133A pdb=" N GLN E 43 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ALA E 85 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE E 41 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 19 through 21 removed outlier: 3.555A pdb=" N ALA F 36 " --> pdb=" O TYR F 44 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ARG F 66 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR F 81 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR F 68 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N GLN F 79 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASP F 70 " --> pdb=" O HIS F 77 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS F 77 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLN F 125 " --> pdb=" O GLU F 116 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE F 118 " --> pdb=" O HIS F 123 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N HIS F 123 " --> pdb=" O PHE F 118 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ALA F 149 " --> pdb=" O THR F 140 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS F 162 " --> pdb=" O PRO F 171 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU F 188 " --> pdb=" O PRO F 168 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS F 180 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLU F 181 " --> pdb=" O GLU F 197 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLU F 197 " --> pdb=" O GLU F 181 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N HIS F 183 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU F 195 " --> pdb=" O HIS F 183 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU F 185 " --> pdb=" O ARG F 193 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG F 187 " --> pdb=" O THR F 191 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N THR F 191 " --> pdb=" O ARG F 187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 94 through 95 Processing sheet with id=AA9, first strand: chain 'G' and resid 441 through 442 removed outlier: 3.600A pdb=" N CYS G 433 " --> pdb=" O ILE G 366 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL G 367 " --> pdb=" O TRP G 355 " (cutoff:3.500A) removed outlier: 19.916A pdb=" N PHE G 642 " --> pdb=" O ILE G 349 " (cutoff:3.500A) removed outlier: 14.667A pdb=" N ARG G 351 " --> pdb=" O PHE G 642 " (cutoff:3.500A) removed outlier: 13.627A pdb=" N ASN G 644 " --> pdb=" O ARG G 351 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ARG G 353 " --> pdb=" O ASN G 644 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N TYR G 646 " --> pdb=" O ARG G 353 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TRP G 355 " --> pdb=" O TYR G 646 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLY G 648 " --> pdb=" O TRP G 355 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS G 357 " --> pdb=" O GLY G 648 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER G 637 " --> pdb=" O ALA G 623 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 496 through 498 Processing sheet with id=AB2, first strand: chain 'G' and resid 502 through 503 Processing sheet with id=AB3, first strand: chain 'H' and resid 83 through 84 removed outlier: 6.665A pdb=" N TYR H 57 " --> pdb=" O ARG H 49 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG H 49 " --> pdb=" O TYR H 57 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE H 59 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 9.457A pdb=" N TYR H 262 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP H 47 " --> pdb=" O TYR H 262 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLY H 264 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG H 49 " --> pdb=" O GLY H 264 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 110 through 111 Processing sheet with id=AB5, first strand: chain 'H' and resid 153 through 155 Processing sheet with id=AB6, first strand: chain 'H' and resid 160 through 162 removed outlier: 3.854A pdb=" N VAL H 166 " --> pdb=" O THR H 162 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 226 through 230 removed outlier: 3.830A pdb=" N GLY H 259 " --> pdb=" O TYR H 250 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 23 through 24 removed outlier: 4.004A pdb=" N GLU I 23 " --> pdb=" O HIS I 31 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N HIS I 31 " --> pdb=" O GLU I 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 34 through 37 removed outlier: 3.567A pdb=" N GLY I 78 " --> pdb=" O TRP I 94 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY I 80 " --> pdb=" O GLY I 92 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY I 92 " --> pdb=" O GLY I 80 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN I 102 " --> pdb=" O GLU I 93 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLY I 101 " --> pdb=" O TRP I 117 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR I 112 " --> pdb=" O LEU I 129 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLN I 125 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR I 140 " --> pdb=" O ALA I 149 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA I 149 " --> pdb=" O THR I 140 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL I 142 " --> pdb=" O GLU I 147 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLU I 147 " --> pdb=" O VAL I 142 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY I 148 " --> pdb=" O PHE I 163 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N PHE I 163 " --> pdb=" O GLY I 148 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS I 162 " --> pdb=" O PRO I 171 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N MET I 164 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL I 169 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N HIS I 183 " --> pdb=" O GLU I 195 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 48 through 49 Processing sheet with id=AC2, first strand: chain 'J' and resid 441 through 442 removed outlier: 6.945A pdb=" N VAL J 367 " --> pdb=" O TRP J 355 " (cutoff:3.500A) removed outlier: 19.667A pdb=" N PHE J 642 " --> pdb=" O ILE J 349 " (cutoff:3.500A) removed outlier: 14.469A pdb=" N ARG J 351 " --> pdb=" O PHE J 642 " (cutoff:3.500A) removed outlier: 14.339A pdb=" N ASN J 644 " --> pdb=" O ARG J 351 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N ARG J 353 " --> pdb=" O ASN J 644 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N TYR J 646 " --> pdb=" O ARG J 353 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TRP J 355 " --> pdb=" O TYR J 646 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N GLY J 648 " --> pdb=" O TRP J 355 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LYS J 357 " --> pdb=" O GLY J 648 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ALA J 633 " --> pdb=" O SER J 627 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 496 through 498 Processing sheet with id=AC4, first strand: chain 'J' and resid 502 through 503 Processing sheet with id=AC5, first strand: chain 'c' and resid 83 through 84 removed outlier: 6.547A pdb=" N TYR c 57 " --> pdb=" O ARG c 49 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG c 49 " --> pdb=" O TYR c 57 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE c 59 " --> pdb=" O TRP c 47 " (cutoff:3.500A) removed outlier: 14.929A pdb=" N TYR c 258 " --> pdb=" O ARG c 43 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N LEU c 45 " --> pdb=" O TYR c 258 " (cutoff:3.500A) removed outlier: 9.382A pdb=" N TYR c 260 " --> pdb=" O LEU c 45 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N TRP c 47 " --> pdb=" O TYR c 260 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY c 264 " --> pdb=" O ARG c 49 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU c 247 " --> pdb=" O SER c 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS c 251 " --> pdb=" O VAL c 237 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 153 through 155 Processing sheet with id=AC7, first strand: chain 'K' and resid 143 through 146 removed outlier: 3.623A pdb=" N LEU K 144 " --> pdb=" O ILE K 214 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS K 216 " --> pdb=" O LEU K 144 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 156 through 160 Processing sheet with id=AC9, first strand: chain 'K' and resid 209 through 210 Processing sheet with id=AD1, first strand: chain 'K' and resid 224 through 225 removed outlier: 6.147A pdb=" N LEU K 230 " --> pdb=" O PHE K 291 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE K 293 " --> pdb=" O LEU K 230 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE K 232 " --> pdb=" O PHE K 293 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 245 through 250 Processing sheet with id=AD3, first strand: chain 'M' and resid 40 through 47 removed outlier: 6.875A pdb=" N ILE M 83 " --> pdb=" O ILE M 42 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG M 44 " --> pdb=" O ALA M 81 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA M 81 " --> pdb=" O ARG M 44 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LYS M 46 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU M 79 " --> pdb=" O LYS M 46 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS M 127 " --> pdb=" O LEU M 18 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 19 through 21 removed outlier: 3.805A pdb=" N TYR N 67 " --> pdb=" O TYR N 59 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN N 79 " --> pdb=" O ASP N 70 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLN N 102 " --> pdb=" O GLU N 93 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ALA N 95 " --> pdb=" O HIS N 100 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N HIS N 100 " --> pdb=" O ALA N 95 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLN N 125 " --> pdb=" O GLU N 116 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N PHE N 118 " --> pdb=" O HIS N 123 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS N 123 " --> pdb=" O PHE N 118 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLN N 160 " --> pdb=" O PRO N 171 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS N 162 " --> pdb=" O VAL N 169 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 19 through 21 removed outlier: 3.805A pdb=" N TYR N 67 " --> pdb=" O TYR N 59 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN N 79 " --> pdb=" O ASP N 70 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLN N 102 " --> pdb=" O GLU N 93 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ALA N 95 " --> pdb=" O HIS N 100 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N HIS N 100 " --> pdb=" O ALA N 95 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLN N 125 " --> pdb=" O GLU N 116 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N PHE N 118 " --> pdb=" O HIS N 123 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS N 123 " --> pdb=" O PHE N 118 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS N 180 " --> pdb=" O PHE N 176 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU N 199 " --> pdb=" O GLU N 181 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 349 through 358 removed outlier: 6.989A pdb=" N VAL O 367 " --> pdb=" O TRP O 355 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS O 357 " --> pdb=" O TYR O 365 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR O 365 " --> pdb=" O LYS O 357 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 496 through 498 Processing sheet with id=AD8, first strand: chain 'O' and resid 502 through 503 removed outlier: 4.020A pdb=" N GLU O 522 " --> pdb=" O GLN O 503 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 609 through 612 Processing sheet with id=AE1, first strand: chain 'P' and resid 83 through 84 removed outlier: 3.529A pdb=" N LYS P 72 " --> pdb=" O GLY P 62 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN P 61 " --> pdb=" O PHE P 46 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE P 46 " --> pdb=" O GLN P 61 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU P 63 " --> pdb=" O VAL P 44 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL P 44 " --> pdb=" O LEU P 63 " (cutoff:3.500A) removed outlier: 13.154A pdb=" N ARG P 43 " --> pdb=" O TYR P 258 " (cutoff:3.500A) removed outlier: 13.090A pdb=" N TYR P 260 " --> pdb=" O ARG P 43 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N LEU P 45 " --> pdb=" O TYR P 260 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N TYR P 262 " --> pdb=" O LEU P 45 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TRP P 47 " --> pdb=" O TYR P 262 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N GLY P 264 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ARG P 49 " --> pdb=" O GLY P 264 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE P 261 " --> pdb=" O THR P 248 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU P 247 " --> pdb=" O SER P 241 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 110 through 111 Processing sheet with id=AE3, first strand: chain 'P' and resid 153 through 155 Processing sheet with id=AE4, first strand: chain 'P' and resid 159 through 162 removed outlier: 3.895A pdb=" N VAL P 166 " --> pdb=" O THR P 162 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 19 through 20 removed outlier: 6.621A pdb=" N SER Q 47 " --> pdb=" O GLN Q 56 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLN Q 56 " --> pdb=" O SER Q 47 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLU Q 49 " --> pdb=" O HIS Q 54 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N HIS Q 54 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLN Q 125 " --> pdb=" O GLU Q 116 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE Q 118 " --> pdb=" O HIS Q 123 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N HIS Q 123 " --> pdb=" O PHE Q 118 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA Q 150 " --> pdb=" O GLY Q 161 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY Q 161 " --> pdb=" O ALA Q 150 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 145 through 146 removed outlier: 3.805A pdb=" N ALA Q 150 " --> pdb=" O GLY Q 161 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY Q 161 " --> pdb=" O ALA Q 150 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN Q 160 " --> pdb=" O LYS Q 173 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 349 through 356 removed outlier: 6.778A pdb=" N GLU R 371 " --> pdb=" O GLN R 350 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N CYS R 352 " --> pdb=" O GLU R 369 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU R 369 " --> pdb=" O CYS R 352 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE R 354 " --> pdb=" O VAL R 367 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL R 367 " --> pdb=" O PHE R 354 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 496 through 498 Processing sheet with id=AE9, first strand: chain 'R' and resid 502 through 503 Processing sheet with id=AF1, first strand: chain 'R' and resid 608 through 612 Processing sheet with id=AF2, first strand: chain 'd' and resid 83 through 85 removed outlier: 4.273A pdb=" N THR d 73 " --> pdb=" O LEU d 85 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY d 62 " --> pdb=" O LYS d 72 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR d 57 " --> pdb=" O ARG d 49 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG d 49 " --> pdb=" O TYR d 57 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE d 59 " --> pdb=" O TRP d 47 " (cutoff:3.500A) removed outlier: 10.434A pdb=" N LEU d 45 " --> pdb=" O TYR d 258 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N TYR d 260 " --> pdb=" O LEU d 45 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N TRP d 47 " --> pdb=" O TYR d 260 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU d 247 " --> pdb=" O SER d 241 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU d 236 " --> pdb=" O GLU d 231 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU d 231 " --> pdb=" O LEU d 236 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'd' and resid 110 through 111 removed outlier: 3.817A pdb=" N ILE d 134 " --> pdb=" O TYR d 111 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'd' and resid 153 through 155 Processing sheet with id=AF5, first strand: chain 'd' and resid 159 through 161 1387 hydrogen bonds defined for protein. 3786 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: 13.94 Time building geometry restraints manager: 13.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5956 1.32 - 1.45: 9635 1.45 - 1.58: 18981 1.58 - 1.70: 16 1.70 - 1.83: 218 Bond restraints: 34806 Sorted by residual: bond pdb=" CB ARG C 41 " pdb=" CG ARG C 41 " ideal model delta sigma weight residual 1.520 1.433 0.087 3.00e-02 1.11e+03 8.48e+00 bond pdb=" C ASN E 196 " pdb=" N PRO E 197 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.59e+00 bond pdb=" CA LEU O 240 " pdb=" C LEU O 240 " ideal model delta sigma weight residual 1.523 1.572 -0.049 1.80e-02 3.09e+03 7.45e+00 bond pdb=" CB MET K 309 " pdb=" CG MET K 309 " ideal model delta sigma weight residual 1.520 1.596 -0.076 3.00e-02 1.11e+03 6.47e+00 bond pdb=" C ALA P 252 " pdb=" N PRO P 253 " ideal model delta sigma weight residual 1.335 1.367 -0.032 1.28e-02 6.10e+03 6.40e+00 ... (remaining 34801 not shown) Histogram of bond angle deviations from ideal: 98.14 - 108.15: 2137 108.15 - 118.15: 23404 118.15 - 128.16: 21140 128.16 - 138.16: 495 138.16 - 148.16: 4 Bond angle restraints: 47180 Sorted by residual: angle pdb=" C ALA R 245 " pdb=" N ASP R 246 " pdb=" CA ASP R 246 " ideal model delta sigma weight residual 121.70 148.16 -26.46 1.80e+00 3.09e-01 2.16e+02 angle pdb=" C GLU P 65 " pdb=" N ASP P 66 " pdb=" CA ASP P 66 " ideal model delta sigma weight residual 121.70 143.05 -21.35 1.80e+00 3.09e-01 1.41e+02 angle pdb=" C LEU J 616 " pdb=" N ILE J 617 " pdb=" CA ILE J 617 " ideal model delta sigma weight residual 121.70 141.50 -19.80 1.80e+00 3.09e-01 1.21e+02 angle pdb=" C TYR Q 159 " pdb=" N GLN Q 160 " pdb=" CA GLN Q 160 " ideal model delta sigma weight residual 121.70 140.12 -18.42 1.80e+00 3.09e-01 1.05e+02 angle pdb=" C ARG Q 99 " pdb=" N HIS Q 100 " pdb=" CA HIS Q 100 " ideal model delta sigma weight residual 121.70 137.54 -15.84 1.80e+00 3.09e-01 7.75e+01 ... (remaining 47175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18244 17.98 - 35.95: 1899 35.95 - 53.93: 418 53.93 - 71.91: 84 71.91 - 89.88: 43 Dihedral angle restraints: 20688 sinusoidal: 8526 harmonic: 12162 Sorted by residual: dihedral pdb=" CA LYS B 216 " pdb=" C LYS B 216 " pdb=" N GLU B 217 " pdb=" CA GLU B 217 " ideal model delta harmonic sigma weight residual 0.00 -43.42 43.42 0 5.00e+00 4.00e-02 7.54e+01 dihedral pdb=" CA SER G 613 " pdb=" C SER G 613 " pdb=" N SER G 614 " pdb=" CA SER G 614 " ideal model delta harmonic sigma weight residual 0.00 -39.36 39.36 0 5.00e+00 4.00e-02 6.20e+01 dihedral pdb=" CA ASP E 183 " pdb=" C ASP E 183 " pdb=" N PRO E 184 " pdb=" CA PRO E 184 " ideal model delta harmonic sigma weight residual -180.00 -143.96 -36.04 0 5.00e+00 4.00e-02 5.20e+01 ... (remaining 20685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4541 0.099 - 0.199: 408 0.199 - 0.298: 13 0.298 - 0.398: 1 0.398 - 0.497: 1 Chirality restraints: 4964 Sorted by residual: chirality pdb=" CG LEU L 295 " pdb=" CB LEU L 295 " pdb=" CD1 LEU L 295 " pdb=" CD2 LEU L 295 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" CA TRP D 294 " pdb=" N TRP D 294 " pdb=" C TRP D 294 " pdb=" CB TRP D 294 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE c 147 " pdb=" CA ILE c 147 " pdb=" CG1 ILE c 147 " pdb=" CG2 ILE c 147 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 4961 not shown) Planarity restraints: 6150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 294 " -0.041 2.00e-02 2.50e+03 4.07e-02 4.14e+01 pdb=" CG TRP D 294 " 0.106 2.00e-02 2.50e+03 pdb=" CD1 TRP D 294 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TRP D 294 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP D 294 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP D 294 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP D 294 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 294 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 294 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP D 294 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU M 7 " -0.064 5.00e-02 4.00e+02 9.61e-02 1.48e+01 pdb=" N PRO M 8 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO M 8 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO M 8 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 294 " 0.030 2.00e-02 2.50e+03 2.42e-02 1.46e+01 pdb=" CG TRP L 294 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP L 294 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP L 294 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP L 294 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP L 294 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP L 294 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 294 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 294 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP L 294 " 0.003 2.00e-02 2.50e+03 ... (remaining 6147 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 378 2.61 - 3.18: 28751 3.18 - 3.75: 53611 3.75 - 4.33: 74191 4.33 - 4.90: 122833 Nonbonded interactions: 279764 Sorted by model distance: nonbonded pdb=" O TYR J 216 " pdb=" OG SER J 219 " model vdw 2.037 2.440 nonbonded pdb=" OH TYR G 216 " pdb=" O PRO J 244 " model vdw 2.045 2.440 nonbonded pdb=" OG SER B 147 " pdb=" OD2 ASP B 150 " model vdw 2.068 2.440 nonbonded pdb=" OD1 ASN O 426 " pdb=" OG SER O 445 " model vdw 2.075 2.440 nonbonded pdb=" OG SER K 147 " pdb=" OD1 ASP K 150 " model vdw 2.079 2.440 ... (remaining 279759 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 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = (chain 'J' and (resid 206 through 261 or resid 273 through 377 or resid 413 thro \ ugh 693)) selection = chain 'O' selection = (chain 'R' and (resid 206 through 261 or resid 273 through 377 or resid 413 thro \ ugh 693)) } ncs_group { reference = chain 'H' selection = chain 'P' selection = (chain 'c' and (resid 1 through 113 or resid 133 through 276)) selection = (chain 'd' and (resid 1 through 113 or resid 133 through 276)) } 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=1.00 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: 9.690 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: 0.040 Extract box with map and model: 36.150 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 84.040 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.230 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: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 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 0.126 34806 Z= 0.462 Angle : 1.218 26.465 47180 Z= 0.647 Chirality : 0.055 0.497 4964 Planarity : 0.009 0.144 6150 Dihedral : 15.704 89.882 12924 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.67 % Favored : 94.14 % Rotamer: Outliers : 0.33 % Allowed : 20.31 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.51 % Twisted Proline : 0.39 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.12), residues: 4110 helix: -0.51 (0.14), residues: 1068 sheet: -1.16 (0.18), residues: 722 loop : -1.01 (0.12), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.002 TRP D 294 HIS 0.028 0.002 HIS Q 157 PHE 0.052 0.003 PHE F 61 TYR 0.056 0.003 TYR R 216 ARG 0.023 0.001 ARG c 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1201 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1189 time to evaluate : 3.777 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: D 294 TRP cc_start: 0.7906 (t60) cc_final: 0.7331 (t60) REVERT: D 298 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7492 (mm-30) REVERT: D 321 VAL cc_start: 0.8804 (t) cc_final: 0.8604 (p) REVERT: D 322 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7396 (mp0) REVERT: D 323 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7918 (ttm-80) REVERT: E 90 ILE cc_start: 0.8713 (mp) cc_final: 0.8044 (mm) REVERT: E 195 ASN cc_start: 0.7619 (m-40) cc_final: 0.7232 (m-40) REVERT: F 122 ARG cc_start: 0.7981 (mpp80) cc_final: 0.7700 (mtm-85) REVERT: F 142 VAL cc_start: 0.8878 (t) cc_final: 0.8513 (m) REVERT: G 251 ILE cc_start: 0.8366 (tt) cc_final: 0.8124 (tp) REVERT: G 257 ASP cc_start: 0.7777 (t70) cc_final: 0.7283 (t0) REVERT: G 281 GLU cc_start: 0.7993 (pt0) cc_final: 0.7764 (pt0) REVERT: G 451 ILE cc_start: 0.7990 (mt) cc_final: 0.7682 (mm) REVERT: G 554 ARG cc_start: 0.7856 (mtp180) cc_final: 0.7623 (mtp-110) REVERT: G 652 LYS cc_start: 0.8665 (ttpt) cc_final: 0.8438 (tttt) REVERT: H 57 TYR cc_start: 0.7390 (m-80) cc_final: 0.6574 (m-80) REVERT: H 67 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8229 (mm-40) REVERT: H 73 THR cc_start: 0.8396 (m) cc_final: 0.8054 (t) REVERT: H 75 TYR cc_start: 0.8219 (p90) cc_final: 0.7891 (p90) REVERT: I 93 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6976 (mp0) REVERT: I 109 ASN cc_start: 0.6862 (p0) cc_final: 0.6635 (p0) REVERT: I 116 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7192 (mt-10) REVERT: I 142 VAL cc_start: 0.8641 (t) cc_final: 0.8366 (p) REVERT: I 147 GLU cc_start: 0.6414 (mm-30) cc_final: 0.6095 (mm-30) REVERT: I 153 ILE cc_start: 0.8529 (mp) cc_final: 0.8252 (mt) REVERT: J 234 LYS cc_start: 0.8424 (mppt) cc_final: 0.7857 (mppt) REVERT: J 332 GLU cc_start: 0.7702 (tp30) cc_final: 0.7458 (tp30) REVERT: J 438 ARG cc_start: 0.8454 (ttm-80) cc_final: 0.8008 (mtt-85) REVERT: J 459 LYS cc_start: 0.8010 (mmtp) cc_final: 0.7450 (ttmm) REVERT: J 464 ARG cc_start: 0.7260 (mtm-85) cc_final: 0.6944 (mtm-85) REVERT: J 479 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: J 533 ILE cc_start: 0.8559 (tp) cc_final: 0.7749 (tp) REVERT: J 537 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7248 (mt-10) REVERT: J 679 MET cc_start: 0.5483 (ppp) cc_final: 0.4124 (ppp) REVERT: c 59 ILE cc_start: 0.8235 (mm) cc_final: 0.7504 (mm) REVERT: c 136 GLU cc_start: 0.7607 (tp30) cc_final: 0.7227 (tp30) REVERT: c 182 ARG cc_start: 0.7919 (mmm-85) cc_final: 0.7633 (mmm-85) REVERT: c 271 ASP cc_start: 0.7499 (m-30) cc_final: 0.7278 (m-30) REVERT: C 38 TYR cc_start: 0.7682 (m-10) cc_final: 0.7462 (m-80) REVERT: K 153 PHE cc_start: 0.7959 (m-80) cc_final: 0.7723 (m-80) REVERT: K 189 ARG cc_start: 0.7510 (mtt-85) cc_final: 0.7174 (mmt90) REVERT: K 192 THR cc_start: 0.8631 (m) cc_final: 0.8290 (p) REVERT: K 217 GLU cc_start: 0.6860 (tp30) cc_final: 0.6321 (tp30) REVERT: L 292 LEU cc_start: 0.9026 (mm) cc_final: 0.8297 (mm) REVERT: L 294 TRP cc_start: 0.7663 (t60) cc_final: 0.7260 (t60) REVERT: L 298 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7127 (mm-30) REVERT: L 301 LYS cc_start: 0.8681 (mtmt) cc_final: 0.8323 (mtmm) REVERT: M 40 THR cc_start: 0.8686 (m) cc_final: 0.8239 (t) REVERT: M 57 PHE cc_start: 0.8539 (t80) cc_final: 0.8297 (t80) REVERT: M 92 TYR cc_start: 0.8518 (t80) cc_final: 0.7521 (t80) REVERT: M 95 GLU cc_start: 0.8218 (mt-10) cc_final: 0.8001 (mt-10) REVERT: M 155 GLN cc_start: 0.7901 (tp40) cc_final: 0.7502 (tm-30) REVERT: N 44 TYR cc_start: 0.7239 (t80) cc_final: 0.6873 (t80) REVERT: N 98 GLN cc_start: 0.8245 (mt0) cc_final: 0.7975 (mt0) REVERT: N 136 LYS cc_start: 0.8515 (mttt) cc_final: 0.8277 (mtpp) REVERT: N 142 VAL cc_start: 0.8907 (t) cc_final: 0.8687 (m) REVERT: N 147 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6499 (mt-10) REVERT: N 185 GLU cc_start: 0.7219 (tt0) cc_final: 0.6828 (tt0) REVERT: N 199 GLU cc_start: 0.6326 (mm-30) cc_final: 0.6095 (mm-30) REVERT: O 281 GLU cc_start: 0.8160 (pt0) cc_final: 0.7702 (pp20) REVERT: O 347 HIS cc_start: 0.8838 (m170) cc_final: 0.8586 (m170) REVERT: O 442 ARG cc_start: 0.8513 (ttt90) cc_final: 0.8192 (ttt180) REVERT: O 502 TYR cc_start: 0.5739 (p90) cc_final: 0.4726 (p90) REVERT: O 641 LYS cc_start: 0.8224 (mmtt) cc_final: 0.8014 (mmtt) REVERT: O 692 MET cc_start: 0.7680 (mtm) cc_final: 0.7318 (mtm) REVERT: P 43 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7301 (mtm-85) REVERT: P 180 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7679 (mt-10) REVERT: P 250 TYR cc_start: 0.5745 (t80) cc_final: 0.5348 (t80) REVERT: Q 105 TYR cc_start: 0.7774 (t80) cc_final: 0.7276 (t80) REVERT: Q 116 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6819 (mt-10) REVERT: Q 151 GLU cc_start: 0.6803 (tp30) cc_final: 0.5894 (tp30) REVERT: Q 158 ARG cc_start: 0.6863 (mtt-85) cc_final: 0.6637 (ttm110) REVERT: R 211 GLN cc_start: 0.7821 (mp10) cc_final: 0.7549 (mp-120) REVERT: R 280 TYR cc_start: 0.6323 (m-10) cc_final: 0.5926 (m-10) REVERT: R 287 LYS cc_start: 0.8368 (pttm) cc_final: 0.7963 (pttm) REVERT: R 313 ASN cc_start: 0.8354 (t0) cc_final: 0.7978 (t0) REVERT: R 316 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7966 (tm-30) REVERT: R 353 ARG cc_start: 0.7782 (ttp80) cc_final: 0.7213 (ttt-90) REVERT: R 433 CYS cc_start: 0.7747 (t) cc_final: 0.7523 (p) REVERT: R 531 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7502 (mm-40) REVERT: R 556 ASN cc_start: 0.8691 (m-40) cc_final: 0.8212 (m-40) REVERT: R 641 LYS cc_start: 0.8006 (pttm) cc_final: 0.7757 (pttm) REVERT: d 73 THR cc_start: 0.9093 (m) cc_final: 0.8660 (t) REVERT: d 78 ASN cc_start: 0.7866 (p0) cc_final: 0.6809 (p0) REVERT: d 81 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6857 (mt-10) REVERT: d 92 MET cc_start: 0.7771 (mtp) cc_final: 0.7557 (mtp) REVERT: d 135 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8148 (mmtt) REVERT: d 180 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7319 (mm-30) REVERT: d 183 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8356 (ptpp) REVERT: d 262 TYR cc_start: 0.8647 (t80) cc_final: 0.8394 (t80) REVERT: d 269 ASN cc_start: 0.8569 (t0) cc_final: 0.8256 (t0) outliers start: 12 outliers final: 4 residues processed: 1192 average time/residue: 0.5201 time to fit residues: 941.5273 Evaluate side-chains 1132 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1127 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain J residue 479 GLU Chi-restraints excluded: chain K residue 155 CYS Chi-restraints excluded: chain P residue 248 THR Chi-restraints excluded: chain d residue 23 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 347 optimal weight: 0.1980 chunk 312 optimal weight: 0.5980 chunk 173 optimal weight: 0.4980 chunk 106 optimal weight: 0.9990 chunk 210 optimal weight: 5.9990 chunk 166 optimal weight: 0.3980 chunk 322 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 240 optimal weight: 0.4980 chunk 374 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS F 54 HIS G 323 GLN G 503 GLN G 531 GLN J 271 HIS J 286 GLN J 342 GLN ** J 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 547 GLN c 78 ASN ** c 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS K 202 GLN ** L 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 HIS ** N 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 657 ASN Q 33 HIS Q 157 HIS ** R 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 342 GLN R 350 GLN ** R 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 95 GLN d 146 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34806 Z= 0.230 Angle : 0.718 14.296 47180 Z= 0.372 Chirality : 0.045 0.246 4964 Planarity : 0.005 0.066 6150 Dihedral : 5.587 47.197 4643 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.72 % Favored : 95.06 % Rotamer: Outliers : 3.51 % Allowed : 18.30 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 4110 helix: -0.06 (0.15), residues: 1140 sheet: -1.03 (0.18), residues: 760 loop : -0.74 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 294 HIS 0.014 0.001 HIS F 120 PHE 0.038 0.002 PHE N 50 TYR 0.023 0.002 TYR H 219 ARG 0.008 0.001 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1302 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1174 time to evaluate : 3.221 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: A 20 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7266 (tm-30) REVERT: B 226 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7072 (mt-10) REVERT: B 256 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8310 (tt) REVERT: D 294 TRP cc_start: 0.7821 (t60) cc_final: 0.7496 (t60) REVERT: D 301 LYS cc_start: 0.8607 (mtmt) cc_final: 0.8055 (mtmt) REVERT: D 307 MET cc_start: 0.7384 (tpp) cc_final: 0.7106 (tpp) REVERT: E 44 ARG cc_start: 0.7684 (ttp-170) cc_final: 0.7382 (ttp-170) REVERT: E 74 MET cc_start: 0.6985 (mmp) cc_final: 0.6149 (mmm) REVERT: E 123 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6804 (mmp80) REVERT: E 158 LYS cc_start: 0.8006 (ptmt) cc_final: 0.7772 (ptmt) REVERT: E 175 GLU cc_start: 0.7276 (pp20) cc_final: 0.6342 (pp20) REVERT: E 186 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6499 (mm) REVERT: F 67 TYR cc_start: 0.7541 (t80) cc_final: 0.6803 (t80) REVERT: F 93 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6810 (mm-30) REVERT: F 121 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6992 (mp10) REVERT: F 142 VAL cc_start: 0.8812 (t) cc_final: 0.8489 (m) REVERT: F 156 ASN cc_start: 0.8117 (p0) cc_final: 0.7625 (p0) REVERT: G 250 ILE cc_start: 0.8421 (mm) cc_final: 0.8205 (tp) REVERT: G 251 ILE cc_start: 0.8262 (tt) cc_final: 0.7894 (tp) REVERT: G 257 ASP cc_start: 0.7819 (t70) cc_final: 0.7276 (t0) REVERT: G 276 MET cc_start: 0.6377 (mmm) cc_final: 0.5827 (mmm) REVERT: G 281 GLU cc_start: 0.8090 (pt0) cc_final: 0.7554 (pp20) REVERT: G 284 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7147 (mm-30) REVERT: G 332 GLU cc_start: 0.8088 (tp30) cc_final: 0.7357 (tp30) REVERT: G 335 ARG cc_start: 0.7254 (tpp80) cc_final: 0.6796 (tpp80) REVERT: G 350 GLN cc_start: 0.8217 (tt0) cc_final: 0.7961 (tp40) REVERT: G 351 ARG cc_start: 0.7433 (ttp-170) cc_final: 0.6741 (ttp-170) REVERT: G 373 ARG cc_start: 0.7610 (mtm-85) cc_final: 0.7091 (mtm-85) REVERT: G 428 TYR cc_start: 0.8084 (m-80) cc_final: 0.7554 (m-10) REVERT: G 503 GLN cc_start: 0.7914 (pt0) cc_final: 0.7685 (pt0) REVERT: G 688 GLN cc_start: 0.8557 (tp40) cc_final: 0.7841 (tp40) REVERT: G 692 MET cc_start: 0.7266 (mmp) cc_final: 0.7033 (mmp) REVERT: H 71 ARG cc_start: 0.7352 (ptt180) cc_final: 0.6905 (ptt180) REVERT: H 230 MET cc_start: 0.8384 (mmm) cc_final: 0.8147 (mmt) REVERT: H 250 TYR cc_start: 0.7248 (p90) cc_final: 0.6951 (p90) REVERT: H 270 MET cc_start: 0.6916 (mmm) cc_final: 0.6716 (mmm) REVERT: I 104 VAL cc_start: 0.7746 (t) cc_final: 0.7412 (p) REVERT: I 111 ASP cc_start: 0.7744 (m-30) cc_final: 0.7340 (m-30) REVERT: I 142 VAL cc_start: 0.8742 (t) cc_final: 0.8382 (p) REVERT: I 147 GLU cc_start: 0.6681 (mm-30) cc_final: 0.6339 (mm-30) REVERT: I 153 ILE cc_start: 0.8694 (mp) cc_final: 0.8265 (mt) REVERT: J 216 TYR cc_start: 0.8096 (t80) cc_final: 0.7751 (t80) REVERT: J 257 ASP cc_start: 0.7827 (t0) cc_final: 0.7549 (t0) REVERT: J 260 MET cc_start: 0.7789 (tmm) cc_final: 0.7527 (tmm) REVERT: J 331 ASP cc_start: 0.7732 (t0) cc_final: 0.7367 (t0) REVERT: J 332 GLU cc_start: 0.7940 (tp30) cc_final: 0.7706 (tp30) REVERT: J 353 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7760 (ptm-80) REVERT: J 438 ARG cc_start: 0.8612 (ttm-80) cc_final: 0.8182 (mtt-85) REVERT: J 458 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8704 (ttmm) REVERT: J 459 LYS cc_start: 0.8084 (mmtp) cc_final: 0.7817 (ttmm) REVERT: J 679 MET cc_start: 0.5570 (ppp) cc_final: 0.4558 (tmm) REVERT: c 57 TYR cc_start: 0.8238 (m-80) cc_final: 0.8033 (m-80) REVERT: c 59 ILE cc_start: 0.8514 (mm) cc_final: 0.8206 (mm) REVERT: c 96 ILE cc_start: 0.8782 (pt) cc_final: 0.8418 (pt) REVERT: c 136 GLU cc_start: 0.7761 (tp30) cc_final: 0.7504 (tp30) REVERT: c 142 SER cc_start: 0.8503 (m) cc_final: 0.7856 (p) REVERT: c 145 ASP cc_start: 0.8213 (t0) cc_final: 0.7767 (t0) REVERT: c 191 ARG cc_start: 0.7277 (mtp180) cc_final: 0.7001 (mtp-110) REVERT: c 248 THR cc_start: 0.8716 (m) cc_final: 0.8355 (t) REVERT: c 258 TYR cc_start: 0.8066 (p90) cc_final: 0.7628 (p90) REVERT: c 262 TYR cc_start: 0.8781 (t80) cc_final: 0.8421 (t80) REVERT: c 271 ASP cc_start: 0.8042 (m-30) cc_final: 0.7409 (m-30) REVERT: C 38 TYR cc_start: 0.7702 (m-10) cc_final: 0.7499 (m-80) REVERT: K 217 GLU cc_start: 0.6882 (tp30) cc_final: 0.6274 (mm-30) REVERT: L 292 LEU cc_start: 0.8952 (mm) cc_final: 0.8438 (mm) REVERT: L 297 ASN cc_start: 0.8587 (m-40) cc_final: 0.8335 (m-40) REVERT: L 301 LYS cc_start: 0.8750 (mtmt) cc_final: 0.8415 (mtmm) REVERT: L 307 MET cc_start: 0.7692 (tpp) cc_final: 0.7439 (tpp) REVERT: M 40 THR cc_start: 0.8610 (m) cc_final: 0.8139 (t) REVERT: M 79 LEU cc_start: 0.6316 (mp) cc_final: 0.6088 (mm) REVERT: M 95 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8002 (mt-10) REVERT: M 139 ILE cc_start: 0.8470 (mt) cc_final: 0.8174 (mm) REVERT: M 155 GLN cc_start: 0.7934 (tp40) cc_final: 0.7389 (tm-30) REVERT: N 98 GLN cc_start: 0.8291 (mt0) cc_final: 0.7928 (mt0) REVERT: N 111 ASP cc_start: 0.7640 (m-30) cc_final: 0.7428 (m-30) REVERT: N 136 LYS cc_start: 0.8628 (mttt) cc_final: 0.8354 (mtpp) REVERT: N 185 GLU cc_start: 0.7239 (tt0) cc_final: 0.6835 (tt0) REVERT: O 241 ASP cc_start: 0.5737 (m-30) cc_final: 0.5204 (p0) REVERT: O 281 GLU cc_start: 0.8442 (pt0) cc_final: 0.7779 (pp20) REVERT: O 284 GLU cc_start: 0.7857 (tp30) cc_final: 0.7613 (tp30) REVERT: O 347 HIS cc_start: 0.8787 (m170) cc_final: 0.8484 (m170) REVERT: O 350 GLN cc_start: 0.8258 (tm-30) cc_final: 0.7554 (tm-30) REVERT: O 371 GLU cc_start: 0.6782 (tp30) cc_final: 0.6204 (tp30) REVERT: O 438 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7673 (mtp85) REVERT: O 451 ILE cc_start: 0.7954 (mt) cc_final: 0.7682 (mt) REVERT: O 502 TYR cc_start: 0.5958 (p90) cc_final: 0.4794 (p90) REVERT: O 626 ARG cc_start: 0.7327 (mtm-85) cc_final: 0.7075 (mtm-85) REVERT: O 686 GLU cc_start: 0.8828 (mp0) cc_final: 0.8608 (mp0) REVERT: O 688 GLN cc_start: 0.8543 (tp40) cc_final: 0.8200 (tm-30) REVERT: O 692 MET cc_start: 0.7790 (mtm) cc_final: 0.6317 (mtm) REVERT: P 10 LEU cc_start: 0.7174 (mm) cc_final: 0.6679 (mt) REVERT: P 33 MET cc_start: 0.8031 (mmt) cc_final: 0.7801 (mmp) REVERT: P 40 ARG cc_start: 0.7661 (ttm110) cc_final: 0.7354 (ttm-80) REVERT: P 78 ASN cc_start: 0.7275 (t0) cc_final: 0.6990 (t0) REVERT: P 180 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7718 (mt-10) REVERT: P 250 TYR cc_start: 0.5960 (t80) cc_final: 0.5724 (t80) REVERT: Q 67 TYR cc_start: 0.6848 (t80) cc_final: 0.6574 (t80) REVERT: Q 138 VAL cc_start: 0.8517 (t) cc_final: 0.8168 (m) REVERT: Q 142 VAL cc_start: 0.8636 (p) cc_final: 0.8411 (m) REVERT: Q 151 GLU cc_start: 0.7019 (tp30) cc_final: 0.6585 (tp30) REVERT: R 249 ASP cc_start: 0.8231 (t0) cc_final: 0.8015 (t0) REVERT: R 313 ASN cc_start: 0.8374 (t0) cc_final: 0.7859 (t0) REVERT: R 322 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7765 (tm-30) REVERT: R 334 TYR cc_start: 0.8009 (t80) cc_final: 0.7720 (t80) REVERT: R 373 ARG cc_start: 0.7052 (ptp90) cc_final: 0.6579 (ptp90) REVERT: R 418 LYS cc_start: 0.8070 (ptmm) cc_final: 0.7712 (ptmm) REVERT: R 438 ARG cc_start: 0.8247 (tpp80) cc_final: 0.8006 (mtt-85) REVERT: R 556 ASN cc_start: 0.8715 (m-40) cc_final: 0.8355 (m-40) REVERT: R 619 GLN cc_start: 0.7993 (tp40) cc_final: 0.7553 (tp40) REVERT: R 640 LYS cc_start: 0.8683 (tptt) cc_final: 0.8469 (tptt) REVERT: R 681 ASP cc_start: 0.6586 (OUTLIER) cc_final: 0.6123 (m-30) REVERT: d 2 ASP cc_start: 0.8088 (t0) cc_final: 0.7792 (t0) REVERT: d 43 ARG cc_start: 0.8235 (ttp80) cc_final: 0.7808 (ttp80) REVERT: d 73 THR cc_start: 0.9073 (m) cc_final: 0.8834 (t) REVERT: d 81 GLU cc_start: 0.7550 (mt-10) cc_final: 0.6908 (mt-10) REVERT: d 92 MET cc_start: 0.7774 (mtp) cc_final: 0.7487 (mtp) REVERT: d 135 LYS cc_start: 0.8418 (mmtt) cc_final: 0.8142 (mmtt) REVERT: d 170 ASN cc_start: 0.7556 (t0) cc_final: 0.7031 (t0) REVERT: d 180 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7362 (mm-30) REVERT: d 183 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8378 (ptpp) REVERT: d 228 ILE cc_start: 0.8844 (mt) cc_final: 0.8545 (tt) REVERT: d 230 MET cc_start: 0.7268 (mmm) cc_final: 0.6890 (mmm) REVERT: d 248 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8610 (p) REVERT: d 262 TYR cc_start: 0.8850 (t80) cc_final: 0.8257 (t80) REVERT: d 269 ASN cc_start: 0.8747 (t0) cc_final: 0.8407 (t0) outliers start: 128 outliers final: 76 residues processed: 1219 average time/residue: 0.5760 time to fit residues: 1079.1821 Evaluate side-chains 1203 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1120 time to evaluate : 4.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 466 ASP Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain G residue 588 VAL Chi-restraints excluded: chain G residue 605 ILE Chi-restraints excluded: chain G residue 617 ILE Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 227 ASN Chi-restraints excluded: chain J residue 458 LYS Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain K residue 222 ARG Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain L residue 289 VAL Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 130 ASN Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain M residue 193 MET Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 155 LEU Chi-restraints excluded: chain O residue 290 PHE Chi-restraints excluded: chain O residue 526 ASP Chi-restraints excluded: chain O residue 540 SER Chi-restraints excluded: chain O residue 556 ASN Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain P residue 271 ASP Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 157 HIS Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 180 CYS Chi-restraints excluded: chain R residue 248 VAL Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain R residue 526 ASP Chi-restraints excluded: chain R residue 641 LYS Chi-restraints excluded: chain R residue 654 CYS Chi-restraints excluded: chain R residue 681 ASP Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 95 GLN Chi-restraints excluded: chain d residue 174 GLU Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 250 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 207 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 311 optimal weight: 0.5980 chunk 254 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 374 optimal weight: 1.9990 chunk 404 optimal weight: 0.8980 chunk 333 optimal weight: 5.9990 chunk 371 optimal weight: 0.5980 chunk 127 optimal weight: 0.6980 chunk 300 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN G 531 GLN G 547 GLN H 95 GLN J 323 GLN J 350 GLN ** J 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 234 ASN ** L 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 162 ASN ** N 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 286 GLN O 531 GLN Q 120 HIS Q 157 HIS ** R 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 146 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 34806 Z= 0.255 Angle : 0.686 15.254 47180 Z= 0.351 Chirality : 0.045 0.198 4964 Planarity : 0.005 0.062 6150 Dihedral : 5.180 41.808 4634 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.72 % Favored : 95.09 % Rotamer: Outliers : 3.76 % Allowed : 19.15 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.13), residues: 4110 helix: 0.14 (0.15), residues: 1142 sheet: -1.00 (0.18), residues: 762 loop : -0.63 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 294 HIS 0.011 0.001 HIS Q 157 PHE 0.022 0.002 PHE O 475 TYR 0.031 0.002 TYR I 44 ARG 0.009 0.001 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1312 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1175 time to evaluate : 3.017 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: A 20 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7207 (tm-30) REVERT: A 41 ARG cc_start: 0.8142 (ttp-170) cc_final: 0.7859 (ttp-170) REVERT: B 146 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7092 (mt) REVERT: B 150 ASP cc_start: 0.7898 (t0) cc_final: 0.7271 (t0) REVERT: B 226 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7080 (mt-10) REVERT: B 253 ASP cc_start: 0.7809 (t0) cc_final: 0.7419 (t0) REVERT: D 294 TRP cc_start: 0.7868 (t60) cc_final: 0.7437 (t60) REVERT: D 307 MET cc_start: 0.7399 (tpp) cc_final: 0.7154 (tpp) REVERT: E 28 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7389 (mm-30) REVERT: E 44 ARG cc_start: 0.7724 (ttp-170) cc_final: 0.7489 (ttp-170) REVERT: E 74 MET cc_start: 0.7035 (mmp) cc_final: 0.6672 (mmp) REVERT: E 92 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7810 (t80) REVERT: E 175 GLU cc_start: 0.7264 (pp20) cc_final: 0.6885 (pp20) REVERT: F 67 TYR cc_start: 0.7659 (t80) cc_final: 0.6880 (t80) REVERT: F 121 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7115 (mp10) REVERT: F 142 VAL cc_start: 0.8822 (t) cc_final: 0.8458 (m) REVERT: F 156 ASN cc_start: 0.8149 (p0) cc_final: 0.7653 (p0) REVERT: G 248 VAL cc_start: 0.8658 (t) cc_final: 0.8344 (t) REVERT: G 250 ILE cc_start: 0.8556 (mm) cc_final: 0.8165 (tp) REVERT: G 251 ILE cc_start: 0.8375 (tt) cc_final: 0.8018 (tp) REVERT: G 257 ASP cc_start: 0.7830 (t70) cc_final: 0.7312 (t0) REVERT: G 276 MET cc_start: 0.6378 (mmm) cc_final: 0.5805 (mmm) REVERT: G 281 GLU cc_start: 0.8087 (pt0) cc_final: 0.7509 (pp20) REVERT: G 284 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7191 (mm-30) REVERT: G 322 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7971 (mm-30) REVERT: G 332 GLU cc_start: 0.8148 (tp30) cc_final: 0.7865 (tp30) REVERT: G 335 ARG cc_start: 0.7227 (tpp80) cc_final: 0.6781 (tpp80) REVERT: G 350 GLN cc_start: 0.8220 (tt0) cc_final: 0.7946 (tp40) REVERT: G 351 ARG cc_start: 0.7493 (ttp-170) cc_final: 0.6753 (ttp-170) REVERT: G 373 ARG cc_start: 0.7658 (mtm-85) cc_final: 0.7112 (mtm-85) REVERT: G 428 TYR cc_start: 0.8104 (m-80) cc_final: 0.7522 (m-10) REVERT: G 451 ILE cc_start: 0.8279 (mt) cc_final: 0.7893 (mm) REVERT: G 688 GLN cc_start: 0.8524 (tp40) cc_final: 0.7612 (tp40) REVERT: G 692 MET cc_start: 0.7381 (mmp) cc_final: 0.7100 (mmp) REVERT: H 145 ASP cc_start: 0.7816 (t0) cc_final: 0.7491 (t0) REVERT: H 183 LYS cc_start: 0.8473 (mtmt) cc_final: 0.8165 (mtmt) REVERT: H 250 TYR cc_start: 0.7351 (p90) cc_final: 0.7055 (p90) REVERT: H 268 LYS cc_start: 0.8456 (ttpp) cc_final: 0.7753 (ttpp) REVERT: H 270 MET cc_start: 0.7139 (mmm) cc_final: 0.6740 (mmm) REVERT: I 93 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6802 (mp0) REVERT: I 104 VAL cc_start: 0.7801 (t) cc_final: 0.7477 (p) REVERT: I 142 VAL cc_start: 0.8821 (t) cc_final: 0.8420 (p) REVERT: I 147 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6554 (mm-30) REVERT: I 153 ILE cc_start: 0.8779 (mp) cc_final: 0.8291 (mt) REVERT: J 216 TYR cc_start: 0.8174 (t80) cc_final: 0.7834 (t80) REVERT: J 256 GLN cc_start: 0.8311 (mt0) cc_final: 0.7972 (mm110) REVERT: J 257 ASP cc_start: 0.7764 (t0) cc_final: 0.7435 (t0) REVERT: J 260 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7462 (tmm) REVERT: J 284 GLU cc_start: 0.7822 (tp30) cc_final: 0.7603 (tp30) REVERT: J 332 GLU cc_start: 0.8124 (tp30) cc_final: 0.7792 (tp30) REVERT: J 353 ARG cc_start: 0.8078 (ttp80) cc_final: 0.7854 (ptm-80) REVERT: J 438 ARG cc_start: 0.8641 (ttm-80) cc_final: 0.8173 (mtt-85) REVERT: J 458 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8791 (ttmm) REVERT: J 459 LYS cc_start: 0.8199 (mmtp) cc_final: 0.7967 (ttmm) REVERT: J 464 ARG cc_start: 0.7450 (mtm-85) cc_final: 0.7194 (mtm-85) REVERT: J 618 PRO cc_start: 0.8838 (Cg_endo) cc_final: 0.8628 (Cg_exo) REVERT: c 45 LEU cc_start: 0.7989 (mp) cc_final: 0.7736 (mt) REVERT: c 59 ILE cc_start: 0.8622 (mm) cc_final: 0.8238 (mm) REVERT: c 96 ILE cc_start: 0.8747 (pt) cc_final: 0.8338 (pt) REVERT: c 142 SER cc_start: 0.8553 (m) cc_final: 0.7883 (p) REVERT: c 191 ARG cc_start: 0.7371 (mtp180) cc_final: 0.7113 (mtp-110) REVERT: c 248 THR cc_start: 0.8690 (m) cc_final: 0.8409 (t) REVERT: c 258 TYR cc_start: 0.8213 (p90) cc_final: 0.7800 (p90) REVERT: c 271 ASP cc_start: 0.8009 (m-30) cc_final: 0.7569 (m-30) REVERT: C 7 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7124 (tppt) REVERT: K 153 PHE cc_start: 0.8227 (m-80) cc_final: 0.7958 (m-80) REVERT: K 217 GLU cc_start: 0.7110 (tp30) cc_final: 0.6758 (tp30) REVERT: K 258 ASN cc_start: 0.8777 (t0) cc_final: 0.8491 (t0) REVERT: L 294 TRP cc_start: 0.7854 (t60) cc_final: 0.7143 (t60) REVERT: L 297 ASN cc_start: 0.8563 (m-40) cc_final: 0.8343 (m-40) REVERT: L 298 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7462 (mm-30) REVERT: L 301 LYS cc_start: 0.8822 (mtmt) cc_final: 0.8416 (mtmm) REVERT: L 307 MET cc_start: 0.7834 (tpp) cc_final: 0.7470 (tpp) REVERT: M 58 TYR cc_start: 0.8050 (m-10) cc_final: 0.7821 (m-10) REVERT: M 79 LEU cc_start: 0.6411 (mp) cc_final: 0.6207 (mm) REVERT: M 88 LYS cc_start: 0.7789 (mmmm) cc_final: 0.7473 (tppp) REVERT: M 95 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7991 (mt-10) REVERT: M 139 ILE cc_start: 0.8480 (mt) cc_final: 0.8133 (tt) REVERT: M 158 LYS cc_start: 0.8311 (mttt) cc_final: 0.7869 (mttt) REVERT: N 91 GLU cc_start: 0.7168 (mp0) cc_final: 0.6949 (mp0) REVERT: N 98 GLN cc_start: 0.8266 (mt0) cc_final: 0.7895 (mt0) REVERT: N 111 ASP cc_start: 0.7681 (m-30) cc_final: 0.7472 (m-30) REVERT: N 136 LYS cc_start: 0.8625 (mttt) cc_final: 0.8343 (mtpp) REVERT: N 185 GLU cc_start: 0.7217 (tt0) cc_final: 0.6607 (tt0) REVERT: O 281 GLU cc_start: 0.8448 (pt0) cc_final: 0.7852 (pp20) REVERT: O 284 GLU cc_start: 0.7924 (tp30) cc_final: 0.7537 (tp30) REVERT: O 347 HIS cc_start: 0.8837 (m170) cc_final: 0.8596 (m170) REVERT: O 350 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7545 (tm-30) REVERT: O 371 GLU cc_start: 0.6820 (tp30) cc_final: 0.6276 (tp30) REVERT: O 438 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7859 (mtp85) REVERT: O 502 TYR cc_start: 0.6171 (p90) cc_final: 0.4828 (p90) REVERT: O 688 GLN cc_start: 0.8527 (tp40) cc_final: 0.8166 (tm-30) REVERT: O 692 MET cc_start: 0.7831 (mtm) cc_final: 0.6308 (mtm) REVERT: P 10 LEU cc_start: 0.7141 (mm) cc_final: 0.6439 (mt) REVERT: P 33 MET cc_start: 0.8011 (mmt) cc_final: 0.7684 (mmp) REVERT: P 43 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7400 (mtm180) REVERT: P 78 ASN cc_start: 0.7385 (t0) cc_final: 0.6938 (t0) REVERT: P 145 ASP cc_start: 0.7909 (t0) cc_final: 0.7699 (t0) REVERT: P 180 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7718 (mt-10) REVERT: P 250 TYR cc_start: 0.6025 (t80) cc_final: 0.5825 (t80) REVERT: Q 67 TYR cc_start: 0.6905 (t80) cc_final: 0.6584 (t80) REVERT: Q 106 TYR cc_start: 0.8122 (m-80) cc_final: 0.7617 (m-80) REVERT: Q 138 VAL cc_start: 0.8531 (t) cc_final: 0.8174 (m) REVERT: Q 142 VAL cc_start: 0.8625 (p) cc_final: 0.8141 (m) REVERT: Q 151 GLU cc_start: 0.6989 (tp30) cc_final: 0.6433 (tp30) REVERT: Q 156 ASN cc_start: 0.7991 (m-40) cc_final: 0.7206 (m110) REVERT: Q 173 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7992 (pttp) REVERT: Q 181 GLU cc_start: 0.7628 (tt0) cc_final: 0.7337 (tt0) REVERT: R 207 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.6363 (mp0) REVERT: R 212 ASN cc_start: 0.7350 (t0) cc_final: 0.6979 (t0) REVERT: R 227 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7801 (p0) REVERT: R 249 ASP cc_start: 0.8322 (t0) cc_final: 0.8084 (t0) REVERT: R 260 MET cc_start: 0.7860 (tpp) cc_final: 0.7636 (mmm) REVERT: R 284 GLU cc_start: 0.7538 (tp30) cc_final: 0.7127 (tp30) REVERT: R 313 ASN cc_start: 0.8340 (t0) cc_final: 0.7763 (t0) REVERT: R 322 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7582 (tm-30) REVERT: R 334 TYR cc_start: 0.8119 (t80) cc_final: 0.7729 (t80) REVERT: R 433 CYS cc_start: 0.7655 (p) cc_final: 0.7392 (p) REVERT: R 438 ARG cc_start: 0.8604 (tpp80) cc_final: 0.7991 (mtt-85) REVERT: R 464 ARG cc_start: 0.7410 (mtm-85) cc_final: 0.7002 (mtm-85) REVERT: R 470 ILE cc_start: 0.8903 (mm) cc_final: 0.8265 (pt) REVERT: R 556 ASN cc_start: 0.8787 (m-40) cc_final: 0.8393 (m-40) REVERT: R 619 GLN cc_start: 0.7976 (tp40) cc_final: 0.7519 (tp-100) REVERT: R 640 LYS cc_start: 0.8686 (tptt) cc_final: 0.8380 (tptm) REVERT: R 679 MET cc_start: 0.4651 (tmm) cc_final: 0.3830 (tmm) REVERT: d 28 LEU cc_start: 0.8603 (tp) cc_final: 0.8394 (tt) REVERT: d 37 ARG cc_start: 0.8652 (ttp80) cc_final: 0.8378 (ttp80) REVERT: d 43 ARG cc_start: 0.8282 (ttp80) cc_final: 0.8013 (ttp-110) REVERT: d 81 GLU cc_start: 0.7574 (mt-10) cc_final: 0.6929 (mt-10) REVERT: d 92 MET cc_start: 0.7768 (mtp) cc_final: 0.7437 (mtp) REVERT: d 135 LYS cc_start: 0.8444 (mmtt) cc_final: 0.8131 (mmtt) REVERT: d 170 ASN cc_start: 0.7625 (t0) cc_final: 0.6963 (t0) REVERT: d 180 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7345 (mm-30) REVERT: d 183 LYS cc_start: 0.8662 (mtmt) cc_final: 0.8413 (ptpp) REVERT: d 228 ILE cc_start: 0.8864 (mt) cc_final: 0.8571 (tt) REVERT: d 230 MET cc_start: 0.7205 (mmm) cc_final: 0.6874 (mmm) REVERT: d 248 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8668 (p) REVERT: d 262 TYR cc_start: 0.8777 (t80) cc_final: 0.8166 (t80) REVERT: d 269 ASN cc_start: 0.8771 (t0) cc_final: 0.8378 (t0) outliers start: 137 outliers final: 89 residues processed: 1223 average time/residue: 0.5424 time to fit residues: 1005.3451 Evaluate side-chains 1237 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1138 time to evaluate : 3.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 165 ASN Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain G residue 588 VAL Chi-restraints excluded: chain G residue 617 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 267 GLU Chi-restraints excluded: chain H residue 275 MET Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain J residue 227 ASN Chi-restraints excluded: chain J residue 260 MET Chi-restraints excluded: chain J residue 458 LYS Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain c residue 67 GLN Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 155 CYS Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 130 ASN Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain N residue 60 LYS Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 140 THR Chi-restraints excluded: chain O residue 290 PHE Chi-restraints excluded: chain O residue 433 CYS Chi-restraints excluded: chain O residue 466 ASP Chi-restraints excluded: chain O residue 540 SER Chi-restraints excluded: chain O residue 556 ASN Chi-restraints excluded: chain O residue 647 ILE Chi-restraints excluded: chain P residue 75 TYR Chi-restraints excluded: chain P residue 172 THR Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 271 ASP Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 157 HIS Chi-restraints excluded: chain Q residue 173 LYS Chi-restraints excluded: chain R residue 207 GLU Chi-restraints excluded: chain R residue 227 ASN Chi-restraints excluded: chain R residue 248 VAL Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain R residue 456 LYS Chi-restraints excluded: chain R residue 526 ASP Chi-restraints excluded: chain R residue 641 LYS Chi-restraints excluded: chain R residue 677 THR Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 85 LEU Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 174 GLU Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 250 TYR Chi-restraints excluded: chain d residue 254 ARG Chi-restraints excluded: chain d residue 271 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 370 optimal weight: 1.9990 chunk 281 optimal weight: 0.0870 chunk 194 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 178 optimal weight: 0.0470 chunk 251 optimal weight: 0.0470 chunk 376 optimal weight: 0.4980 chunk 398 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 356 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 ASN E 195 ASN F 154 HIS ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 503 GLN G 547 GLN G 552 GLN G 688 GLN I 125 GLN J 323 GLN J 350 GLN ** J 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 220 HIS ** L 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 162 ASN N 183 HIS O 286 GLN O 323 GLN O 531 GLN Q 54 HIS Q 157 HIS ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 229 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34806 Z= 0.186 Angle : 0.646 13.137 47180 Z= 0.331 Chirality : 0.043 0.181 4964 Planarity : 0.005 0.061 6150 Dihedral : 4.992 41.223 4634 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.57 % Favored : 95.26 % Rotamer: Outliers : 3.90 % Allowed : 20.06 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 4110 helix: 0.33 (0.15), residues: 1138 sheet: -0.91 (0.18), residues: 750 loop : -0.59 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP M 187 HIS 0.007 0.001 HIS F 157 PHE 0.017 0.001 PHE E 141 TYR 0.029 0.001 TYR I 44 ARG 0.008 0.001 ARG G 442 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1307 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1165 time to evaluate : 3.830 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: A 3 THR cc_start: 0.8882 (p) cc_final: 0.8564 (m) REVERT: A 7 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7456 (mptp) REVERT: A 20 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7187 (tm-30) REVERT: B 150 ASP cc_start: 0.7930 (t0) cc_final: 0.7453 (t0) REVERT: B 253 ASP cc_start: 0.7721 (t0) cc_final: 0.7174 (t0) REVERT: D 294 TRP cc_start: 0.7855 (t60) cc_final: 0.7626 (t60) REVERT: D 307 MET cc_start: 0.7394 (tpp) cc_final: 0.6942 (tpp) REVERT: D 323 ARG cc_start: 0.8324 (ttm110) cc_final: 0.8028 (ttm-80) REVERT: E 28 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7328 (mm-30) REVERT: E 44 ARG cc_start: 0.7743 (ttp-170) cc_final: 0.7337 (ttp-170) REVERT: E 56 ASN cc_start: 0.8391 (m-40) cc_final: 0.7854 (p0) REVERT: E 92 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7683 (t80) REVERT: E 141 PHE cc_start: 0.7094 (t80) cc_final: 0.6628 (t80) REVERT: F 67 TYR cc_start: 0.7632 (t80) cc_final: 0.6832 (t80) REVERT: F 121 GLN cc_start: 0.7370 (mp10) cc_final: 0.7055 (mp10) REVERT: F 142 VAL cc_start: 0.8811 (t) cc_final: 0.7935 (m) REVERT: F 147 GLU cc_start: 0.7173 (tt0) cc_final: 0.6549 (tt0) REVERT: F 156 ASN cc_start: 0.8172 (p0) cc_final: 0.7690 (p0) REVERT: G 238 LYS cc_start: 0.7512 (ttpt) cc_final: 0.7099 (ttpt) REVERT: G 251 ILE cc_start: 0.8276 (tt) cc_final: 0.7936 (tp) REVERT: G 257 ASP cc_start: 0.7807 (t70) cc_final: 0.7358 (t0) REVERT: G 276 MET cc_start: 0.6292 (mmm) cc_final: 0.5703 (mmm) REVERT: G 281 GLU cc_start: 0.8066 (pt0) cc_final: 0.7470 (pp20) REVERT: G 284 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7136 (mm-30) REVERT: G 322 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7888 (mm-30) REVERT: G 331 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7735 (t0) REVERT: G 351 ARG cc_start: 0.7472 (ttp-170) cc_final: 0.6833 (ttp-170) REVERT: G 373 ARG cc_start: 0.7651 (mtm-85) cc_final: 0.7132 (mtm-85) REVERT: G 428 TYR cc_start: 0.8065 (m-80) cc_final: 0.7385 (m-10) REVERT: G 451 ILE cc_start: 0.8237 (mt) cc_final: 0.7841 (mm) REVERT: G 688 GLN cc_start: 0.8482 (tp-100) cc_final: 0.7564 (tp40) REVERT: G 692 MET cc_start: 0.7358 (mmp) cc_final: 0.7069 (mmp) REVERT: H 39 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7730 (m-80) REVERT: H 54 VAL cc_start: 0.9209 (t) cc_final: 0.8915 (m) REVERT: H 57 TYR cc_start: 0.7675 (m-80) cc_final: 0.6639 (m-80) REVERT: H 95 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.7178 (mp10) REVERT: H 145 ASP cc_start: 0.7822 (t0) cc_final: 0.7466 (t0) REVERT: H 183 LYS cc_start: 0.8467 (mtmt) cc_final: 0.8131 (mtmt) REVERT: H 250 TYR cc_start: 0.7251 (p90) cc_final: 0.7014 (p90) REVERT: H 268 LYS cc_start: 0.8481 (ttpp) cc_final: 0.7781 (ttpp) REVERT: H 270 MET cc_start: 0.7140 (mmm) cc_final: 0.6665 (mmm) REVERT: I 142 VAL cc_start: 0.8813 (t) cc_final: 0.8434 (p) REVERT: I 153 ILE cc_start: 0.8767 (mp) cc_final: 0.8341 (mt) REVERT: J 216 TYR cc_start: 0.8203 (t80) cc_final: 0.7796 (t80) REVERT: J 260 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7374 (tmm) REVERT: J 284 GLU cc_start: 0.7824 (tp30) cc_final: 0.7559 (tp30) REVERT: J 332 GLU cc_start: 0.8058 (tp30) cc_final: 0.7697 (tp30) REVERT: J 362 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7365 (mt-10) REVERT: J 438 ARG cc_start: 0.8648 (ttm-80) cc_final: 0.8161 (mtt-85) REVERT: J 458 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8693 (ttmm) REVERT: J 459 LYS cc_start: 0.8205 (mmtp) cc_final: 0.7992 (ttmm) REVERT: J 464 ARG cc_start: 0.7444 (mtm-85) cc_final: 0.7180 (mtm-85) REVERT: c 45 LEU cc_start: 0.8027 (mp) cc_final: 0.7773 (mt) REVERT: c 59 ILE cc_start: 0.8638 (mm) cc_final: 0.8236 (mm) REVERT: c 96 ILE cc_start: 0.8755 (pt) cc_final: 0.8374 (pt) REVERT: c 136 GLU cc_start: 0.7712 (tp30) cc_final: 0.7488 (tp30) REVERT: c 142 SER cc_start: 0.8526 (m) cc_final: 0.7888 (p) REVERT: c 191 ARG cc_start: 0.7434 (mtp180) cc_final: 0.7134 (mtp180) REVERT: c 248 THR cc_start: 0.8620 (m) cc_final: 0.8415 (t) REVERT: c 258 TYR cc_start: 0.8195 (p90) cc_final: 0.7759 (p90) REVERT: c 262 TYR cc_start: 0.8869 (t80) cc_final: 0.8237 (t80) REVERT: c 271 ASP cc_start: 0.8018 (m-30) cc_final: 0.7578 (m-30) REVERT: c 275 MET cc_start: 0.8118 (mtt) cc_final: 0.7905 (mtt) REVERT: C 7 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.6920 (tppt) REVERT: K 153 PHE cc_start: 0.8182 (m-80) cc_final: 0.7870 (m-80) REVERT: K 183 ASP cc_start: 0.6280 (t0) cc_final: 0.5842 (t0) REVERT: K 217 GLU cc_start: 0.7135 (tp30) cc_final: 0.6910 (tp30) REVERT: L 294 TRP cc_start: 0.7910 (t60) cc_final: 0.7412 (t60) REVERT: L 296 MET cc_start: 0.8117 (mmp) cc_final: 0.7914 (mmp) REVERT: L 297 ASN cc_start: 0.8602 (m-40) cc_final: 0.8299 (m-40) REVERT: L 301 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8445 (mtmm) REVERT: M 27 GLU cc_start: 0.7849 (tt0) cc_final: 0.7348 (tm-30) REVERT: M 79 LEU cc_start: 0.6421 (mp) cc_final: 0.6189 (mm) REVERT: M 88 LYS cc_start: 0.7760 (mmmm) cc_final: 0.7431 (tppp) REVERT: M 95 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7987 (mt-10) REVERT: M 138 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7396 (mt-10) REVERT: M 158 LYS cc_start: 0.8345 (mttt) cc_final: 0.7933 (mttt) REVERT: N 49 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6907 (tm-30) REVERT: N 98 GLN cc_start: 0.8245 (mt0) cc_final: 0.7849 (mt0) REVERT: N 111 ASP cc_start: 0.7704 (m-30) cc_final: 0.7492 (m-30) REVERT: N 136 LYS cc_start: 0.8604 (mttt) cc_final: 0.8338 (mtpp) REVERT: N 185 GLU cc_start: 0.7261 (tt0) cc_final: 0.6653 (tt0) REVERT: O 281 GLU cc_start: 0.8458 (pt0) cc_final: 0.7853 (pp20) REVERT: O 347 HIS cc_start: 0.8832 (m170) cc_final: 0.8614 (m170) REVERT: O 350 GLN cc_start: 0.8354 (tm-30) cc_final: 0.7505 (tm-30) REVERT: O 371 GLU cc_start: 0.6822 (tp30) cc_final: 0.6187 (tp30) REVERT: O 438 ARG cc_start: 0.8099 (ttm-80) cc_final: 0.7848 (mtp85) REVERT: O 502 TYR cc_start: 0.6090 (p90) cc_final: 0.4773 (p90) REVERT: O 543 VAL cc_start: 0.8649 (m) cc_final: 0.7973 (p) REVERT: O 547 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8089 (mt0) REVERT: O 641 LYS cc_start: 0.8218 (mmtt) cc_final: 0.8001 (mmtt) REVERT: P 10 LEU cc_start: 0.7040 (mm) cc_final: 0.6423 (mt) REVERT: P 33 MET cc_start: 0.8032 (mmt) cc_final: 0.7734 (mmp) REVERT: P 43 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7339 (mtm180) REVERT: P 67 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7133 (mm-40) REVERT: P 78 ASN cc_start: 0.7373 (t0) cc_final: 0.6926 (t0) REVERT: P 180 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7676 (mt-10) REVERT: Q 89 ARG cc_start: 0.7816 (mtm110) cc_final: 0.7601 (mtm110) REVERT: Q 106 TYR cc_start: 0.8129 (m-80) cc_final: 0.7615 (m-80) REVERT: Q 121 GLN cc_start: 0.6091 (mp10) cc_final: 0.5756 (mp10) REVERT: Q 138 VAL cc_start: 0.8545 (t) cc_final: 0.8180 (m) REVERT: Q 151 GLU cc_start: 0.6942 (tp30) cc_final: 0.6466 (tp30) REVERT: Q 156 ASN cc_start: 0.8140 (m-40) cc_final: 0.7462 (m110) REVERT: Q 173 LYS cc_start: 0.8504 (ptpp) cc_final: 0.7910 (pttp) REVERT: Q 181 GLU cc_start: 0.7570 (tt0) cc_final: 0.7241 (tt0) REVERT: R 207 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.6632 (mp0) REVERT: R 212 ASN cc_start: 0.7348 (t0) cc_final: 0.6961 (t0) REVERT: R 249 ASP cc_start: 0.8343 (t0) cc_final: 0.8094 (t0) REVERT: R 260 MET cc_start: 0.7811 (tpp) cc_final: 0.7607 (mmm) REVERT: R 284 GLU cc_start: 0.7538 (tp30) cc_final: 0.7073 (tp30) REVERT: R 313 ASN cc_start: 0.8324 (t0) cc_final: 0.7728 (t0) REVERT: R 322 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7568 (tm-30) REVERT: R 334 TYR cc_start: 0.8022 (t80) cc_final: 0.7728 (t80) REVERT: R 433 CYS cc_start: 0.7565 (p) cc_final: 0.7271 (p) REVERT: R 438 ARG cc_start: 0.8601 (tpp80) cc_final: 0.7993 (mtt-85) REVERT: R 464 ARG cc_start: 0.7431 (mtm-85) cc_final: 0.7115 (mtm-85) REVERT: R 470 ILE cc_start: 0.8861 (mm) cc_final: 0.8227 (pt) REVERT: R 530 ILE cc_start: 0.8891 (mm) cc_final: 0.8496 (tp) REVERT: R 556 ASN cc_start: 0.8791 (m-40) cc_final: 0.8394 (m-40) REVERT: R 619 GLN cc_start: 0.7963 (tp40) cc_final: 0.7468 (tp-100) REVERT: R 640 LYS cc_start: 0.8660 (tptt) cc_final: 0.8373 (tptm) REVERT: R 679 MET cc_start: 0.4461 (tmm) cc_final: 0.3936 (tmm) REVERT: d 28 LEU cc_start: 0.8579 (tp) cc_final: 0.8372 (tt) REVERT: d 33 MET cc_start: 0.7918 (tpp) cc_final: 0.7701 (tpp) REVERT: d 38 ASP cc_start: 0.8065 (m-30) cc_final: 0.7693 (m-30) REVERT: d 43 ARG cc_start: 0.8289 (ttp80) cc_final: 0.7991 (ttp-110) REVERT: d 81 GLU cc_start: 0.7560 (mt-10) cc_final: 0.6935 (mt-10) REVERT: d 92 MET cc_start: 0.7740 (mtp) cc_final: 0.7383 (mtp) REVERT: d 135 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8143 (mmtt) REVERT: d 170 ASN cc_start: 0.7639 (t0) cc_final: 0.7026 (t0) REVERT: d 180 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7274 (mm-30) REVERT: d 183 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8403 (ptpp) REVERT: d 230 MET cc_start: 0.7176 (mmm) cc_final: 0.6926 (mmm) REVERT: d 248 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8633 (p) REVERT: d 262 TYR cc_start: 0.8788 (t80) cc_final: 0.7898 (t80) REVERT: d 269 ASN cc_start: 0.8819 (t0) cc_final: 0.8434 (t0) REVERT: d 270 MET cc_start: 0.7472 (mmt) cc_final: 0.7047 (mmt) outliers start: 142 outliers final: 100 residues processed: 1221 average time/residue: 0.5319 time to fit residues: 986.3007 Evaluate side-chains 1247 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1136 time to evaluate : 3.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 48 TYR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain G residue 588 VAL Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 267 GLU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain J residue 260 MET Chi-restraints excluded: chain J residue 458 LYS Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain J residue 654 CYS Chi-restraints excluded: chain c residue 67 GLN Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 167 THR Chi-restraints excluded: chain c residue 172 THR Chi-restraints excluded: chain c residue 174 GLU Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain K residue 155 CYS Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 220 HIS Chi-restraints excluded: chain K residue 228 ASP Chi-restraints excluded: chain M residue 130 ASN Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain N residue 60 LYS Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 290 PHE Chi-restraints excluded: chain O residue 314 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain O residue 433 CYS Chi-restraints excluded: chain O residue 466 ASP Chi-restraints excluded: chain O residue 526 ASP Chi-restraints excluded: chain O residue 547 GLN Chi-restraints excluded: chain O residue 556 ASN Chi-restraints excluded: chain O residue 647 ILE Chi-restraints excluded: chain P residue 75 TYR Chi-restraints excluded: chain P residue 172 THR Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain P residue 271 ASP Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain Q residue 114 THR Chi-restraints excluded: chain Q residue 120 HIS Chi-restraints excluded: chain Q residue 157 HIS Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain R residue 207 GLU Chi-restraints excluded: chain R residue 234 LYS Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain R residue 456 LYS Chi-restraints excluded: chain R residue 526 ASP Chi-restraints excluded: chain R residue 641 LYS Chi-restraints excluded: chain R residue 654 CYS Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 85 LEU Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 174 GLU Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 250 TYR Chi-restraints excluded: chain d residue 254 ARG Chi-restraints excluded: chain d residue 271 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 331 optimal weight: 9.9990 chunk 226 optimal weight: 0.8980 chunk 5 optimal weight: 0.0370 chunk 296 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 339 optimal weight: 0.5980 chunk 275 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 203 optimal weight: 0.0670 chunk 357 optimal weight: 0.0470 chunk 100 optimal weight: 1.9990 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN E 31 GLN ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 547 GLN I 125 GLN I 143 HIS ** J 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 234 ASN K 220 HIS L 297 ASN M 162 ASN N 157 HIS O 286 GLN O 531 GLN ** O 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 157 HIS ** R 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34806 Z= 0.186 Angle : 0.643 12.919 47180 Z= 0.327 Chirality : 0.043 0.238 4964 Planarity : 0.005 0.090 6150 Dihedral : 4.926 47.743 4634 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.99 % Favored : 94.84 % Rotamer: Outliers : 3.81 % Allowed : 21.19 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 4110 helix: 0.43 (0.15), residues: 1140 sheet: -0.91 (0.18), residues: 771 loop : -0.54 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP M 187 HIS 0.018 0.001 HIS K 220 PHE 0.015 0.001 PHE E 141 TYR 0.027 0.001 TYR N 67 ARG 0.009 0.001 ARG H 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1278 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1139 time to evaluate : 4.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.6581 (mptp) REVERT: A 20 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7189 (tm-30) REVERT: B 150 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7468 (t0) REVERT: B 226 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6494 (mt-10) REVERT: B 231 PHE cc_start: 0.8177 (m-80) cc_final: 0.7492 (m-80) REVERT: B 253 ASP cc_start: 0.7785 (t0) cc_final: 0.7168 (t0) REVERT: D 294 TRP cc_start: 0.7837 (t60) cc_final: 0.6543 (t60) REVERT: D 298 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7444 (mm-30) REVERT: D 307 MET cc_start: 0.7437 (tpp) cc_final: 0.7178 (tpp) REVERT: D 323 ARG cc_start: 0.8348 (ttm110) cc_final: 0.8058 (ttm-80) REVERT: E 28 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7275 (mm-30) REVERT: E 44 ARG cc_start: 0.7756 (ttp-170) cc_final: 0.7412 (ttp-170) REVERT: E 56 ASN cc_start: 0.8340 (m-40) cc_final: 0.7843 (p0) REVERT: E 74 MET cc_start: 0.6539 (mmp) cc_final: 0.5975 (mmm) REVERT: E 92 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7691 (t80) REVERT: E 141 PHE cc_start: 0.7073 (t80) cc_final: 0.6665 (t80) REVERT: F 59 TYR cc_start: 0.6650 (t80) cc_final: 0.6286 (t80) REVERT: F 67 TYR cc_start: 0.7648 (t80) cc_final: 0.6860 (t80) REVERT: F 142 VAL cc_start: 0.8807 (t) cc_final: 0.7920 (m) REVERT: F 147 GLU cc_start: 0.7186 (tt0) cc_final: 0.6551 (tt0) REVERT: F 156 ASN cc_start: 0.8183 (p0) cc_final: 0.7704 (p0) REVERT: G 238 LYS cc_start: 0.7488 (ttpt) cc_final: 0.7132 (ttpt) REVERT: G 251 ILE cc_start: 0.8210 (tt) cc_final: 0.7971 (tp) REVERT: G 257 ASP cc_start: 0.7821 (t70) cc_final: 0.7316 (t0) REVERT: G 276 MET cc_start: 0.6414 (mmm) cc_final: 0.5782 (mmm) REVERT: G 281 GLU cc_start: 0.8061 (pt0) cc_final: 0.7466 (pp20) REVERT: G 284 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7134 (mm-30) REVERT: G 322 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7862 (mm-30) REVERT: G 351 ARG cc_start: 0.7410 (ttp-170) cc_final: 0.6881 (ttp-170) REVERT: G 373 ARG cc_start: 0.7616 (mtm-85) cc_final: 0.7068 (mtm-85) REVERT: G 428 TYR cc_start: 0.8057 (m-80) cc_final: 0.7349 (m-10) REVERT: G 451 ILE cc_start: 0.8219 (mt) cc_final: 0.7845 (mm) REVERT: G 688 GLN cc_start: 0.8558 (tp-100) cc_final: 0.7694 (tp40) REVERT: G 692 MET cc_start: 0.7397 (mmp) cc_final: 0.7044 (mmp) REVERT: H 54 VAL cc_start: 0.9217 (t) cc_final: 0.8983 (m) REVERT: H 57 TYR cc_start: 0.7672 (m-80) cc_final: 0.6793 (m-80) REVERT: H 95 GLN cc_start: 0.7466 (mp10) cc_final: 0.7119 (mp10) REVERT: H 145 ASP cc_start: 0.7856 (t0) cc_final: 0.7490 (t0) REVERT: H 183 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8184 (mtmt) REVERT: H 270 MET cc_start: 0.7097 (mmm) cc_final: 0.6758 (mmm) REVERT: I 93 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6624 (mp0) REVERT: I 142 VAL cc_start: 0.8711 (t) cc_final: 0.8435 (p) REVERT: I 147 GLU cc_start: 0.6696 (mm-30) cc_final: 0.6346 (mm-30) REVERT: I 153 ILE cc_start: 0.8780 (mp) cc_final: 0.8355 (mt) REVERT: I 181 GLU cc_start: 0.7173 (pm20) cc_final: 0.6842 (pm20) REVERT: I 185 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7247 (mt-10) REVERT: J 260 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7338 (tmm) REVERT: J 284 GLU cc_start: 0.7823 (tp30) cc_final: 0.7549 (tp30) REVERT: J 332 GLU cc_start: 0.8102 (tp30) cc_final: 0.7757 (tp30) REVERT: J 438 ARG cc_start: 0.8649 (ttm-80) cc_final: 0.8257 (mtt-85) REVERT: J 458 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8853 (ttpp) REVERT: J 464 ARG cc_start: 0.7441 (mtm-85) cc_final: 0.7210 (mtm-85) REVERT: c 28 LEU cc_start: 0.7913 (mt) cc_final: 0.7665 (mm) REVERT: c 45 LEU cc_start: 0.8033 (mp) cc_final: 0.7790 (mt) REVERT: c 59 ILE cc_start: 0.8674 (mm) cc_final: 0.8262 (mm) REVERT: c 96 ILE cc_start: 0.8756 (pt) cc_final: 0.8371 (pt) REVERT: c 136 GLU cc_start: 0.7699 (tp30) cc_final: 0.7460 (tp30) REVERT: c 142 SER cc_start: 0.8508 (m) cc_final: 0.7976 (p) REVERT: c 182 ARG cc_start: 0.8019 (mmm-85) cc_final: 0.7810 (mmm-85) REVERT: c 191 ARG cc_start: 0.7463 (mtp180) cc_final: 0.7159 (mtp180) REVERT: c 248 THR cc_start: 0.8640 (m) cc_final: 0.8435 (t) REVERT: c 258 TYR cc_start: 0.8214 (p90) cc_final: 0.7771 (p90) REVERT: c 262 TYR cc_start: 0.8847 (t80) cc_final: 0.8270 (t80) REVERT: c 271 ASP cc_start: 0.7995 (m-30) cc_final: 0.7525 (m-30) REVERT: C 7 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7231 (tppt) REVERT: K 183 ASP cc_start: 0.6216 (t0) cc_final: 0.5776 (t0) REVERT: K 189 ARG cc_start: 0.7692 (mmt90) cc_final: 0.7392 (mmt90) REVERT: K 258 ASN cc_start: 0.8699 (t0) cc_final: 0.8481 (t0) REVERT: L 294 TRP cc_start: 0.7872 (t60) cc_final: 0.7427 (t60) REVERT: L 296 MET cc_start: 0.8102 (mmp) cc_final: 0.7843 (mmp) REVERT: L 297 ASN cc_start: 0.8623 (m110) cc_final: 0.8277 (m110) REVERT: L 301 LYS cc_start: 0.8876 (mtmt) cc_final: 0.8479 (mtmm) REVERT: M 27 GLU cc_start: 0.7860 (tt0) cc_final: 0.7340 (tm-30) REVERT: M 79 LEU cc_start: 0.6468 (mp) cc_final: 0.6248 (mm) REVERT: M 88 LYS cc_start: 0.7820 (mmmm) cc_final: 0.7484 (tppp) REVERT: M 92 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.7587 (t80) REVERT: M 95 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7976 (mt-10) REVERT: M 138 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7390 (mt-10) REVERT: M 158 LYS cc_start: 0.8375 (mttt) cc_final: 0.7983 (mttt) REVERT: M 193 MET cc_start: 0.7567 (mmm) cc_final: 0.7112 (tmm) REVERT: N 98 GLN cc_start: 0.8221 (mt0) cc_final: 0.7830 (mt0) REVERT: N 111 ASP cc_start: 0.7716 (m-30) cc_final: 0.7474 (m-30) REVERT: N 116 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7058 (mm-30) REVERT: N 181 GLU cc_start: 0.6521 (mp0) cc_final: 0.6205 (mp0) REVERT: N 185 GLU cc_start: 0.7219 (tt0) cc_final: 0.6585 (tt0) REVERT: O 281 GLU cc_start: 0.8439 (pt0) cc_final: 0.7841 (pp20) REVERT: O 350 GLN cc_start: 0.8358 (tm-30) cc_final: 0.7627 (tm-30) REVERT: O 502 TYR cc_start: 0.6051 (p90) cc_final: 0.4747 (p90) REVERT: O 547 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8082 (mt0) REVERT: O 641 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7936 (mmtt) REVERT: O 688 GLN cc_start: 0.8502 (tm-30) cc_final: 0.7871 (tm-30) REVERT: O 692 MET cc_start: 0.7754 (mtm) cc_final: 0.7101 (mtm) REVERT: P 10 LEU cc_start: 0.6794 (mm) cc_final: 0.6588 (mt) REVERT: P 24 ARG cc_start: 0.8097 (mpt-90) cc_final: 0.7879 (mmt90) REVERT: P 33 MET cc_start: 0.8056 (mmt) cc_final: 0.7770 (mmp) REVERT: P 43 ARG cc_start: 0.7783 (mtm-85) cc_final: 0.7558 (mtm180) REVERT: P 78 ASN cc_start: 0.7359 (t0) cc_final: 0.6893 (t0) REVERT: P 94 MET cc_start: 0.7398 (mmp) cc_final: 0.7168 (mmp) REVERT: P 180 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7661 (mt-10) REVERT: P 250 TYR cc_start: 0.5990 (t80) cc_final: 0.5771 (t80) REVERT: P 267 GLU cc_start: 0.7126 (mp0) cc_final: 0.6262 (mp0) REVERT: Q 106 TYR cc_start: 0.8168 (m-80) cc_final: 0.7742 (m-80) REVERT: Q 116 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6958 (mt-10) REVERT: Q 121 GLN cc_start: 0.6130 (mp10) cc_final: 0.5749 (mp10) REVERT: Q 138 VAL cc_start: 0.8531 (t) cc_final: 0.8169 (m) REVERT: Q 151 GLU cc_start: 0.6955 (tp30) cc_final: 0.6494 (tp30) REVERT: Q 156 ASN cc_start: 0.8290 (m-40) cc_final: 0.7548 (m110) REVERT: Q 173 LYS cc_start: 0.8505 (ptpp) cc_final: 0.7885 (pttp) REVERT: Q 181 GLU cc_start: 0.7521 (tt0) cc_final: 0.7171 (tt0) REVERT: R 205 MET cc_start: 0.5118 (tpt) cc_final: 0.4093 (tpt) REVERT: R 207 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.6421 (mp0) REVERT: R 212 ASN cc_start: 0.7411 (t0) cc_final: 0.7007 (t0) REVERT: R 227 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7839 (p0) REVERT: R 242 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7520 (tm-30) REVERT: R 249 ASP cc_start: 0.8348 (t0) cc_final: 0.8091 (t0) REVERT: R 260 MET cc_start: 0.7816 (tpp) cc_final: 0.7429 (tpp) REVERT: R 313 ASN cc_start: 0.8323 (t0) cc_final: 0.7708 (t0) REVERT: R 316 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8039 (tm-30) REVERT: R 322 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7555 (tm-30) REVERT: R 334 TYR cc_start: 0.8037 (t80) cc_final: 0.7739 (t80) REVERT: R 371 GLU cc_start: 0.7424 (tm-30) cc_final: 0.6792 (tm-30) REVERT: R 433 CYS cc_start: 0.7584 (p) cc_final: 0.7172 (p) REVERT: R 438 ARG cc_start: 0.8605 (tpp80) cc_final: 0.7955 (mtt-85) REVERT: R 464 ARG cc_start: 0.7447 (mtm-85) cc_final: 0.7130 (mtm-85) REVERT: R 470 ILE cc_start: 0.8867 (mm) cc_final: 0.8252 (pt) REVERT: R 530 ILE cc_start: 0.8859 (mm) cc_final: 0.8463 (tp) REVERT: R 556 ASN cc_start: 0.8784 (m-40) cc_final: 0.8398 (m-40) REVERT: R 640 LYS cc_start: 0.8670 (tptt) cc_final: 0.8377 (tptm) REVERT: R 679 MET cc_start: 0.4209 (tmm) cc_final: 0.3714 (tmm) REVERT: d 28 LEU cc_start: 0.8579 (tp) cc_final: 0.8376 (tt) REVERT: d 33 MET cc_start: 0.7942 (tpp) cc_final: 0.7713 (tpp) REVERT: d 38 ASP cc_start: 0.8004 (m-30) cc_final: 0.7727 (m-30) REVERT: d 43 ARG cc_start: 0.8289 (ttp80) cc_final: 0.7725 (ttp80) REVERT: d 81 GLU cc_start: 0.7572 (mt-10) cc_final: 0.6948 (mt-10) REVERT: d 92 MET cc_start: 0.7745 (mtp) cc_final: 0.7378 (mtp) REVERT: d 170 ASN cc_start: 0.7664 (t0) cc_final: 0.7046 (t0) REVERT: d 180 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7237 (mm-30) REVERT: d 183 LYS cc_start: 0.8689 (mtmt) cc_final: 0.8398 (ptpp) REVERT: d 248 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8590 (p) REVERT: d 262 TYR cc_start: 0.8789 (t80) cc_final: 0.7787 (t80) REVERT: d 269 ASN cc_start: 0.8791 (t0) cc_final: 0.8429 (t0) outliers start: 139 outliers final: 101 residues processed: 1186 average time/residue: 0.5620 time to fit residues: 1020.4675 Evaluate side-chains 1228 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1116 time to evaluate : 3.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 48 TYR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 267 GLU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain J residue 260 MET Chi-restraints excluded: chain J residue 458 LYS Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain c residue 67 GLN Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 167 THR Chi-restraints excluded: chain c residue 172 THR Chi-restraints excluded: chain c residue 174 GLU Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 155 CYS Chi-restraints excluded: chain K residue 220 HIS Chi-restraints excluded: chain L residue 289 VAL Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 130 ASN Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 60 LYS Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 290 PHE Chi-restraints excluded: chain O residue 314 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain O residue 466 ASP Chi-restraints excluded: chain O residue 540 SER Chi-restraints excluded: chain O residue 547 GLN Chi-restraints excluded: chain O residue 556 ASN Chi-restraints excluded: chain O residue 647 ILE Chi-restraints excluded: chain P residue 75 TYR Chi-restraints excluded: chain P residue 172 THR Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 271 ASP Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain Q residue 114 THR Chi-restraints excluded: chain Q residue 120 HIS Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 157 HIS Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain R residue 207 GLU Chi-restraints excluded: chain R residue 210 ILE Chi-restraints excluded: chain R residue 227 ASN Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain R residue 526 ASP Chi-restraints excluded: chain R residue 641 LYS Chi-restraints excluded: chain R residue 677 THR Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 174 GLU Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 250 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 133 optimal weight: 1.9990 chunk 358 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 233 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 398 optimal weight: 2.9990 chunk 330 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 209 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN F 160 GLN ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 547 GLN I 143 HIS ** J 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 234 ASN K 266 HIS M 162 ASN O 286 GLN O 323 GLN O 347 HIS Q 157 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 34806 Z= 0.286 Angle : 0.670 12.934 47180 Z= 0.343 Chirality : 0.044 0.221 4964 Planarity : 0.005 0.136 6150 Dihedral : 4.925 44.288 4634 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.28 % Favored : 94.53 % Rotamer: Outliers : 4.20 % Allowed : 21.46 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 4110 helix: 0.38 (0.15), residues: 1142 sheet: -0.95 (0.17), residues: 803 loop : -0.53 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP M 187 HIS 0.022 0.001 HIS K 220 PHE 0.021 0.002 PHE R 636 TYR 0.027 0.002 TYR H 250 ARG 0.010 0.001 ARG H 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1156 time to evaluate : 3.927 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: A 7 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.6555 (mptp) REVERT: B 150 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7393 (t0) REVERT: D 294 TRP cc_start: 0.7925 (t60) cc_final: 0.6619 (t60) REVERT: D 298 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7476 (mm-30) REVERT: D 307 MET cc_start: 0.7444 (tpp) cc_final: 0.7189 (tpp) REVERT: D 323 ARG cc_start: 0.8413 (ttm110) cc_final: 0.8115 (ttm-80) REVERT: E 26 LYS cc_start: 0.8104 (mttm) cc_final: 0.7855 (mttm) REVERT: E 28 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7281 (mm-30) REVERT: E 56 ASN cc_start: 0.8440 (m-40) cc_final: 0.7996 (p0) REVERT: E 141 PHE cc_start: 0.7178 (t80) cc_final: 0.6763 (t80) REVERT: E 175 GLU cc_start: 0.7274 (pp20) cc_final: 0.6860 (pp20) REVERT: F 67 TYR cc_start: 0.7765 (t80) cc_final: 0.6965 (t80) REVERT: F 142 VAL cc_start: 0.8840 (t) cc_final: 0.8450 (m) REVERT: F 156 ASN cc_start: 0.8283 (p0) cc_final: 0.7903 (p0) REVERT: G 210 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7437 (tp) REVERT: G 238 LYS cc_start: 0.7553 (ttpt) cc_final: 0.7267 (ttpt) REVERT: G 251 ILE cc_start: 0.8345 (tt) cc_final: 0.7975 (tp) REVERT: G 257 ASP cc_start: 0.7770 (t70) cc_final: 0.7294 (t0) REVERT: G 276 MET cc_start: 0.6542 (mmm) cc_final: 0.5869 (mmm) REVERT: G 281 GLU cc_start: 0.8103 (pt0) cc_final: 0.7506 (pp20) REVERT: G 284 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7277 (mm-30) REVERT: G 351 ARG cc_start: 0.7394 (ttp-170) cc_final: 0.7032 (ttp-170) REVERT: G 373 ARG cc_start: 0.7579 (mtm-85) cc_final: 0.7282 (mtm-85) REVERT: G 451 ILE cc_start: 0.8254 (mt) cc_final: 0.7892 (mm) REVERT: G 688 GLN cc_start: 0.8612 (tp-100) cc_final: 0.7682 (tp40) REVERT: G 692 MET cc_start: 0.7435 (mmp) cc_final: 0.7147 (mmp) REVERT: H 54 VAL cc_start: 0.9251 (t) cc_final: 0.8978 (m) REVERT: H 145 ASP cc_start: 0.7870 (t0) cc_final: 0.7510 (t0) REVERT: H 270 MET cc_start: 0.7112 (mmm) cc_final: 0.6626 (mmm) REVERT: I 93 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6616 (mp0) REVERT: I 116 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7229 (mt-10) REVERT: I 122 ARG cc_start: 0.8108 (mpp80) cc_final: 0.6477 (mtt90) REVERT: I 136 LYS cc_start: 0.8216 (mttt) cc_final: 0.7985 (mttt) REVERT: I 142 VAL cc_start: 0.8789 (t) cc_final: 0.8528 (p) REVERT: I 147 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6780 (mm-30) REVERT: I 153 ILE cc_start: 0.8847 (mp) cc_final: 0.8399 (mt) REVERT: I 185 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7232 (mt-10) REVERT: J 216 TYR cc_start: 0.8297 (t80) cc_final: 0.7921 (t80) REVERT: J 256 GLN cc_start: 0.8379 (mt0) cc_final: 0.8122 (mm-40) REVERT: J 260 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7299 (tmm) REVERT: J 284 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7541 (tp30) REVERT: J 332 GLU cc_start: 0.8175 (tp30) cc_final: 0.7823 (tp30) REVERT: J 458 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.9006 (ttpp) REVERT: J 641 LYS cc_start: 0.7966 (pttt) cc_final: 0.7637 (pttm) REVERT: c 45 LEU cc_start: 0.8096 (mp) cc_final: 0.7862 (mt) REVERT: c 96 ILE cc_start: 0.8755 (pt) cc_final: 0.8354 (pt) REVERT: c 136 GLU cc_start: 0.7720 (tp30) cc_final: 0.7456 (tp30) REVERT: c 142 SER cc_start: 0.8488 (m) cc_final: 0.8013 (p) REVERT: c 183 LYS cc_start: 0.8249 (mtmm) cc_final: 0.8045 (mtpp) REVERT: c 191 ARG cc_start: 0.7507 (mtp180) cc_final: 0.7220 (mtp180) REVERT: c 258 TYR cc_start: 0.8344 (p90) cc_final: 0.7901 (p90) REVERT: c 262 TYR cc_start: 0.8886 (t80) cc_final: 0.8159 (t80) REVERT: c 271 ASP cc_start: 0.7954 (m-30) cc_final: 0.7552 (m-30) REVERT: C 7 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.6818 (tppt) REVERT: K 183 ASP cc_start: 0.6322 (t0) cc_final: 0.5869 (t0) REVERT: K 189 ARG cc_start: 0.7813 (mmt90) cc_final: 0.7523 (mmt90) REVERT: K 253 ASP cc_start: 0.7721 (m-30) cc_final: 0.7287 (t0) REVERT: L 294 TRP cc_start: 0.7998 (t60) cc_final: 0.7395 (t60) REVERT: L 296 MET cc_start: 0.8169 (mmp) cc_final: 0.7861 (mmp) REVERT: L 297 ASN cc_start: 0.8711 (m110) cc_final: 0.8391 (m-40) REVERT: L 301 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8468 (mtmm) REVERT: L 323 ARG cc_start: 0.8337 (ttm110) cc_final: 0.7954 (ttm-80) REVERT: M 47 LEU cc_start: 0.7211 (mm) cc_final: 0.6669 (mp) REVERT: M 88 LYS cc_start: 0.7911 (mmmm) cc_final: 0.7583 (tppp) REVERT: M 92 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.7668 (t80) REVERT: M 95 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7987 (mt-10) REVERT: M 158 LYS cc_start: 0.8465 (mttt) cc_final: 0.8036 (mttt) REVERT: M 193 MET cc_start: 0.7686 (mmm) cc_final: 0.7211 (tmm) REVERT: N 98 GLN cc_start: 0.8244 (mt0) cc_final: 0.7807 (mt0) REVERT: N 111 ASP cc_start: 0.7708 (m-30) cc_final: 0.7496 (m-30) REVERT: N 116 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7119 (mm-30) REVERT: N 136 LYS cc_start: 0.8650 (mttt) cc_final: 0.8394 (mtpp) REVERT: N 185 GLU cc_start: 0.7202 (tt0) cc_final: 0.6568 (tt0) REVERT: O 281 GLU cc_start: 0.8458 (pt0) cc_final: 0.8176 (pt0) REVERT: O 350 GLN cc_start: 0.8430 (tm-30) cc_final: 0.7642 (tm-30) REVERT: O 371 GLU cc_start: 0.7081 (tp30) cc_final: 0.6524 (tp30) REVERT: O 502 TYR cc_start: 0.6242 (p90) cc_final: 0.4878 (p90) REVERT: O 547 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8113 (mt0) REVERT: O 641 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7950 (mmtt) REVERT: O 656 GLU cc_start: 0.7887 (mp0) cc_final: 0.7659 (pm20) REVERT: O 688 GLN cc_start: 0.8494 (tm-30) cc_final: 0.7984 (tm-30) REVERT: O 692 MET cc_start: 0.7771 (mtm) cc_final: 0.7342 (mtm) REVERT: P 78 ASN cc_start: 0.7414 (t0) cc_final: 0.6937 (t0) REVERT: P 94 MET cc_start: 0.7443 (mmp) cc_final: 0.7129 (mmp) REVERT: P 180 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7694 (mt-10) REVERT: P 250 TYR cc_start: 0.6040 (t80) cc_final: 0.5809 (t80) REVERT: P 267 GLU cc_start: 0.7178 (mp0) cc_final: 0.6281 (mp0) REVERT: Q 89 ARG cc_start: 0.7899 (mtm110) cc_final: 0.7647 (mtm110) REVERT: Q 106 TYR cc_start: 0.8144 (m-80) cc_final: 0.7487 (m-80) REVERT: Q 116 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7061 (mt-10) REVERT: Q 120 HIS cc_start: 0.4665 (OUTLIER) cc_final: 0.4278 (t-90) REVERT: Q 121 GLN cc_start: 0.6229 (mp10) cc_final: 0.5822 (mp10) REVERT: Q 151 GLU cc_start: 0.6979 (tp30) cc_final: 0.6354 (tp30) REVERT: Q 156 ASN cc_start: 0.8374 (m-40) cc_final: 0.7651 (m-40) REVERT: Q 158 ARG cc_start: 0.7194 (mtt-85) cc_final: 0.6931 (ttm110) REVERT: Q 173 LYS cc_start: 0.8573 (ptpp) cc_final: 0.7891 (pttp) REVERT: Q 181 GLU cc_start: 0.7723 (tt0) cc_final: 0.7310 (tt0) REVERT: R 205 MET cc_start: 0.5214 (tpt) cc_final: 0.4088 (tpt) REVERT: R 207 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.6045 (mp0) REVERT: R 212 ASN cc_start: 0.7540 (t0) cc_final: 0.7160 (t0) REVERT: R 227 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7832 (p0) REVERT: R 249 ASP cc_start: 0.8400 (t0) cc_final: 0.8173 (t0) REVERT: R 260 MET cc_start: 0.7890 (tpp) cc_final: 0.7440 (tpp) REVERT: R 313 ASN cc_start: 0.8344 (t0) cc_final: 0.7592 (t0) REVERT: R 322 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7583 (tm-30) REVERT: R 334 TYR cc_start: 0.8172 (t80) cc_final: 0.7933 (t80) REVERT: R 433 CYS cc_start: 0.7680 (p) cc_final: 0.7293 (p) REVERT: R 464 ARG cc_start: 0.7488 (mtm-85) cc_final: 0.7233 (mtm-85) REVERT: R 470 ILE cc_start: 0.8936 (mm) cc_final: 0.8280 (pt) REVERT: R 530 ILE cc_start: 0.8871 (mm) cc_final: 0.8448 (tp) REVERT: R 531 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7520 (mm-40) REVERT: R 556 ASN cc_start: 0.8812 (m-40) cc_final: 0.8445 (m-40) REVERT: R 640 LYS cc_start: 0.8714 (tptt) cc_final: 0.8411 (tptm) REVERT: R 679 MET cc_start: 0.4383 (tmm) cc_final: 0.3935 (tmm) REVERT: d 38 ASP cc_start: 0.8063 (m-30) cc_final: 0.7838 (m-30) REVERT: d 43 ARG cc_start: 0.8295 (ttp80) cc_final: 0.7714 (ttp80) REVERT: d 81 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7006 (mt-10) REVERT: d 92 MET cc_start: 0.7798 (mtp) cc_final: 0.7429 (mtp) REVERT: d 170 ASN cc_start: 0.7653 (t0) cc_final: 0.7080 (t0) REVERT: d 180 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7269 (mm-30) REVERT: d 183 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8382 (ptpp) REVERT: d 230 MET cc_start: 0.7444 (mmm) cc_final: 0.7146 (mtp) REVERT: d 232 ARG cc_start: 0.7007 (mtm110) cc_final: 0.6790 (mtm110) REVERT: d 248 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8579 (p) REVERT: d 258 TYR cc_start: 0.8755 (p90) cc_final: 0.8551 (p90) REVERT: d 262 TYR cc_start: 0.8816 (t80) cc_final: 0.7781 (t80) REVERT: d 269 ASN cc_start: 0.8776 (t0) cc_final: 0.8410 (t0) outliers start: 153 outliers final: 115 residues processed: 1204 average time/residue: 0.5273 time to fit residues: 962.5434 Evaluate side-chains 1249 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1121 time to evaluate : 3.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 165 ASN Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain G residue 617 ILE Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 267 GLU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 260 MET Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 458 LYS Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain J residue 611 GLN Chi-restraints excluded: chain J residue 654 CYS Chi-restraints excluded: chain c residue 67 GLN Chi-restraints excluded: chain c residue 73 THR Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 167 THR Chi-restraints excluded: chain c residue 172 THR Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 155 CYS Chi-restraints excluded: chain L residue 289 VAL Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 130 ASN Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 60 LYS Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 290 PHE Chi-restraints excluded: chain O residue 314 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain O residue 433 CYS Chi-restraints excluded: chain O residue 466 ASP Chi-restraints excluded: chain O residue 540 SER Chi-restraints excluded: chain O residue 547 GLN Chi-restraints excluded: chain O residue 556 ASN Chi-restraints excluded: chain O residue 647 ILE Chi-restraints excluded: chain P residue 75 TYR Chi-restraints excluded: chain P residue 92 MET Chi-restraints excluded: chain P residue 106 ASP Chi-restraints excluded: chain P residue 135 LYS Chi-restraints excluded: chain P residue 172 THR Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 271 ASP Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain Q residue 114 THR Chi-restraints excluded: chain Q residue 120 HIS Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain R residue 207 GLU Chi-restraints excluded: chain R residue 227 ASN Chi-restraints excluded: chain R residue 238 LYS Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain R residue 526 ASP Chi-restraints excluded: chain R residue 616 LEU Chi-restraints excluded: chain R residue 641 LYS Chi-restraints excluded: chain R residue 677 THR Chi-restraints excluded: chain d residue 10 LEU Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain d residue 174 GLU Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 250 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 384 optimal weight: 0.1980 chunk 44 optimal weight: 0.6980 chunk 227 optimal weight: 2.9990 chunk 291 optimal weight: 0.6980 chunk 225 optimal weight: 0.6980 chunk 335 optimal weight: 0.0980 chunk 222 optimal weight: 1.9990 chunk 397 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 242 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 547 GLN ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 GLN ** J 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 269 ASN K 220 HIS M 162 ASN ** O 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 323 GLN O 347 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34806 Z= 0.222 Angle : 0.672 12.920 47180 Z= 0.342 Chirality : 0.043 0.194 4964 Planarity : 0.005 0.150 6150 Dihedral : 4.896 43.456 4634 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.16 % Favored : 94.67 % Rotamer: Outliers : 4.36 % Allowed : 21.79 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 4110 helix: 0.36 (0.15), residues: 1134 sheet: -0.92 (0.17), residues: 807 loop : -0.46 (0.14), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP M 187 HIS 0.009 0.001 HIS I 157 PHE 0.034 0.001 PHE R 636 TYR 0.028 0.002 TYR N 67 ARG 0.013 0.001 ARG J 373 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1320 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1161 time to evaluate : 3.894 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: A 7 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.6511 (mptp) REVERT: A 20 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7399 (tm-30) REVERT: B 150 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7418 (t0) REVERT: D 294 TRP cc_start: 0.7907 (t60) cc_final: 0.6955 (t60) REVERT: D 298 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7855 (mm-30) REVERT: D 307 MET cc_start: 0.7464 (tpp) cc_final: 0.7212 (tpp) REVERT: D 323 ARG cc_start: 0.8394 (ttm110) cc_final: 0.8106 (ttm-80) REVERT: E 26 LYS cc_start: 0.7992 (mttm) cc_final: 0.7779 (mttm) REVERT: E 28 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7220 (mm-30) REVERT: E 44 ARG cc_start: 0.7488 (ttp-170) cc_final: 0.7236 (ttp-110) REVERT: E 74 MET cc_start: 0.6581 (mmp) cc_final: 0.6068 (mmm) REVERT: E 92 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.7722 (t80) REVERT: E 175 GLU cc_start: 0.7145 (pp20) cc_final: 0.6839 (pp20) REVERT: F 67 TYR cc_start: 0.7722 (t80) cc_final: 0.6902 (t80) REVERT: F 97 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7392 (t70) REVERT: F 142 VAL cc_start: 0.8824 (t) cc_final: 0.8430 (m) REVERT: F 156 ASN cc_start: 0.8256 (p0) cc_final: 0.7929 (p0) REVERT: G 238 LYS cc_start: 0.7477 (ttpt) cc_final: 0.7082 (ttpt) REVERT: G 251 ILE cc_start: 0.8254 (tt) cc_final: 0.7964 (tp) REVERT: G 257 ASP cc_start: 0.7737 (t70) cc_final: 0.7262 (t0) REVERT: G 276 MET cc_start: 0.6502 (mmm) cc_final: 0.5820 (mmm) REVERT: G 281 GLU cc_start: 0.8088 (pt0) cc_final: 0.7502 (pp20) REVERT: G 284 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7241 (mm-30) REVERT: G 316 GLU cc_start: 0.8150 (tt0) cc_final: 0.7726 (tt0) REVERT: G 373 ARG cc_start: 0.7657 (mtm-85) cc_final: 0.7092 (mtm-85) REVERT: G 451 ILE cc_start: 0.8253 (mt) cc_final: 0.7974 (mm) REVERT: G 501 PHE cc_start: 0.8351 (t80) cc_final: 0.7901 (t80) REVERT: G 592 LEU cc_start: 0.8199 (mm) cc_final: 0.7913 (tp) REVERT: G 688 GLN cc_start: 0.8617 (tp-100) cc_final: 0.7589 (tp40) REVERT: G 692 MET cc_start: 0.7420 (mmp) cc_final: 0.7154 (mmp) REVERT: H 95 GLN cc_start: 0.7453 (mm-40) cc_final: 0.6986 (mm-40) REVERT: H 106 ASP cc_start: 0.7725 (t0) cc_final: 0.7318 (t0) REVERT: H 145 ASP cc_start: 0.7899 (t0) cc_final: 0.7526 (t0) REVERT: H 171 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7940 (ptm-80) REVERT: H 270 MET cc_start: 0.6968 (mmm) cc_final: 0.6453 (mmm) REVERT: I 116 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7184 (mt-10) REVERT: I 122 ARG cc_start: 0.8070 (mpp80) cc_final: 0.6466 (mtt90) REVERT: I 125 GLN cc_start: 0.8409 (mm110) cc_final: 0.8097 (mm-40) REVERT: I 136 LYS cc_start: 0.8191 (mttt) cc_final: 0.7960 (mttt) REVERT: I 142 VAL cc_start: 0.8818 (t) cc_final: 0.8576 (p) REVERT: I 147 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6788 (mm-30) REVERT: I 151 GLU cc_start: 0.6917 (mp0) cc_final: 0.6585 (mp0) REVERT: I 153 ILE cc_start: 0.8858 (mp) cc_final: 0.8423 (mt) REVERT: I 160 GLN cc_start: 0.7805 (mt0) cc_final: 0.7526 (mt0) REVERT: I 181 GLU cc_start: 0.7171 (pm20) cc_final: 0.5482 (pm20) REVERT: I 185 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7169 (mt-10) REVERT: J 211 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7765 (mp10) REVERT: J 256 GLN cc_start: 0.8386 (mt0) cc_final: 0.8174 (mm-40) REVERT: J 260 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7273 (tmm) REVERT: J 284 GLU cc_start: 0.7829 (tp30) cc_final: 0.7546 (tp30) REVERT: J 332 GLU cc_start: 0.8163 (tp30) cc_final: 0.7851 (tp30) REVERT: J 438 ARG cc_start: 0.8764 (ttm-80) cc_final: 0.8438 (mtm-85) REVERT: J 458 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8961 (ttpp) REVERT: c 12 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7111 (tp) REVERT: c 28 LEU cc_start: 0.7947 (mt) cc_final: 0.7743 (mm) REVERT: c 45 LEU cc_start: 0.8153 (mp) cc_final: 0.7920 (mt) REVERT: c 136 GLU cc_start: 0.7691 (tp30) cc_final: 0.7416 (tp30) REVERT: c 145 ASP cc_start: 0.8184 (m-30) cc_final: 0.7787 (m-30) REVERT: c 191 ARG cc_start: 0.7532 (mtp180) cc_final: 0.7259 (mtp180) REVERT: c 258 TYR cc_start: 0.8310 (p90) cc_final: 0.7898 (p90) REVERT: c 262 TYR cc_start: 0.8875 (t80) cc_final: 0.8166 (t80) REVERT: c 271 ASP cc_start: 0.7991 (m-30) cc_final: 0.7628 (m-30) REVERT: C 7 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.6720 (tppt) REVERT: K 149 GLU cc_start: 0.7766 (mp0) cc_final: 0.7475 (mp0) REVERT: K 183 ASP cc_start: 0.6291 (t0) cc_final: 0.5874 (t0) REVERT: K 189 ARG cc_start: 0.7785 (mmt90) cc_final: 0.7491 (mmt90) REVERT: K 253 ASP cc_start: 0.7779 (m-30) cc_final: 0.7242 (t0) REVERT: L 294 TRP cc_start: 0.7995 (t60) cc_final: 0.7397 (t60) REVERT: L 296 MET cc_start: 0.8167 (mmp) cc_final: 0.7855 (mmp) REVERT: L 307 MET cc_start: 0.7769 (tpp) cc_final: 0.7472 (tpp) REVERT: L 323 ARG cc_start: 0.8312 (ttm110) cc_final: 0.7911 (ttm-80) REVERT: M 88 LYS cc_start: 0.7911 (mmmm) cc_final: 0.7570 (tppp) REVERT: M 92 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.7768 (t80) REVERT: M 95 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7967 (mt-10) REVERT: M 97 MET cc_start: 0.5412 (mmt) cc_final: 0.5091 (mmt) REVERT: M 158 LYS cc_start: 0.8408 (mttt) cc_final: 0.8010 (mttt) REVERT: M 193 MET cc_start: 0.7628 (mmm) cc_final: 0.7167 (tmm) REVERT: N 98 GLN cc_start: 0.8217 (mt0) cc_final: 0.7821 (mt0) REVERT: N 111 ASP cc_start: 0.7770 (m-30) cc_final: 0.7530 (m-30) REVERT: N 116 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7085 (mm-30) REVERT: N 136 LYS cc_start: 0.8645 (mttt) cc_final: 0.8380 (mtpp) REVERT: N 185 GLU cc_start: 0.7178 (tt0) cc_final: 0.6543 (tt0) REVERT: O 281 GLU cc_start: 0.8446 (pt0) cc_final: 0.7866 (pp20) REVERT: O 284 GLU cc_start: 0.7852 (tp30) cc_final: 0.7237 (tp30) REVERT: O 287 LYS cc_start: 0.9030 (mmmt) cc_final: 0.8816 (mmmt) REVERT: O 350 GLN cc_start: 0.8396 (tm-30) cc_final: 0.7739 (tm-30) REVERT: O 371 GLU cc_start: 0.7087 (tp30) cc_final: 0.6759 (tp30) REVERT: O 502 TYR cc_start: 0.6186 (p90) cc_final: 0.4789 (p90) REVERT: O 524 ASN cc_start: 0.8823 (t0) cc_final: 0.8472 (t0) REVERT: O 547 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8088 (mt0) REVERT: O 643 GLU cc_start: 0.7549 (pm20) cc_final: 0.6956 (pm20) REVERT: O 688 GLN cc_start: 0.8496 (tm-30) cc_final: 0.7978 (tm-30) REVERT: O 692 MET cc_start: 0.7759 (mtm) cc_final: 0.7330 (mtm) REVERT: P 10 LEU cc_start: 0.7065 (mt) cc_final: 0.6838 (mt) REVERT: P 24 ARG cc_start: 0.8233 (mmt-90) cc_final: 0.8015 (mmt-90) REVERT: P 43 ARG cc_start: 0.7819 (mtm180) cc_final: 0.7460 (mtm180) REVERT: P 94 MET cc_start: 0.7405 (mmp) cc_final: 0.7105 (mmp) REVERT: P 180 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7685 (mt-10) REVERT: P 250 TYR cc_start: 0.5925 (t80) cc_final: 0.5583 (t80) REVERT: P 267 GLU cc_start: 0.7212 (mp0) cc_final: 0.6290 (mp0) REVERT: Q 89 ARG cc_start: 0.7855 (mtm110) cc_final: 0.7655 (mtm110) REVERT: Q 106 TYR cc_start: 0.8158 (m-80) cc_final: 0.7658 (m-80) REVERT: Q 116 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7010 (mt-10) REVERT: Q 120 HIS cc_start: 0.4578 (OUTLIER) cc_final: 0.4229 (t-90) REVERT: Q 121 GLN cc_start: 0.6180 (mp10) cc_final: 0.5768 (mp10) REVERT: Q 151 GLU cc_start: 0.7004 (tp30) cc_final: 0.6760 (tp30) REVERT: Q 156 ASN cc_start: 0.8282 (m-40) cc_final: 0.7614 (m-40) REVERT: Q 164 MET cc_start: 0.7248 (tmm) cc_final: 0.7034 (tmm) REVERT: Q 173 LYS cc_start: 0.8557 (ptpp) cc_final: 0.7862 (pttp) REVERT: Q 181 GLU cc_start: 0.7723 (tt0) cc_final: 0.7301 (tt0) REVERT: Q 193 ARG cc_start: 0.7012 (tmt170) cc_final: 0.6778 (tmt170) REVERT: R 205 MET cc_start: 0.5096 (tpt) cc_final: 0.4286 (tpt) REVERT: R 207 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.6379 (mp0) REVERT: R 212 ASN cc_start: 0.7543 (t0) cc_final: 0.7159 (t0) REVERT: R 227 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7829 (p0) REVERT: R 242 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7606 (tm-30) REVERT: R 260 MET cc_start: 0.7868 (tpp) cc_final: 0.7513 (tpp) REVERT: R 313 ASN cc_start: 0.8296 (t0) cc_final: 0.7598 (t0) REVERT: R 322 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7525 (tm-30) REVERT: R 334 TYR cc_start: 0.8195 (t80) cc_final: 0.7942 (t80) REVERT: R 335 ARG cc_start: 0.8429 (mmt90) cc_final: 0.8187 (mtt-85) REVERT: R 371 GLU cc_start: 0.7457 (tm-30) cc_final: 0.6918 (tm-30) REVERT: R 433 CYS cc_start: 0.7703 (p) cc_final: 0.7236 (p) REVERT: R 438 ARG cc_start: 0.8683 (tpp80) cc_final: 0.8239 (mtt90) REVERT: R 464 ARG cc_start: 0.7571 (mtm-85) cc_final: 0.6940 (mtm-85) REVERT: R 466 ASP cc_start: 0.8796 (p0) cc_final: 0.8542 (p0) REVERT: R 470 ILE cc_start: 0.8916 (mm) cc_final: 0.8217 (pt) REVERT: R 522 GLU cc_start: 0.7408 (pm20) cc_final: 0.7166 (pm20) REVERT: R 523 GLU cc_start: 0.7786 (tp30) cc_final: 0.7499 (mm-30) REVERT: R 530 ILE cc_start: 0.8866 (mm) cc_final: 0.8437 (tp) REVERT: R 531 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7527 (mm-40) REVERT: R 556 ASN cc_start: 0.8816 (m-40) cc_final: 0.8439 (m-40) REVERT: R 640 LYS cc_start: 0.8684 (tptt) cc_final: 0.8363 (tptm) REVERT: R 643 GLU cc_start: 0.7405 (pm20) cc_final: 0.7172 (pm20) REVERT: R 679 MET cc_start: 0.4360 (tmm) cc_final: 0.3864 (tmm) REVERT: d 25 ARG cc_start: 0.8545 (ttm-80) cc_final: 0.8285 (ttm-80) REVERT: d 33 MET cc_start: 0.7922 (tpp) cc_final: 0.7575 (tpp) REVERT: d 38 ASP cc_start: 0.8067 (m-30) cc_final: 0.7842 (m-30) REVERT: d 43 ARG cc_start: 0.8277 (ttp80) cc_final: 0.7624 (ttp80) REVERT: d 81 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7025 (mt-10) REVERT: d 92 MET cc_start: 0.7789 (mtp) cc_final: 0.7419 (mtp) REVERT: d 170 ASN cc_start: 0.7652 (t0) cc_final: 0.7083 (t0) REVERT: d 180 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7233 (mm-30) REVERT: d 183 LYS cc_start: 0.8684 (mtmt) cc_final: 0.8347 (ptpp) REVERT: d 230 MET cc_start: 0.7490 (mmm) cc_final: 0.7193 (mtp) REVERT: d 248 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8570 (p) REVERT: d 262 TYR cc_start: 0.8748 (t80) cc_final: 0.7679 (t80) REVERT: d 269 ASN cc_start: 0.8735 (t0) cc_final: 0.8404 (t0) outliers start: 159 outliers final: 114 residues processed: 1217 average time/residue: 0.5335 time to fit residues: 984.3160 Evaluate side-chains 1274 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1144 time to evaluate : 3.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain G residue 657 ASN Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 267 GLU Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 157 HIS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 260 MET Chi-restraints excluded: chain J residue 458 LYS Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain J residue 611 GLN Chi-restraints excluded: chain J residue 654 CYS Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 67 GLN Chi-restraints excluded: chain c residue 73 THR Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 167 THR Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain c residue 172 THR Chi-restraints excluded: chain c residue 174 GLU Chi-restraints excluded: chain c residue 248 THR Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 155 CYS Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 130 ASN Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 234 LYS Chi-restraints excluded: chain O residue 290 PHE Chi-restraints excluded: chain O residue 314 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain O residue 466 ASP Chi-restraints excluded: chain O residue 540 SER Chi-restraints excluded: chain O residue 547 GLN Chi-restraints excluded: chain O residue 556 ASN Chi-restraints excluded: chain O residue 647 ILE Chi-restraints excluded: chain P residue 75 TYR Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 106 ASP Chi-restraints excluded: chain P residue 135 LYS Chi-restraints excluded: chain P residue 172 THR Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 215 ASP Chi-restraints excluded: chain P residue 248 THR Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 271 ASP Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain Q residue 114 THR Chi-restraints excluded: chain Q residue 120 HIS Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain R residue 207 GLU Chi-restraints excluded: chain R residue 227 ASN Chi-restraints excluded: chain R residue 238 LYS Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain R residue 456 LYS Chi-restraints excluded: chain R residue 526 ASP Chi-restraints excluded: chain R residue 677 THR Chi-restraints excluded: chain d residue 10 LEU Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain d residue 174 GLU Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 250 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 245 optimal weight: 0.9990 chunk 158 optimal weight: 0.0050 chunk 237 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 252 optimal weight: 9.9990 chunk 270 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 312 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN E 162 ASN G 231 HIS G 547 GLN ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 HIS ** J 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 547 GLN c 146 GLN c 234 ASN L 297 ASN M 195 ASN O 323 GLN O 347 HIS P 78 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 34806 Z= 0.252 Angle : 0.691 12.958 47180 Z= 0.351 Chirality : 0.044 0.316 4964 Planarity : 0.005 0.125 6150 Dihedral : 4.903 44.043 4634 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.55 % Favored : 94.26 % Rotamer: Outliers : 4.25 % Allowed : 22.06 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 4110 helix: 0.38 (0.15), residues: 1146 sheet: -0.94 (0.17), residues: 816 loop : -0.43 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 187 HIS 0.008 0.001 HIS I 157 PHE 0.032 0.002 PHE B 213 TYR 0.027 0.002 TYR N 67 ARG 0.011 0.001 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1318 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1163 time to evaluate : 3.843 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: A 7 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.6527 (mptp) REVERT: A 20 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: B 150 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7356 (t0) REVERT: D 294 TRP cc_start: 0.7956 (t60) cc_final: 0.7132 (t60) REVERT: D 307 MET cc_start: 0.7444 (tpp) cc_final: 0.7190 (tpp) REVERT: D 323 ARG cc_start: 0.8390 (ttm110) cc_final: 0.8104 (ttm-80) REVERT: E 26 LYS cc_start: 0.7988 (mttm) cc_final: 0.7760 (mttm) REVERT: E 44 ARG cc_start: 0.7531 (ttp-170) cc_final: 0.7272 (ttp-110) REVERT: E 46 LYS cc_start: 0.7515 (tttm) cc_final: 0.7057 (tmtm) REVERT: E 74 MET cc_start: 0.6781 (mmp) cc_final: 0.6136 (mmm) REVERT: E 92 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7799 (t80) REVERT: F 67 TYR cc_start: 0.7759 (t80) cc_final: 0.7018 (t80) REVERT: F 97 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7393 (t70) REVERT: F 106 TYR cc_start: 0.8516 (m-80) cc_final: 0.8313 (m-80) REVERT: F 142 VAL cc_start: 0.8834 (t) cc_final: 0.7639 (m) REVERT: F 147 GLU cc_start: 0.7176 (tt0) cc_final: 0.6668 (tt0) REVERT: F 156 ASN cc_start: 0.8294 (p0) cc_final: 0.7997 (p0) REVERT: G 238 LYS cc_start: 0.7474 (ttpt) cc_final: 0.7069 (ttpt) REVERT: G 251 ILE cc_start: 0.8237 (tt) cc_final: 0.7927 (tp) REVERT: G 257 ASP cc_start: 0.7697 (t70) cc_final: 0.7222 (t0) REVERT: G 276 MET cc_start: 0.6572 (mmm) cc_final: 0.5950 (mmm) REVERT: G 281 GLU cc_start: 0.8086 (pt0) cc_final: 0.7526 (pp20) REVERT: G 284 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7362 (mm-30) REVERT: G 316 GLU cc_start: 0.8111 (tt0) cc_final: 0.7693 (tt0) REVERT: G 373 ARG cc_start: 0.7658 (mtm-85) cc_final: 0.7260 (mtm-85) REVERT: G 451 ILE cc_start: 0.8263 (mt) cc_final: 0.7995 (mm) REVERT: G 592 LEU cc_start: 0.8169 (mm) cc_final: 0.7912 (tp) REVERT: G 688 GLN cc_start: 0.8638 (tp-100) cc_final: 0.7606 (tp40) REVERT: G 692 MET cc_start: 0.7443 (mmp) cc_final: 0.7140 (mmp) REVERT: H 95 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7300 (mm110) REVERT: H 106 ASP cc_start: 0.7753 (t0) cc_final: 0.7368 (t0) REVERT: H 145 ASP cc_start: 0.7896 (t0) cc_final: 0.7519 (t0) REVERT: H 171 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7996 (ptm-80) REVERT: H 268 LYS cc_start: 0.8173 (tttm) cc_final: 0.7684 (tttp) REVERT: I 116 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7260 (mt-10) REVERT: I 122 ARG cc_start: 0.8072 (mpp80) cc_final: 0.7697 (mtt90) REVERT: I 125 GLN cc_start: 0.8404 (mm110) cc_final: 0.8112 (mm-40) REVERT: I 136 LYS cc_start: 0.8208 (mttt) cc_final: 0.7976 (mttt) REVERT: I 142 VAL cc_start: 0.8824 (t) cc_final: 0.8585 (p) REVERT: I 147 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6846 (mm-30) REVERT: I 151 GLU cc_start: 0.6889 (mp0) cc_final: 0.6435 (mp0) REVERT: I 153 ILE cc_start: 0.8879 (mp) cc_final: 0.8421 (mt) REVERT: I 160 GLN cc_start: 0.7844 (mt0) cc_final: 0.7417 (mt0) REVERT: I 185 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7183 (mt-10) REVERT: J 216 TYR cc_start: 0.8330 (t80) cc_final: 0.8022 (t80) REVERT: J 256 GLN cc_start: 0.8404 (mt0) cc_final: 0.8107 (mm110) REVERT: J 260 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7232 (tmm) REVERT: J 284 GLU cc_start: 0.7846 (tp30) cc_final: 0.7557 (tp30) REVERT: J 332 GLU cc_start: 0.8146 (tp30) cc_final: 0.7902 (tp30) REVERT: J 438 ARG cc_start: 0.8774 (ttm-80) cc_final: 0.8456 (mtm-85) REVERT: J 458 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8932 (ttpp) REVERT: J 537 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7321 (mt-10) REVERT: c 12 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7114 (tp) REVERT: c 24 ARG cc_start: 0.8189 (mmt-90) cc_final: 0.7455 (tpp80) REVERT: c 28 LEU cc_start: 0.7915 (mt) cc_final: 0.7649 (mm) REVERT: c 45 LEU cc_start: 0.8180 (mp) cc_final: 0.7965 (mt) REVERT: c 136 GLU cc_start: 0.7736 (tp30) cc_final: 0.7450 (tp30) REVERT: c 145 ASP cc_start: 0.8154 (m-30) cc_final: 0.7818 (m-30) REVERT: c 191 ARG cc_start: 0.7554 (mtp180) cc_final: 0.7284 (mtp180) REVERT: c 258 TYR cc_start: 0.8339 (p90) cc_final: 0.7936 (p90) REVERT: c 262 TYR cc_start: 0.8881 (t80) cc_final: 0.8071 (t80) REVERT: c 271 ASP cc_start: 0.8025 (m-30) cc_final: 0.7612 (m-30) REVERT: C 7 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.6653 (tppt) REVERT: K 149 GLU cc_start: 0.7754 (mp0) cc_final: 0.7476 (mp0) REVERT: K 183 ASP cc_start: 0.6316 (t0) cc_final: 0.5879 (t0) REVERT: K 253 ASP cc_start: 0.7786 (m-30) cc_final: 0.7277 (t0) REVERT: L 294 TRP cc_start: 0.8055 (t60) cc_final: 0.7417 (t60) REVERT: L 296 MET cc_start: 0.8166 (mmp) cc_final: 0.7832 (mmp) REVERT: L 307 MET cc_start: 0.7803 (tpp) cc_final: 0.7470 (tpp) REVERT: M 88 LYS cc_start: 0.7975 (mmmm) cc_final: 0.7639 (tppp) REVERT: M 92 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.7717 (t80) REVERT: M 95 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7996 (mt-10) REVERT: M 101 ASN cc_start: 0.8458 (m-40) cc_final: 0.8188 (m-40) REVERT: M 158 LYS cc_start: 0.8417 (mttt) cc_final: 0.8026 (mttt) REVERT: M 193 MET cc_start: 0.7592 (mmm) cc_final: 0.7159 (tmm) REVERT: N 98 GLN cc_start: 0.8190 (mt0) cc_final: 0.7772 (mt0) REVERT: N 111 ASP cc_start: 0.7857 (m-30) cc_final: 0.7642 (m-30) REVERT: N 116 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7106 (mm-30) REVERT: N 136 LYS cc_start: 0.8634 (mttt) cc_final: 0.8383 (mtpp) REVERT: N 185 GLU cc_start: 0.7190 (tt0) cc_final: 0.6585 (tt0) REVERT: O 281 GLU cc_start: 0.8460 (pt0) cc_final: 0.8169 (pt0) REVERT: O 350 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7773 (tm-30) REVERT: O 371 GLU cc_start: 0.7109 (tp30) cc_final: 0.6797 (tp30) REVERT: O 502 TYR cc_start: 0.6219 (p90) cc_final: 0.4870 (p90) REVERT: O 524 ASN cc_start: 0.8856 (t0) cc_final: 0.8509 (t0) REVERT: O 547 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8098 (mt0) REVERT: O 688 GLN cc_start: 0.8457 (tm-30) cc_final: 0.7935 (tm-30) REVERT: O 692 MET cc_start: 0.7775 (mtm) cc_final: 0.7326 (mtm) REVERT: P 10 LEU cc_start: 0.7078 (mt) cc_final: 0.6872 (tp) REVERT: P 43 ARG cc_start: 0.7850 (mtm180) cc_final: 0.7467 (mtm180) REVERT: P 81 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7174 (mt-10) REVERT: P 94 MET cc_start: 0.7396 (mmp) cc_final: 0.7073 (mmp) REVERT: P 180 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7688 (mt-10) REVERT: P 250 TYR cc_start: 0.6180 (t80) cc_final: 0.5795 (t80) REVERT: P 267 GLU cc_start: 0.7216 (mp0) cc_final: 0.6287 (mp0) REVERT: Q 89 ARG cc_start: 0.7880 (mtm110) cc_final: 0.7675 (mtm110) REVERT: Q 106 TYR cc_start: 0.8141 (m-80) cc_final: 0.7667 (m-80) REVERT: Q 116 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7030 (mt-10) REVERT: Q 120 HIS cc_start: 0.4672 (OUTLIER) cc_final: 0.4365 (t-90) REVERT: Q 121 GLN cc_start: 0.6195 (mp10) cc_final: 0.5744 (mp10) REVERT: Q 151 GLU cc_start: 0.6995 (tp30) cc_final: 0.6707 (tp30) REVERT: Q 156 ASN cc_start: 0.8333 (m-40) cc_final: 0.7701 (m-40) REVERT: Q 173 LYS cc_start: 0.8551 (ptpp) cc_final: 0.7835 (pttp) REVERT: Q 181 GLU cc_start: 0.7780 (tt0) cc_final: 0.7337 (tt0) REVERT: Q 193 ARG cc_start: 0.6982 (tmt170) cc_final: 0.6613 (tmt170) REVERT: R 205 MET cc_start: 0.5084 (OUTLIER) cc_final: 0.4700 (tpt) REVERT: R 207 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.6857 (pp20) REVERT: R 212 ASN cc_start: 0.7604 (t0) cc_final: 0.7292 (t0) REVERT: R 227 ASN cc_start: 0.8199 (OUTLIER) cc_final: 0.7832 (p0) REVERT: R 242 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7623 (tm-30) REVERT: R 260 MET cc_start: 0.7874 (tpp) cc_final: 0.7483 (tpp) REVERT: R 313 ASN cc_start: 0.8293 (t0) cc_final: 0.7595 (t0) REVERT: R 322 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7455 (tm-30) REVERT: R 334 TYR cc_start: 0.8223 (t80) cc_final: 0.7963 (t80) REVERT: R 335 ARG cc_start: 0.8460 (mmt90) cc_final: 0.8212 (mtt-85) REVERT: R 371 GLU cc_start: 0.7476 (tm-30) cc_final: 0.6868 (tm-30) REVERT: R 433 CYS cc_start: 0.7754 (p) cc_final: 0.7404 (p) REVERT: R 438 ARG cc_start: 0.8692 (tpp80) cc_final: 0.8253 (mtt90) REVERT: R 464 ARG cc_start: 0.7598 (mtm-85) cc_final: 0.6991 (mtm-85) REVERT: R 466 ASP cc_start: 0.8785 (p0) cc_final: 0.8503 (p0) REVERT: R 470 ILE cc_start: 0.8934 (mm) cc_final: 0.8230 (pt) REVERT: R 522 GLU cc_start: 0.7398 (pm20) cc_final: 0.7147 (pm20) REVERT: R 523 GLU cc_start: 0.7801 (tp30) cc_final: 0.7535 (mm-30) REVERT: R 530 ILE cc_start: 0.8881 (mm) cc_final: 0.8606 (tp) REVERT: R 531 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7527 (mm-40) REVERT: R 556 ASN cc_start: 0.8820 (m-40) cc_final: 0.8385 (m-40) REVERT: R 640 LYS cc_start: 0.8688 (tptt) cc_final: 0.8383 (tptm) REVERT: R 679 MET cc_start: 0.4413 (tmm) cc_final: 0.4061 (tmm) REVERT: d 2 ASP cc_start: 0.8379 (t0) cc_final: 0.8083 (t0) REVERT: d 33 MET cc_start: 0.7954 (tpp) cc_final: 0.7675 (tpp) REVERT: d 38 ASP cc_start: 0.8084 (m-30) cc_final: 0.7707 (m-30) REVERT: d 43 ARG cc_start: 0.8286 (ttp80) cc_final: 0.7594 (ttp80) REVERT: d 49 ARG cc_start: 0.8164 (ttp80) cc_final: 0.7872 (ttp80) REVERT: d 81 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7049 (mt-10) REVERT: d 92 MET cc_start: 0.7811 (mtp) cc_final: 0.7449 (mtp) REVERT: d 170 ASN cc_start: 0.7706 (t0) cc_final: 0.7163 (t0) REVERT: d 180 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7217 (mm-30) REVERT: d 183 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8355 (ptpp) REVERT: d 248 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8577 (p) REVERT: d 262 TYR cc_start: 0.8746 (t80) cc_final: 0.7617 (t80) REVERT: d 269 ASN cc_start: 0.8775 (t0) cc_final: 0.8427 (t0) outliers start: 155 outliers final: 118 residues processed: 1212 average time/residue: 0.5438 time to fit residues: 990.1270 Evaluate side-chains 1273 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1138 time to evaluate : 4.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 456 LYS Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain G residue 657 ASN Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 156 ARG Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 275 MET Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 157 HIS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 260 MET Chi-restraints excluded: chain J residue 458 LYS Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain J residue 611 GLN Chi-restraints excluded: chain J residue 654 CYS Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 73 THR Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 146 GLN Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 167 THR Chi-restraints excluded: chain c residue 172 THR Chi-restraints excluded: chain c residue 174 GLU Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 248 THR Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 155 CYS Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain L residue 289 VAL Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain M residue 65 MET Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 130 ASN Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 234 LYS Chi-restraints excluded: chain O residue 290 PHE Chi-restraints excluded: chain O residue 314 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain O residue 433 CYS Chi-restraints excluded: chain O residue 466 ASP Chi-restraints excluded: chain O residue 547 GLN Chi-restraints excluded: chain O residue 647 ILE Chi-restraints excluded: chain P residue 75 TYR Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 106 ASP Chi-restraints excluded: chain P residue 135 LYS Chi-restraints excluded: chain P residue 172 THR Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 248 THR Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain Q residue 114 THR Chi-restraints excluded: chain Q residue 120 HIS Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain R residue 205 MET Chi-restraints excluded: chain R residue 207 GLU Chi-restraints excluded: chain R residue 227 ASN Chi-restraints excluded: chain R residue 238 LYS Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain R residue 316 GLU Chi-restraints excluded: chain R residue 456 LYS Chi-restraints excluded: chain R residue 526 ASP Chi-restraints excluded: chain R residue 641 LYS Chi-restraints excluded: chain R residue 677 THR Chi-restraints excluded: chain d residue 10 LEU Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain d residue 174 GLU Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 250 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 361 optimal weight: 0.9980 chunk 380 optimal weight: 0.7980 chunk 347 optimal weight: 0.0870 chunk 370 optimal weight: 0.5980 chunk 222 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 290 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 334 optimal weight: 8.9990 chunk 349 optimal weight: 0.9990 chunk 368 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN G 486 GLN G 547 GLN H 95 GLN I 143 HIS J 323 GLN J 350 GLN ** J 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 547 GLN J 586 GLN c 146 GLN ** O 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 323 GLN O 347 HIS ** O 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 18 GLN d 229 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 34806 Z= 0.259 Angle : 0.706 12.964 47180 Z= 0.358 Chirality : 0.044 0.260 4964 Planarity : 0.005 0.099 6150 Dihedral : 4.945 43.964 4634 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.47 % Favored : 94.36 % Rotamer: Outliers : 4.23 % Allowed : 22.45 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 4110 helix: 0.35 (0.15), residues: 1137 sheet: -0.93 (0.17), residues: 821 loop : -0.42 (0.14), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 294 HIS 0.009 0.001 HIS G 545 PHE 0.037 0.002 PHE R 321 TYR 0.038 0.002 TYR F 59 ARG 0.012 0.001 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1321 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1167 time to evaluate : 3.754 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: A 7 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.6473 (mptp) REVERT: A 20 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7578 (tm-30) REVERT: B 150 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7393 (t0) REVERT: B 180 LEU cc_start: 0.7068 (mt) cc_final: 0.6841 (mt) REVERT: B 212 ILE cc_start: 0.7570 (mt) cc_final: 0.7351 (tt) REVERT: D 294 TRP cc_start: 0.7953 (t60) cc_final: 0.7033 (t60) REVERT: D 298 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7845 (mm-30) REVERT: D 307 MET cc_start: 0.7395 (tpp) cc_final: 0.7131 (tpp) REVERT: E 26 LYS cc_start: 0.7980 (mttm) cc_final: 0.7773 (mttm) REVERT: E 44 ARG cc_start: 0.7546 (ttp-110) cc_final: 0.7304 (ttp-110) REVERT: E 46 LYS cc_start: 0.7505 (tttm) cc_final: 0.7052 (tmtm) REVERT: E 92 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7776 (t80) REVERT: E 142 MET cc_start: 0.7498 (ttm) cc_final: 0.7172 (ttm) REVERT: E 175 GLU cc_start: 0.7213 (pp20) cc_final: 0.6881 (pp20) REVERT: E 188 LEU cc_start: 0.7967 (tp) cc_final: 0.7712 (tt) REVERT: F 67 TYR cc_start: 0.7755 (t80) cc_final: 0.7000 (t80) REVERT: F 97 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7418 (t70) REVERT: F 142 VAL cc_start: 0.8823 (t) cc_final: 0.8426 (m) REVERT: F 156 ASN cc_start: 0.8311 (p0) cc_final: 0.8021 (p0) REVERT: G 238 LYS cc_start: 0.7461 (ttpt) cc_final: 0.7145 (ttpt) REVERT: G 251 ILE cc_start: 0.8232 (tt) cc_final: 0.7892 (tp) REVERT: G 257 ASP cc_start: 0.7711 (t70) cc_final: 0.7194 (t0) REVERT: G 276 MET cc_start: 0.6589 (mmm) cc_final: 0.5968 (mmm) REVERT: G 281 GLU cc_start: 0.8095 (pt0) cc_final: 0.7536 (pp20) REVERT: G 284 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7369 (mm-30) REVERT: G 316 GLU cc_start: 0.8118 (tt0) cc_final: 0.7698 (tt0) REVERT: G 373 ARG cc_start: 0.7687 (mtm-85) cc_final: 0.7399 (mtm-85) REVERT: G 451 ILE cc_start: 0.8262 (mt) cc_final: 0.8001 (mm) REVERT: G 501 PHE cc_start: 0.8385 (t80) cc_final: 0.7964 (t80) REVERT: G 503 GLN cc_start: 0.7716 (pt0) cc_final: 0.7508 (pt0) REVERT: G 521 TYR cc_start: 0.7626 (p90) cc_final: 0.7407 (p90) REVERT: G 592 LEU cc_start: 0.8184 (mm) cc_final: 0.7939 (tp) REVERT: G 688 GLN cc_start: 0.8650 (tp-100) cc_final: 0.7586 (tp40) REVERT: G 692 MET cc_start: 0.7431 (mmp) cc_final: 0.7163 (mmp) REVERT: H 95 GLN cc_start: 0.7673 (mm110) cc_final: 0.7336 (mm110) REVERT: H 106 ASP cc_start: 0.7822 (t0) cc_final: 0.7376 (t0) REVERT: H 145 ASP cc_start: 0.7881 (t0) cc_final: 0.7539 (t0) REVERT: H 171 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8035 (ptm-80) REVERT: I 59 TYR cc_start: 0.7119 (t80) cc_final: 0.6870 (t80) REVERT: I 116 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7262 (mt-10) REVERT: I 121 GLN cc_start: 0.6142 (mp-120) cc_final: 0.5908 (mp-120) REVERT: I 122 ARG cc_start: 0.8069 (mpp80) cc_final: 0.7701 (mtt90) REVERT: I 125 GLN cc_start: 0.8399 (mm110) cc_final: 0.8114 (mm-40) REVERT: I 136 LYS cc_start: 0.8220 (mttt) cc_final: 0.7982 (mttt) REVERT: I 142 VAL cc_start: 0.8830 (t) cc_final: 0.8579 (p) REVERT: I 147 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6856 (mm-30) REVERT: I 151 GLU cc_start: 0.6922 (mp0) cc_final: 0.6457 (mp0) REVERT: I 153 ILE cc_start: 0.8867 (mp) cc_final: 0.8422 (mt) REVERT: I 160 GLN cc_start: 0.7833 (mt0) cc_final: 0.7382 (mt0) REVERT: I 185 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7091 (mt-10) REVERT: J 216 TYR cc_start: 0.8352 (t80) cc_final: 0.8037 (t80) REVERT: J 256 GLN cc_start: 0.8393 (mt0) cc_final: 0.8115 (mm110) REVERT: J 260 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7216 (tmm) REVERT: J 284 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7565 (tp30) REVERT: J 313 ASN cc_start: 0.8153 (t0) cc_final: 0.7689 (t0) REVERT: J 332 GLU cc_start: 0.8200 (tp30) cc_final: 0.7867 (tp30) REVERT: J 438 ARG cc_start: 0.8773 (ttm-80) cc_final: 0.8441 (mtm-85) REVERT: J 537 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7314 (mt-10) REVERT: J 670 TYR cc_start: 0.7616 (t80) cc_final: 0.7227 (t80) REVERT: c 12 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7115 (tp) REVERT: c 24 ARG cc_start: 0.8192 (mmt-90) cc_final: 0.7508 (tpp80) REVERT: c 28 LEU cc_start: 0.7925 (mt) cc_final: 0.7720 (mm) REVERT: c 45 LEU cc_start: 0.8200 (mp) cc_final: 0.7980 (mt) REVERT: c 145 ASP cc_start: 0.8130 (m-30) cc_final: 0.7756 (m-30) REVERT: c 191 ARG cc_start: 0.7563 (mtp180) cc_final: 0.7300 (mtp180) REVERT: c 258 TYR cc_start: 0.8341 (p90) cc_final: 0.7944 (p90) REVERT: c 262 TYR cc_start: 0.8865 (t80) cc_final: 0.8053 (t80) REVERT: c 269 ASN cc_start: 0.7972 (t0) cc_final: 0.7653 (t0) REVERT: c 271 ASP cc_start: 0.8007 (m-30) cc_final: 0.7556 (m-30) REVERT: C 7 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.6897 (tppt) REVERT: C 41 ARG cc_start: 0.7773 (mtt180) cc_final: 0.7501 (mmm-85) REVERT: K 149 GLU cc_start: 0.7738 (mp0) cc_final: 0.7480 (mp0) REVERT: K 183 ASP cc_start: 0.6293 (t0) cc_final: 0.5874 (t0) REVERT: K 253 ASP cc_start: 0.7811 (m-30) cc_final: 0.7270 (t0) REVERT: L 294 TRP cc_start: 0.8132 (t60) cc_final: 0.7375 (t60) REVERT: L 296 MET cc_start: 0.8157 (mmp) cc_final: 0.7875 (mmp) REVERT: L 307 MET cc_start: 0.7801 (tpp) cc_final: 0.7417 (tpp) REVERT: M 88 LYS cc_start: 0.8007 (mmmm) cc_final: 0.7675 (tppp) REVERT: M 92 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.7753 (t80) REVERT: M 95 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7964 (mt-10) REVERT: M 97 MET cc_start: 0.5402 (mmt) cc_final: 0.5141 (mmt) REVERT: M 101 ASN cc_start: 0.8447 (m-40) cc_final: 0.8186 (m-40) REVERT: M 113 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7688 (pt) REVERT: M 139 ILE cc_start: 0.8531 (mt) cc_final: 0.8150 (mm) REVERT: M 158 LYS cc_start: 0.8436 (mttt) cc_final: 0.8043 (mttt) REVERT: M 191 TRP cc_start: 0.8197 (t-100) cc_final: 0.7905 (t-100) REVERT: M 193 MET cc_start: 0.7565 (mmm) cc_final: 0.7150 (tmm) REVERT: N 98 GLN cc_start: 0.8186 (mt0) cc_final: 0.7771 (mt0) REVERT: N 111 ASP cc_start: 0.7902 (m-30) cc_final: 0.7697 (m-30) REVERT: N 116 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7113 (mm-30) REVERT: N 136 LYS cc_start: 0.8625 (mttt) cc_final: 0.8375 (mtpp) REVERT: N 185 GLU cc_start: 0.7216 (tt0) cc_final: 0.6640 (tt0) REVERT: O 281 GLU cc_start: 0.8455 (pt0) cc_final: 0.8172 (pt0) REVERT: O 284 GLU cc_start: 0.7877 (tp30) cc_final: 0.7269 (tp30) REVERT: O 316 GLU cc_start: 0.8294 (tt0) cc_final: 0.8085 (tt0) REVERT: O 350 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7802 (tm-30) REVERT: O 371 GLU cc_start: 0.7111 (tp30) cc_final: 0.6811 (tp30) REVERT: O 502 TYR cc_start: 0.6246 (p90) cc_final: 0.4837 (p90) REVERT: O 547 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8087 (mt0) REVERT: O 688 GLN cc_start: 0.8435 (tm-30) cc_final: 0.7916 (tm-30) REVERT: O 692 MET cc_start: 0.7773 (mtm) cc_final: 0.7353 (mtm) REVERT: P 43 ARG cc_start: 0.7850 (mtm180) cc_final: 0.7470 (mtm180) REVERT: P 94 MET cc_start: 0.7374 (mmp) cc_final: 0.7065 (mmp) REVERT: P 156 ARG cc_start: 0.7588 (tpt90) cc_final: 0.7179 (tpt90) REVERT: P 180 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7685 (mt-10) REVERT: P 267 GLU cc_start: 0.7244 (mp0) cc_final: 0.6322 (mp0) REVERT: Q 106 TYR cc_start: 0.8144 (m-80) cc_final: 0.7630 (m-80) REVERT: Q 116 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7025 (mt-10) REVERT: Q 121 GLN cc_start: 0.6219 (mp10) cc_final: 0.5774 (mp10) REVERT: Q 151 GLU cc_start: 0.7005 (tp30) cc_final: 0.6718 (tp30) REVERT: Q 156 ASN cc_start: 0.8329 (m-40) cc_final: 0.7702 (m-40) REVERT: Q 173 LYS cc_start: 0.8551 (ptpp) cc_final: 0.7810 (pttp) REVERT: Q 181 GLU cc_start: 0.7803 (tt0) cc_final: 0.7343 (tt0) REVERT: Q 193 ARG cc_start: 0.6974 (tmt170) cc_final: 0.6573 (tmt170) REVERT: R 205 MET cc_start: 0.5031 (OUTLIER) cc_final: 0.4777 (tpt) REVERT: R 207 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: R 212 ASN cc_start: 0.7630 (t0) cc_final: 0.7383 (t0) REVERT: R 227 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7848 (p0) REVERT: R 242 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7670 (tm-30) REVERT: R 260 MET cc_start: 0.7874 (tpp) cc_final: 0.7587 (tpp) REVERT: R 313 ASN cc_start: 0.8282 (t0) cc_final: 0.7604 (t0) REVERT: R 322 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7403 (tm-30) REVERT: R 334 TYR cc_start: 0.8237 (t80) cc_final: 0.8018 (t80) REVERT: R 335 ARG cc_start: 0.8463 (mmt90) cc_final: 0.8210 (mtt-85) REVERT: R 371 GLU cc_start: 0.7499 (tm-30) cc_final: 0.6870 (tm-30) REVERT: R 427 LYS cc_start: 0.8718 (tttp) cc_final: 0.8425 (tttp) REVERT: R 433 CYS cc_start: 0.7779 (p) cc_final: 0.7415 (p) REVERT: R 464 ARG cc_start: 0.7598 (mtm-85) cc_final: 0.6992 (mtm-85) REVERT: R 466 ASP cc_start: 0.8785 (p0) cc_final: 0.8481 (p0) REVERT: R 470 ILE cc_start: 0.8932 (mm) cc_final: 0.8224 (pt) REVERT: R 530 ILE cc_start: 0.8883 (mm) cc_final: 0.8623 (tp) REVERT: R 531 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7494 (mp10) REVERT: R 537 GLU cc_start: 0.7554 (pp20) cc_final: 0.7337 (pp20) REVERT: R 556 ASN cc_start: 0.8779 (m-40) cc_final: 0.8560 (m-40) REVERT: R 640 LYS cc_start: 0.8703 (tptt) cc_final: 0.8397 (tptm) REVERT: R 679 MET cc_start: 0.4423 (tmm) cc_final: 0.4041 (tmm) REVERT: d 2 ASP cc_start: 0.8396 (t0) cc_final: 0.8072 (t0) REVERT: d 33 MET cc_start: 0.7950 (tpp) cc_final: 0.7617 (tpp) REVERT: d 38 ASP cc_start: 0.8010 (m-30) cc_final: 0.7786 (m-30) REVERT: d 43 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7623 (ttp80) REVERT: d 81 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7066 (mt-10) REVERT: d 92 MET cc_start: 0.7820 (mtp) cc_final: 0.7473 (mtp) REVERT: d 170 ASN cc_start: 0.7680 (t0) cc_final: 0.7093 (t0) REVERT: d 180 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7186 (mm-30) REVERT: d 183 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8346 (ptpp) REVERT: d 220 ASP cc_start: 0.7160 (t0) cc_final: 0.6706 (t0) REVERT: d 248 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8577 (p) REVERT: d 262 TYR cc_start: 0.8733 (t80) cc_final: 0.7648 (t80) REVERT: d 269 ASN cc_start: 0.8778 (t0) cc_final: 0.8432 (t0) outliers start: 154 outliers final: 121 residues processed: 1210 average time/residue: 0.5391 time to fit residues: 981.8746 Evaluate side-chains 1294 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1156 time to evaluate : 3.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain G residue 456 LYS Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain G residue 617 ILE Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 156 ARG Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 157 HIS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 260 MET Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 586 GLN Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain J residue 611 GLN Chi-restraints excluded: chain J residue 654 CYS Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 73 THR Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 167 THR Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain c residue 172 THR Chi-restraints excluded: chain c residue 174 GLU Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 248 THR Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 275 MET Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 155 CYS Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 228 ASP Chi-restraints excluded: chain L residue 289 VAL Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain M residue 65 MET Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 130 ASN Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain N residue 155 LEU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 234 LYS Chi-restraints excluded: chain O residue 290 PHE Chi-restraints excluded: chain O residue 314 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain O residue 433 CYS Chi-restraints excluded: chain O residue 466 ASP Chi-restraints excluded: chain O residue 547 GLN Chi-restraints excluded: chain O residue 556 ASN Chi-restraints excluded: chain O residue 647 ILE Chi-restraints excluded: chain P residue 75 TYR Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 106 ASP Chi-restraints excluded: chain P residue 135 LYS Chi-restraints excluded: chain P residue 172 THR Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 215 ASP Chi-restraints excluded: chain P residue 248 THR Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain Q residue 114 THR Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain R residue 205 MET Chi-restraints excluded: chain R residue 207 GLU Chi-restraints excluded: chain R residue 227 ASN Chi-restraints excluded: chain R residue 238 LYS Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain R residue 316 GLU Chi-restraints excluded: chain R residue 456 LYS Chi-restraints excluded: chain R residue 526 ASP Chi-restraints excluded: chain R residue 641 LYS Chi-restraints excluded: chain R residue 677 THR Chi-restraints excluded: chain d residue 10 LEU Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain d residue 174 GLU Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 250 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 242 optimal weight: 0.5980 chunk 391 optimal weight: 0.7980 chunk 238 optimal weight: 1.9990 chunk 185 optimal weight: 0.6980 chunk 272 optimal weight: 0.9990 chunk 410 optimal weight: 0.5980 chunk 377 optimal weight: 0.6980 chunk 326 optimal weight: 0.1980 chunk 33 optimal weight: 0.8980 chunk 252 optimal weight: 9.9990 chunk 200 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN E 162 ASN ** G 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 547 GLN H 67 GLN I 143 HIS ** J 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 GLN J 350 GLN ** J 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 586 GLN c 146 GLN L 330 HIS ** O 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 323 GLN O 347 HIS ** O 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.362 34806 Z= 0.317 Angle : 0.860 59.200 47180 Z= 0.470 Chirality : 0.045 0.408 4964 Planarity : 0.005 0.102 6150 Dihedral : 4.942 43.964 4634 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.47 % Favored : 94.33 % Rotamer: Outliers : 4.09 % Allowed : 22.86 % Favored : 73.05 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 4110 helix: 0.34 (0.15), residues: 1137 sheet: -0.93 (0.17), residues: 821 loop : -0.43 (0.14), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Q 141 HIS 0.008 0.001 HIS I 157 PHE 0.033 0.002 PHE B 213 TYR 0.041 0.002 TYR P 250 ARG 0.041 0.001 ARG Q 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1300 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1151 time to evaluate : 3.997 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: A 7 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.6446 (mptp) REVERT: A 20 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7574 (tm-30) REVERT: B 150 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7364 (t0) REVERT: B 180 LEU cc_start: 0.7074 (mt) cc_final: 0.6844 (mt) REVERT: B 212 ILE cc_start: 0.7572 (mt) cc_final: 0.7351 (tt) REVERT: D 294 TRP cc_start: 0.7962 (t60) cc_final: 0.7022 (t60) REVERT: D 298 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7837 (mm-30) REVERT: D 307 MET cc_start: 0.7388 (tpp) cc_final: 0.7125 (tpp) REVERT: E 26 LYS cc_start: 0.7978 (mttm) cc_final: 0.7769 (mttm) REVERT: E 44 ARG cc_start: 0.7545 (ttp-110) cc_final: 0.7295 (ttp-110) REVERT: E 46 LYS cc_start: 0.7503 (tttm) cc_final: 0.7061 (tmtm) REVERT: E 92 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7776 (t80) REVERT: E 175 GLU cc_start: 0.7169 (pp20) cc_final: 0.6866 (pp20) REVERT: F 67 TYR cc_start: 0.7756 (t80) cc_final: 0.6997 (t80) REVERT: F 97 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7417 (t70) REVERT: F 142 VAL cc_start: 0.8822 (t) cc_final: 0.8427 (m) REVERT: F 156 ASN cc_start: 0.8308 (p0) cc_final: 0.8018 (p0) REVERT: F 181 GLU cc_start: 0.7171 (mp0) cc_final: 0.6779 (mp0) REVERT: G 238 LYS cc_start: 0.7558 (ttpt) cc_final: 0.7150 (ttpt) REVERT: G 251 ILE cc_start: 0.8193 (tt) cc_final: 0.7894 (tp) REVERT: G 257 ASP cc_start: 0.7715 (t70) cc_final: 0.7194 (t0) REVERT: G 276 MET cc_start: 0.6586 (mmm) cc_final: 0.5969 (mmm) REVERT: G 281 GLU cc_start: 0.8092 (pt0) cc_final: 0.7539 (pp20) REVERT: G 284 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7360 (mm-30) REVERT: G 316 GLU cc_start: 0.8119 (tt0) cc_final: 0.7690 (tt0) REVERT: G 373 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7274 (mtm-85) REVERT: G 451 ILE cc_start: 0.8259 (mt) cc_final: 0.7999 (mm) REVERT: G 503 GLN cc_start: 0.7718 (pt0) cc_final: 0.7500 (pt0) REVERT: G 521 TYR cc_start: 0.7655 (p90) cc_final: 0.7381 (p90) REVERT: G 592 LEU cc_start: 0.8183 (mm) cc_final: 0.7936 (tp) REVERT: G 688 GLN cc_start: 0.8649 (tp-100) cc_final: 0.7587 (tp40) REVERT: G 692 MET cc_start: 0.7431 (mmp) cc_final: 0.7163 (mmp) REVERT: H 95 GLN cc_start: 0.7646 (mm110) cc_final: 0.7320 (mm110) REVERT: H 106 ASP cc_start: 0.7819 (t0) cc_final: 0.7373 (t0) REVERT: H 145 ASP cc_start: 0.7882 (t0) cc_final: 0.7535 (t0) REVERT: H 171 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8032 (ptm-80) REVERT: I 59 TYR cc_start: 0.7112 (t80) cc_final: 0.6892 (t80) REVERT: I 116 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7265 (mt-10) REVERT: I 121 GLN cc_start: 0.6143 (mp-120) cc_final: 0.5910 (mp-120) REVERT: I 122 ARG cc_start: 0.8068 (mpp80) cc_final: 0.7697 (mtt90) REVERT: I 125 GLN cc_start: 0.8404 (mm110) cc_final: 0.8114 (mm-40) REVERT: I 136 LYS cc_start: 0.8210 (mttt) cc_final: 0.7984 (mttt) REVERT: I 142 VAL cc_start: 0.8830 (t) cc_final: 0.8574 (p) REVERT: I 147 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6854 (mm-30) REVERT: I 151 GLU cc_start: 0.6926 (mp0) cc_final: 0.6465 (mp0) REVERT: I 153 ILE cc_start: 0.8862 (mp) cc_final: 0.8424 (mt) REVERT: I 160 GLN cc_start: 0.7825 (mt0) cc_final: 0.7371 (mt0) REVERT: I 185 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7093 (mt-10) REVERT: J 211 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7749 (mp10) REVERT: J 216 TYR cc_start: 0.8352 (t80) cc_final: 0.8033 (t80) REVERT: J 256 GLN cc_start: 0.8393 (mt0) cc_final: 0.8193 (mm-40) REVERT: J 260 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7208 (tmm) REVERT: J 284 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7565 (tp30) REVERT: J 313 ASN cc_start: 0.8144 (t0) cc_final: 0.7690 (t0) REVERT: J 332 GLU cc_start: 0.8147 (tp30) cc_final: 0.7869 (tp30) REVERT: J 438 ARG cc_start: 0.8766 (ttm-80) cc_final: 0.8442 (mtm-85) REVERT: J 537 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7316 (mt-10) REVERT: J 670 TYR cc_start: 0.7617 (t80) cc_final: 0.7222 (t80) REVERT: c 12 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7114 (tp) REVERT: c 24 ARG cc_start: 0.8198 (mmt-90) cc_final: 0.7465 (tpp80) REVERT: c 28 LEU cc_start: 0.7940 (mt) cc_final: 0.7666 (mm) REVERT: c 45 LEU cc_start: 0.8198 (mp) cc_final: 0.7980 (mt) REVERT: c 145 ASP cc_start: 0.8127 (m-30) cc_final: 0.7763 (m-30) REVERT: c 191 ARG cc_start: 0.7563 (mtp180) cc_final: 0.7300 (mtp180) REVERT: c 258 TYR cc_start: 0.8337 (p90) cc_final: 0.7944 (p90) REVERT: c 262 TYR cc_start: 0.8861 (t80) cc_final: 0.8052 (t80) REVERT: c 269 ASN cc_start: 0.7988 (t0) cc_final: 0.7682 (t0) REVERT: c 271 ASP cc_start: 0.7972 (m-30) cc_final: 0.7551 (m-30) REVERT: C 7 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.6865 (tppt) REVERT: K 149 GLU cc_start: 0.7724 (mp0) cc_final: 0.7480 (mp0) REVERT: K 183 ASP cc_start: 0.6288 (t0) cc_final: 0.5876 (t0) REVERT: K 253 ASP cc_start: 0.7854 (m-30) cc_final: 0.7274 (t0) REVERT: L 294 TRP cc_start: 0.7970 (t60) cc_final: 0.7348 (t60) REVERT: L 296 MET cc_start: 0.8190 (mmp) cc_final: 0.7861 (mmp) REVERT: L 298 GLU cc_start: 0.8524 (mm-30) cc_final: 0.7997 (mm-30) REVERT: L 307 MET cc_start: 0.7794 (tpp) cc_final: 0.7395 (tpp) REVERT: M 88 LYS cc_start: 0.8020 (mmmm) cc_final: 0.7676 (tppp) REVERT: M 92 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.7749 (t80) REVERT: M 95 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7962 (mt-10) REVERT: M 101 ASN cc_start: 0.8450 (m-40) cc_final: 0.8182 (m-40) REVERT: M 113 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7677 (pt) REVERT: M 139 ILE cc_start: 0.8533 (mt) cc_final: 0.8149 (mm) REVERT: M 158 LYS cc_start: 0.8432 (mttt) cc_final: 0.8044 (mttt) REVERT: M 191 TRP cc_start: 0.8207 (t-100) cc_final: 0.7910 (t-100) REVERT: M 193 MET cc_start: 0.7563 (mmm) cc_final: 0.7142 (tmm) REVERT: N 98 GLN cc_start: 0.8185 (mt0) cc_final: 0.7771 (mt0) REVERT: N 116 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7113 (mm-30) REVERT: N 136 LYS cc_start: 0.8630 (mttt) cc_final: 0.8374 (mtpp) REVERT: N 185 GLU cc_start: 0.7222 (tt0) cc_final: 0.6641 (tt0) REVERT: O 281 GLU cc_start: 0.8454 (pt0) cc_final: 0.8177 (pt0) REVERT: O 284 GLU cc_start: 0.7879 (tp30) cc_final: 0.7271 (tp30) REVERT: O 316 GLU cc_start: 0.8291 (tt0) cc_final: 0.8048 (tt0) REVERT: O 350 GLN cc_start: 0.8405 (tm-30) cc_final: 0.7797 (tm-30) REVERT: O 371 GLU cc_start: 0.7112 (tp30) cc_final: 0.6816 (tp30) REVERT: O 502 TYR cc_start: 0.6227 (p90) cc_final: 0.4837 (p90) REVERT: O 547 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8085 (mt0) REVERT: O 688 GLN cc_start: 0.8435 (tm-30) cc_final: 0.7912 (tm-30) REVERT: O 692 MET cc_start: 0.7773 (mtm) cc_final: 0.7351 (mtm) REVERT: P 43 ARG cc_start: 0.7854 (mtm180) cc_final: 0.7470 (mtm180) REVERT: P 94 MET cc_start: 0.7376 (mmp) cc_final: 0.7065 (mmp) REVERT: P 180 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7691 (mt-10) REVERT: P 250 TYR cc_start: 0.6149 (t80) cc_final: 0.5794 (t80) REVERT: P 267 GLU cc_start: 0.7235 (mp0) cc_final: 0.6325 (mp0) REVERT: Q 106 TYR cc_start: 0.8010 (m-80) cc_final: 0.7623 (m-80) REVERT: Q 116 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7026 (mt-10) REVERT: Q 121 GLN cc_start: 0.6218 (mp10) cc_final: 0.5769 (mp10) REVERT: Q 151 GLU cc_start: 0.7021 (tp30) cc_final: 0.6737 (tp30) REVERT: Q 156 ASN cc_start: 0.8327 (m-40) cc_final: 0.7701 (m-40) REVERT: Q 173 LYS cc_start: 0.8548 (ptpp) cc_final: 0.7809 (pttp) REVERT: Q 181 GLU cc_start: 0.7801 (tt0) cc_final: 0.7342 (tt0) REVERT: Q 193 ARG cc_start: 0.7000 (tmt170) cc_final: 0.6597 (tmt170) REVERT: R 205 MET cc_start: 0.5038 (OUTLIER) cc_final: 0.4729 (tpt) REVERT: R 207 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.6769 (mp0) REVERT: R 212 ASN cc_start: 0.7692 (t0) cc_final: 0.7382 (t0) REVERT: R 227 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7846 (p0) REVERT: R 260 MET cc_start: 0.7870 (tpp) cc_final: 0.7582 (tpp) REVERT: R 313 ASN cc_start: 0.8281 (t0) cc_final: 0.7593 (t0) REVERT: R 322 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7400 (tm-30) REVERT: R 334 TYR cc_start: 0.8239 (t80) cc_final: 0.8022 (t80) REVERT: R 335 ARG cc_start: 0.8460 (mmt90) cc_final: 0.8208 (mtt-85) REVERT: R 371 GLU cc_start: 0.7507 (tm-30) cc_final: 0.6862 (tm-30) REVERT: R 427 LYS cc_start: 0.8752 (tttp) cc_final: 0.8426 (tttp) REVERT: R 433 CYS cc_start: 0.7784 (p) cc_final: 0.7419 (p) REVERT: R 464 ARG cc_start: 0.7598 (mtm-85) cc_final: 0.6994 (mtm-85) REVERT: R 466 ASP cc_start: 0.8783 (p0) cc_final: 0.8487 (p0) REVERT: R 470 ILE cc_start: 0.8931 (mm) cc_final: 0.8225 (pt) REVERT: R 530 ILE cc_start: 0.8881 (mm) cc_final: 0.8620 (tp) REVERT: R 531 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7502 (mp10) REVERT: R 556 ASN cc_start: 0.8779 (m-40) cc_final: 0.8560 (m-40) REVERT: R 640 LYS cc_start: 0.8688 (tptt) cc_final: 0.8390 (tptm) REVERT: R 679 MET cc_start: 0.4377 (tmm) cc_final: 0.4023 (tmm) REVERT: R 687 GLU cc_start: 0.8572 (pt0) cc_final: 0.8191 (pp20) REVERT: d 2 ASP cc_start: 0.8386 (t0) cc_final: 0.8076 (t0) REVERT: d 33 MET cc_start: 0.7957 (tpp) cc_final: 0.7619 (tpp) REVERT: d 38 ASP cc_start: 0.7990 (m-30) cc_final: 0.7781 (m-30) REVERT: d 43 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7621 (ttp80) REVERT: d 81 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7063 (mt-10) REVERT: d 92 MET cc_start: 0.7821 (mtp) cc_final: 0.7474 (mtp) REVERT: d 170 ASN cc_start: 0.7684 (t0) cc_final: 0.7093 (t0) REVERT: d 180 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7197 (mm-30) REVERT: d 183 LYS cc_start: 0.8704 (mtmt) cc_final: 0.8345 (ptpp) REVERT: d 220 ASP cc_start: 0.7192 (t0) cc_final: 0.6724 (t0) REVERT: d 248 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8578 (p) REVERT: d 262 TYR cc_start: 0.8729 (t80) cc_final: 0.7645 (t80) REVERT: d 269 ASN cc_start: 0.8780 (t0) cc_final: 0.8431 (t0) outliers start: 149 outliers final: 125 residues processed: 1194 average time/residue: 0.5408 time to fit residues: 970.2634 Evaluate side-chains 1295 residues out of total 3644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1153 time to evaluate : 3.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 165 ASN Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain G residue 456 LYS Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain G residue 617 ILE Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain G residue 657 ASN Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 156 ARG Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 157 HIS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 260 MET Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain J residue 654 CYS Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 73 THR Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 167 THR Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain c residue 172 THR Chi-restraints excluded: chain c residue 174 GLU Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 248 THR Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 275 MET Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 155 CYS Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 228 ASP Chi-restraints excluded: chain L residue 289 VAL Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain M residue 65 MET Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 130 ASN Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain N residue 155 LEU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 234 LYS Chi-restraints excluded: chain O residue 249 ASP Chi-restraints excluded: chain O residue 290 PHE Chi-restraints excluded: chain O residue 314 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain O residue 433 CYS Chi-restraints excluded: chain O residue 466 ASP Chi-restraints excluded: chain O residue 540 SER Chi-restraints excluded: chain O residue 547 GLN Chi-restraints excluded: chain O residue 556 ASN Chi-restraints excluded: chain O residue 647 ILE Chi-restraints excluded: chain P residue 75 TYR Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 106 ASP Chi-restraints excluded: chain P residue 135 LYS Chi-restraints excluded: chain P residue 172 THR Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 215 ASP Chi-restraints excluded: chain P residue 232 ARG Chi-restraints excluded: chain P residue 248 THR Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain Q residue 66 ARG Chi-restraints excluded: chain Q residue 114 THR Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain R residue 205 MET Chi-restraints excluded: chain R residue 207 GLU Chi-restraints excluded: chain R residue 227 ASN Chi-restraints excluded: chain R residue 238 LYS Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain R residue 316 GLU Chi-restraints excluded: chain R residue 456 LYS Chi-restraints excluded: chain R residue 526 ASP Chi-restraints excluded: chain R residue 641 LYS Chi-restraints excluded: chain R residue 677 THR Chi-restraints excluded: chain d residue 10 LEU Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain d residue 174 GLU Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 250 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 259 optimal weight: 3.9990 chunk 348 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 301 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 327 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 336 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 547 GLN I 143 HIS ** J 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 330 HIS ** O 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 323 GLN O 347 HIS ** O 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.131346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.110403 restraints weight = 72608.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.114272 restraints weight = 34882.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.116747 restraints weight = 21215.026| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.362 34806 Z= 0.317 Angle : 0.860 59.200 47180 Z= 0.470 Chirality : 0.045 0.408 4964 Planarity : 0.005 0.105 6150 Dihedral : 4.942 43.964 4634 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.47 % Favored : 94.33 % Rotamer: Outliers : 3.92 % Allowed : 23.16 % Favored : 72.91 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 4110 helix: 0.34 (0.15), residues: 1137 sheet: -0.93 (0.17), residues: 821 loop : -0.43 (0.14), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Q 141 HIS 0.008 0.001 HIS I 157 PHE 0.033 0.002 PHE B 213 TYR 0.041 0.002 TYR P 250 ARG 0.041 0.001 ARG Q 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13523.69 seconds wall clock time: 240 minutes 26.65 seconds (14426.65 seconds total)