Starting phenix.real_space_refine on Fri Mar 15 12:49:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxd_13698/03_2024/7pxd_13698_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxd_13698/03_2024/7pxd_13698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxd_13698/03_2024/7pxd_13698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxd_13698/03_2024/7pxd_13698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxd_13698/03_2024/7pxd_13698_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxd_13698/03_2024/7pxd_13698_neut_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 179 5.16 5 C 43207 2.51 5 N 12113 2.21 5 O 13377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 14": "NH1" <-> "NH2" Residue "0 GLU 15": "OE1" <-> "OE2" Residue "2 GLU 119": "OE1" <-> "OE2" Residue "4 GLU 15": "OE1" <-> "OE2" Residue "6 GLU 10": "OE1" <-> "OE2" Residue "8 GLU 10": "OE1" <-> "OE2" Residue "8 ARG 26": "NH1" <-> "NH2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A ARG 494": "NH1" <-> "NH2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B ARG 318": "NH1" <-> "NH2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B ARG 427": "NH1" <-> "NH2" Residue "B TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B GLU 559": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C GLU 239": "OE1" <-> "OE2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "C ARG 378": "NH1" <-> "NH2" Residue "C GLU 418": "OE1" <-> "OE2" Residue "C ARG 427": "NH1" <-> "NH2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C ARG 494": "NH1" <-> "NH2" Residue "C GLU 536": "OE1" <-> "OE2" Residue "C GLU 557": "OE1" <-> "OE2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D GLU 245": "OE1" <-> "OE2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D GLU 276": "OE1" <-> "OE2" Residue "D GLU 336": "OE1" <-> "OE2" Residue "D GLU 418": "OE1" <-> "OE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D GLU 536": "OE1" <-> "OE2" Residue "D ARG 543": "NH1" <-> "NH2" Residue "D GLU 557": "OE1" <-> "OE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E GLU 237": "OE1" <-> "OE2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "E GLU 336": "OE1" <-> "OE2" Residue "E GLU 362": "OE1" <-> "OE2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "E ARG 378": "NH1" <-> "NH2" Residue "E ARG 380": "NH1" <-> "NH2" Residue "E GLU 404": "OE1" <-> "OE2" Residue "E GLU 407": "OE1" <-> "OE2" Residue "E GLU 455": "OE1" <-> "OE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E ARG 494": "NH1" <-> "NH2" Residue "E GLU 497": "OE1" <-> "OE2" Residue "E GLU 536": "OE1" <-> "OE2" Residue "E GLU 554": "OE1" <-> "OE2" Residue "E GLU 579": "OE1" <-> "OE2" Residue "E ARG 580": "NH1" <-> "NH2" Residue "E TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 151": "OE1" <-> "OE2" Residue "F GLU 182": "OE1" <-> "OE2" Residue "F GLU 276": "OE1" <-> "OE2" Residue "F GLU 280": "OE1" <-> "OE2" Residue "F GLU 336": "OE1" <-> "OE2" Residue "F GLU 344": "OE1" <-> "OE2" Residue "F GLU 372": "OE1" <-> "OE2" Residue "F GLU 418": "OE1" <-> "OE2" Residue "F GLU 506": "OE1" <-> "OE2" Residue "F GLU 536": "OE1" <-> "OE2" Residue "F GLU 559": "OE1" <-> "OE2" Residue "F GLU 579": "OE1" <-> "OE2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "H TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 382": "NH1" <-> "NH2" Residue "H GLU 432": "OE1" <-> "OE2" Residue "H ARG 488": "NH1" <-> "NH2" Residue "I PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 382": "NH1" <-> "NH2" Residue "J ARG 488": "NH1" <-> "NH2" Residue "K PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 132": "OE1" <-> "OE2" Residue "K GLU 173": "OE1" <-> "OE2" Residue "L GLU 432": "OE1" <-> "OE2" Residue "L ARG 488": "NH1" <-> "NH2" Residue "L GLU 512": "OE1" <-> "OE2" Residue "L ARG 515": "NH1" <-> "NH2" Residue "M GLU 434": "OE1" <-> "OE2" Residue "M ARG 488": "NH1" <-> "NH2" Residue "M GLU 512": "OE1" <-> "OE2" Residue "N ARG 382": "NH1" <-> "NH2" Residue "N GLU 434": "OE1" <-> "OE2" Residue "N ARG 488": "NH1" <-> "NH2" Residue "N ARG 515": "NH1" <-> "NH2" Residue "O PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 132": "OE1" <-> "OE2" Residue "O GLU 173": "OE1" <-> "OE2" Residue "P ARG 465": "NH1" <-> "NH2" Residue "P ARG 488": "NH1" <-> "NH2" Residue "P GLU 512": "OE1" <-> "OE2" Residue "Q GLU 18": "OE1" <-> "OE2" Residue "Q PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 357": "NH1" <-> "NH2" Residue "R GLU 434": "OE1" <-> "OE2" Residue "R ARG 488": "NH1" <-> "NH2" Residue "R GLU 512": "OE1" <-> "OE2" Residue "S GLU 433": "OE1" <-> "OE2" Residue "S GLU 434": "OE1" <-> "OE2" Residue "S ARG 488": "NH1" <-> "NH2" Residue "S GLU 512": "OE1" <-> "OE2" Residue "T GLU 15": "OE1" <-> "OE2" Residue "T GLU 18": "OE1" <-> "OE2" Residue "T PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 97": "NH1" <-> "NH2" Residue "T GLU 132": "OE1" <-> "OE2" Residue "U ARG 357": "NH1" <-> "NH2" Residue "U ARG 382": "NH1" <-> "NH2" Residue "U GLU 434": "OE1" <-> "OE2" Residue "U ARG 488": "NH1" <-> "NH2" Residue "U GLU 512": "OE1" <-> "OE2" Residue "U ARG 515": "NH1" <-> "NH2" Residue "V ARG 488": "NH1" <-> "NH2" Residue "W GLU 354": "OE1" <-> "OE2" Residue "W ARG 382": "NH1" <-> "NH2" Residue "W ARG 488": "NH1" <-> "NH2" Residue "W GLU 533": "OE1" <-> "OE2" Residue "X GLU 15": "OE1" <-> "OE2" Residue "X ARG 76": "NH1" <-> "NH2" Residue "X PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 173": "OE1" <-> "OE2" Residue "Y ARG 382": "NH1" <-> "NH2" Residue "Y GLU 432": "OE1" <-> "OE2" Residue "Y ARG 488": "NH1" <-> "NH2" Residue "Y GLU 512": "OE1" <-> "OE2" Residue "Z GLU 132": "OE1" <-> "OE2" Residue "a ARG 382": "NH1" <-> "NH2" Residue "a ARG 388": "NH1" <-> "NH2" Residue "a GLU 434": "OE1" <-> "OE2" Residue "a ARG 488": "NH1" <-> "NH2" Residue "a ARG 509": "NH1" <-> "NH2" Residue "a GLU 512": "OE1" <-> "OE2" Residue "b ARG 382": "NH1" <-> "NH2" Residue "b ARG 488": "NH1" <-> "NH2" Residue "d GLU 18": "OE1" <-> "OE2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "f GLU 18": "OE1" <-> "OE2" Residue "f ARG 21": "NH1" <-> "NH2" Time to flip residues: 0.24s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 68900 Number of models: 1 Model: "" Number of chains: 42 Chain: "0" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "1" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "2" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "4" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "6" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "8" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "A" Number of atoms: 3692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3692 Classifications: {'peptide': 471} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain breaks: 4 Chain: "B" Number of atoms: 3761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3761 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 458} Chain breaks: 2 Chain: "C" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3685 Classifications: {'peptide': 471} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 448} Chain breaks: 3 Chain: "D" Number of atoms: 3584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3584 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 433} Chain breaks: 4 Chain: "E" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3775 Classifications: {'peptide': 483} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 460} Chain breaks: 2 Chain: "F" Number of atoms: 3773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3773 Classifications: {'peptide': 483} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 460} Chain breaks: 2 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 112 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain breaks: 1 Chain: "J" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1668 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Chain: "L" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "P" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "R" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain breaks: 1 Chain: "U" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1715 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 226} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1715 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 226} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain breaks: 1 Chain: "Y" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Z" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "a" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "f" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 26.80, per 1000 atoms: 0.39 Number of scatterers: 68900 At special positions: 0 Unit cell: (140.53, 153.972, 282.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 179 16.00 P 18 15.00 Mg 6 11.99 O 13377 8.00 N 12113 7.00 C 43207 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: 20.33 Conformation dependent library (CDL) restraints added in 9.4 seconds 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16466 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 287 helices and 95 sheets defined 39.7% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.74 Creating SS restraints... Processing helix chain '0' and resid 9 through 25 removed outlier: 3.538A pdb=" N ALA 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) Processing helix chain '0' and resid 68 through 88 Processing helix chain '0' and resid 91 through 93 No H-bonds generated for 'chain '0' and resid 91 through 93' Processing helix chain '0' and resid 96 through 113 Processing helix chain '0' and resid 160 through 170 Processing helix chain '0' and resid 177 through 189 Processing helix chain '0' and resid 227 through 233 Processing helix chain '2' and resid 9 through 26 Processing helix chain '2' and resid 68 through 88 removed outlier: 4.228A pdb=" N ASN 2 73 " --> pdb=" O ASN 2 69 " (cutoff:3.500A) Processing helix chain '2' and resid 91 through 93 No H-bonds generated for 'chain '2' and resid 91 through 93' Processing helix chain '2' and resid 96 through 113 Processing helix chain '2' and resid 160 through 170 Processing helix chain '2' and resid 177 through 189 Processing helix chain '2' and resid 227 through 233 Processing helix chain '4' and resid 9 through 25 Processing helix chain '4' and resid 68 through 88 Processing helix chain '4' and resid 91 through 93 No H-bonds generated for 'chain '4' and resid 91 through 93' Processing helix chain '4' and resid 96 through 113 Processing helix chain '4' and resid 160 through 170 Processing helix chain '4' and resid 177 through 189 Processing helix chain '4' and resid 227 through 233 Processing helix chain '6' and resid 9 through 25 Processing helix chain '6' and resid 68 through 88 Processing helix chain '6' and resid 91 through 93 No H-bonds generated for 'chain '6' and resid 91 through 93' Processing helix chain '6' and resid 96 through 113 Processing helix chain '6' and resid 160 through 170 Processing helix chain '6' and resid 177 through 189 Processing helix chain '6' and resid 227 through 233 Processing helix chain '8' and resid 9 through 25 Processing helix chain '8' and resid 68 through 88 Processing helix chain '8' and resid 91 through 93 No H-bonds generated for 'chain '8' and resid 91 through 93' Processing helix chain '8' and resid 96 through 113 Processing helix chain '8' and resid 160 through 170 Processing helix chain '8' and resid 177 through 189 Processing helix chain '8' and resid 227 through 233 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 238 through 241 No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 259 through 273 removed outlier: 4.456A pdb=" N LEU A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 275 through 281 Processing helix chain 'A' and resid 299 through 317 Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 345 through 362 removed outlier: 3.890A pdb=" N ILE A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 403 removed outlier: 4.511A pdb=" N VAL A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 442 through 452 Processing helix chain 'A' and resid 461 through 467 removed outlier: 3.961A pdb=" N GLU A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 486 Processing helix chain 'A' and resid 491 through 493 No H-bonds generated for 'chain 'A' and resid 491 through 493' Processing helix chain 'A' and resid 510 through 513 Processing helix chain 'A' and resid 516 through 536 Processing helix chain 'A' and resid 544 through 557 removed outlier: 3.684A pdb=" N VAL A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 567 through 577 Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 260 through 273 Proline residue: B 271 - end of helix Processing helix chain 'B' and resid 275 through 281 Processing helix chain 'B' and resid 299 through 317 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 442 through 452 Processing helix chain 'B' and resid 461 through 466 Processing helix chain 'B' and resid 471 through 486 Processing helix chain 'B' and resid 510 through 513 Processing helix chain 'B' and resid 516 through 537 Processing helix chain 'B' and resid 544 through 560 removed outlier: 5.150A pdb=" N ASP B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 577 Processing helix chain 'C' and resid 237 through 241 Processing helix chain 'C' and resid 258 through 273 removed outlier: 3.634A pdb=" N ALA C 267 " --> pdb=" O GLN C 263 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) Proline residue: C 271 - end of helix Processing helix chain 'C' and resid 275 through 281 Processing helix chain 'C' and resid 299 through 313 Processing helix chain 'C' and resid 344 through 360 Processing helix chain 'C' and resid 389 through 400 Proline residue: C 394 - end of helix Processing helix chain 'C' and resid 442 through 452 Processing helix chain 'C' and resid 461 through 466 Processing helix chain 'C' and resid 471 through 486 Processing helix chain 'C' and resid 491 through 493 No H-bonds generated for 'chain 'C' and resid 491 through 493' Processing helix chain 'C' and resid 510 through 513 Processing helix chain 'C' and resid 516 through 537 Processing helix chain 'C' and resid 544 through 553 removed outlier: 3.753A pdb=" N VAL C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 577 Processing helix chain 'D' and resid 258 through 267 Processing helix chain 'D' and resid 269 through 280 removed outlier: 3.567A pdb=" N LEU D 273 " --> pdb=" O GLU D 269 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS D 274 " --> pdb=" O LEU D 270 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU D 276 " --> pdb=" O PHE D 272 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 314 Processing helix chain 'D' and resid 334 through 337 No H-bonds generated for 'chain 'D' and resid 334 through 337' Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 373 through 375 No H-bonds generated for 'chain 'D' and resid 373 through 375' Processing helix chain 'D' and resid 392 through 402 Processing helix chain 'D' and resid 423 through 426 No H-bonds generated for 'chain 'D' and resid 423 through 426' Processing helix chain 'D' and resid 442 through 452 Processing helix chain 'D' and resid 461 through 467 removed outlier: 3.964A pdb=" N GLU D 466 " --> pdb=" O ASP D 462 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE D 467 " --> pdb=" O ASP D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 486 Processing helix chain 'D' and resid 491 through 493 No H-bonds generated for 'chain 'D' and resid 491 through 493' Processing helix chain 'D' and resid 516 through 537 removed outlier: 3.558A pdb=" N GLU D 536 " --> pdb=" O LYS D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 558 Processing helix chain 'D' and resid 570 through 577 removed outlier: 3.508A pdb=" N SER D 574 " --> pdb=" O TRP D 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 134 No H-bonds generated for 'chain 'E' and resid 132 through 134' Processing helix chain 'E' and resid 236 through 242 Processing helix chain 'E' and resid 251 through 253 No H-bonds generated for 'chain 'E' and resid 251 through 253' Processing helix chain 'E' and resid 259 through 273 removed outlier: 4.298A pdb=" N LEU E 270 " --> pdb=" O ASP E 266 " (cutoff:3.500A) Proline residue: E 271 - end of helix Processing helix chain 'E' and resid 275 through 281 Processing helix chain 'E' and resid 299 through 317 removed outlier: 3.669A pdb=" N ALA E 307 " --> pdb=" O ALA E 303 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN E 308 " --> pdb=" O LYS E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 328 removed outlier: 4.065A pdb=" N TYR E 328 " --> pdb=" O GLU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 337 No H-bonds generated for 'chain 'E' and resid 335 through 337' Processing helix chain 'E' and resid 344 through 359 removed outlier: 3.604A pdb=" N LYS E 359 " --> pdb=" O ARG E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 388 through 400 Proline residue: E 394 - end of helix Processing helix chain 'E' and resid 442 through 452 Processing helix chain 'E' and resid 461 through 466 removed outlier: 4.260A pdb=" N GLU E 466 " --> pdb=" O ASP E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 486 Processing helix chain 'E' and resid 491 through 493 No H-bonds generated for 'chain 'E' and resid 491 through 493' Processing helix chain 'E' and resid 516 through 537 Processing helix chain 'E' and resid 544 through 557 removed outlier: 3.600A pdb=" N VAL E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 577 Processing helix chain 'F' and resid 190 through 192 No H-bonds generated for 'chain 'F' and resid 190 through 192' Processing helix chain 'F' and resid 251 through 253 No H-bonds generated for 'chain 'F' and resid 251 through 253' Processing helix chain 'F' and resid 258 through 273 removed outlier: 4.438A pdb=" N LEU F 270 " --> pdb=" O ASP F 266 " (cutoff:3.500A) Proline residue: F 271 - end of helix Processing helix chain 'F' and resid 275 through 281 Processing helix chain 'F' and resid 300 through 315 Processing helix chain 'F' and resid 324 through 327 No H-bonds generated for 'chain 'F' and resid 324 through 327' Processing helix chain 'F' and resid 335 through 337 No H-bonds generated for 'chain 'F' and resid 335 through 337' Processing helix chain 'F' and resid 345 through 359 Processing helix chain 'F' and resid 388 through 399 removed outlier: 3.778A pdb=" N VAL F 392 " --> pdb=" O GLU F 389 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL F 393 " --> pdb=" O THR F 390 " (cutoff:3.500A) Proline residue: F 394 - end of helix removed outlier: 3.577A pdb=" N GLU F 399 " --> pdb=" O LEU F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 420 No H-bonds generated for 'chain 'F' and resid 418 through 420' Processing helix chain 'F' and resid 442 through 452 Processing helix chain 'F' and resid 461 through 467 removed outlier: 4.332A pdb=" N GLU F 466 " --> pdb=" O ASP F 462 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N PHE F 467 " --> pdb=" O ASP F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 486 Processing helix chain 'F' and resid 491 through 493 No H-bonds generated for 'chain 'F' and resid 491 through 493' Processing helix chain 'F' and resid 510 through 513 Processing helix chain 'F' and resid 516 through 537 Processing helix chain 'F' and resid 544 through 557 removed outlier: 3.577A pdb=" N VAL F 552 " --> pdb=" O LEU F 548 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 577 No H-bonds generated for 'chain 'F' and resid 574 through 577' Processing helix chain 'H' and resid 349 through 370 Processing helix chain 'H' and resid 376 through 395 removed outlier: 3.520A pdb=" N ASN H 390 " --> pdb=" O MET H 386 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU H 391 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ALA H 392 " --> pdb=" O ARG H 388 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ALA H 393 " --> pdb=" O GLY H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 416 No H-bonds generated for 'chain 'H' and resid 414 through 416' Processing helix chain 'H' and resid 443 through 456 removed outlier: 4.062A pdb=" N LYS H 452 " --> pdb=" O SER H 448 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER H 455 " --> pdb=" O LYS H 451 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLN H 456 " --> pdb=" O LYS H 452 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 477 Processing helix chain 'H' and resid 507 through 521 Processing helix chain 'I' and resid 9 through 25 Processing helix chain 'I' and resid 68 through 88 Processing helix chain 'I' and resid 91 through 93 No H-bonds generated for 'chain 'I' and resid 91 through 93' Processing helix chain 'I' and resid 96 through 113 Processing helix chain 'I' and resid 160 through 170 Processing helix chain 'I' and resid 177 through 189 Processing helix chain 'I' and resid 205 through 207 No H-bonds generated for 'chain 'I' and resid 205 through 207' Processing helix chain 'I' and resid 227 through 233 Processing helix chain 'J' and resid 349 through 370 Processing helix chain 'J' and resid 376 through 395 removed outlier: 3.591A pdb=" N ASN J 390 " --> pdb=" O MET J 386 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU J 391 " --> pdb=" O VAL J 387 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA J 392 " --> pdb=" O ARG J 388 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ALA J 393 " --> pdb=" O GLY J 389 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 416 No H-bonds generated for 'chain 'J' and resid 414 through 416' Processing helix chain 'J' and resid 441 through 456 removed outlier: 4.513A pdb=" N LEU J 444 " --> pdb=" O SER J 441 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET J 450 " --> pdb=" O LYS J 447 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS J 451 " --> pdb=" O SER J 448 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR J 454 " --> pdb=" O LYS J 451 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER J 455 " --> pdb=" O LYS J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 460 through 477 Processing helix chain 'J' and resid 507 through 521 Processing helix chain 'K' and resid 9 through 25 Processing helix chain 'K' and resid 68 through 88 Processing helix chain 'K' and resid 91 through 93 No H-bonds generated for 'chain 'K' and resid 91 through 93' Processing helix chain 'K' and resid 96 through 113 Processing helix chain 'K' and resid 160 through 170 Processing helix chain 'K' and resid 177 through 189 Processing helix chain 'K' and resid 205 through 207 No H-bonds generated for 'chain 'K' and resid 205 through 207' Processing helix chain 'K' and resid 227 through 232 Processing helix chain 'L' and resid 349 through 370 Processing helix chain 'L' and resid 376 through 395 removed outlier: 3.669A pdb=" N LEU L 391 " --> pdb=" O VAL L 387 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ALA L 392 " --> pdb=" O ARG L 388 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA L 393 " --> pdb=" O GLY L 389 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 416 No H-bonds generated for 'chain 'L' and resid 414 through 416' Processing helix chain 'L' and resid 441 through 456 removed outlier: 4.481A pdb=" N LEU L 444 " --> pdb=" O SER L 441 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS L 451 " --> pdb=" O SER L 448 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR L 454 " --> pdb=" O LYS L 451 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER L 455 " --> pdb=" O LYS L 452 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 477 Processing helix chain 'L' and resid 507 through 521 Processing helix chain 'M' and resid 349 through 370 Processing helix chain 'M' and resid 376 through 389 Processing helix chain 'M' and resid 391 through 395 Processing helix chain 'M' and resid 414 through 416 No H-bonds generated for 'chain 'M' and resid 414 through 416' Processing helix chain 'M' and resid 443 through 456 removed outlier: 4.009A pdb=" N LYS M 452 " --> pdb=" O SER M 448 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER M 455 " --> pdb=" O LYS M 451 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLN M 456 " --> pdb=" O LYS M 452 " (cutoff:3.500A) Processing helix chain 'M' and resid 460 through 477 Processing helix chain 'M' and resid 507 through 521 Processing helix chain 'N' and resid 349 through 370 Processing helix chain 'N' and resid 376 through 395 removed outlier: 3.712A pdb=" N LEU N 391 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ALA N 392 " --> pdb=" O ARG N 388 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ALA N 393 " --> pdb=" O GLY N 389 " (cutoff:3.500A) Processing helix chain 'N' and resid 414 through 416 No H-bonds generated for 'chain 'N' and resid 414 through 416' Processing helix chain 'N' and resid 443 through 456 removed outlier: 4.094A pdb=" N LYS N 452 " --> pdb=" O SER N 448 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER N 455 " --> pdb=" O LYS N 451 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLN N 456 " --> pdb=" O LYS N 452 " (cutoff:3.500A) Processing helix chain 'N' and resid 460 through 477 Processing helix chain 'N' and resid 507 through 521 Processing helix chain 'O' and resid 9 through 25 removed outlier: 3.643A pdb=" N ARG O 14 " --> pdb=" O GLU O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 88 Processing helix chain 'O' and resid 91 through 93 No H-bonds generated for 'chain 'O' and resid 91 through 93' Processing helix chain 'O' and resid 96 through 113 Processing helix chain 'O' and resid 161 through 170 Processing helix chain 'O' and resid 177 through 189 Processing helix chain 'O' and resid 227 through 233 Processing helix chain 'P' and resid 349 through 370 Processing helix chain 'P' and resid 376 through 396 removed outlier: 3.587A pdb=" N ASN P 390 " --> pdb=" O MET P 386 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU P 391 " --> pdb=" O VAL P 387 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA P 392 " --> pdb=" O ARG P 388 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA P 393 " --> pdb=" O GLY P 389 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN P 396 " --> pdb=" O ALA P 392 " (cutoff:3.500A) Processing helix chain 'P' and resid 414 through 416 No H-bonds generated for 'chain 'P' and resid 414 through 416' Processing helix chain 'P' and resid 441 through 456 removed outlier: 4.412A pdb=" N LEU P 444 " --> pdb=" O SER P 441 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET P 450 " --> pdb=" O LYS P 447 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS P 451 " --> pdb=" O SER P 448 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR P 454 " --> pdb=" O LYS P 451 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER P 455 " --> pdb=" O LYS P 452 " (cutoff:3.500A) Processing helix chain 'P' and resid 460 through 477 Processing helix chain 'P' and resid 507 through 522 Processing helix chain 'Q' and resid 9 through 25 Processing helix chain 'Q' and resid 68 through 88 Processing helix chain 'Q' and resid 91 through 93 No H-bonds generated for 'chain 'Q' and resid 91 through 93' Processing helix chain 'Q' and resid 96 through 113 Processing helix chain 'Q' and resid 161 through 170 Processing helix chain 'Q' and resid 177 through 189 Processing helix chain 'Q' and resid 205 through 207 No H-bonds generated for 'chain 'Q' and resid 205 through 207' Processing helix chain 'Q' and resid 227 through 233 Processing helix chain 'R' and resid 349 through 370 Processing helix chain 'R' and resid 376 through 395 removed outlier: 3.617A pdb=" N LEU R 391 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ALA R 392 " --> pdb=" O ARG R 388 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ALA R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) Processing helix chain 'R' and resid 414 through 416 No H-bonds generated for 'chain 'R' and resid 414 through 416' Processing helix chain 'R' and resid 441 through 456 removed outlier: 4.486A pdb=" N LEU R 444 " --> pdb=" O SER R 441 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS R 451 " --> pdb=" O SER R 448 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TYR R 454 " --> pdb=" O LYS R 451 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N SER R 455 " --> pdb=" O LYS R 452 " (cutoff:3.500A) Processing helix chain 'R' and resid 460 through 477 Processing helix chain 'R' and resid 507 through 521 Processing helix chain 'S' and resid 349 through 370 Processing helix chain 'S' and resid 376 through 389 Processing helix chain 'S' and resid 391 through 395 Processing helix chain 'S' and resid 414 through 416 No H-bonds generated for 'chain 'S' and resid 414 through 416' Processing helix chain 'S' and resid 443 through 456 removed outlier: 4.024A pdb=" N LYS S 452 " --> pdb=" O SER S 448 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER S 455 " --> pdb=" O LYS S 451 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLN S 456 " --> pdb=" O LYS S 452 " (cutoff:3.500A) Processing helix chain 'S' and resid 460 through 477 Processing helix chain 'S' and resid 507 through 521 Processing helix chain 'T' and resid 9 through 25 Processing helix chain 'T' and resid 68 through 88 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing helix chain 'T' and resid 96 through 113 Processing helix chain 'T' and resid 161 through 170 Processing helix chain 'T' and resid 177 through 189 Processing helix chain 'T' and resid 205 through 207 No H-bonds generated for 'chain 'T' and resid 205 through 207' Processing helix chain 'T' and resid 227 through 232 Processing helix chain 'U' and resid 349 through 370 Processing helix chain 'U' and resid 376 through 395 removed outlier: 3.512A pdb=" N LEU U 391 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA U 392 " --> pdb=" O ARG U 388 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ALA U 393 " --> pdb=" O GLY U 389 " (cutoff:3.500A) Processing helix chain 'U' and resid 414 through 416 No H-bonds generated for 'chain 'U' and resid 414 through 416' Processing helix chain 'U' and resid 441 through 456 removed outlier: 4.565A pdb=" N LEU U 444 " --> pdb=" O SER U 441 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS U 451 " --> pdb=" O SER U 448 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR U 454 " --> pdb=" O LYS U 451 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER U 455 " --> pdb=" O LYS U 452 " (cutoff:3.500A) Processing helix chain 'U' and resid 460 through 477 Processing helix chain 'U' and resid 507 through 527 Processing helix chain 'V' and resid 349 through 370 Processing helix chain 'V' and resid 376 through 395 removed outlier: 3.769A pdb=" N LEU V 391 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ALA V 392 " --> pdb=" O ARG V 388 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ALA V 393 " --> pdb=" O GLY V 389 " (cutoff:3.500A) Processing helix chain 'V' and resid 414 through 416 No H-bonds generated for 'chain 'V' and resid 414 through 416' Processing helix chain 'V' and resid 443 through 456 removed outlier: 4.082A pdb=" N LYS V 452 " --> pdb=" O SER V 448 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER V 455 " --> pdb=" O LYS V 451 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLN V 456 " --> pdb=" O LYS V 452 " (cutoff:3.500A) Processing helix chain 'V' and resid 460 through 477 Processing helix chain 'V' and resid 507 through 522 Processing helix chain 'W' and resid 349 through 370 Processing helix chain 'W' and resid 376 through 395 removed outlier: 3.522A pdb=" N ASN W 390 " --> pdb=" O MET W 386 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU W 391 " --> pdb=" O VAL W 387 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA W 392 " --> pdb=" O ARG W 388 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA W 393 " --> pdb=" O GLY W 389 " (cutoff:3.500A) Processing helix chain 'W' and resid 414 through 416 No H-bonds generated for 'chain 'W' and resid 414 through 416' Processing helix chain 'W' and resid 443 through 456 removed outlier: 4.097A pdb=" N LYS W 452 " --> pdb=" O SER W 448 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N SER W 455 " --> pdb=" O LYS W 451 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLN W 456 " --> pdb=" O LYS W 452 " (cutoff:3.500A) Processing helix chain 'W' and resid 460 through 477 Processing helix chain 'W' and resid 507 through 527 Processing helix chain 'X' and resid 9 through 25 removed outlier: 3.544A pdb=" N ARG X 14 " --> pdb=" O GLU X 10 " (cutoff:3.500A) Processing helix chain 'X' and resid 68 through 88 Processing helix chain 'X' and resid 91 through 93 No H-bonds generated for 'chain 'X' and resid 91 through 93' Processing helix chain 'X' and resid 96 through 113 Processing helix chain 'X' and resid 160 through 170 Processing helix chain 'X' and resid 177 through 189 Processing helix chain 'X' and resid 227 through 232 Processing helix chain 'Y' and resid 349 through 370 Processing helix chain 'Y' and resid 376 through 395 removed outlier: 3.611A pdb=" N LEU Y 391 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ALA Y 392 " --> pdb=" O ARG Y 388 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ALA Y 393 " --> pdb=" O GLY Y 389 " (cutoff:3.500A) Processing helix chain 'Y' and resid 414 through 416 No H-bonds generated for 'chain 'Y' and resid 414 through 416' Processing helix chain 'Y' and resid 441 through 456 removed outlier: 4.548A pdb=" N LEU Y 444 " --> pdb=" O SER Y 441 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET Y 450 " --> pdb=" O LYS Y 447 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS Y 451 " --> pdb=" O SER Y 448 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR Y 454 " --> pdb=" O LYS Y 451 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER Y 455 " --> pdb=" O LYS Y 452 " (cutoff:3.500A) Processing helix chain 'Y' and resid 460 through 477 Processing helix chain 'Y' and resid 507 through 522 Processing helix chain 'Z' and resid 9 through 25 removed outlier: 4.151A pdb=" N MET Z 13 " --> pdb=" O PRO Z 9 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG Z 14 " --> pdb=" O GLU Z 10 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 88 Processing helix chain 'Z' and resid 91 through 93 No H-bonds generated for 'chain 'Z' and resid 91 through 93' Processing helix chain 'Z' and resid 96 through 113 Processing helix chain 'Z' and resid 161 through 170 Processing helix chain 'Z' and resid 177 through 189 Processing helix chain 'Z' and resid 205 through 207 No H-bonds generated for 'chain 'Z' and resid 205 through 207' Processing helix chain 'Z' and resid 227 through 232 Processing helix chain 'a' and resid 349 through 370 Processing helix chain 'a' and resid 376 through 395 removed outlier: 3.634A pdb=" N ASN a 390 " --> pdb=" O MET a 386 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU a 391 " --> pdb=" O VAL a 387 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ALA a 392 " --> pdb=" O ARG a 388 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ALA a 393 " --> pdb=" O GLY a 389 " (cutoff:3.500A) Processing helix chain 'a' and resid 414 through 416 No H-bonds generated for 'chain 'a' and resid 414 through 416' Processing helix chain 'a' and resid 441 through 456 removed outlier: 4.515A pdb=" N LEU a 444 " --> pdb=" O SER a 441 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET a 450 " --> pdb=" O LYS a 447 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS a 451 " --> pdb=" O SER a 448 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR a 454 " --> pdb=" O LYS a 451 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N SER a 455 " --> pdb=" O LYS a 452 " (cutoff:3.500A) Processing helix chain 'a' and resid 460 through 477 Processing helix chain 'a' and resid 507 through 522 Processing helix chain 'b' and resid 349 through 370 Processing helix chain 'b' and resid 376 through 395 removed outlier: 3.799A pdb=" N LEU b 391 " --> pdb=" O VAL b 387 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ALA b 392 " --> pdb=" O ARG b 388 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ALA b 393 " --> pdb=" O GLY b 389 " (cutoff:3.500A) Processing helix chain 'b' and resid 414 through 416 No H-bonds generated for 'chain 'b' and resid 414 through 416' Processing helix chain 'b' and resid 443 through 456 removed outlier: 4.078A pdb=" N LYS b 452 " --> pdb=" O SER b 448 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N SER b 455 " --> pdb=" O LYS b 451 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLN b 456 " --> pdb=" O LYS b 452 " (cutoff:3.500A) Processing helix chain 'b' and resid 460 through 477 Processing helix chain 'b' and resid 507 through 521 Processing helix chain 'd' and resid 9 through 25 removed outlier: 3.662A pdb=" N ARG d 16 " --> pdb=" O ALA d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 88 Processing helix chain 'd' and resid 91 through 93 No H-bonds generated for 'chain 'd' and resid 91 through 93' Processing helix chain 'd' and resid 96 through 113 Processing helix chain 'd' and resid 160 through 170 Processing helix chain 'd' and resid 177 through 189 Processing helix chain 'd' and resid 227 through 233 Processing helix chain 'f' and resid 9 through 25 Processing helix chain 'f' and resid 68 through 88 Processing helix chain 'f' and resid 91 through 93 No H-bonds generated for 'chain 'f' and resid 91 through 93' Processing helix chain 'f' and resid 96 through 113 removed outlier: 3.687A pdb=" N PHE f 111 " --> pdb=" O LEU f 107 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR f 112 " --> pdb=" O GLY f 108 " (cutoff:3.500A) Processing helix chain 'f' and resid 160 through 170 Processing helix chain 'f' and resid 177 through 189 Processing helix chain 'f' and resid 227 through 233 Processing sheet with id= A, first strand: chain '0' and resid 153 through 156 Processing sheet with id= B, first strand: chain '0' and resid 147 through 150 removed outlier: 3.740A pdb=" N LEU 0 138 " --> pdb=" O GLU 0 150 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE 0 62 " --> pdb=" O GLU 0 55 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU 0 55 " --> pdb=" O PHE 0 62 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA 0 64 " --> pdb=" O ILE 0 53 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE 0 53 " --> pdb=" O ALA 0 64 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 153 through 156 Processing sheet with id= D, first strand: chain '2' and resid 147 through 150 removed outlier: 3.727A pdb=" N LEU 2 138 " --> pdb=" O GLU 2 150 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE 2 62 " --> pdb=" O GLU 2 55 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLU 2 55 " --> pdb=" O PHE 2 62 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ALA 2 64 " --> pdb=" O ILE 2 53 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE 2 53 " --> pdb=" O ALA 2 64 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '4' and resid 153 through 156 Processing sheet with id= F, first strand: chain '4' and resid 147 through 150 removed outlier: 3.714A pdb=" N LEU 4 138 " --> pdb=" O GLU 4 150 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE 4 62 " --> pdb=" O GLU 4 55 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU 4 55 " --> pdb=" O PHE 4 62 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ALA 4 64 " --> pdb=" O ILE 4 53 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE 4 53 " --> pdb=" O ALA 4 64 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '6' and resid 153 through 156 Processing sheet with id= H, first strand: chain '6' and resid 147 through 150 removed outlier: 3.676A pdb=" N LEU 6 138 " --> pdb=" O GLU 6 150 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE 6 62 " --> pdb=" O GLU 6 55 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU 6 55 " --> pdb=" O PHE 6 62 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA 6 64 " --> pdb=" O ILE 6 53 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE 6 53 " --> pdb=" O ALA 6 64 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '8' and resid 153 through 156 Processing sheet with id= J, first strand: chain '8' and resid 147 through 150 removed outlier: 3.665A pdb=" N LEU 8 138 " --> pdb=" O GLU 8 150 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE 8 62 " --> pdb=" O GLU 8 55 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLU 8 55 " --> pdb=" O PHE 8 62 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ALA 8 64 " --> pdb=" O ILE 8 53 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE 8 53 " --> pdb=" O ALA 8 64 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 140 through 142 removed outlier: 6.672A pdb=" N ASP A 114 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N THR A 107 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR A 112 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 184 through 187 removed outlier: 6.113A pdb=" N VAL A 177 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU A 164 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU A 231 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASP A 223 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ALA A 229 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 433 through 437 removed outlier: 8.574A pdb=" N VAL A 289 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 411 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU A 291 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLY A 413 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N GLY A 293 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N SER A 415 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL A 366 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE A 412 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL A 368 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ALA A 414 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE A 370 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 584 through 586 removed outlier: 6.581A pdb=" N MET A 508 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLU A 497 " --> pdb=" O GLU A 506 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU A 506 " --> pdb=" O GLU A 497 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 140 through 142 removed outlier: 6.641A pdb=" N ASP B 114 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N THR B 107 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N THR B 112 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 183 through 187 removed outlier: 6.519A pdb=" N VAL B 177 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU B 164 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU B 231 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASP B 223 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA B 229 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 433 through 437 removed outlier: 7.659A pdb=" N VAL B 289 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL B 411 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU B 291 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLY B 413 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N GLY B 293 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER B 415 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL B 366 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE B 412 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL B 368 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N ALA B 414 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N PHE B 370 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 505 through 509 Processing sheet with id= S, first strand: chain 'C' and resid 140 through 142 removed outlier: 6.679A pdb=" N ASP C 114 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N THR C 107 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR C 112 " --> pdb=" O THR C 107 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 183 through 187 removed outlier: 3.839A pdb=" N GLU C 166 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL C 177 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU C 164 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER C 219 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU C 231 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ASP C 223 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ALA C 229 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 433 through 437 removed outlier: 8.299A pdb=" N VAL C 289 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL C 411 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU C 291 " --> pdb=" O VAL C 411 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY C 413 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N GLY C 293 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER C 415 " --> pdb=" O GLY C 293 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL C 366 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE C 412 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL C 368 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA C 414 " --> pdb=" O VAL C 368 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE C 370 " --> pdb=" O ALA C 414 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR C 328 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N PHE C 369 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU C 330 " --> pdb=" O PHE C 369 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 507 through 509 removed outlier: 3.989A pdb=" N TYR C 583 " --> pdb=" O THR C 499 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 140 through 142 removed outlier: 6.560A pdb=" N ASP D 114 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N THR D 107 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N THR D 112 " --> pdb=" O THR D 107 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 183 through 187 removed outlier: 6.187A pdb=" N VAL D 177 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU D 164 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER D 219 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU D 231 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ASP D 223 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ALA D 229 " --> pdb=" O ASP D 223 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 433 through 436 removed outlier: 6.942A pdb=" N VAL D 411 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU D 291 " --> pdb=" O VAL D 411 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY D 413 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TYR D 328 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE D 369 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU D 330 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP D 371 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE D 332 " --> pdb=" O ASP D 371 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 496 through 499 Processing sheet with id= AA, first strand: chain 'E' and resid 151 through 153 removed outlier: 3.903A pdb=" N GLU E 151 " --> pdb=" O ARG E 142 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR E 140 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASP E 114 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N THR E 107 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR E 112 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 219 through 222 removed outlier: 3.607A pdb=" N GLU E 160 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU E 175 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ILE E 167 " --> pdb=" O ARG E 173 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ARG E 173 " --> pdb=" O ILE E 167 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 433 through 437 removed outlier: 3.601A pdb=" N VAL E 433 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL E 289 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL E 411 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU E 291 " --> pdb=" O VAL E 411 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY E 413 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N GLY E 293 " --> pdb=" O GLY E 413 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER E 415 " --> pdb=" O GLY E 293 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL E 366 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE E 412 " --> pdb=" O VAL E 366 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL E 368 " --> pdb=" O ILE E 412 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ALA E 414 " --> pdb=" O VAL E 368 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE E 370 " --> pdb=" O ALA E 414 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 494 through 498 removed outlier: 6.790A pdb=" N MET E 508 " --> pdb=" O PHE E 495 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU E 497 " --> pdb=" O GLU E 506 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLU E 506 " --> pdb=" O GLU E 497 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 140 through 142 removed outlier: 6.908A pdb=" N ASP F 114 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N THR F 107 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR F 112 " --> pdb=" O THR F 107 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 160 through 163 removed outlier: 4.368A pdb=" N SER F 219 " --> pdb=" O ILE F 233 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU F 231 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASP F 223 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA F 229 " --> pdb=" O ASP F 223 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 184 through 187 Processing sheet with id= AH, first strand: chain 'F' and resid 433 through 437 removed outlier: 6.234A pdb=" N VAL F 366 " --> pdb=" O ILE F 410 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE F 412 " --> pdb=" O VAL F 366 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL F 368 " --> pdb=" O ILE F 412 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ALA F 414 " --> pdb=" O VAL F 368 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE F 370 " --> pdb=" O ALA F 414 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU F 330 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ASP F 371 " --> pdb=" O LEU F 330 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE F 332 " --> pdb=" O ASP F 371 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 584 through 586 removed outlier: 6.774A pdb=" N MET F 508 " --> pdb=" O PHE F 495 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU F 497 " --> pdb=" O GLU F 506 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLU F 506 " --> pdb=" O GLU F 497 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 436 through 440 Processing sheet with id= AK, first strand: chain 'H' and resid 341 through 347 removed outlier: 3.675A pdb=" N PHE H 423 " --> pdb=" O PRO H 402 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 320 through 322 removed outlier: 6.496A pdb=" N GLN H 322 " --> pdb=" O ILE H 326 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE H 326 " --> pdb=" O GLN H 322 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'I' and resid 153 through 156 Processing sheet with id= AN, first strand: chain 'I' and resid 147 through 150 removed outlier: 3.876A pdb=" N LEU I 138 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N PHE I 62 " --> pdb=" O GLU I 55 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLU I 55 " --> pdb=" O PHE I 62 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ALA I 64 " --> pdb=" O ILE I 53 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE I 53 " --> pdb=" O ALA I 64 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'J' and resid 436 through 440 Processing sheet with id= AP, first strand: chain 'J' and resid 429 through 431 removed outlier: 3.750A pdb=" N PHE J 423 " --> pdb=" O PRO J 402 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP J 338 " --> pdb=" O THR J 341 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR J 343 " --> pdb=" O ILE J 336 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ILE J 336 " --> pdb=" O THR J 343 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE J 345 " --> pdb=" O VAL J 334 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL J 334 " --> pdb=" O ILE J 345 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'J' and resid 320 through 322 removed outlier: 6.296A pdb=" N GLN J 322 " --> pdb=" O ILE J 326 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE J 326 " --> pdb=" O GLN J 322 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'K' and resid 153 through 156 Processing sheet with id= AS, first strand: chain 'K' and resid 147 through 150 removed outlier: 3.940A pdb=" N LEU K 138 " --> pdb=" O GLU K 150 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N PHE K 62 " --> pdb=" O GLU K 55 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLU K 55 " --> pdb=" O PHE K 62 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA K 64 " --> pdb=" O ILE K 53 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ILE K 53 " --> pdb=" O ALA K 64 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'L' and resid 436 through 440 Processing sheet with id= AU, first strand: chain 'L' and resid 429 through 431 removed outlier: 3.714A pdb=" N PHE L 423 " --> pdb=" O PRO L 402 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR L 343 " --> pdb=" O ILE L 336 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ILE L 336 " --> pdb=" O THR L 343 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE L 345 " --> pdb=" O VAL L 334 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL L 334 " --> pdb=" O ILE L 345 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'L' and resid 320 through 322 removed outlier: 6.348A pdb=" N GLN L 322 " --> pdb=" O ILE L 326 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE L 326 " --> pdb=" O GLN L 322 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'M' and resid 436 through 440 Processing sheet with id= AX, first strand: chain 'M' and resid 341 through 347 removed outlier: 3.718A pdb=" N PHE M 423 " --> pdb=" O PRO M 402 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'M' and resid 320 through 322 removed outlier: 6.492A pdb=" N GLN M 322 " --> pdb=" O ILE M 326 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE M 326 " --> pdb=" O GLN M 322 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'N' and resid 436 through 439 Processing sheet with id= BA, first strand: chain 'N' and resid 429 through 431 removed outlier: 3.722A pdb=" N PHE N 423 " --> pdb=" O PRO N 402 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR N 343 " --> pdb=" O ILE N 336 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE N 336 " --> pdb=" O THR N 343 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE N 345 " --> pdb=" O VAL N 334 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL N 334 " --> pdb=" O ILE N 345 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'N' and resid 320 through 322 removed outlier: 6.553A pdb=" N GLN N 322 " --> pdb=" O ILE N 326 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE N 326 " --> pdb=" O GLN N 322 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'O' and resid 153 through 156 Processing sheet with id= BD, first strand: chain 'O' and resid 147 through 150 removed outlier: 3.950A pdb=" N LEU O 138 " --> pdb=" O GLU O 150 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE O 62 " --> pdb=" O GLU O 55 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU O 55 " --> pdb=" O PHE O 62 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ALA O 64 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE O 53 " --> pdb=" O ALA O 64 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'P' and resid 436 through 440 Processing sheet with id= BF, first strand: chain 'P' and resid 429 through 431 removed outlier: 3.719A pdb=" N PHE P 423 " --> pdb=" O PRO P 402 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR P 343 " --> pdb=" O ILE P 336 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE P 336 " --> pdb=" O THR P 343 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE P 345 " --> pdb=" O VAL P 334 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL P 334 " --> pdb=" O ILE P 345 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'P' and resid 320 through 322 removed outlier: 6.351A pdb=" N GLN P 322 " --> pdb=" O ILE P 326 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE P 326 " --> pdb=" O GLN P 322 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'Q' and resid 153 through 156 Processing sheet with id= BI, first strand: chain 'Q' and resid 147 through 150 removed outlier: 3.955A pdb=" N LEU Q 138 " --> pdb=" O GLU Q 150 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE Q 62 " --> pdb=" O GLU Q 55 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLU Q 55 " --> pdb=" O PHE Q 62 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA Q 64 " --> pdb=" O ILE Q 53 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE Q 53 " --> pdb=" O ALA Q 64 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'R' and resid 436 through 440 Processing sheet with id= BK, first strand: chain 'R' and resid 429 through 431 removed outlier: 3.746A pdb=" N PHE R 423 " --> pdb=" O PRO R 402 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR R 343 " --> pdb=" O ILE R 336 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE R 336 " --> pdb=" O THR R 343 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE R 345 " --> pdb=" O VAL R 334 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL R 334 " --> pdb=" O ILE R 345 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'R' and resid 320 through 322 removed outlier: 6.311A pdb=" N GLN R 322 " --> pdb=" O ILE R 326 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE R 326 " --> pdb=" O GLN R 322 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'S' and resid 436 through 440 Processing sheet with id= BN, first strand: chain 'S' and resid 429 through 431 removed outlier: 3.666A pdb=" N PHE S 423 " --> pdb=" O PRO S 402 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR S 343 " --> pdb=" O ILE S 336 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE S 336 " --> pdb=" O THR S 343 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE S 345 " --> pdb=" O VAL S 334 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL S 334 " --> pdb=" O ILE S 345 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'S' and resid 320 through 322 removed outlier: 6.475A pdb=" N GLN S 322 " --> pdb=" O ILE S 326 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE S 326 " --> pdb=" O GLN S 322 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'T' and resid 153 through 156 Processing sheet with id= BQ, first strand: chain 'T' and resid 147 through 150 removed outlier: 3.956A pdb=" N LEU T 138 " --> pdb=" O GLU T 150 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE T 62 " --> pdb=" O GLU T 55 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLU T 55 " --> pdb=" O PHE T 62 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA T 64 " --> pdb=" O ILE T 53 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE T 53 " --> pdb=" O ALA T 64 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'U' and resid 436 through 440 Processing sheet with id= BS, first strand: chain 'U' and resid 429 through 432 removed outlier: 4.750A pdb=" N ILE U 420 " --> pdb=" O GLU U 432 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE U 423 " --> pdb=" O PRO U 402 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR U 343 " --> pdb=" O ILE U 336 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE U 336 " --> pdb=" O THR U 343 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE U 345 " --> pdb=" O VAL U 334 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL U 334 " --> pdb=" O ILE U 345 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'U' and resid 320 through 322 removed outlier: 6.288A pdb=" N GLN U 322 " --> pdb=" O ILE U 326 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE U 326 " --> pdb=" O GLN U 322 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'V' and resid 436 through 439 Processing sheet with id= BV, first strand: chain 'V' and resid 429 through 431 removed outlier: 3.672A pdb=" N PHE V 423 " --> pdb=" O PRO V 402 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR V 343 " --> pdb=" O ILE V 336 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE V 336 " --> pdb=" O THR V 343 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE V 345 " --> pdb=" O VAL V 334 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL V 334 " --> pdb=" O ILE V 345 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'V' and resid 320 through 322 removed outlier: 6.462A pdb=" N GLN V 322 " --> pdb=" O ILE V 326 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE V 326 " --> pdb=" O GLN V 322 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'W' and resid 436 through 440 Processing sheet with id= BY, first strand: chain 'W' and resid 341 through 347 removed outlier: 3.677A pdb=" N PHE W 423 " --> pdb=" O PRO W 402 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'W' and resid 320 through 322 removed outlier: 6.496A pdb=" N GLN W 322 " --> pdb=" O ILE W 326 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE W 326 " --> pdb=" O GLN W 322 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'X' and resid 153 through 156 Processing sheet with id= CB, first strand: chain 'X' and resid 147 through 150 removed outlier: 3.953A pdb=" N LEU X 138 " --> pdb=" O GLU X 150 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE X 62 " --> pdb=" O GLU X 55 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLU X 55 " --> pdb=" O PHE X 62 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA X 64 " --> pdb=" O ILE X 53 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ILE X 53 " --> pdb=" O ALA X 64 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'Y' and resid 436 through 440 Processing sheet with id= CD, first strand: chain 'Y' and resid 429 through 431 removed outlier: 3.737A pdb=" N PHE Y 423 " --> pdb=" O PRO Y 402 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP Y 338 " --> pdb=" O THR Y 341 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR Y 343 " --> pdb=" O ILE Y 336 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE Y 336 " --> pdb=" O THR Y 343 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE Y 345 " --> pdb=" O VAL Y 334 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL Y 334 " --> pdb=" O ILE Y 345 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'Y' and resid 320 through 322 removed outlier: 6.303A pdb=" N GLN Y 322 " --> pdb=" O ILE Y 326 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE Y 326 " --> pdb=" O GLN Y 322 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'Z' and resid 153 through 156 Processing sheet with id= CG, first strand: chain 'Z' and resid 147 through 150 removed outlier: 3.930A pdb=" N LEU Z 138 " --> pdb=" O GLU Z 150 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N PHE Z 62 " --> pdb=" O GLU Z 55 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLU Z 55 " --> pdb=" O PHE Z 62 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ALA Z 64 " --> pdb=" O ILE Z 53 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ILE Z 53 " --> pdb=" O ALA Z 64 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'a' and resid 436 through 440 Processing sheet with id= CI, first strand: chain 'a' and resid 429 through 431 removed outlier: 3.732A pdb=" N PHE a 423 " --> pdb=" O PRO a 402 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP a 338 " --> pdb=" O THR a 341 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR a 343 " --> pdb=" O ILE a 336 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE a 336 " --> pdb=" O THR a 343 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE a 345 " --> pdb=" O VAL a 334 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL a 334 " --> pdb=" O ILE a 345 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'a' and resid 320 through 322 removed outlier: 6.396A pdb=" N GLN a 322 " --> pdb=" O ILE a 326 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE a 326 " --> pdb=" O GLN a 322 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'b' and resid 436 through 440 Processing sheet with id= CL, first strand: chain 'b' and resid 341 through 347 removed outlier: 3.712A pdb=" N PHE b 423 " --> pdb=" O PRO b 402 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'b' and resid 320 through 322 removed outlier: 6.509A pdb=" N GLN b 322 " --> pdb=" O ILE b 326 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE b 326 " --> pdb=" O GLN b 322 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'd' and resid 153 through 156 Processing sheet with id= CO, first strand: chain 'd' and resid 147 through 150 removed outlier: 3.707A pdb=" N LEU d 138 " --> pdb=" O GLU d 150 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE d 62 " --> pdb=" O GLU d 55 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLU d 55 " --> pdb=" O PHE d 62 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ALA d 64 " --> pdb=" O ILE d 53 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE d 53 " --> pdb=" O ALA d 64 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'f' and resid 153 through 156 Processing sheet with id= CQ, first strand: chain 'f' and resid 147 through 150 removed outlier: 3.740A pdb=" N LEU f 138 " --> pdb=" O GLU f 150 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N PHE f 62 " --> pdb=" O GLU f 55 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU f 55 " --> pdb=" O PHE f 62 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ALA f 64 " --> pdb=" O ILE f 53 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE f 53 " --> pdb=" O ALA f 64 " (cutoff:3.500A) 3522 hydrogen bonds defined for protein. 9897 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: 28.42 Time building geometry restraints manager: 22.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 19764 1.33 - 1.46: 13417 1.46 - 1.58: 36418 1.58 - 1.70: 32 1.70 - 1.83: 326 Bond restraints: 69957 Sorted by residual: bond pdb=" C4 ATP E 701 " pdb=" C5 ATP E 701 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.88e+01 bond pdb=" C4 ATP C 701 " pdb=" C5 ATP C 701 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.72e+01 bond pdb=" CA TYR Z 89 " pdb=" C TYR Z 89 " ideal model delta sigma weight residual 1.517 1.466 0.051 6.30e-03 2.52e+04 6.68e+01 bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.66e+01 bond pdb=" C4 ATP B 701 " pdb=" C5 ATP B 701 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.59e+01 ... (remaining 69952 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.47: 1354 105.47 - 113.08: 37579 113.08 - 120.70: 32115 120.70 - 128.31: 23383 128.31 - 135.93: 263 Bond angle restraints: 94694 Sorted by residual: angle pdb=" PB ATP D 701 " pdb=" O3B ATP D 701 " pdb=" PG ATP D 701 " ideal model delta sigma weight residual 139.87 118.62 21.25 1.00e+00 1.00e+00 4.51e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 118.03 18.80 1.00e+00 1.00e+00 3.53e+02 angle pdb=" PA ATP B 701 " pdb=" O3A ATP B 701 " pdb=" PB ATP B 701 " ideal model delta sigma weight residual 136.83 118.22 18.61 1.00e+00 1.00e+00 3.46e+02 angle pdb=" PA ATP C 701 " pdb=" O3A ATP C 701 " pdb=" PB ATP C 701 " ideal model delta sigma weight residual 136.83 118.38 18.45 1.00e+00 1.00e+00 3.40e+02 angle pdb=" PA ATP E 701 " pdb=" O3A ATP E 701 " pdb=" PB ATP E 701 " ideal model delta sigma weight residual 136.83 118.77 18.06 1.00e+00 1.00e+00 3.26e+02 ... (remaining 94689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.26: 39011 18.26 - 36.52: 2589 36.52 - 54.78: 603 54.78 - 73.04: 156 73.04 - 91.30: 98 Dihedral angle restraints: 42457 sinusoidal: 16692 harmonic: 25765 Sorted by residual: dihedral pdb=" CA ARG D 439 " pdb=" C ARG D 439 " pdb=" N PRO D 440 " pdb=" CA PRO D 440 " ideal model delta harmonic sigma weight residual -180.00 -153.38 -26.62 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA VAL D 242 " pdb=" C VAL D 242 " pdb=" N LEU D 243 " pdb=" CA LEU D 243 " ideal model delta harmonic sigma weight residual 180.00 156.85 23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA LYS D 340 " pdb=" C LYS D 340 " pdb=" N PHE D 341 " pdb=" CA PHE D 341 " ideal model delta harmonic sigma weight residual 180.00 -158.00 -22.00 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 42454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 9064 0.069 - 0.138: 1557 0.138 - 0.208: 119 0.208 - 0.277: 17 0.277 - 0.346: 2 Chirality restraints: 10759 Sorted by residual: chirality pdb=" CA ASP B 504 " pdb=" N ASP B 504 " pdb=" C ASP B 504 " pdb=" CB ASP B 504 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA ARG 0 26 " pdb=" N ARG 0 26 " pdb=" C ARG 0 26 " pdb=" CB ARG 0 26 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA TYR 8 103 " pdb=" N TYR 8 103 " pdb=" C TYR 8 103 " pdb=" CB TYR 8 103 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 10756 not shown) Planarity restraints: 12440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 566 " 0.053 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO E 567 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO E 567 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 567 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU W 401 " 0.050 5.00e-02 4.00e+02 7.58e-02 9.19e+00 pdb=" N PRO W 402 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO W 402 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO W 402 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU M 401 " -0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO M 402 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO M 402 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO M 402 " -0.036 5.00e-02 4.00e+02 ... (remaining 12437 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 615 2.63 - 3.20: 62970 3.20 - 3.77: 105825 3.77 - 4.33: 150648 4.33 - 4.90: 241953 Nonbonded interactions: 562011 Sorted by model distance: nonbonded pdb=" O1B ATP A 701 " pdb="MG MG A 702 " model vdw 2.068 2.170 nonbonded pdb=" O1B ATP E 701 " pdb="MG MG E 702 " model vdw 2.076 2.170 nonbonded pdb=" O1B ATP C 701 " pdb="MG MG C 702 " model vdw 2.077 2.170 nonbonded pdb=" O1B ATP B 701 " pdb="MG MG B 702 " model vdw 2.079 2.170 nonbonded pdb=" O1B ATP D 701 " pdb="MG MG D 702 " model vdw 2.097 2.170 ... (remaining 562006 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 '0' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '2' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '4' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '6' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '8' and (resid 8 through 190 or resid 204 through 234)) selection = chain 'I' selection = (chain 'K' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'O' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'Q' and (resid 8 through 190 or resid 204 through 234)) selection = chain 'T' selection = chain 'X' selection = (chain 'Z' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'd' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'f' and (resid 8 through 190 or resid 204 through 234)) } ncs_group { reference = (chain 'A' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587 or resid 605 through 609 or resid 701 through 702)) selection = (chain 'B' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587 or resid 605 through 609 or resid 701 through 702)) selection = (chain 'C' and (resid 97 through 377 or resid 390 through 587 or resid 605 throu \ gh 609 or resid 701 through 702)) selection = chain 'D' selection = (chain 'E' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587 or resid 605 through 609 or resid 701 through 702)) selection = (chain 'F' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587 or resid 605 through 609 or resid 701 through 702)) } ncs_group { reference = chain 'H' selection = (chain 'J' and resid 301 through 522) selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = (chain 'P' and resid 301 through 522) selection = chain 'R' selection = chain 'S' selection = (chain 'U' and resid 301 through 522) selection = (chain 'V' and resid 301 through 522) selection = (chain 'W' and resid 301 through 522) selection = (chain 'Y' and resid 301 through 522) selection = (chain 'a' and resid 301 through 522) selection = (chain 'b' and resid 301 through 522) } 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 11.160 Check model and map are aligned: 0.780 Set scattering table: 0.500 Process input model: 145.360 Find NCS groups from input model: 4.420 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 69957 Z= 0.414 Angle : 0.929 21.248 94694 Z= 0.595 Chirality : 0.051 0.346 10759 Planarity : 0.005 0.081 12440 Dihedral : 14.198 91.299 25991 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.92 % Rotamer: Outliers : 3.29 % Allowed : 4.67 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.08), residues: 8881 helix: -0.60 (0.08), residues: 3515 sheet: -0.44 (0.11), residues: 2027 loop : -0.74 (0.11), residues: 3339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 187 HIS 0.007 0.001 HIS V 365 PHE 0.034 0.003 PHE K 71 TYR 0.022 0.002 TYR 6 130 ARG 0.008 0.001 ARG d 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1850 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1618 time to evaluate : 6.028 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: 0 29 SER cc_start: 0.7095 (m) cc_final: 0.6676 (p) REVERT: 0 44 GLU cc_start: 0.5889 (tt0) cc_final: 0.5619 (tm-30) REVERT: 0 54 SER cc_start: 0.7318 (t) cc_final: 0.6921 (m) REVERT: 0 101 ASN cc_start: 0.6627 (t0) cc_final: 0.6398 (m-40) REVERT: 0 233 LEU cc_start: 0.7090 (mp) cc_final: 0.6773 (mm) REVERT: 2 28 LYS cc_start: 0.6990 (mmtt) cc_final: 0.6745 (mmtt) REVERT: 2 130 TYR cc_start: 0.7587 (t80) cc_final: 0.7375 (t80) REVERT: 4 21 ARG cc_start: 0.6079 (ttp80) cc_final: 0.5844 (ttp80) REVERT: 4 44 GLU cc_start: 0.6927 (tt0) cc_final: 0.6405 (pt0) REVERT: 4 97 ARG cc_start: 0.6093 (ttt-90) cc_final: 0.5844 (ttm-80) REVERT: 4 101 ASN cc_start: 0.6767 (t0) cc_final: 0.6334 (m-40) REVERT: 4 163 ILE cc_start: 0.6454 (mt) cc_final: 0.6126 (mt) REVERT: 4 171 TYR cc_start: 0.6329 (t80) cc_final: 0.5839 (t80) REVERT: 6 13 MET cc_start: 0.5839 (mtt) cc_final: 0.5613 (mmp) REVERT: 6 44 GLU cc_start: 0.7339 (tt0) cc_final: 0.6588 (tm-30) REVERT: 6 67 LYS cc_start: 0.7182 (tttm) cc_final: 0.6928 (ttmt) REVERT: 6 97 ARG cc_start: 0.5948 (ttt-90) cc_final: 0.5621 (ttt-90) REVERT: 6 101 ASN cc_start: 0.6823 (t0) cc_final: 0.6506 (m-40) REVERT: 6 113 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6094 (tt0) REVERT: 6 182 ARG cc_start: 0.4883 (OUTLIER) cc_final: 0.4631 (mtm-85) REVERT: 6 233 LEU cc_start: 0.7609 (mp) cc_final: 0.7111 (mt) REVERT: 6 234 LEU cc_start: 0.5533 (OUTLIER) cc_final: 0.4950 (pt) REVERT: 8 44 GLU cc_start: 0.6973 (tt0) cc_final: 0.6771 (tp30) REVERT: 8 69 ASN cc_start: 0.7099 (OUTLIER) cc_final: 0.6653 (p0) REVERT: 8 73 ASN cc_start: 0.6529 (OUTLIER) cc_final: 0.5916 (m-40) REVERT: 8 74 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7212 (mt) REVERT: 8 97 ARG cc_start: 0.6946 (ttt-90) cc_final: 0.6586 (ttt90) REVERT: 8 110 ILE cc_start: 0.7599 (mt) cc_final: 0.6286 (mt) REVERT: 8 118 TYR cc_start: 0.7737 (m-10) cc_final: 0.6953 (m-10) REVERT: 8 156 MET cc_start: 0.7519 (mtm) cc_final: 0.7131 (mtm) REVERT: 8 163 ILE cc_start: 0.6951 (mt) cc_final: 0.6335 (mt) REVERT: 8 169 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6757 (mp0) REVERT: 8 209 GLU cc_start: 0.7683 (tt0) cc_final: 0.7447 (mt-10) REVERT: A 160 GLU cc_start: 0.7466 (tp30) cc_final: 0.6839 (tp30) REVERT: B 314 MET cc_start: 0.8268 (mmm) cc_final: 0.7745 (mmt) REVERT: B 395 GLN cc_start: 0.7793 (tp40) cc_final: 0.5857 (tp40) REVERT: B 426 LEU cc_start: 0.8899 (mp) cc_final: 0.8555 (mp) REVERT: C 332 ILE cc_start: 0.8895 (mp) cc_final: 0.8560 (mm) REVERT: D 164 LEU cc_start: 0.6867 (tp) cc_final: 0.6523 (tp) REVERT: D 314 MET cc_start: 0.5950 (ptt) cc_final: 0.5405 (tpt) REVERT: D 406 LEU cc_start: 0.7098 (mt) cc_final: 0.6702 (mt) REVERT: D 446 GLN cc_start: 0.8917 (mt0) cc_final: 0.8664 (tm-30) REVERT: D 474 CYS cc_start: 0.7648 (t) cc_final: 0.7133 (p) REVERT: D 520 GLN cc_start: 0.8240 (mm110) cc_final: 0.7680 (mm110) REVERT: E 124 LEU cc_start: 0.7720 (mp) cc_final: 0.7515 (mp) REVERT: E 520 GLN cc_start: 0.8266 (tt0) cc_final: 0.8014 (tt0) REVERT: F 314 MET cc_start: 0.5929 (mmt) cc_final: 0.5507 (mmp) REVERT: F 529 ASN cc_start: 0.8654 (m-40) cc_final: 0.8325 (t0) REVERT: G 1 MET cc_start: 0.6043 (pmm) cc_final: 0.5531 (mtp) REVERT: H 325 MET cc_start: 0.7834 (mtm) cc_final: 0.7604 (mtt) REVERT: H 363 LEU cc_start: 0.5859 (OUTLIER) cc_final: 0.5630 (mp) REVERT: H 388 ARG cc_start: 0.6199 (tpt-90) cc_final: 0.5999 (ttm170) REVERT: H 519 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7122 (tp30) REVERT: I 17 SER cc_start: 0.5856 (m) cc_final: 0.5648 (t) REVERT: I 18 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6311 (tp30) REVERT: I 85 ARG cc_start: 0.7246 (mmt90) cc_final: 0.6820 (tpp80) REVERT: I 105 GLN cc_start: 0.7369 (tt0) cc_final: 0.7002 (tm-30) REVERT: I 121 GLU cc_start: 0.6663 (tt0) cc_final: 0.6439 (tp30) REVERT: I 140 ARG cc_start: 0.7127 (ttp-110) cc_final: 0.6561 (ttm110) REVERT: I 153 PHE cc_start: 0.5306 (p90) cc_final: 0.4865 (p90) REVERT: I 209 GLU cc_start: 0.5050 (tt0) cc_final: 0.4363 (tt0) REVERT: I 233 LEU cc_start: 0.5967 (mm) cc_final: 0.5407 (tp) REVERT: J 325 MET cc_start: 0.7929 (mtm) cc_final: 0.7508 (ttp) REVERT: J 354 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6587 (mt-10) REVERT: J 361 VAL cc_start: 0.7553 (OUTLIER) cc_final: 0.7173 (t) REVERT: J 364 GLU cc_start: 0.7200 (tt0) cc_final: 0.6983 (pt0) REVERT: J 431 ILE cc_start: 0.7959 (mt) cc_final: 0.7670 (mp) REVERT: J 433 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6696 (mp0) REVERT: J 507 GLU cc_start: 0.7306 (tt0) cc_final: 0.7058 (tp30) REVERT: K 13 MET cc_start: 0.5988 (tpt) cc_final: 0.5696 (mmt) REVERT: K 18 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6086 (mm-30) REVERT: K 26 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.6104 (ptt90) REVERT: K 89 TYR cc_start: 0.7626 (m-80) cc_final: 0.7274 (m-80) REVERT: K 112 THR cc_start: 0.7524 (m) cc_final: 0.7223 (p) REVERT: K 116 LYS cc_start: 0.6694 (ttpp) cc_final: 0.6320 (ttpt) REVERT: K 119 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6677 (mp0) REVERT: K 130 TYR cc_start: 0.7520 (t80) cc_final: 0.7317 (t80) REVERT: K 146 SER cc_start: 0.7503 (m) cc_final: 0.6961 (p) REVERT: K 209 GLU cc_start: 0.5686 (tt0) cc_final: 0.5395 (tt0) REVERT: K 216 ASN cc_start: 0.7414 (t0) cc_final: 0.6612 (m-40) REVERT: L 325 MET cc_start: 0.7870 (mtm) cc_final: 0.6938 (ttm) REVERT: L 332 ARG cc_start: 0.7488 (mtt-85) cc_final: 0.6493 (mtt180) REVERT: L 361 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7280 (t) REVERT: L 364 GLU cc_start: 0.7788 (tt0) cc_final: 0.7282 (pt0) REVERT: L 388 ARG cc_start: 0.6175 (tpt-90) cc_final: 0.5786 (ttm-80) REVERT: M 307 LYS cc_start: 0.7732 (mtpt) cc_final: 0.7446 (mtmm) REVERT: M 325 MET cc_start: 0.7835 (mtm) cc_final: 0.7408 (ttt) REVERT: M 370 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6726 (mm-30) REVERT: M 390 ASN cc_start: 0.7497 (t0) cc_final: 0.7182 (t0) REVERT: M 395 MET cc_start: 0.7260 (mtm) cc_final: 0.7002 (mtt) REVERT: M 432 GLU cc_start: 0.6753 (tp30) cc_final: 0.6340 (mm-30) REVERT: N 325 MET cc_start: 0.7599 (mtm) cc_final: 0.7286 (ttp) REVERT: N 364 GLU cc_start: 0.7805 (tt0) cc_final: 0.7508 (pt0) REVERT: N 432 GLU cc_start: 0.6550 (tp30) cc_final: 0.5893 (mm-30) REVERT: N 434 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6390 (pm20) REVERT: N 461 ASP cc_start: 0.5942 (t70) cc_final: 0.5523 (t0) REVERT: N 509 ARG cc_start: 0.5600 (OUTLIER) cc_final: 0.5221 (tpt-90) REVERT: N 519 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6813 (mm-30) REVERT: O 19 LEU cc_start: 0.6432 (tt) cc_final: 0.6208 (mt) REVERT: O 26 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6664 (ppt170) REVERT: O 33 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6619 (pp) REVERT: O 74 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6546 (mt) REVERT: O 101 ASN cc_start: 0.6948 (t0) cc_final: 0.6648 (m-40) REVERT: O 116 LYS cc_start: 0.7019 (ttpp) cc_final: 0.6640 (mttt) REVERT: O 137 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7109 (mt-10) REVERT: O 143 TYR cc_start: 0.5210 (p90) cc_final: 0.4803 (p90) REVERT: O 155 VAL cc_start: 0.7112 (t) cc_final: 0.6891 (p) REVERT: O 156 MET cc_start: 0.6344 (mtm) cc_final: 0.6098 (mtm) REVERT: O 174 ASN cc_start: 0.6787 (t0) cc_final: 0.6490 (t0) REVERT: O 178 THR cc_start: 0.5778 (m) cc_final: 0.5571 (p) REVERT: O 181 LEU cc_start: 0.5733 (tp) cc_final: 0.5515 (tt) REVERT: O 228 SER cc_start: 0.4914 (p) cc_final: 0.4551 (p) REVERT: P 325 MET cc_start: 0.7816 (mtm) cc_final: 0.7138 (ttp) REVERT: P 361 VAL cc_start: 0.8089 (OUTLIER) cc_final: 0.7811 (t) REVERT: P 364 GLU cc_start: 0.7556 (tt0) cc_final: 0.7282 (pt0) REVERT: P 388 ARG cc_start: 0.5866 (tpt-90) cc_final: 0.5391 (ttm110) REVERT: P 509 ARG cc_start: 0.6558 (ttp80) cc_final: 0.6079 (tpt90) REVERT: P 519 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7037 (tp30) REVERT: Q 10 GLU cc_start: 0.4363 (OUTLIER) cc_final: 0.4122 (mp0) REVERT: Q 44 GLU cc_start: 0.6286 (tt0) cc_final: 0.6045 (mt-10) REVERT: Q 105 GLN cc_start: 0.7166 (mt0) cc_final: 0.6861 (tm-30) REVERT: Q 135 ARG cc_start: 0.6891 (ttm110) cc_final: 0.6579 (ttm110) REVERT: Q 146 SER cc_start: 0.6794 (m) cc_final: 0.6495 (p) REVERT: Q 155 VAL cc_start: 0.6339 (t) cc_final: 0.5800 (m) REVERT: Q 156 MET cc_start: 0.6218 (mtm) cc_final: 0.5840 (mtm) REVERT: Q 159 THR cc_start: 0.3872 (p) cc_final: 0.2968 (m) REVERT: Q 169 GLU cc_start: 0.5905 (OUTLIER) cc_final: 0.5700 (tp30) REVERT: Q 234 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6089 (tp) REVERT: R 322 GLN cc_start: 0.8008 (mt0) cc_final: 0.7757 (mt0) REVERT: R 325 MET cc_start: 0.7385 (mtm) cc_final: 0.6437 (mmt) REVERT: R 330 ASP cc_start: 0.7474 (p0) cc_final: 0.7235 (p0) REVERT: R 354 GLU cc_start: 0.7520 (tt0) cc_final: 0.7106 (tp30) REVERT: R 507 GLU cc_start: 0.7435 (tt0) cc_final: 0.6433 (tp30) REVERT: S 322 GLN cc_start: 0.7225 (mt0) cc_final: 0.6993 (mt0) REVERT: S 324 ASN cc_start: 0.6996 (m-40) cc_final: 0.6705 (m-40) REVERT: S 325 MET cc_start: 0.7305 (mtm) cc_final: 0.6464 (mmt) REVERT: S 345 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6813 (mt) REVERT: S 370 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6883 (mm-30) REVERT: S 432 GLU cc_start: 0.6764 (tp30) cc_final: 0.6477 (mm-30) REVERT: S 519 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7345 (tm-30) REVERT: T 49 SER cc_start: 0.7213 (m) cc_final: 0.6857 (m) REVERT: T 97 ARG cc_start: 0.5538 (ttp80) cc_final: 0.4966 (ttt180) REVERT: T 106 THR cc_start: 0.6752 (m) cc_final: 0.6393 (t) REVERT: T 111 PHE cc_start: 0.6814 (t80) cc_final: 0.6468 (t80) REVERT: T 112 THR cc_start: 0.7136 (m) cc_final: 0.6574 (p) REVERT: T 119 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7430 (mp0) REVERT: T 121 GLU cc_start: 0.7042 (tt0) cc_final: 0.6500 (tp30) REVERT: T 134 LYS cc_start: 0.7212 (ttpt) cc_final: 0.6825 (ttpt) REVERT: T 174 ASN cc_start: 0.7219 (m-40) cc_final: 0.6538 (m110) REVERT: T 178 THR cc_start: 0.5840 (m) cc_final: 0.5617 (p) REVERT: T 228 SER cc_start: 0.6261 (p) cc_final: 0.5918 (t) REVERT: U 314 MET cc_start: 0.8496 (ttm) cc_final: 0.7949 (ttm) REVERT: U 330 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6923 (p0) REVERT: U 447 LYS cc_start: 0.6613 (mtmt) cc_final: 0.6332 (mtmt) REVERT: V 390 ASN cc_start: 0.7092 (t0) cc_final: 0.6648 (t0) REVERT: V 432 GLU cc_start: 0.5850 (mm-30) cc_final: 0.5312 (mm-30) REVERT: V 509 ARG cc_start: 0.6172 (OUTLIER) cc_final: 0.5617 (ttt180) REVERT: V 519 GLU cc_start: 0.7422 (tt0) cc_final: 0.7092 (tp30) REVERT: W 307 LYS cc_start: 0.7496 (mtpt) cc_final: 0.7144 (mtpt) REVERT: W 354 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6584 (tt0) REVERT: W 364 GLU cc_start: 0.7348 (tt0) cc_final: 0.7011 (pt0) REVERT: W 509 ARG cc_start: 0.6483 (tpt170) cc_final: 0.6050 (ttp-170) REVERT: W 519 GLU cc_start: 0.6485 (mt-10) cc_final: 0.6107 (mm-30) REVERT: W 522 SER cc_start: 0.5773 (t) cc_final: 0.5555 (m) REVERT: X 24 ILE cc_start: 0.6347 (mt) cc_final: 0.6140 (mt) REVERT: X 69 ASN cc_start: 0.6914 (OUTLIER) cc_final: 0.6528 (p0) REVERT: X 101 ASN cc_start: 0.6573 (t0) cc_final: 0.6296 (m-40) REVERT: X 111 PHE cc_start: 0.6473 (t80) cc_final: 0.6265 (t80) REVERT: X 119 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7579 (mp0) REVERT: X 130 TYR cc_start: 0.7257 (t80) cc_final: 0.6239 (t80) REVERT: X 135 ARG cc_start: 0.7231 (ttm110) cc_final: 0.6903 (mmp80) REVERT: X 156 MET cc_start: 0.4841 (mtm) cc_final: 0.4571 (mtm) REVERT: X 163 ILE cc_start: 0.6538 (mt) cc_final: 0.6200 (mt) REVERT: X 216 ASN cc_start: 0.7490 (t0) cc_final: 0.6990 (t0) REVERT: X 233 LEU cc_start: 0.6735 (mp) cc_final: 0.6332 (mm) REVERT: Y 314 MET cc_start: 0.8247 (ttm) cc_final: 0.7939 (ttm) REVERT: Y 325 MET cc_start: 0.7760 (mtm) cc_final: 0.6863 (ttm) REVERT: Y 430 ASN cc_start: 0.7711 (t0) cc_final: 0.6969 (t0) REVERT: Y 432 GLU cc_start: 0.6355 (tp30) cc_final: 0.5894 (mm-30) REVERT: Y 450 MET cc_start: 0.6867 (mtm) cc_final: 0.6631 (mtm) REVERT: Y 509 ARG cc_start: 0.7237 (tpt170) cc_final: 0.6157 (ttt180) REVERT: Z 28 LYS cc_start: 0.7476 (mmtt) cc_final: 0.7213 (mmtp) REVERT: Z 33 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6377 (pt) REVERT: Z 52 LYS cc_start: 0.7462 (mtpt) cc_final: 0.6885 (mttm) REVERT: Z 98 GLN cc_start: 0.6091 (mt0) cc_final: 0.5844 (mt0) REVERT: Z 101 ASN cc_start: 0.7428 (t0) cc_final: 0.7065 (m-40) REVERT: Z 121 GLU cc_start: 0.7534 (tt0) cc_final: 0.7281 (tt0) REVERT: Z 138 LEU cc_start: 0.7837 (mt) cc_final: 0.7617 (mp) REVERT: Z 178 THR cc_start: 0.5281 (m) cc_final: 0.5065 (p) REVERT: Z 209 GLU cc_start: 0.5530 (tt0) cc_final: 0.4822 (tt0) REVERT: Z 216 ASN cc_start: 0.8141 (t0) cc_final: 0.7462 (m-40) REVERT: a 325 MET cc_start: 0.7623 (mtm) cc_final: 0.6955 (ttp) REVERT: a 345 ILE cc_start: 0.6765 (OUTLIER) cc_final: 0.6525 (mt) REVERT: a 354 GLU cc_start: 0.7148 (tt0) cc_final: 0.6816 (mt-10) REVERT: a 432 GLU cc_start: 0.6937 (tp30) cc_final: 0.6700 (tp30) REVERT: b 354 GLU cc_start: 0.7019 (tt0) cc_final: 0.6551 (mm-30) REVERT: b 355 PHE cc_start: 0.7118 (m-10) cc_final: 0.6746 (m-80) REVERT: b 390 ASN cc_start: 0.7212 (t0) cc_final: 0.6882 (t0) REVERT: b 432 GLU cc_start: 0.6695 (tp30) cc_final: 0.6442 (mm-30) REVERT: b 461 ASP cc_start: 0.5951 (t70) cc_final: 0.5747 (t0) REVERT: b 519 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6426 (mm-30) REVERT: d 19 LEU cc_start: 0.8166 (tt) cc_final: 0.7633 (tp) REVERT: d 97 ARG cc_start: 0.6062 (ttt-90) cc_final: 0.5820 (ttt180) REVERT: d 101 ASN cc_start: 0.7256 (t0) cc_final: 0.6705 (m110) REVERT: d 110 ILE cc_start: 0.8189 (mt) cc_final: 0.7940 (mm) REVERT: d 118 TYR cc_start: 0.7512 (m-10) cc_final: 0.7102 (m-10) REVERT: d 146 SER cc_start: 0.7735 (m) cc_final: 0.7287 (t) REVERT: d 179 ASP cc_start: 0.7044 (m-30) cc_final: 0.6624 (t0) REVERT: d 234 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5857 (pt) REVERT: f 15 GLU cc_start: 0.7825 (tt0) cc_final: 0.7476 (tp30) REVERT: f 26 ARG cc_start: 0.6920 (ttt180) cc_final: 0.6498 (ttp80) REVERT: f 44 GLU cc_start: 0.7019 (tt0) cc_final: 0.6508 (tm-30) REVERT: f 69 ASN cc_start: 0.7178 (OUTLIER) cc_final: 0.6566 (m-40) REVERT: f 101 ASN cc_start: 0.6682 (t0) cc_final: 0.6279 (m-40) REVERT: f 146 SER cc_start: 0.7306 (p) cc_final: 0.6796 (p) REVERT: f 163 ILE cc_start: 0.6400 (mt) cc_final: 0.5941 (mm) REVERT: f 165 ASN cc_start: 0.5712 (m-40) cc_final: 0.5459 (m110) REVERT: f 234 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6759 (pt) outliers start: 232 outliers final: 42 residues processed: 1791 average time/residue: 0.7437 time to fit residues: 2209.0937 Evaluate side-chains 990 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 920 time to evaluate : 6.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 205 VAL Chi-restraints excluded: chain 0 residue 234 LEU Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 205 VAL Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 205 VAL Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 69 ASN Chi-restraints excluded: chain 8 residue 73 ASN Chi-restraints excluded: chain 8 residue 74 LEU Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 234 LEU Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 354 GLU Chi-restraints excluded: chain J residue 361 VAL Chi-restraints excluded: chain J residue 486 LEU Chi-restraints excluded: chain K residue 26 ARG Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 361 VAL Chi-restraints excluded: chain L residue 441 SER Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain M residue 503 VAL Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 509 ARG Chi-restraints excluded: chain O residue 26 ARG Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 123 CYS Chi-restraints excluded: chain P residue 361 VAL Chi-restraints excluded: chain P residue 444 LEU Chi-restraints excluded: chain Q residue 10 GLU Chi-restraints excluded: chain Q residue 123 CYS Chi-restraints excluded: chain Q residue 169 GLU Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 361 VAL Chi-restraints excluded: chain R residue 363 LEU Chi-restraints excluded: chain S residue 345 ILE Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain U residue 330 ASP Chi-restraints excluded: chain U residue 345 ILE Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 345 ILE Chi-restraints excluded: chain W residue 354 GLU Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain Y residue 345 ILE Chi-restraints excluded: chain Y residue 361 VAL Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 123 CYS Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain a residue 345 ILE Chi-restraints excluded: chain d residue 74 LEU Chi-restraints excluded: chain d residue 144 ASP Chi-restraints excluded: chain d residue 205 VAL Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 69 ASN Chi-restraints excluded: chain f residue 234 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 749 optimal weight: 8.9990 chunk 673 optimal weight: 1.9990 chunk 373 optimal weight: 2.9990 chunk 229 optimal weight: 10.0000 chunk 454 optimal weight: 9.9990 chunk 359 optimal weight: 5.9990 chunk 696 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 chunk 423 optimal weight: 6.9990 chunk 518 optimal weight: 0.9990 chunk 806 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 114 GLN 6 114 GLN 8 69 ASN 8 80 GLN 8 114 GLN 8 165 ASN 8 231 GLN A 529 ASN B 139 GLN B 460 HIS B 502 ASN B 566 ASN C 172 HIS C 446 GLN ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN F 339 ASN F 348 HIS F 395 GLN F 607 GLN G 5 GLN H 456 GLN I 45 ASN I 98 GLN I 114 GLN I 129 HIS J 456 GLN K 80 GLN K 114 GLN L 322 GLN ** L 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 396 GLN L 456 GLN M 381 ASN M 456 GLN N 456 GLN O 51 GLN O 80 GLN ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 456 GLN Q 11 GLN ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 456 GLN S 456 GLN T 69 ASN T 80 GLN T 174 ASN U 322 GLN U 456 GLN V 322 GLN V 415 GLN V 456 GLN W 456 GLN X 69 ASN X 73 ASN X 80 GLN X 114 GLN Y 456 GLN Z 114 GLN a 456 GLN b 322 GLN b 456 GLN d 11 GLN ** d 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 114 GLN f 45 ASN f 69 ASN f 114 GLN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 69957 Z= 0.320 Angle : 0.669 10.596 94694 Z= 0.351 Chirality : 0.047 0.247 10759 Planarity : 0.006 0.113 12440 Dihedral : 6.815 111.198 10316 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.68 % Favored : 97.31 % Rotamer: Outliers : 2.63 % Allowed : 10.41 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.09), residues: 8881 helix: 1.48 (0.08), residues: 3488 sheet: 0.24 (0.11), residues: 2007 loop : -0.39 (0.11), residues: 3386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 187 HIS 0.014 0.002 HIS F 546 PHE 0.036 0.003 PHE 0 71 TYR 0.029 0.002 TYR L 359 ARG 0.010 0.001 ARG W 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 937 time to evaluate : 6.069 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: 0 28 LYS cc_start: 0.7143 (mmtt) cc_final: 0.6799 (mmtm) REVERT: 0 114 GLN cc_start: 0.5865 (mp10) cc_final: 0.5400 (mp10) REVERT: 0 143 TYR cc_start: 0.6138 (p90) cc_final: 0.5789 (p90) REVERT: 2 135 ARG cc_start: 0.7742 (tpp80) cc_final: 0.6841 (ttm-80) REVERT: 2 234 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6343 (pt) REVERT: 4 45 ASN cc_start: 0.7531 (t0) cc_final: 0.6769 (t0) REVERT: 4 121 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7350 (tt0) REVERT: 4 130 TYR cc_start: 0.8113 (t80) cc_final: 0.7739 (t80) REVERT: 6 44 GLU cc_start: 0.7273 (tt0) cc_final: 0.6703 (tm-30) REVERT: 6 97 ARG cc_start: 0.6266 (ttt-90) cc_final: 0.5964 (ttt-90) REVERT: 6 113 GLU cc_start: 0.6985 (mm-30) cc_final: 0.6331 (tt0) REVERT: 6 118 TYR cc_start: 0.8212 (m-10) cc_final: 0.7931 (m-80) REVERT: 6 171 TYR cc_start: 0.6082 (t80) cc_final: 0.5767 (t80) REVERT: 6 182 ARG cc_start: 0.4864 (OUTLIER) cc_final: 0.4590 (mtm-85) REVERT: 6 233 LEU cc_start: 0.7612 (mp) cc_final: 0.7186 (mt) REVERT: 6 234 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.5992 (pt) REVERT: 8 14 ARG cc_start: 0.5598 (mmm160) cc_final: 0.5359 (mmp-170) REVERT: 8 73 ASN cc_start: 0.6822 (OUTLIER) cc_final: 0.6569 (m-40) REVERT: 8 80 GLN cc_start: 0.7420 (tp40) cc_final: 0.7140 (tp40) REVERT: 8 179 ASP cc_start: 0.7215 (m-30) cc_final: 0.6992 (t0) REVERT: A 160 GLU cc_start: 0.7510 (tp30) cc_final: 0.7032 (tp30) REVERT: B 137 LYS cc_start: 0.7085 (ttmt) cc_final: 0.6525 (tptt) REVERT: B 274 HIS cc_start: 0.8808 (OUTLIER) cc_final: 0.8519 (m90) REVERT: B 373 MET cc_start: 0.8733 (tpp) cc_final: 0.8528 (tpp) REVERT: C 110 ASP cc_start: 0.6201 (OUTLIER) cc_final: 0.5876 (p0) REVERT: C 260 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7599 (mp10) REVERT: C 332 ILE cc_start: 0.8964 (mp) cc_final: 0.8671 (mm) REVERT: C 344 GLU cc_start: 0.7185 (tp30) cc_final: 0.6736 (tp30) REVERT: C 460 HIS cc_start: 0.6160 (t70) cc_final: 0.5932 (t-90) REVERT: D 122 MET cc_start: 0.8072 (mpp) cc_final: 0.7710 (mpp) REVERT: D 164 LEU cc_start: 0.6975 (tp) cc_final: 0.6586 (tp) REVERT: D 314 MET cc_start: 0.5964 (ptt) cc_final: 0.5072 (tpt) REVERT: D 520 GLN cc_start: 0.8193 (mm110) cc_final: 0.7993 (tp40) REVERT: E 379 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.8023 (p) REVERT: E 520 GLN cc_start: 0.8260 (tt0) cc_final: 0.7994 (tt0) REVERT: E 607 GLN cc_start: 0.4919 (OUTLIER) cc_final: 0.4715 (tt0) REVERT: F 122 MET cc_start: 0.6819 (mmm) cc_final: 0.6459 (mmm) REVERT: F 149 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8102 (p) REVERT: F 529 ASN cc_start: 0.8550 (m-40) cc_final: 0.8211 (t0) REVERT: F 537 THR cc_start: 0.7727 (p) cc_final: 0.6708 (p) REVERT: G 1 MET cc_start: 0.6011 (pmm) cc_final: 0.5626 (mtp) REVERT: H 325 MET cc_start: 0.8214 (mtm) cc_final: 0.7974 (mtt) REVERT: H 434 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7310 (mm-30) REVERT: H 519 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7164 (mm-30) REVERT: I 73 ASN cc_start: 0.6827 (t0) cc_final: 0.6552 (t0) REVERT: I 105 GLN cc_start: 0.7371 (tt0) cc_final: 0.6877 (tm-30) REVERT: I 111 PHE cc_start: 0.7022 (t80) cc_final: 0.6517 (t80) REVERT: I 153 PHE cc_start: 0.5891 (p90) cc_final: 0.5643 (p90) REVERT: J 325 MET cc_start: 0.7811 (mtm) cc_final: 0.7439 (ttm) REVERT: J 364 GLU cc_start: 0.7370 (tt0) cc_final: 0.7077 (pt0) REVERT: J 509 ARG cc_start: 0.6598 (tpt90) cc_final: 0.6198 (tpt-90) REVERT: K 18 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6843 (mm-30) REVERT: K 26 ARG cc_start: 0.6450 (ttm110) cc_final: 0.6035 (ppt170) REVERT: K 112 THR cc_start: 0.7443 (m) cc_final: 0.7109 (p) REVERT: K 146 SER cc_start: 0.6742 (m) cc_final: 0.6320 (p) REVERT: K 150 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7001 (mm-30) REVERT: K 209 GLU cc_start: 0.6310 (tt0) cc_final: 0.6060 (tt0) REVERT: K 216 ASN cc_start: 0.7361 (t0) cc_final: 0.6652 (m-40) REVERT: K 234 LEU cc_start: 0.6220 (mt) cc_final: 0.6015 (mm) REVERT: L 325 MET cc_start: 0.7806 (mtm) cc_final: 0.7067 (ttp) REVERT: L 332 ARG cc_start: 0.7446 (mtt-85) cc_final: 0.6409 (mtt180) REVERT: L 364 GLU cc_start: 0.7880 (tt0) cc_final: 0.7143 (pt0) REVERT: L 401 LEU cc_start: 0.7463 (mt) cc_final: 0.7123 (tp) REVERT: M 307 LYS cc_start: 0.7962 (mtpt) cc_final: 0.7714 (mtmm) REVERT: M 325 MET cc_start: 0.7944 (mtm) cc_final: 0.7510 (ttt) REVERT: M 500 ASP cc_start: 0.7585 (m-30) cc_final: 0.7271 (m-30) REVERT: N 325 MET cc_start: 0.7672 (mtm) cc_final: 0.7389 (ttp) REVERT: N 364 GLU cc_start: 0.7830 (tt0) cc_final: 0.7384 (pt0) REVERT: N 432 GLU cc_start: 0.6714 (tp30) cc_final: 0.6175 (mm-30) REVERT: N 433 GLU cc_start: 0.7887 (tp30) cc_final: 0.7528 (mt-10) REVERT: N 434 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7445 (pm20) REVERT: O 21 ARG cc_start: 0.6623 (ttm110) cc_final: 0.6314 (ptp-170) REVERT: O 22 LYS cc_start: 0.6796 (mtmt) cc_final: 0.6580 (ptpt) REVERT: O 26 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6497 (ppt170) REVERT: O 97 ARG cc_start: 0.6662 (ttt-90) cc_final: 0.6448 (tmm-80) REVERT: O 116 LYS cc_start: 0.7113 (ttpp) cc_final: 0.6757 (mttt) REVERT: O 146 SER cc_start: 0.6858 (m) cc_final: 0.6585 (t) REVERT: O 174 ASN cc_start: 0.7137 (t0) cc_final: 0.6925 (t0) REVERT: O 214 ASP cc_start: 0.7002 (t0) cc_final: 0.6695 (t0) REVERT: O 226 THR cc_start: 0.5817 (t) cc_final: 0.5424 (m) REVERT: P 325 MET cc_start: 0.7779 (mtm) cc_final: 0.7136 (ttp) REVERT: P 388 ARG cc_start: 0.6930 (tpt-90) cc_final: 0.6225 (ttm110) REVERT: Q 113 GLU cc_start: 0.7286 (tp30) cc_final: 0.6675 (tt0) REVERT: Q 135 ARG cc_start: 0.7254 (ttm110) cc_final: 0.6981 (ttm110) REVERT: Q 146 SER cc_start: 0.6743 (m) cc_final: 0.6333 (p) REVERT: Q 156 MET cc_start: 0.5918 (mtm) cc_final: 0.5599 (mtm) REVERT: Q 228 SER cc_start: 0.6833 (p) cc_final: 0.6591 (p) REVERT: Q 234 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.5866 (tp) REVERT: R 325 MET cc_start: 0.7302 (mtm) cc_final: 0.6635 (ttp) REVERT: R 357 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.7117 (mtp-110) REVERT: R 430 ASN cc_start: 0.7944 (t0) cc_final: 0.7663 (t0) REVERT: S 519 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7046 (mm-30) REVERT: T 52 LYS cc_start: 0.7256 (mtpt) cc_final: 0.6887 (mtmm) REVERT: T 111 PHE cc_start: 0.6621 (t80) cc_final: 0.6339 (t80) REVERT: T 113 GLU cc_start: 0.7220 (tp30) cc_final: 0.6991 (tm-30) REVERT: T 121 GLU cc_start: 0.7179 (tt0) cc_final: 0.6607 (mm-30) REVERT: T 134 LYS cc_start: 0.7207 (ttpt) cc_final: 0.6950 (ttpt) REVERT: T 156 MET cc_start: 0.6058 (mtm) cc_final: 0.5767 (mtm) REVERT: T 214 ASP cc_start: 0.6228 (t0) cc_final: 0.5821 (t0) REVERT: T 216 ASN cc_start: 0.7540 (t0) cc_final: 0.6813 (m110) REVERT: U 314 MET cc_start: 0.8230 (ttm) cc_final: 0.7667 (ttm) REVERT: U 330 ASP cc_start: 0.7523 (p0) cc_final: 0.7250 (p0) REVERT: U 430 ASN cc_start: 0.8415 (t0) cc_final: 0.8156 (t0) REVERT: U 432 GLU cc_start: 0.6351 (tp30) cc_final: 0.6137 (mm-30) REVERT: V 325 MET cc_start: 0.7426 (ttp) cc_final: 0.6320 (mmt) REVERT: V 395 MET cc_start: 0.6820 (mmp) cc_final: 0.6548 (mtm) REVERT: V 434 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7784 (mt-10) REVERT: V 509 ARG cc_start: 0.6153 (OUTLIER) cc_final: 0.5638 (ttt180) REVERT: V 519 GLU cc_start: 0.7316 (tt0) cc_final: 0.6845 (mt-10) REVERT: W 307 LYS cc_start: 0.7456 (mtpt) cc_final: 0.7092 (mtpt) REVERT: W 345 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7499 (mp) REVERT: W 364 GLU cc_start: 0.7063 (tt0) cc_final: 0.6602 (pt0) REVERT: W 509 ARG cc_start: 0.6120 (tpt170) cc_final: 0.5517 (ttt-90) REVERT: X 26 ARG cc_start: 0.7317 (ptm-80) cc_final: 0.7083 (ptm-80) REVERT: X 52 LYS cc_start: 0.7378 (mtpt) cc_final: 0.6920 (mtmm) REVERT: X 130 TYR cc_start: 0.7309 (t80) cc_final: 0.5841 (t80) REVERT: X 135 ARG cc_start: 0.7078 (ttm110) cc_final: 0.6754 (mmp-170) REVERT: X 179 ASP cc_start: 0.6707 (m-30) cc_final: 0.6055 (t0) REVERT: X 216 ASN cc_start: 0.7653 (t0) cc_final: 0.7039 (t0) REVERT: Y 324 ASN cc_start: 0.7569 (m-40) cc_final: 0.7236 (t0) REVERT: Y 325 MET cc_start: 0.7815 (mtm) cc_final: 0.6824 (ttt) REVERT: Z 52 LYS cc_start: 0.7313 (mtpt) cc_final: 0.6746 (mttm) REVERT: Z 121 GLU cc_start: 0.7371 (tt0) cc_final: 0.7045 (tt0) REVERT: Z 152 HIS cc_start: 0.7356 (m-70) cc_final: 0.6944 (m-70) REVERT: Z 216 ASN cc_start: 0.8461 (t0) cc_final: 0.7926 (m-40) REVERT: a 325 MET cc_start: 0.7391 (mtm) cc_final: 0.6711 (ttm) REVERT: a 354 GLU cc_start: 0.6850 (tt0) cc_final: 0.6321 (tp30) REVERT: a 370 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6910 (mm-30) REVERT: a 401 LEU cc_start: 0.7149 (mt) cc_final: 0.6790 (mp) REVERT: d 19 LEU cc_start: 0.8240 (tt) cc_final: 0.8039 (tt) REVERT: d 101 ASN cc_start: 0.7217 (t0) cc_final: 0.6841 (m-40) REVERT: d 169 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7267 (mp0) REVERT: d 234 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6615 (pt) REVERT: f 15 GLU cc_start: 0.7568 (tt0) cc_final: 0.7278 (tp30) REVERT: f 26 ARG cc_start: 0.6957 (ttt180) cc_final: 0.6620 (ttp80) REVERT: f 69 ASN cc_start: 0.7198 (p0) cc_final: 0.6390 (m-40) REVERT: f 101 ASN cc_start: 0.6698 (t0) cc_final: 0.6181 (m-40) REVERT: f 112 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7764 (p) REVERT: f 146 SER cc_start: 0.7509 (p) cc_final: 0.7254 (p) REVERT: f 165 ASN cc_start: 0.5610 (m-40) cc_final: 0.5359 (m110) outliers start: 185 outliers final: 89 residues processed: 1065 average time/residue: 0.6660 time to fit residues: 1189.9905 Evaluate side-chains 875 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 769 time to evaluate : 6.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 2 residue 133 THR Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 170 SER Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 121 GLU Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 29 SER Chi-restraints excluded: chain 8 residue 73 ASN Chi-restraints excluded: chain 8 residue 147 ILE Chi-restraints excluded: chain 8 residue 226 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain E residue 607 GLN Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 474 CYS Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 450 MET Chi-restraints excluded: chain O residue 26 ARG Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 444 LEU Chi-restraints excluded: chain Q residue 10 GLU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain S residue 386 MET Chi-restraints excluded: chain S residue 409 ILE Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 345 ILE Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 412 SER Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 331 VAL Chi-restraints excluded: chain W residue 345 ILE Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain X residue 147 ILE Chi-restraints excluded: chain Y residue 307 LYS Chi-restraints excluded: chain Y residue 345 ILE Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain a residue 409 ILE Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 144 ASP Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 147 ILE Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Chi-restraints excluded: chain f residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 448 optimal weight: 0.9990 chunk 250 optimal weight: 0.0020 chunk 671 optimal weight: 2.9990 chunk 549 optimal weight: 0.0170 chunk 222 optimal weight: 6.9990 chunk 807 optimal weight: 1.9990 chunk 872 optimal weight: 0.7980 chunk 719 optimal weight: 5.9990 chunk 801 optimal weight: 9.9990 chunk 275 optimal weight: 0.2980 chunk 648 optimal weight: 0.9980 overall best weight: 0.4226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 69 ASN 8 73 ASN ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 ASN ** F 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN I 174 ASN ** J 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 11 GLN ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 GLN T 80 GLN U 322 GLN X 80 GLN Y 390 ASN Z 98 GLN b 322 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 69957 Z= 0.131 Angle : 0.502 10.819 94694 Z= 0.262 Chirality : 0.042 0.246 10759 Planarity : 0.004 0.086 12440 Dihedral : 5.840 89.660 10239 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.32 % Favored : 97.67 % Rotamer: Outliers : 2.10 % Allowed : 11.93 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.09), residues: 8881 helix: 2.24 (0.09), residues: 3490 sheet: 0.55 (0.11), residues: 1995 loop : -0.21 (0.11), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 187 HIS 0.008 0.001 HIS O 152 PHE 0.029 0.002 PHE K 71 TYR 0.012 0.001 TYR O 171 ARG 0.006 0.000 ARG K 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 849 time to evaluate : 6.204 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: 0 114 GLN cc_start: 0.5843 (mp10) cc_final: 0.5232 (mp10) REVERT: 2 13 MET cc_start: 0.5643 (ttp) cc_final: 0.5208 (tmm) REVERT: 2 135 ARG cc_start: 0.7724 (tpp80) cc_final: 0.6774 (ttm-80) REVERT: 2 149 ASP cc_start: 0.7909 (m-30) cc_final: 0.7709 (m-30) REVERT: 2 234 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6387 (pt) REVERT: 4 45 ASN cc_start: 0.7592 (t0) cc_final: 0.6924 (t0) REVERT: 4 121 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6945 (tt0) REVERT: 4 156 MET cc_start: 0.7227 (mtm) cc_final: 0.6512 (mtp) REVERT: 6 44 GLU cc_start: 0.7285 (tt0) cc_final: 0.6714 (tm-30) REVERT: 6 113 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6381 (tt0) REVERT: 6 171 TYR cc_start: 0.5999 (t80) cc_final: 0.5732 (t80) REVERT: 6 182 ARG cc_start: 0.5301 (OUTLIER) cc_final: 0.4921 (mtm-85) REVERT: 6 233 LEU cc_start: 0.7555 (mp) cc_final: 0.7169 (mt) REVERT: 6 234 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.5873 (pt) REVERT: 8 21 ARG cc_start: 0.6444 (ttp80) cc_final: 0.6204 (ttm-80) REVERT: 8 44 GLU cc_start: 0.6559 (tp30) cc_final: 0.6330 (tp30) REVERT: 8 52 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.7116 (mtpt) REVERT: 8 73 ASN cc_start: 0.7168 (OUTLIER) cc_final: 0.6758 (m110) REVERT: 8 80 GLN cc_start: 0.7357 (tp40) cc_final: 0.7075 (tp40) REVERT: A 122 MET cc_start: 0.8839 (mmm) cc_final: 0.8548 (mmm) REVERT: A 160 GLU cc_start: 0.7515 (tp30) cc_final: 0.7005 (tp30) REVERT: B 137 LYS cc_start: 0.7289 (ttmt) cc_final: 0.6564 (tptt) REVERT: B 139 GLN cc_start: 0.8247 (tp-100) cc_final: 0.8018 (tp-100) REVERT: B 274 HIS cc_start: 0.8783 (OUTLIER) cc_final: 0.8482 (m90) REVERT: C 110 ASP cc_start: 0.6209 (OUTLIER) cc_final: 0.5863 (p0) REVERT: C 314 MET cc_start: 0.6154 (tpt) cc_final: 0.5753 (tpt) REVERT: C 460 HIS cc_start: 0.6204 (t70) cc_final: 0.5989 (t-90) REVERT: D 122 MET cc_start: 0.7919 (mpp) cc_final: 0.7204 (mpp) REVERT: D 314 MET cc_start: 0.6347 (ptt) cc_final: 0.5256 (tpt) REVERT: D 486 MET cc_start: 0.7765 (tpp) cc_final: 0.7181 (tpp) REVERT: E 124 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6921 (tp) REVERT: E 379 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7904 (p) REVERT: E 520 GLN cc_start: 0.8133 (tt0) cc_final: 0.7818 (tt0) REVERT: F 314 MET cc_start: 0.6083 (mmt) cc_final: 0.5760 (mmp) REVERT: F 529 ASN cc_start: 0.8593 (m-40) cc_final: 0.8246 (t0) REVERT: F 537 THR cc_start: 0.7746 (p) cc_final: 0.7203 (t) REVERT: F 544 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8458 (tp) REVERT: G 1 MET cc_start: 0.5847 (pmm) cc_final: 0.5551 (mtp) REVERT: H 325 MET cc_start: 0.8236 (mtm) cc_final: 0.8025 (mtt) REVERT: H 519 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7172 (mm-30) REVERT: I 73 ASN cc_start: 0.6641 (t0) cc_final: 0.6379 (t0) REVERT: I 105 GLN cc_start: 0.7184 (tt0) cc_final: 0.6741 (tm-30) REVERT: I 233 LEU cc_start: 0.6291 (OUTLIER) cc_final: 0.5997 (mm) REVERT: J 325 MET cc_start: 0.7799 (mtm) cc_final: 0.7442 (ttm) REVERT: J 364 GLU cc_start: 0.7123 (tt0) cc_final: 0.6675 (pt0) REVERT: J 507 GLU cc_start: 0.7472 (tt0) cc_final: 0.7110 (tp30) REVERT: J 509 ARG cc_start: 0.6454 (tpt90) cc_final: 0.6060 (ttt180) REVERT: K 26 ARG cc_start: 0.6438 (ttm110) cc_final: 0.6111 (ppt170) REVERT: K 89 TYR cc_start: 0.7700 (m-80) cc_final: 0.7439 (m-80) REVERT: K 101 ASN cc_start: 0.7067 (t0) cc_final: 0.6609 (m-40) REVERT: K 112 THR cc_start: 0.7198 (m) cc_final: 0.6829 (p) REVERT: K 146 SER cc_start: 0.6824 (m) cc_final: 0.6403 (p) REVERT: K 150 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7017 (mm-30) REVERT: K 216 ASN cc_start: 0.7411 (t0) cc_final: 0.6639 (m-40) REVERT: K 234 LEU cc_start: 0.6193 (mt) cc_final: 0.5857 (mm) REVERT: L 325 MET cc_start: 0.7872 (mtm) cc_final: 0.7082 (ttp) REVERT: L 332 ARG cc_start: 0.7405 (mtt-85) cc_final: 0.6502 (mtt180) REVERT: L 401 LEU cc_start: 0.7708 (mt) cc_final: 0.7342 (tp) REVERT: M 307 LYS cc_start: 0.7882 (mtpt) cc_final: 0.7617 (mtmm) REVERT: M 325 MET cc_start: 0.8031 (mtm) cc_final: 0.7597 (ttt) REVERT: M 338 ASP cc_start: 0.7420 (p0) cc_final: 0.7037 (p0) REVERT: N 325 MET cc_start: 0.7700 (mtm) cc_final: 0.7391 (ttp) REVERT: N 364 GLU cc_start: 0.7713 (tt0) cc_final: 0.7239 (pt0) REVERT: N 432 GLU cc_start: 0.6651 (tp30) cc_final: 0.6199 (mm-30) REVERT: N 433 GLU cc_start: 0.7906 (tp30) cc_final: 0.7486 (mt-10) REVERT: N 434 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7422 (pm20) REVERT: O 26 ARG cc_start: 0.7233 (ttp80) cc_final: 0.6546 (ppt170) REVERT: O 116 LYS cc_start: 0.7102 (ttpp) cc_final: 0.6730 (mttt) REVERT: O 152 HIS cc_start: 0.7148 (m170) cc_final: 0.6292 (m-70) REVERT: O 174 ASN cc_start: 0.7121 (t0) cc_final: 0.6917 (t0) REVERT: O 226 THR cc_start: 0.5738 (t) cc_final: 0.5294 (m) REVERT: P 325 MET cc_start: 0.7790 (mtm) cc_final: 0.7144 (ttp) REVERT: P 388 ARG cc_start: 0.6814 (tpt-90) cc_final: 0.6205 (ttm110) REVERT: Q 24 ILE cc_start: 0.6302 (mt) cc_final: 0.6061 (mt) REVERT: Q 49 SER cc_start: 0.7355 (m) cc_final: 0.6903 (p) REVERT: Q 113 GLU cc_start: 0.7508 (tp30) cc_final: 0.6818 (tt0) REVERT: Q 135 ARG cc_start: 0.7259 (ttm110) cc_final: 0.6974 (ttm110) REVERT: Q 146 SER cc_start: 0.6955 (m) cc_final: 0.6529 (p) REVERT: Q 156 MET cc_start: 0.5763 (mtm) cc_final: 0.5442 (mtm) REVERT: Q 228 SER cc_start: 0.6820 (p) cc_final: 0.6585 (p) REVERT: Q 234 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5731 (tp) REVERT: R 325 MET cc_start: 0.7421 (mtm) cc_final: 0.6782 (ttp) REVERT: R 504 ASP cc_start: 0.8241 (m-30) cc_final: 0.8026 (m-30) REVERT: S 519 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7288 (tm-30) REVERT: T 52 LYS cc_start: 0.7396 (mtpt) cc_final: 0.6975 (mtmm) REVERT: T 72 ASP cc_start: 0.7934 (t70) cc_final: 0.7692 (t70) REVERT: T 113 GLU cc_start: 0.7341 (tp30) cc_final: 0.6959 (tm-30) REVERT: T 121 GLU cc_start: 0.7036 (tt0) cc_final: 0.6290 (mm-30) REVERT: T 134 LYS cc_start: 0.7222 (ttpt) cc_final: 0.6997 (ttpt) REVERT: T 135 ARG cc_start: 0.7389 (ttp-170) cc_final: 0.7181 (ttp-170) REVERT: T 214 ASP cc_start: 0.6163 (t0) cc_final: 0.5824 (t0) REVERT: T 216 ASN cc_start: 0.7523 (t0) cc_final: 0.6879 (m110) REVERT: U 314 MET cc_start: 0.8240 (ttm) cc_final: 0.7741 (ttm) REVERT: U 395 MET cc_start: 0.7386 (tpp) cc_final: 0.6751 (ttm) REVERT: U 432 GLU cc_start: 0.6314 (tp30) cc_final: 0.6089 (mm-30) REVERT: U 509 ARG cc_start: 0.6203 (tpt170) cc_final: 0.5948 (ttp80) REVERT: V 351 VAL cc_start: 0.7196 (p) cc_final: 0.6991 (t) REVERT: V 358 LEU cc_start: 0.7213 (tp) cc_final: 0.6898 (mt) REVERT: V 395 MET cc_start: 0.6832 (mmp) cc_final: 0.6577 (mtm) REVERT: V 434 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7844 (mt-10) REVERT: V 509 ARG cc_start: 0.6126 (OUTLIER) cc_final: 0.5783 (ttt180) REVERT: V 519 GLU cc_start: 0.7175 (tt0) cc_final: 0.6780 (mt-10) REVERT: W 307 LYS cc_start: 0.7404 (mtpt) cc_final: 0.6563 (mttt) REVERT: W 345 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7391 (mm) REVERT: W 364 GLU cc_start: 0.7040 (tt0) cc_final: 0.6549 (pt0) REVERT: W 509 ARG cc_start: 0.6065 (tpt170) cc_final: 0.5469 (ttt180) REVERT: X 26 ARG cc_start: 0.7421 (ptm-80) cc_final: 0.7014 (mtm110) REVERT: X 51 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6868 (mp10) REVERT: X 52 LYS cc_start: 0.7439 (mtpt) cc_final: 0.7058 (mtmm) REVERT: X 130 TYR cc_start: 0.7326 (t80) cc_final: 0.5787 (t80) REVERT: X 135 ARG cc_start: 0.7027 (ttm110) cc_final: 0.6738 (mmp-170) REVERT: X 179 ASP cc_start: 0.6744 (m-30) cc_final: 0.6083 (t0) REVERT: X 216 ASN cc_start: 0.7629 (t0) cc_final: 0.7000 (t0) REVERT: Y 324 ASN cc_start: 0.7576 (m-40) cc_final: 0.7236 (t0) REVERT: Y 325 MET cc_start: 0.7916 (mtm) cc_final: 0.6907 (ttt) REVERT: Y 399 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7305 (tp) REVERT: Z 28 LYS cc_start: 0.7044 (mmtm) cc_final: 0.6777 (mmtm) REVERT: Z 52 LYS cc_start: 0.7200 (mtpt) cc_final: 0.6682 (mttm) REVERT: Z 121 GLU cc_start: 0.7125 (tt0) cc_final: 0.6809 (tt0) REVERT: Z 216 ASN cc_start: 0.8456 (t0) cc_final: 0.7956 (m-40) REVERT: a 325 MET cc_start: 0.7635 (mtm) cc_final: 0.6994 (ttm) REVERT: a 354 GLU cc_start: 0.6768 (tt0) cc_final: 0.6557 (pt0) REVERT: a 401 LEU cc_start: 0.7444 (mt) cc_final: 0.7157 (mp) REVERT: a 433 GLU cc_start: 0.7310 (pm20) cc_final: 0.7103 (pm20) REVERT: b 339 ASP cc_start: 0.8114 (t0) cc_final: 0.7690 (m-30) REVERT: d 101 ASN cc_start: 0.7200 (t0) cc_final: 0.6870 (m-40) REVERT: d 189 ARG cc_start: 0.5652 (ttm-80) cc_final: 0.5173 (mtm-85) REVERT: d 234 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6284 (pt) REVERT: f 15 GLU cc_start: 0.7751 (tt0) cc_final: 0.7340 (tp30) REVERT: f 26 ARG cc_start: 0.6765 (ttt180) cc_final: 0.6452 (ttp80) REVERT: f 52 LYS cc_start: 0.6621 (OUTLIER) cc_final: 0.6311 (mtpt) REVERT: f 101 ASN cc_start: 0.6887 (t0) cc_final: 0.6487 (m-40) REVERT: f 112 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7708 (p) REVERT: f 209 GLU cc_start: 0.6931 (tt0) cc_final: 0.6265 (mt-10) outliers start: 148 outliers final: 64 residues processed: 948 average time/residue: 0.7156 time to fit residues: 1145.7673 Evaluate side-chains 841 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 757 time to evaluate : 6.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 170 SER Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 121 GLU Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 8 residue 73 ASN Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 147 ILE Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain F residue 474 CYS Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 519 GLU Chi-restraints excluded: chain K residue 13 MET Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain M residue 461 ASP Chi-restraints excluded: chain N residue 307 LYS Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 345 ILE Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 51 GLN Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 307 LYS Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain d residue 74 LEU Chi-restraints excluded: chain d residue 144 ASP Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 233 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 798 optimal weight: 3.9990 chunk 607 optimal weight: 6.9990 chunk 419 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 385 optimal weight: 0.9980 chunk 542 optimal weight: 4.9990 chunk 810 optimal weight: 0.8980 chunk 858 optimal weight: 0.0870 chunk 423 optimal weight: 0.0670 chunk 768 optimal weight: 0.9990 chunk 231 optimal weight: 20.0000 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 69 ASN B 546 HIS ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 GLN ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 GLN E 172 HIS F 348 HIS ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN I 174 ASN J 390 ASN ** L 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 174 ASN U 322 GLN X 80 GLN b 322 GLN d 98 GLN f 80 GLN f 165 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 69957 Z= 0.138 Angle : 0.484 8.373 94694 Z= 0.253 Chirality : 0.041 0.148 10759 Planarity : 0.004 0.052 12440 Dihedral : 5.484 87.935 10214 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.13 % Allowed : 12.63 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.09), residues: 8881 helix: 2.50 (0.09), residues: 3487 sheet: 0.69 (0.12), residues: 1985 loop : -0.10 (0.11), residues: 3409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 187 HIS 0.004 0.001 HIS F 348 PHE 0.028 0.002 PHE f 71 TYR 0.017 0.001 TYR D 583 ARG 0.007 0.000 ARG D 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 822 time to evaluate : 6.242 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: 2 135 ARG cc_start: 0.7705 (tpp80) cc_final: 0.6763 (ttm-80) REVERT: 2 149 ASP cc_start: 0.7893 (m-30) cc_final: 0.7670 (m-30) REVERT: 2 234 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6451 (pt) REVERT: 4 44 GLU cc_start: 0.6803 (tt0) cc_final: 0.6460 (pt0) REVERT: 4 45 ASN cc_start: 0.7593 (t0) cc_final: 0.6896 (t0) REVERT: 4 51 GLN cc_start: 0.6706 (mm-40) cc_final: 0.5994 (mm-40) REVERT: 4 173 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7096 (mm-30) REVERT: 6 44 GLU cc_start: 0.7315 (tt0) cc_final: 0.6784 (tm-30) REVERT: 6 113 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6410 (tt0) REVERT: 6 171 TYR cc_start: 0.5995 (t80) cc_final: 0.5697 (t80) REVERT: 6 182 ARG cc_start: 0.5387 (OUTLIER) cc_final: 0.5141 (mpt-90) REVERT: 6 233 LEU cc_start: 0.7572 (mp) cc_final: 0.7245 (mt) REVERT: 6 234 LEU cc_start: 0.6386 (OUTLIER) cc_final: 0.5738 (pt) REVERT: 8 21 ARG cc_start: 0.6362 (ttp80) cc_final: 0.6150 (ttm-80) REVERT: 8 52 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.7034 (mtpt) REVERT: 8 73 ASN cc_start: 0.7160 (OUTLIER) cc_final: 0.6808 (m110) REVERT: 8 80 GLN cc_start: 0.7317 (tp40) cc_final: 0.7072 (tp40) REVERT: 8 156 MET cc_start: 0.7328 (mtm) cc_final: 0.7022 (mtm) REVERT: A 122 MET cc_start: 0.8742 (mmm) cc_final: 0.8397 (mmm) REVERT: A 160 GLU cc_start: 0.7691 (tp30) cc_final: 0.7159 (tp30) REVERT: B 122 MET cc_start: 0.7965 (mpp) cc_final: 0.7672 (mpp) REVERT: B 137 LYS cc_start: 0.7274 (ttmt) cc_final: 0.6434 (tptt) REVERT: B 274 HIS cc_start: 0.8752 (OUTLIER) cc_final: 0.8476 (m90) REVERT: B 395 GLN cc_start: 0.7903 (tp40) cc_final: 0.7695 (tp40) REVERT: C 110 ASP cc_start: 0.6429 (OUTLIER) cc_final: 0.6061 (p0) REVERT: C 314 MET cc_start: 0.6198 (tpt) cc_final: 0.5791 (tpt) REVERT: C 344 GLU cc_start: 0.6745 (tp30) cc_final: 0.6102 (tp30) REVERT: C 420 MET cc_start: 0.7039 (mtm) cc_final: 0.6706 (mtm) REVERT: D 122 MET cc_start: 0.8126 (mpp) cc_final: 0.7827 (mpp) REVERT: D 314 MET cc_start: 0.6349 (ptt) cc_final: 0.5251 (tpt) REVERT: D 480 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7795 (tp30) REVERT: D 518 MET cc_start: 0.7811 (ttp) cc_final: 0.7606 (ttp) REVERT: D 520 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7759 (mm110) REVERT: E 124 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7052 (tp) REVERT: E 379 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7900 (p) REVERT: E 520 GLN cc_start: 0.8096 (tt0) cc_final: 0.7783 (tt0) REVERT: F 314 MET cc_start: 0.6251 (mmt) cc_final: 0.5878 (mmp) REVERT: F 373 MET cc_start: 0.7929 (mmm) cc_final: 0.7574 (mmm) REVERT: F 529 ASN cc_start: 0.8598 (m-40) cc_final: 0.8251 (t0) REVERT: G 1 MET cc_start: 0.5913 (pmm) cc_final: 0.5548 (mtp) REVERT: H 325 MET cc_start: 0.8228 (mtm) cc_final: 0.7959 (mtt) REVERT: H 519 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7191 (mm-30) REVERT: I 73 ASN cc_start: 0.6535 (t0) cc_final: 0.6259 (t0) REVERT: I 105 GLN cc_start: 0.7176 (tt0) cc_final: 0.6744 (tm-30) REVERT: I 111 PHE cc_start: 0.6929 (t80) cc_final: 0.6622 (t80) REVERT: I 233 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6356 (mm) REVERT: J 325 MET cc_start: 0.7797 (mtm) cc_final: 0.7440 (ttm) REVERT: J 364 GLU cc_start: 0.7033 (tt0) cc_final: 0.6688 (mt-10) REVERT: J 395 MET cc_start: 0.7739 (mmm) cc_final: 0.7537 (mmm) REVERT: J 433 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7262 (mp0) REVERT: J 509 ARG cc_start: 0.6285 (tpt90) cc_final: 0.5934 (ttt180) REVERT: K 26 ARG cc_start: 0.6732 (ttm110) cc_final: 0.6231 (ppt170) REVERT: K 101 ASN cc_start: 0.7052 (t0) cc_final: 0.6680 (m-40) REVERT: K 112 THR cc_start: 0.7247 (m) cc_final: 0.6893 (p) REVERT: K 146 SER cc_start: 0.6831 (m) cc_final: 0.6399 (p) REVERT: K 150 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6796 (mm-30) REVERT: K 216 ASN cc_start: 0.7404 (t0) cc_final: 0.6621 (m-40) REVERT: K 234 LEU cc_start: 0.6249 (mt) cc_final: 0.5918 (mm) REVERT: L 325 MET cc_start: 0.7835 (mtm) cc_final: 0.7093 (ttp) REVERT: L 332 ARG cc_start: 0.7397 (mtt-85) cc_final: 0.6500 (mtt180) REVERT: M 307 LYS cc_start: 0.7846 (mtpt) cc_final: 0.7585 (mtmm) REVERT: M 325 MET cc_start: 0.8035 (mtm) cc_final: 0.7592 (ttt) REVERT: N 325 MET cc_start: 0.7739 (mtm) cc_final: 0.7405 (ttp) REVERT: N 364 GLU cc_start: 0.7711 (tt0) cc_final: 0.7116 (pt0) REVERT: N 432 GLU cc_start: 0.6691 (tp30) cc_final: 0.6218 (mm-30) REVERT: N 433 GLU cc_start: 0.7849 (tp30) cc_final: 0.7530 (mt-10) REVERT: N 434 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7469 (pm20) REVERT: O 26 ARG cc_start: 0.7070 (ttp80) cc_final: 0.6377 (ppt170) REVERT: O 146 SER cc_start: 0.6729 (m) cc_final: 0.6448 (t) REVERT: O 151 PRO cc_start: 0.7788 (Cg_endo) cc_final: 0.7459 (Cg_exo) REVERT: O 152 HIS cc_start: 0.7239 (m170) cc_final: 0.6471 (m-70) REVERT: O 156 MET cc_start: 0.6125 (mtm) cc_final: 0.5840 (mtm) REVERT: O 226 THR cc_start: 0.5786 (t) cc_final: 0.5360 (m) REVERT: P 325 MET cc_start: 0.7794 (mtm) cc_final: 0.7129 (ttp) REVERT: P 388 ARG cc_start: 0.6899 (tpt-90) cc_final: 0.6289 (ttm110) REVERT: Q 44 GLU cc_start: 0.6678 (pt0) cc_final: 0.6313 (pm20) REVERT: Q 49 SER cc_start: 0.7305 (m) cc_final: 0.6864 (p) REVERT: Q 113 GLU cc_start: 0.7549 (tp30) cc_final: 0.7105 (tm-30) REVERT: Q 146 SER cc_start: 0.6954 (m) cc_final: 0.6513 (p) REVERT: Q 156 MET cc_start: 0.5896 (mtm) cc_final: 0.5610 (mtm) REVERT: Q 234 LEU cc_start: 0.6081 (OUTLIER) cc_final: 0.5670 (tp) REVERT: R 325 MET cc_start: 0.7410 (mtm) cc_final: 0.6785 (ttp) REVERT: S 519 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7184 (tm-30) REVERT: T 52 LYS cc_start: 0.7386 (mtpt) cc_final: 0.6966 (mtmm) REVERT: T 72 ASP cc_start: 0.7931 (t70) cc_final: 0.7687 (t70) REVERT: T 113 GLU cc_start: 0.7258 (tp30) cc_final: 0.6908 (tm-30) REVERT: T 121 GLU cc_start: 0.7017 (tt0) cc_final: 0.6342 (mm-30) REVERT: T 134 LYS cc_start: 0.7172 (ttpt) cc_final: 0.6935 (ttpt) REVERT: T 214 ASP cc_start: 0.5868 (t0) cc_final: 0.5498 (t0) REVERT: T 216 ASN cc_start: 0.7544 (t0) cc_final: 0.6903 (m110) REVERT: U 314 MET cc_start: 0.8218 (ttm) cc_final: 0.7741 (ttm) REVERT: U 509 ARG cc_start: 0.6177 (tpt170) cc_final: 0.5952 (ttp80) REVERT: V 395 MET cc_start: 0.6639 (mmp) cc_final: 0.6310 (mtm) REVERT: V 509 ARG cc_start: 0.6165 (OUTLIER) cc_final: 0.5864 (ttt180) REVERT: V 519 GLU cc_start: 0.7159 (tt0) cc_final: 0.6590 (mm-30) REVERT: W 307 LYS cc_start: 0.7367 (mtpt) cc_final: 0.7137 (mtpt) REVERT: W 364 GLU cc_start: 0.7039 (tt0) cc_final: 0.6525 (pt0) REVERT: W 509 ARG cc_start: 0.6096 (tpt170) cc_final: 0.5437 (ttt180) REVERT: X 26 ARG cc_start: 0.7379 (ptm-80) cc_final: 0.7064 (mtm110) REVERT: X 33 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6910 (pp) REVERT: X 52 LYS cc_start: 0.7524 (mtpt) cc_final: 0.7061 (mtmm) REVERT: X 130 TYR cc_start: 0.7570 (t80) cc_final: 0.6155 (t80) REVERT: X 135 ARG cc_start: 0.7017 (ttm110) cc_final: 0.6718 (mmp-170) REVERT: X 179 ASP cc_start: 0.6627 (m-30) cc_final: 0.5936 (t0) REVERT: X 216 ASN cc_start: 0.7495 (t0) cc_final: 0.6927 (t0) REVERT: Y 324 ASN cc_start: 0.7556 (m-40) cc_final: 0.7236 (t0) REVERT: Y 325 MET cc_start: 0.7763 (mtm) cc_final: 0.6844 (ttt) REVERT: Y 399 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7203 (tp) REVERT: Z 31 VAL cc_start: 0.7572 (m) cc_final: 0.7295 (p) REVERT: Z 52 LYS cc_start: 0.7194 (mtpt) cc_final: 0.6652 (mttm) REVERT: Z 113 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6471 (tm-30) REVERT: Z 121 GLU cc_start: 0.7025 (tt0) cc_final: 0.6753 (tt0) REVERT: Z 216 ASN cc_start: 0.8467 (t0) cc_final: 0.8041 (m-40) REVERT: a 325 MET cc_start: 0.7559 (mtm) cc_final: 0.6957 (ttm) REVERT: a 401 LEU cc_start: 0.7503 (mt) cc_final: 0.7175 (mp) REVERT: b 339 ASP cc_start: 0.8060 (t0) cc_final: 0.7584 (m-30) REVERT: d 69 ASN cc_start: 0.7582 (OUTLIER) cc_final: 0.7190 (m-40) REVERT: d 101 ASN cc_start: 0.7163 (t0) cc_final: 0.6860 (m-40) REVERT: d 189 ARG cc_start: 0.5737 (ttm-80) cc_final: 0.5252 (mtm-85) REVERT: d 234 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6310 (pt) REVERT: f 15 GLU cc_start: 0.7826 (tt0) cc_final: 0.7410 (tp30) REVERT: f 26 ARG cc_start: 0.6789 (ttt180) cc_final: 0.6525 (ttp80) REVERT: f 73 ASN cc_start: 0.6992 (t0) cc_final: 0.6775 (t0) REVERT: f 101 ASN cc_start: 0.6891 (t0) cc_final: 0.6455 (m-40) REVERT: f 105 GLN cc_start: 0.6690 (mm110) cc_final: 0.6475 (mm-40) REVERT: f 112 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7853 (p) REVERT: f 209 GLU cc_start: 0.6935 (tt0) cc_final: 0.6649 (tt0) outliers start: 150 outliers final: 81 residues processed: 920 average time/residue: 0.6811 time to fit residues: 1052.8119 Evaluate side-chains 855 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 755 time to evaluate : 6.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 67 LYS Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 170 SER Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 173 GLU Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 8 residue 73 ASN Chi-restraints excluded: chain 8 residue 226 THR Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 474 CYS Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 519 GLU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 149 ASP Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 338 ASP Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain V residue 412 SER Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain Y residue 307 LYS Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain d residue 69 ASN Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 147 ILE Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 714 optimal weight: 0.8980 chunk 487 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 639 optimal weight: 0.7980 chunk 354 optimal weight: 4.9990 chunk 732 optimal weight: 6.9990 chunk 593 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 438 optimal weight: 4.9990 chunk 770 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 69 ASN 2 114 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 HIS ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 ASN F 348 HIS F 416 ASN G 5 GLN I 174 ASN ** L 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN ** P 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 GLN V 322 GLN Y 396 GLN f 80 GLN f 165 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 69957 Z= 0.159 Angle : 0.488 7.395 94694 Z= 0.255 Chirality : 0.042 0.190 10759 Planarity : 0.004 0.053 12440 Dihedral : 5.315 84.673 10206 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.44 % Allowed : 13.00 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.09), residues: 8881 helix: 2.60 (0.09), residues: 3487 sheet: 0.71 (0.11), residues: 2023 loop : -0.06 (0.11), residues: 3371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 570 HIS 0.005 0.001 HIS F 348 PHE 0.032 0.002 PHE F 341 TYR 0.016 0.001 TYR 6 118 ARG 0.010 0.000 ARG 4 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 787 time to evaluate : 6.164 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: 0 156 MET cc_start: 0.7421 (mtm) cc_final: 0.6926 (mtm) REVERT: 2 135 ARG cc_start: 0.7773 (tpp80) cc_final: 0.6913 (ttm-80) REVERT: 2 205 VAL cc_start: 0.5950 (m) cc_final: 0.5619 (p) REVERT: 2 234 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6373 (pt) REVERT: 4 44 GLU cc_start: 0.6857 (tt0) cc_final: 0.6637 (pt0) REVERT: 4 45 ASN cc_start: 0.7791 (t0) cc_final: 0.7215 (t0) REVERT: 4 51 GLN cc_start: 0.6567 (mm-40) cc_final: 0.5806 (mm-40) REVERT: 4 156 MET cc_start: 0.6730 (mtt) cc_final: 0.6491 (mtp) REVERT: 4 173 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7249 (mm-30) REVERT: 4 179 ASP cc_start: 0.7525 (m-30) cc_final: 0.7282 (m-30) REVERT: 6 44 GLU cc_start: 0.7335 (tt0) cc_final: 0.6754 (tm-30) REVERT: 6 113 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6465 (tt0) REVERT: 6 182 ARG cc_start: 0.5229 (OUTLIER) cc_final: 0.5027 (mpt-90) REVERT: 6 233 LEU cc_start: 0.7572 (mp) cc_final: 0.7230 (mt) REVERT: 6 234 LEU cc_start: 0.6159 (OUTLIER) cc_final: 0.5546 (pt) REVERT: 8 52 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.7003 (mtpt) REVERT: 8 73 ASN cc_start: 0.7199 (OUTLIER) cc_final: 0.6743 (m110) REVERT: A 122 MET cc_start: 0.8887 (mmm) cc_final: 0.8481 (mmm) REVERT: A 160 GLU cc_start: 0.7711 (tp30) cc_final: 0.7169 (tp30) REVERT: B 137 LYS cc_start: 0.7238 (ttmt) cc_final: 0.6439 (tptt) REVERT: C 110 ASP cc_start: 0.6502 (OUTLIER) cc_final: 0.6092 (p0) REVERT: C 344 GLU cc_start: 0.6824 (tp30) cc_final: 0.6088 (tp30) REVERT: D 314 MET cc_start: 0.6399 (ptt) cc_final: 0.5210 (tpt) REVERT: D 480 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: E 124 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7029 (tp) REVERT: E 323 HIS cc_start: 0.6222 (p-80) cc_final: 0.5983 (p-80) REVERT: E 379 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7832 (p) REVERT: E 520 GLN cc_start: 0.8154 (tt0) cc_final: 0.7843 (tt0) REVERT: F 297 CYS cc_start: 0.8858 (m) cc_final: 0.8396 (m) REVERT: F 314 MET cc_start: 0.6277 (mmt) cc_final: 0.5921 (mmp) REVERT: F 373 MET cc_start: 0.7946 (mmm) cc_final: 0.7609 (mmm) REVERT: F 529 ASN cc_start: 0.8638 (m-40) cc_final: 0.8285 (t0) REVERT: H 519 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7206 (mm-30) REVERT: I 73 ASN cc_start: 0.6481 (t0) cc_final: 0.6215 (t0) REVERT: I 105 GLN cc_start: 0.7204 (tt0) cc_final: 0.6718 (tm-30) REVERT: I 111 PHE cc_start: 0.7335 (t80) cc_final: 0.7080 (t80) REVERT: J 325 MET cc_start: 0.7824 (mtm) cc_final: 0.7436 (ttm) REVERT: J 364 GLU cc_start: 0.7117 (tt0) cc_final: 0.6819 (mt-10) REVERT: J 395 MET cc_start: 0.7708 (mmm) cc_final: 0.7471 (mmm) REVERT: J 433 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7245 (mp0) REVERT: J 509 ARG cc_start: 0.6291 (tpt90) cc_final: 0.5940 (ttt180) REVERT: K 13 MET cc_start: 0.5929 (mmt) cc_final: 0.4470 (ttp) REVERT: K 22 LYS cc_start: 0.7637 (pttt) cc_final: 0.7383 (pttm) REVERT: K 101 ASN cc_start: 0.6574 (t0) cc_final: 0.6141 (m-40) REVERT: K 112 THR cc_start: 0.7081 (m) cc_final: 0.6858 (p) REVERT: K 146 SER cc_start: 0.6840 (m) cc_final: 0.6395 (p) REVERT: K 150 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6724 (mm-30) REVERT: K 216 ASN cc_start: 0.7384 (t0) cc_final: 0.6597 (m-40) REVERT: K 234 LEU cc_start: 0.6233 (mt) cc_final: 0.5910 (mm) REVERT: L 325 MET cc_start: 0.7886 (mtm) cc_final: 0.7125 (ttp) REVERT: L 332 ARG cc_start: 0.7408 (mtt-85) cc_final: 0.6503 (mtt180) REVERT: M 307 LYS cc_start: 0.7831 (mtpt) cc_final: 0.7597 (mtmm) REVERT: M 325 MET cc_start: 0.7976 (mtm) cc_final: 0.7546 (ttt) REVERT: N 325 MET cc_start: 0.7764 (mtm) cc_final: 0.7415 (ttp) REVERT: N 364 GLU cc_start: 0.7758 (tt0) cc_final: 0.7167 (pt0) REVERT: N 399 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7536 (tt) REVERT: N 432 GLU cc_start: 0.6825 (tp30) cc_final: 0.6545 (mm-30) REVERT: O 26 ARG cc_start: 0.7177 (ttp80) cc_final: 0.6593 (ppt170) REVERT: O 146 SER cc_start: 0.6635 (m) cc_final: 0.6323 (t) REVERT: O 151 PRO cc_start: 0.7917 (Cg_endo) cc_final: 0.7650 (Cg_exo) REVERT: O 156 MET cc_start: 0.6242 (mtm) cc_final: 0.5908 (mtm) REVERT: O 226 THR cc_start: 0.5820 (t) cc_final: 0.5388 (m) REVERT: P 325 MET cc_start: 0.7725 (mtm) cc_final: 0.7077 (ttp) REVERT: P 388 ARG cc_start: 0.7020 (tpt-90) cc_final: 0.6385 (ttm110) REVERT: Q 49 SER cc_start: 0.7310 (m) cc_final: 0.6902 (p) REVERT: Q 111 PHE cc_start: 0.6628 (t80) cc_final: 0.6284 (t80) REVERT: Q 113 GLU cc_start: 0.7689 (tp30) cc_final: 0.7241 (tm-30) REVERT: Q 146 SER cc_start: 0.6975 (m) cc_final: 0.6557 (p) REVERT: Q 234 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.5886 (tp) REVERT: R 325 MET cc_start: 0.7350 (mtm) cc_final: 0.6764 (ttp) REVERT: S 519 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7172 (tm-30) REVERT: T 17 SER cc_start: 0.6178 (t) cc_final: 0.5969 (p) REVERT: T 33 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.7033 (pt) REVERT: T 52 LYS cc_start: 0.7422 (mtpt) cc_final: 0.7014 (mtmm) REVERT: T 72 ASP cc_start: 0.7972 (t70) cc_final: 0.7761 (t70) REVERT: T 80 GLN cc_start: 0.6847 (tp-100) cc_final: 0.6511 (tp-100) REVERT: T 113 GLU cc_start: 0.7377 (tp30) cc_final: 0.7068 (tm-30) REVERT: T 121 GLU cc_start: 0.7006 (tt0) cc_final: 0.6351 (mm-30) REVERT: T 134 LYS cc_start: 0.7155 (ttpt) cc_final: 0.6899 (ttpt) REVERT: T 214 ASP cc_start: 0.5973 (t0) cc_final: 0.5627 (t0) REVERT: T 216 ASN cc_start: 0.7609 (t0) cc_final: 0.6979 (m110) REVERT: U 314 MET cc_start: 0.8202 (ttm) cc_final: 0.7752 (ttm) REVERT: U 509 ARG cc_start: 0.6296 (tpt170) cc_final: 0.6042 (ttp80) REVERT: V 395 MET cc_start: 0.6681 (mmp) cc_final: 0.6251 (mtm) REVERT: V 509 ARG cc_start: 0.6146 (OUTLIER) cc_final: 0.5773 (ttt180) REVERT: V 519 GLU cc_start: 0.7145 (tt0) cc_final: 0.6685 (mm-30) REVERT: W 307 LYS cc_start: 0.7364 (mtpt) cc_final: 0.6594 (mttt) REVERT: W 364 GLU cc_start: 0.7073 (tt0) cc_final: 0.6545 (pt0) REVERT: W 416 SER cc_start: 0.6817 (p) cc_final: 0.6273 (t) REVERT: W 509 ARG cc_start: 0.6093 (tpt170) cc_final: 0.5468 (ttt180) REVERT: X 26 ARG cc_start: 0.7463 (ptm-80) cc_final: 0.7171 (mtm110) REVERT: X 33 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6879 (pp) REVERT: X 52 LYS cc_start: 0.7591 (mtpt) cc_final: 0.7109 (mtmm) REVERT: X 130 TYR cc_start: 0.7515 (t80) cc_final: 0.6063 (t80) REVERT: X 156 MET cc_start: 0.4346 (mtm) cc_final: 0.4083 (mtm) REVERT: X 179 ASP cc_start: 0.6667 (m-30) cc_final: 0.5981 (t0) REVERT: X 216 ASN cc_start: 0.7475 (t0) cc_final: 0.6907 (t0) REVERT: Y 324 ASN cc_start: 0.7575 (m-40) cc_final: 0.7216 (t0) REVERT: Y 325 MET cc_start: 0.7815 (mtm) cc_final: 0.7061 (ttt) REVERT: Y 399 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7222 (tp) REVERT: Y 410 HIS cc_start: 0.7593 (m90) cc_final: 0.7359 (m-70) REVERT: Z 31 VAL cc_start: 0.7590 (m) cc_final: 0.7358 (p) REVERT: Z 52 LYS cc_start: 0.7340 (mtpt) cc_final: 0.7008 (mttp) REVERT: Z 113 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6501 (tm-30) REVERT: Z 216 ASN cc_start: 0.8479 (t0) cc_final: 0.8037 (m-40) REVERT: a 325 MET cc_start: 0.7560 (mtm) cc_final: 0.6949 (ttm) REVERT: a 401 LEU cc_start: 0.7376 (mt) cc_final: 0.6955 (mp) REVERT: a 432 GLU cc_start: 0.6698 (tp30) cc_final: 0.6440 (mm-30) REVERT: b 339 ASP cc_start: 0.8043 (t0) cc_final: 0.7617 (m-30) REVERT: d 69 ASN cc_start: 0.7473 (OUTLIER) cc_final: 0.7142 (m110) REVERT: d 101 ASN cc_start: 0.7222 (t0) cc_final: 0.6917 (m-40) REVERT: d 189 ARG cc_start: 0.5698 (ttm-80) cc_final: 0.5215 (mtm-85) REVERT: d 234 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6506 (pt) REVERT: f 15 GLU cc_start: 0.7827 (tt0) cc_final: 0.7398 (tp30) REVERT: f 26 ARG cc_start: 0.6790 (ttt180) cc_final: 0.6450 (ttp80) REVERT: f 52 LYS cc_start: 0.6514 (OUTLIER) cc_final: 0.6096 (mtpt) REVERT: f 101 ASN cc_start: 0.6933 (t0) cc_final: 0.6451 (m-40) REVERT: f 112 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7915 (p) REVERT: f 209 GLU cc_start: 0.6858 (tt0) cc_final: 0.6564 (tt0) outliers start: 172 outliers final: 95 residues processed: 908 average time/residue: 0.6796 time to fit residues: 1048.9360 Evaluate side-chains 855 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 740 time to evaluate : 6.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 69 ASN Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 170 SER Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 173 GLU Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 8 residue 73 ASN Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 545 GLN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 474 CYS Chi-restraints excluded: chain H residue 434 GLU Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 461 ASP Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain P residue 396 GLN Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 174 ASN Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 149 ASP Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 225 ILE Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain V residue 412 SER Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain Y residue 307 LYS Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 69 ASN Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 147 ILE Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 288 optimal weight: 20.0000 chunk 772 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 503 optimal weight: 0.7980 chunk 211 optimal weight: 20.0000 chunk 859 optimal weight: 8.9990 chunk 713 optimal weight: 0.7980 chunk 397 optimal weight: 0.9990 chunk 71 optimal weight: 0.0070 chunk 284 optimal weight: 6.9990 chunk 451 optimal weight: 4.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 45 ASN 2 69 ASN 2 114 GLN B 546 HIS C 514 ASN ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 514 ASN ** F 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN I 174 ASN ** L 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 GLN O 174 ASN ** P 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 GLN V 322 GLN f 165 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 69957 Z= 0.153 Angle : 0.483 9.254 94694 Z= 0.252 Chirality : 0.041 0.179 10759 Planarity : 0.003 0.042 12440 Dihedral : 5.213 81.638 10204 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.19 % Allowed : 13.61 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.09), residues: 8881 helix: 2.65 (0.09), residues: 3494 sheet: 0.74 (0.11), residues: 2012 loop : -0.03 (0.11), residues: 3375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 570 HIS 0.005 0.001 HIS C 460 PHE 0.031 0.002 PHE 2 71 TYR 0.014 0.001 TYR 6 118 ARG 0.008 0.000 ARG 4 182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 774 time to evaluate : 6.133 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: 0 156 MET cc_start: 0.7493 (mtm) cc_final: 0.7162 (mtt) REVERT: 2 135 ARG cc_start: 0.7936 (tpp80) cc_final: 0.7176 (ttm-80) REVERT: 2 170 SER cc_start: 0.6802 (OUTLIER) cc_final: 0.6575 (t) REVERT: 2 205 VAL cc_start: 0.5996 (m) cc_final: 0.5665 (p) REVERT: 2 234 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6391 (pt) REVERT: 4 45 ASN cc_start: 0.7776 (t0) cc_final: 0.7231 (t0) REVERT: 4 51 GLN cc_start: 0.6573 (mm-40) cc_final: 0.5706 (mm-40) REVERT: 4 156 MET cc_start: 0.6951 (mtm) cc_final: 0.6681 (mtp) REVERT: 4 173 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7286 (mm-30) REVERT: 4 179 ASP cc_start: 0.7758 (m-30) cc_final: 0.7514 (m-30) REVERT: 6 44 GLU cc_start: 0.7406 (tt0) cc_final: 0.6793 (tm-30) REVERT: 6 113 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6536 (tt0) REVERT: 6 233 LEU cc_start: 0.7560 (mp) cc_final: 0.7202 (mt) REVERT: 6 234 LEU cc_start: 0.5961 (OUTLIER) cc_final: 0.5368 (pt) REVERT: 8 52 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6844 (mtpp) REVERT: 8 73 ASN cc_start: 0.7439 (OUTLIER) cc_final: 0.7079 (m110) REVERT: A 122 MET cc_start: 0.8894 (mmm) cc_final: 0.8540 (mmm) REVERT: A 160 GLU cc_start: 0.7737 (tp30) cc_final: 0.7191 (tp30) REVERT: A 396 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7844 (tt) REVERT: B 122 MET cc_start: 0.7908 (mpp) cc_final: 0.7627 (mpp) REVERT: B 137 LYS cc_start: 0.7113 (ttmt) cc_final: 0.6344 (tptt) REVERT: C 110 ASP cc_start: 0.6508 (OUTLIER) cc_final: 0.6030 (p0) REVERT: C 344 GLU cc_start: 0.6874 (tp30) cc_final: 0.6199 (tp30) REVERT: C 570 TRP cc_start: 0.2635 (m100) cc_final: 0.2128 (t60) REVERT: D 164 LEU cc_start: 0.6540 (tp) cc_final: 0.6250 (tp) REVERT: D 314 MET cc_start: 0.6391 (ptt) cc_final: 0.5200 (tpt) REVERT: D 480 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7866 (tm-30) REVERT: E 124 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7048 (tp) REVERT: E 373 MET cc_start: 0.7741 (mmp) cc_final: 0.7405 (mmp) REVERT: E 379 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7931 (p) REVERT: E 520 GLN cc_start: 0.8166 (tt0) cc_final: 0.7838 (tt0) REVERT: F 297 CYS cc_start: 0.8859 (m) cc_final: 0.8404 (m) REVERT: F 314 MET cc_start: 0.6086 (mmt) cc_final: 0.5820 (mmp) REVERT: F 529 ASN cc_start: 0.8636 (m-40) cc_final: 0.8314 (t0) REVERT: G 5 GLN cc_start: 0.7743 (mt0) cc_final: 0.7509 (mt0) REVERT: H 519 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7204 (mm-30) REVERT: I 73 ASN cc_start: 0.6410 (t0) cc_final: 0.6171 (t0) REVERT: I 105 GLN cc_start: 0.7190 (tt0) cc_final: 0.6711 (tm-30) REVERT: J 325 MET cc_start: 0.7824 (mtm) cc_final: 0.7435 (ttm) REVERT: J 364 GLU cc_start: 0.6860 (tt0) cc_final: 0.6568 (mt-10) REVERT: J 395 MET cc_start: 0.7702 (mmm) cc_final: 0.7458 (mmm) REVERT: J 433 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7262 (mp0) REVERT: J 509 ARG cc_start: 0.6264 (tpt90) cc_final: 0.5915 (ttt180) REVERT: K 13 MET cc_start: 0.5935 (mmt) cc_final: 0.4585 (ttp) REVERT: K 18 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6900 (mm-30) REVERT: K 22 LYS cc_start: 0.7566 (pttt) cc_final: 0.7223 (ptpp) REVERT: K 101 ASN cc_start: 0.6544 (t0) cc_final: 0.6163 (m-40) REVERT: K 112 THR cc_start: 0.7146 (m) cc_final: 0.6898 (p) REVERT: K 146 SER cc_start: 0.6829 (m) cc_final: 0.6412 (p) REVERT: K 150 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6569 (mm-30) REVERT: K 216 ASN cc_start: 0.7370 (t0) cc_final: 0.6576 (m-40) REVERT: K 234 LEU cc_start: 0.6243 (mt) cc_final: 0.5912 (mm) REVERT: L 325 MET cc_start: 0.7886 (mtm) cc_final: 0.7126 (ttp) REVERT: L 332 ARG cc_start: 0.7362 (mtt-85) cc_final: 0.6465 (mtt180) REVERT: M 307 LYS cc_start: 0.7841 (mtpt) cc_final: 0.7633 (mtmm) REVERT: M 325 MET cc_start: 0.7981 (mtm) cc_final: 0.7558 (ttt) REVERT: M 424 ASP cc_start: 0.6591 (p0) cc_final: 0.6372 (p0) REVERT: N 325 MET cc_start: 0.7764 (mtm) cc_final: 0.7431 (ttp) REVERT: N 364 GLU cc_start: 0.7760 (tt0) cc_final: 0.7159 (pt0) REVERT: N 399 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7457 (tt) REVERT: N 432 GLU cc_start: 0.6894 (tp30) cc_final: 0.6537 (mm-30) REVERT: N 434 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7415 (pm20) REVERT: O 26 ARG cc_start: 0.7252 (ttp80) cc_final: 0.6632 (ppt170) REVERT: O 146 SER cc_start: 0.6532 (m) cc_final: 0.6177 (t) REVERT: O 151 PRO cc_start: 0.7935 (Cg_endo) cc_final: 0.7671 (Cg_exo) REVERT: O 152 HIS cc_start: 0.7330 (m170) cc_final: 0.6386 (m-70) REVERT: O 156 MET cc_start: 0.6133 (mtm) cc_final: 0.5822 (mtm) REVERT: O 226 THR cc_start: 0.5806 (t) cc_final: 0.5374 (m) REVERT: P 325 MET cc_start: 0.7544 (mtm) cc_final: 0.6898 (ttp) REVERT: P 388 ARG cc_start: 0.7052 (tpt-90) cc_final: 0.6422 (ttm110) REVERT: P 432 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: Q 49 SER cc_start: 0.7251 (m) cc_final: 0.6912 (p) REVERT: Q 111 PHE cc_start: 0.6674 (t80) cc_final: 0.6292 (t80) REVERT: Q 113 GLU cc_start: 0.7597 (tp30) cc_final: 0.7029 (tm-30) REVERT: Q 126 GLU cc_start: 0.7529 (tt0) cc_final: 0.7310 (tt0) REVERT: Q 146 SER cc_start: 0.6984 (m) cc_final: 0.6546 (p) REVERT: Q 234 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6141 (tp) REVERT: R 325 MET cc_start: 0.7360 (mtm) cc_final: 0.6786 (ttp) REVERT: S 519 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7155 (tm-30) REVERT: T 33 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6997 (pt) REVERT: T 52 LYS cc_start: 0.7405 (mtpt) cc_final: 0.6892 (mtmm) REVERT: T 113 GLU cc_start: 0.7411 (tp30) cc_final: 0.7080 (tm-30) REVERT: T 121 GLU cc_start: 0.6930 (tt0) cc_final: 0.6343 (mm-30) REVERT: T 134 LYS cc_start: 0.7120 (ttpt) cc_final: 0.6854 (ttpt) REVERT: T 214 ASP cc_start: 0.5984 (t0) cc_final: 0.5649 (t0) REVERT: T 216 ASN cc_start: 0.7613 (t0) cc_final: 0.7133 (m110) REVERT: U 314 MET cc_start: 0.8192 (ttm) cc_final: 0.7726 (ttm) REVERT: U 401 LEU cc_start: 0.7612 (mt) cc_final: 0.7293 (mt) REVERT: U 509 ARG cc_start: 0.6260 (tpt170) cc_final: 0.6035 (ttp80) REVERT: V 395 MET cc_start: 0.6724 (mmp) cc_final: 0.6288 (mtm) REVERT: V 509 ARG cc_start: 0.6098 (OUTLIER) cc_final: 0.5791 (ttt180) REVERT: V 519 GLU cc_start: 0.7137 (tt0) cc_final: 0.6697 (mm-30) REVERT: W 307 LYS cc_start: 0.7352 (mtpt) cc_final: 0.6591 (mttt) REVERT: W 364 GLU cc_start: 0.7000 (tt0) cc_final: 0.6486 (pt0) REVERT: W 416 SER cc_start: 0.6844 (p) cc_final: 0.6320 (t) REVERT: W 509 ARG cc_start: 0.6058 (tpt170) cc_final: 0.5450 (ttt180) REVERT: X 26 ARG cc_start: 0.7474 (ptm-80) cc_final: 0.7196 (mtm110) REVERT: X 33 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6946 (pp) REVERT: X 52 LYS cc_start: 0.7690 (mtpt) cc_final: 0.7228 (mtmm) REVERT: X 130 TYR cc_start: 0.7514 (t80) cc_final: 0.6069 (t80) REVERT: X 156 MET cc_start: 0.4520 (mtm) cc_final: 0.4273 (mtm) REVERT: X 179 ASP cc_start: 0.6746 (m-30) cc_final: 0.5983 (t0) REVERT: X 216 ASN cc_start: 0.7446 (t0) cc_final: 0.6900 (t0) REVERT: Y 324 ASN cc_start: 0.7539 (m-40) cc_final: 0.7113 (t0) REVERT: Y 325 MET cc_start: 0.7804 (mtm) cc_final: 0.7057 (ttt) REVERT: Y 399 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7218 (tp) REVERT: Y 410 HIS cc_start: 0.7618 (m90) cc_final: 0.7368 (m-70) REVERT: Y 432 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6652 (mm-30) REVERT: Z 28 LYS cc_start: 0.7278 (mmtm) cc_final: 0.6505 (mmtm) REVERT: Z 52 LYS cc_start: 0.7629 (mtpt) cc_final: 0.7266 (mttp) REVERT: Z 113 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6552 (tm-30) REVERT: Z 156 MET cc_start: 0.6654 (mtm) cc_final: 0.6253 (mtm) REVERT: Z 216 ASN cc_start: 0.8455 (t0) cc_final: 0.8013 (m-40) REVERT: a 325 MET cc_start: 0.7566 (mtm) cc_final: 0.6950 (ttm) REVERT: a 401 LEU cc_start: 0.7423 (mt) cc_final: 0.7149 (mt) REVERT: a 432 GLU cc_start: 0.6505 (tp30) cc_final: 0.6286 (mm-30) REVERT: b 339 ASP cc_start: 0.8037 (t0) cc_final: 0.7631 (m-30) REVERT: d 13 MET cc_start: 0.4458 (ttp) cc_final: 0.3930 (ttm) REVERT: d 69 ASN cc_start: 0.7428 (OUTLIER) cc_final: 0.7211 (m-40) REVERT: d 101 ASN cc_start: 0.7186 (t0) cc_final: 0.6897 (m-40) REVERT: d 189 ARG cc_start: 0.5651 (ttm-80) cc_final: 0.5177 (mtm-85) REVERT: d 234 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6497 (pt) REVERT: f 15 GLU cc_start: 0.7828 (tt0) cc_final: 0.7394 (tp30) REVERT: f 26 ARG cc_start: 0.6745 (ttt180) cc_final: 0.6417 (ttp80) REVERT: f 52 LYS cc_start: 0.6624 (OUTLIER) cc_final: 0.6225 (mtpt) REVERT: f 101 ASN cc_start: 0.6943 (t0) cc_final: 0.6444 (m-40) REVERT: f 112 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7945 (p) outliers start: 154 outliers final: 97 residues processed: 875 average time/residue: 0.6712 time to fit residues: 990.5053 Evaluate side-chains 860 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 741 time to evaluate : 6.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 45 ASN Chi-restraints excluded: chain 2 residue 69 ASN Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 170 SER Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 173 GLU Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 112 THR Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 8 residue 73 ASN Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 474 CYS Chi-restraints excluded: chain H residue 434 GLU Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain M residue 461 ASP Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 412 SER Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 149 ASP Chi-restraints excluded: chain Q residue 174 ASN Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 149 ASP Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 225 ILE Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 338 ASP Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain V residue 412 SER Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 69 ASN Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 13 MET Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Chi-restraints excluded: chain f residue 233 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 828 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 489 optimal weight: 0.9990 chunk 627 optimal weight: 0.8980 chunk 486 optimal weight: 0.4980 chunk 723 optimal weight: 0.9990 chunk 479 optimal weight: 1.9990 chunk 855 optimal weight: 2.9990 chunk 535 optimal weight: 4.9990 chunk 521 optimal weight: 0.6980 chunk 395 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 69 ASN 2 114 GLN B 546 HIS ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 ASN E 514 ASN ** F 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 545 GLN I 174 ASN O 174 ASN ** P 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 GLN V 322 GLN Y 396 GLN d 80 GLN f 80 GLN f 165 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 69957 Z= 0.145 Angle : 0.475 10.082 94694 Z= 0.248 Chirality : 0.041 0.183 10759 Planarity : 0.003 0.042 12440 Dihedral : 5.099 79.566 10196 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.14 % Allowed : 13.86 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.09), residues: 8881 helix: 2.71 (0.09), residues: 3487 sheet: 0.73 (0.11), residues: 2029 loop : 0.01 (0.11), residues: 3365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 570 HIS 0.007 0.001 HIS F 348 PHE 0.032 0.002 PHE 2 71 TYR 0.016 0.001 TYR 6 118 ARG 0.008 0.000 ARG X 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 764 time to evaluate : 6.105 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: 0 156 MET cc_start: 0.7615 (mtm) cc_final: 0.7370 (mtm) REVERT: 2 135 ARG cc_start: 0.7949 (tpp80) cc_final: 0.7185 (ttm-80) REVERT: 2 205 VAL cc_start: 0.6051 (m) cc_final: 0.5717 (p) REVERT: 2 234 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6448 (pt) REVERT: 4 45 ASN cc_start: 0.7665 (t0) cc_final: 0.7129 (t0) REVERT: 4 51 GLN cc_start: 0.6559 (mm-40) cc_final: 0.5669 (mm-40) REVERT: 4 156 MET cc_start: 0.7030 (mtm) cc_final: 0.6788 (mtp) REVERT: 4 173 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7354 (mm-30) REVERT: 4 179 ASP cc_start: 0.7755 (m-30) cc_final: 0.7519 (m-30) REVERT: 6 44 GLU cc_start: 0.7425 (tt0) cc_final: 0.6801 (tm-30) REVERT: 6 113 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6365 (tt0) REVERT: 6 233 LEU cc_start: 0.7521 (mp) cc_final: 0.7315 (mt) REVERT: 6 234 LEU cc_start: 0.5789 (OUTLIER) cc_final: 0.5411 (pt) REVERT: 8 52 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6940 (mtpp) REVERT: 8 73 ASN cc_start: 0.7354 (OUTLIER) cc_final: 0.7029 (m110) REVERT: A 122 MET cc_start: 0.8871 (mmm) cc_final: 0.8551 (mmm) REVERT: A 155 PHE cc_start: 0.5003 (m-80) cc_final: 0.4718 (m-10) REVERT: A 160 GLU cc_start: 0.7758 (tp30) cc_final: 0.7435 (tp30) REVERT: A 243 LEU cc_start: 0.7335 (mt) cc_final: 0.7076 (pp) REVERT: A 396 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7851 (tt) REVERT: B 122 MET cc_start: 0.7965 (mpp) cc_final: 0.7643 (mpp) REVERT: B 137 LYS cc_start: 0.7123 (ttmt) cc_final: 0.6337 (tptt) REVERT: C 314 MET cc_start: 0.6124 (tpt) cc_final: 0.5804 (tpt) REVERT: C 344 GLU cc_start: 0.6855 (tp30) cc_final: 0.6174 (tp30) REVERT: C 570 TRP cc_start: 0.2543 (m100) cc_final: 0.2072 (t60) REVERT: D 164 LEU cc_start: 0.6586 (tp) cc_final: 0.6285 (tp) REVERT: D 314 MET cc_start: 0.6275 (ptt) cc_final: 0.5181 (tpt) REVERT: D 480 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: E 124 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7205 (tp) REVERT: E 323 HIS cc_start: 0.6196 (p-80) cc_final: 0.5988 (p-80) REVERT: E 373 MET cc_start: 0.7665 (mmp) cc_final: 0.7453 (mmp) REVERT: E 379 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.8013 (p) REVERT: E 520 GLN cc_start: 0.8172 (tt0) cc_final: 0.7823 (tt0) REVERT: F 297 CYS cc_start: 0.8843 (m) cc_final: 0.8419 (m) REVERT: F 314 MET cc_start: 0.6062 (mmt) cc_final: 0.5774 (mmp) REVERT: F 529 ASN cc_start: 0.8614 (m-40) cc_final: 0.8307 (t0) REVERT: H 519 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7204 (mm-30) REVERT: I 101 ASN cc_start: 0.6763 (t0) cc_final: 0.6312 (m-40) REVERT: I 105 GLN cc_start: 0.7184 (tt0) cc_final: 0.6709 (tm-30) REVERT: J 325 MET cc_start: 0.7826 (mtm) cc_final: 0.7440 (ttm) REVERT: J 364 GLU cc_start: 0.6852 (tt0) cc_final: 0.6560 (mt-10) REVERT: J 395 MET cc_start: 0.7746 (mmm) cc_final: 0.7498 (mmm) REVERT: J 430 ASN cc_start: 0.7286 (t0) cc_final: 0.6617 (t0) REVERT: J 433 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7277 (mp0) REVERT: J 509 ARG cc_start: 0.6244 (tpt90) cc_final: 0.5920 (ttt180) REVERT: K 13 MET cc_start: 0.6021 (mmt) cc_final: 0.4595 (ttp) REVERT: K 22 LYS cc_start: 0.7574 (pttt) cc_final: 0.7242 (ptpp) REVERT: K 101 ASN cc_start: 0.6529 (t0) cc_final: 0.6260 (m-40) REVERT: K 112 THR cc_start: 0.7113 (m) cc_final: 0.6881 (p) REVERT: K 146 SER cc_start: 0.6836 (m) cc_final: 0.6406 (p) REVERT: K 150 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6517 (mm-30) REVERT: K 216 ASN cc_start: 0.7367 (t0) cc_final: 0.6577 (m-40) REVERT: K 234 LEU cc_start: 0.6242 (mt) cc_final: 0.5916 (mm) REVERT: L 325 MET cc_start: 0.7881 (mtm) cc_final: 0.7128 (ttp) REVERT: L 332 ARG cc_start: 0.7357 (mtt-85) cc_final: 0.6476 (mtt180) REVERT: M 307 LYS cc_start: 0.7829 (mtpt) cc_final: 0.7617 (mtmm) REVERT: M 325 MET cc_start: 0.7981 (mtm) cc_final: 0.7581 (ttm) REVERT: M 338 ASP cc_start: 0.7304 (p0) cc_final: 0.6832 (p0) REVERT: M 424 ASP cc_start: 0.6640 (p0) cc_final: 0.6399 (p0) REVERT: N 325 MET cc_start: 0.7762 (mtm) cc_final: 0.7428 (ttp) REVERT: N 364 GLU cc_start: 0.7763 (tt0) cc_final: 0.7154 (pt0) REVERT: N 399 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7457 (tt) REVERT: O 26 ARG cc_start: 0.7237 (ttp80) cc_final: 0.6625 (ppt170) REVERT: O 146 SER cc_start: 0.6525 (m) cc_final: 0.6190 (t) REVERT: O 151 PRO cc_start: 0.7992 (Cg_endo) cc_final: 0.7731 (Cg_exo) REVERT: O 152 HIS cc_start: 0.7300 (m170) cc_final: 0.6347 (m-70) REVERT: O 156 MET cc_start: 0.6138 (mtm) cc_final: 0.5808 (mtm) REVERT: P 325 MET cc_start: 0.7542 (mtm) cc_final: 0.6897 (ttp) REVERT: P 345 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7523 (mm) REVERT: P 388 ARG cc_start: 0.7067 (tpt-90) cc_final: 0.6430 (ttm110) REVERT: P 432 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6250 (mp0) REVERT: Q 49 SER cc_start: 0.7209 (m) cc_final: 0.6866 (p) REVERT: Q 70 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6425 (mm-30) REVERT: Q 111 PHE cc_start: 0.6688 (t80) cc_final: 0.6445 (t80) REVERT: Q 113 GLU cc_start: 0.7544 (tp30) cc_final: 0.6976 (tm-30) REVERT: Q 126 GLU cc_start: 0.7521 (tt0) cc_final: 0.7314 (tt0) REVERT: Q 146 SER cc_start: 0.6992 (m) cc_final: 0.6549 (p) REVERT: Q 234 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6234 (tp) REVERT: R 325 MET cc_start: 0.7382 (mtm) cc_final: 0.6824 (ttp) REVERT: S 519 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7170 (tm-30) REVERT: T 17 SER cc_start: 0.6523 (t) cc_final: 0.5902 (p) REVERT: T 33 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.7016 (pt) REVERT: T 52 LYS cc_start: 0.7440 (mtpt) cc_final: 0.6918 (mtmm) REVERT: T 113 GLU cc_start: 0.7424 (tp30) cc_final: 0.7097 (tm-30) REVERT: T 121 GLU cc_start: 0.6898 (tt0) cc_final: 0.6313 (mm-30) REVERT: T 134 LYS cc_start: 0.7112 (ttpt) cc_final: 0.6843 (ttpt) REVERT: T 214 ASP cc_start: 0.5902 (t0) cc_final: 0.5576 (t0) REVERT: T 216 ASN cc_start: 0.7540 (t0) cc_final: 0.7083 (m110) REVERT: U 314 MET cc_start: 0.8189 (ttm) cc_final: 0.7692 (ttm) REVERT: U 401 LEU cc_start: 0.7580 (mt) cc_final: 0.7114 (mt) REVERT: U 509 ARG cc_start: 0.6242 (tpt170) cc_final: 0.6032 (ttp80) REVERT: V 395 MET cc_start: 0.6725 (mmp) cc_final: 0.6294 (mtm) REVERT: V 509 ARG cc_start: 0.6105 (OUTLIER) cc_final: 0.5787 (ttt180) REVERT: V 519 GLU cc_start: 0.7135 (tt0) cc_final: 0.6699 (mm-30) REVERT: W 307 LYS cc_start: 0.7343 (mtpt) cc_final: 0.6582 (mttt) REVERT: W 364 GLU cc_start: 0.7004 (tt0) cc_final: 0.6484 (pt0) REVERT: W 416 SER cc_start: 0.6860 (p) cc_final: 0.6347 (t) REVERT: X 26 ARG cc_start: 0.7455 (ptm-80) cc_final: 0.7213 (mtm110) REVERT: X 33 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6988 (pp) REVERT: X 52 LYS cc_start: 0.7696 (mtpt) cc_final: 0.7234 (mtmm) REVERT: X 80 GLN cc_start: 0.7258 (tp40) cc_final: 0.6708 (tp40) REVERT: X 130 TYR cc_start: 0.7503 (t80) cc_final: 0.5978 (t80) REVERT: X 179 ASP cc_start: 0.6644 (m-30) cc_final: 0.6103 (t0) REVERT: X 216 ASN cc_start: 0.7401 (t0) cc_final: 0.6904 (t0) REVERT: Y 324 ASN cc_start: 0.7548 (m-40) cc_final: 0.7143 (t0) REVERT: Y 325 MET cc_start: 0.7794 (mtm) cc_final: 0.7221 (ttm) REVERT: Y 399 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7234 (tp) REVERT: Y 410 HIS cc_start: 0.7614 (m90) cc_final: 0.7380 (m-70) REVERT: Z 28 LYS cc_start: 0.7246 (mmtm) cc_final: 0.6524 (mmtm) REVERT: Z 52 LYS cc_start: 0.7634 (mtpt) cc_final: 0.7258 (mttp) REVERT: Z 70 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6604 (mm-30) REVERT: Z 113 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6514 (tm-30) REVERT: Z 143 TYR cc_start: 0.5265 (p90) cc_final: 0.4561 (p90) REVERT: Z 156 MET cc_start: 0.6675 (mtm) cc_final: 0.6315 (mtm) REVERT: Z 216 ASN cc_start: 0.8404 (t0) cc_final: 0.8003 (m-40) REVERT: a 325 MET cc_start: 0.7579 (mtm) cc_final: 0.6958 (ttm) REVERT: a 401 LEU cc_start: 0.7404 (mt) cc_final: 0.7123 (mt) REVERT: b 339 ASP cc_start: 0.8035 (t0) cc_final: 0.7548 (m-30) REVERT: d 13 MET cc_start: 0.4480 (ttp) cc_final: 0.4036 (ttm) REVERT: d 69 ASN cc_start: 0.7428 (OUTLIER) cc_final: 0.7159 (m110) REVERT: d 101 ASN cc_start: 0.7219 (t0) cc_final: 0.6936 (m-40) REVERT: d 189 ARG cc_start: 0.5610 (ttm-80) cc_final: 0.5070 (mtm-85) REVERT: d 214 ASP cc_start: 0.6274 (t0) cc_final: 0.5975 (t0) REVERT: d 234 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6482 (pt) REVERT: f 15 GLU cc_start: 0.7827 (tt0) cc_final: 0.7393 (tp30) REVERT: f 26 ARG cc_start: 0.6728 (ttt180) cc_final: 0.6396 (ttp80) REVERT: f 52 LYS cc_start: 0.6644 (OUTLIER) cc_final: 0.6226 (mtpt) REVERT: f 101 ASN cc_start: 0.6903 (t0) cc_final: 0.6447 (m-40) REVERT: f 112 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7935 (p) outliers start: 151 outliers final: 106 residues processed: 860 average time/residue: 0.7213 time to fit residues: 1052.8274 Evaluate side-chains 867 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 738 time to evaluate : 6.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 67 LYS Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 69 ASN Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 168 LYS Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 73 ASN Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 173 GLU Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 112 THR Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 8 residue 73 ASN Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 474 CYS Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain M residue 461 ASP Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 412 SER Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 174 ASN Chi-restraints excluded: chain P residue 345 ILE Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 174 ASN Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 386 MET Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 149 ASP Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 225 ILE Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 338 ASP Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain V residue 412 SER Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain Y residue 307 LYS Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain Z residue 70 GLU Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 307 LYS Chi-restraints excluded: chain b residue 345 ILE Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 69 ASN Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 13 MET Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Chi-restraints excluded: chain f residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 529 optimal weight: 5.9990 chunk 341 optimal weight: 8.9990 chunk 511 optimal weight: 4.9990 chunk 257 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 544 optimal weight: 5.9990 chunk 583 optimal weight: 2.9990 chunk 423 optimal weight: 0.0980 chunk 79 optimal weight: 5.9990 chunk 672 optimal weight: 5.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 45 ASN 2 69 ASN 2 114 GLN B 446 GLN B 502 ASN B 546 HIS ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 ASN E 514 ASN F 607 GLN G 5 GLN I 174 ASN K 129 HIS M 437 GLN ** N 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 ASN ** T 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 GLN V 322 GLN Z 69 ASN Z 129 HIS f 165 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 69957 Z= 0.410 Angle : 0.644 10.190 94694 Z= 0.337 Chirality : 0.047 0.220 10759 Planarity : 0.005 0.054 12440 Dihedral : 5.545 76.915 10196 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.30 % Allowed : 14.15 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.09), residues: 8881 helix: 2.16 (0.09), residues: 3481 sheet: 0.62 (0.12), residues: 1953 loop : -0.25 (0.11), residues: 3447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 570 HIS 0.009 0.002 HIS X 129 PHE 0.038 0.003 PHE 6 71 TYR 0.019 0.002 TYR J 454 ARG 0.013 0.001 ARG V 521 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 719 time to evaluate : 6.220 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: 2 44 GLU cc_start: 0.7787 (tt0) cc_final: 0.7494 (tm-30) REVERT: 2 110 ILE cc_start: 0.7950 (mt) cc_final: 0.7643 (tp) REVERT: 2 135 ARG cc_start: 0.7963 (tpp80) cc_final: 0.7229 (ttm-80) REVERT: 2 205 VAL cc_start: 0.5963 (m) cc_final: 0.5720 (p) REVERT: 2 234 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6785 (pt) REVERT: 4 45 ASN cc_start: 0.7668 (t0) cc_final: 0.7330 (t0) REVERT: 6 44 GLU cc_start: 0.7503 (tt0) cc_final: 0.6855 (tm-30) REVERT: 6 113 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6481 (tt0) REVERT: 6 233 LEU cc_start: 0.7687 (mp) cc_final: 0.7475 (mt) REVERT: 8 52 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.7030 (mtpp) REVERT: 8 174 ASN cc_start: 0.7848 (m110) cc_final: 0.7642 (m110) REVERT: A 122 MET cc_start: 0.8940 (mmm) cc_final: 0.8624 (mmm) REVERT: A 260 GLN cc_start: 0.8767 (mp10) cc_final: 0.8550 (mp10) REVERT: A 396 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7931 (tt) REVERT: B 384 VAL cc_start: 0.8409 (m) cc_final: 0.8037 (t) REVERT: C 314 MET cc_start: 0.6250 (tpt) cc_final: 0.5966 (tpt) REVERT: C 344 GLU cc_start: 0.7271 (tp30) cc_final: 0.6796 (tp30) REVERT: C 570 TRP cc_start: 0.2658 (m100) cc_final: 0.2110 (t60) REVERT: D 164 LEU cc_start: 0.6724 (tp) cc_final: 0.6400 (tp) REVERT: D 480 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.8018 (tm-30) REVERT: E 124 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7446 (tp) REVERT: E 373 MET cc_start: 0.7904 (mmp) cc_final: 0.7690 (mmp) REVERT: E 379 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8119 (p) REVERT: E 520 GLN cc_start: 0.8402 (tt0) cc_final: 0.8128 (tt0) REVERT: F 297 CYS cc_start: 0.9113 (m) cc_final: 0.8732 (m) REVERT: F 314 MET cc_start: 0.6169 (mmt) cc_final: 0.5884 (mmp) REVERT: F 529 ASN cc_start: 0.8570 (m-40) cc_final: 0.8240 (t0) REVERT: H 519 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7378 (mm-30) REVERT: I 101 ASN cc_start: 0.6595 (t0) cc_final: 0.6261 (m-40) REVERT: I 111 PHE cc_start: 0.7166 (t80) cc_final: 0.6869 (t80) REVERT: J 325 MET cc_start: 0.7953 (mtm) cc_final: 0.7484 (ttm) REVERT: J 364 GLU cc_start: 0.6620 (tt0) cc_final: 0.6332 (pt0) REVERT: J 386 MET cc_start: 0.7393 (ttm) cc_final: 0.7179 (ttm) REVERT: J 509 ARG cc_start: 0.6542 (tpt90) cc_final: 0.6031 (ttt-90) REVERT: K 13 MET cc_start: 0.6292 (mmt) cc_final: 0.4841 (ttp) REVERT: K 101 ASN cc_start: 0.6522 (t0) cc_final: 0.6149 (m-40) REVERT: K 112 THR cc_start: 0.7258 (m) cc_final: 0.6914 (p) REVERT: K 146 SER cc_start: 0.6623 (m) cc_final: 0.6187 (p) REVERT: K 150 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6681 (mm-30) REVERT: K 216 ASN cc_start: 0.7356 (t0) cc_final: 0.6562 (m-40) REVERT: L 325 MET cc_start: 0.7904 (mtm) cc_final: 0.7178 (ttm) REVERT: L 332 ARG cc_start: 0.7267 (mtt-85) cc_final: 0.6272 (mtt180) REVERT: M 307 LYS cc_start: 0.7889 (mtpt) cc_final: 0.7539 (mtmm) REVERT: M 325 MET cc_start: 0.8140 (mtm) cc_final: 0.7655 (ttm) REVERT: M 338 ASP cc_start: 0.7509 (p0) cc_final: 0.7126 (p0) REVERT: N 325 MET cc_start: 0.7727 (mtm) cc_final: 0.7184 (ttt) REVERT: N 364 GLU cc_start: 0.7932 (tt0) cc_final: 0.7344 (pt0) REVERT: N 399 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7515 (tt) REVERT: O 26 ARG cc_start: 0.7319 (ttp80) cc_final: 0.6755 (ppt170) REVERT: O 156 MET cc_start: 0.5933 (mtm) cc_final: 0.5620 (mtm) REVERT: O 214 ASP cc_start: 0.7027 (t0) cc_final: 0.6666 (t0) REVERT: P 325 MET cc_start: 0.7336 (mtm) cc_final: 0.6878 (ttp) REVERT: P 345 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7597 (mm) REVERT: P 432 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6523 (mp0) REVERT: Q 70 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6794 (mm-30) REVERT: Q 113 GLU cc_start: 0.7650 (tp30) cc_final: 0.7120 (tm-30) REVERT: Q 146 SER cc_start: 0.6831 (m) cc_final: 0.6410 (p) REVERT: R 325 MET cc_start: 0.7329 (mtm) cc_final: 0.6669 (ttp) REVERT: R 430 ASN cc_start: 0.8027 (t0) cc_final: 0.7506 (m-40) REVERT: S 519 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7139 (tm-30) REVERT: T 52 LYS cc_start: 0.7201 (mtpt) cc_final: 0.6665 (mtmm) REVERT: T 113 GLU cc_start: 0.7427 (tp30) cc_final: 0.7131 (tm-30) REVERT: T 121 GLU cc_start: 0.7030 (tt0) cc_final: 0.6352 (mm-30) REVERT: T 214 ASP cc_start: 0.6502 (t0) cc_final: 0.6203 (t0) REVERT: T 216 ASN cc_start: 0.7635 (t0) cc_final: 0.7289 (m110) REVERT: U 314 MET cc_start: 0.8091 (ttm) cc_final: 0.7682 (ttm) REVERT: U 509 ARG cc_start: 0.6406 (tpt170) cc_final: 0.6030 (ttp80) REVERT: V 325 MET cc_start: 0.7677 (ttp) cc_final: 0.6506 (mmt) REVERT: V 395 MET cc_start: 0.6710 (mmp) cc_final: 0.6246 (mtm) REVERT: V 401 LEU cc_start: 0.7258 (tp) cc_final: 0.6916 (mt) REVERT: V 461 ASP cc_start: 0.7241 (p0) cc_final: 0.6703 (t0) REVERT: V 509 ARG cc_start: 0.6382 (OUTLIER) cc_final: 0.5745 (ttt180) REVERT: V 519 GLU cc_start: 0.7243 (tt0) cc_final: 0.6906 (mt-10) REVERT: W 307 LYS cc_start: 0.7370 (mtpt) cc_final: 0.6619 (mttt) REVERT: W 364 GLU cc_start: 0.7216 (tt0) cc_final: 0.6701 (pt0) REVERT: W 388 ARG cc_start: 0.6918 (ttt180) cc_final: 0.6228 (ttm110) REVERT: W 416 SER cc_start: 0.6858 (p) cc_final: 0.6338 (t) REVERT: X 26 ARG cc_start: 0.7482 (ptm-80) cc_final: 0.7119 (mtm110) REVERT: X 52 LYS cc_start: 0.7651 (mtpt) cc_final: 0.7304 (mtmm) REVERT: X 130 TYR cc_start: 0.7452 (t80) cc_final: 0.5976 (t80) REVERT: X 156 MET cc_start: 0.4897 (mtm) cc_final: 0.4514 (mtm) REVERT: X 179 ASP cc_start: 0.6724 (m-30) cc_final: 0.6221 (t0) REVERT: X 209 GLU cc_start: 0.5987 (OUTLIER) cc_final: 0.5547 (mt-10) REVERT: X 216 ASN cc_start: 0.7639 (t0) cc_final: 0.7057 (t0) REVERT: Y 324 ASN cc_start: 0.7489 (m-40) cc_final: 0.7126 (t0) REVERT: Y 325 MET cc_start: 0.7856 (mtm) cc_final: 0.7192 (ttm) REVERT: Z 113 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6697 (tm-30) REVERT: Z 143 TYR cc_start: 0.5346 (p90) cc_final: 0.4707 (p90) REVERT: Z 216 ASN cc_start: 0.8426 (t0) cc_final: 0.8052 (m-40) REVERT: a 325 MET cc_start: 0.7293 (mtm) cc_final: 0.6645 (ttm) REVERT: b 339 ASP cc_start: 0.7917 (t0) cc_final: 0.7518 (m-30) REVERT: b 355 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.6746 (t80) REVERT: d 13 MET cc_start: 0.5313 (ttp) cc_final: 0.4733 (ttm) REVERT: d 51 GLN cc_start: 0.7145 (mt0) cc_final: 0.6852 (mt0) REVERT: d 101 ASN cc_start: 0.7275 (t0) cc_final: 0.6812 (m-40) REVERT: d 189 ARG cc_start: 0.5781 (ttm-80) cc_final: 0.5324 (mtm-85) REVERT: d 234 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6735 (pt) REVERT: f 15 GLU cc_start: 0.7627 (tt0) cc_final: 0.7275 (tp30) REVERT: f 69 ASN cc_start: 0.6856 (p0) cc_final: 0.6421 (m-40) REVERT: f 101 ASN cc_start: 0.6588 (t0) cc_final: 0.6239 (m-40) REVERT: f 112 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7998 (p) outliers start: 162 outliers final: 109 residues processed: 833 average time/residue: 0.6625 time to fit residues: 932.6848 Evaluate side-chains 809 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 685 time to evaluate : 6.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 22 LYS Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 112 THR Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 474 CYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain J residue 434 GLU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain N residue 341 THR Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 412 SER Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 461 ASP Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain P residue 345 ILE Chi-restraints excluded: chain P residue 396 GLN Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 149 ASP Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 225 ILE Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 396 GLN Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 209 GLU Chi-restraints excluded: chain Y residue 307 LYS Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 13 MET Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 778 optimal weight: 1.9990 chunk 819 optimal weight: 3.9990 chunk 748 optimal weight: 2.9990 chunk 797 optimal weight: 9.9990 chunk 480 optimal weight: 0.9980 chunk 347 optimal weight: 6.9990 chunk 626 optimal weight: 1.9990 chunk 244 optimal weight: 20.0000 chunk 720 optimal weight: 0.8980 chunk 754 optimal weight: 7.9990 chunk 794 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 174 ASN 2 45 ASN B 546 HIS ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 ASN ** F 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN I 174 ASN O 101 ASN ** P 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 ASN Q 165 ASN U 322 GLN V 322 GLN d 69 ASN d 80 GLN f 105 GLN f 165 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 69957 Z= 0.228 Angle : 0.532 9.390 94694 Z= 0.279 Chirality : 0.043 0.180 10759 Planarity : 0.004 0.046 12440 Dihedral : 5.309 79.107 10190 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.86 % Allowed : 14.85 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.09), residues: 8881 helix: 2.37 (0.09), residues: 3489 sheet: 0.66 (0.12), residues: 1982 loop : -0.18 (0.11), residues: 3410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 187 HIS 0.006 0.001 HIS Y 365 PHE 0.030 0.002 PHE 0 71 TYR 0.020 0.001 TYR B 328 ARG 0.008 0.000 ARG X 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 735 time to evaluate : 6.232 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: 0 67 LYS cc_start: 0.6984 (tttm) cc_final: 0.6750 (tttm) REVERT: 0 156 MET cc_start: 0.7512 (mtm) cc_final: 0.7062 (mtt) REVERT: 2 44 GLU cc_start: 0.7776 (tt0) cc_final: 0.7492 (tm-30) REVERT: 2 110 ILE cc_start: 0.8032 (mt) cc_final: 0.7730 (tp) REVERT: 2 135 ARG cc_start: 0.7981 (tpp80) cc_final: 0.7263 (ttm-80) REVERT: 2 205 VAL cc_start: 0.6035 (m) cc_final: 0.5748 (p) REVERT: 2 234 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6888 (pt) REVERT: 4 45 ASN cc_start: 0.7608 (t0) cc_final: 0.7290 (t0) REVERT: 4 98 GLN cc_start: 0.6850 (mt0) cc_final: 0.6525 (mt0) REVERT: 4 225 ILE cc_start: 0.8374 (mt) cc_final: 0.7920 (mm) REVERT: 6 44 GLU cc_start: 0.7514 (tt0) cc_final: 0.6852 (tm-30) REVERT: 6 51 GLN cc_start: 0.6819 (mm-40) cc_final: 0.6385 (mm-40) REVERT: 6 113 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6616 (tt0) REVERT: 8 52 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.7123 (mtpp) REVERT: 8 113 GLU cc_start: 0.7572 (mm-30) cc_final: 0.6903 (tt0) REVERT: 8 174 ASN cc_start: 0.7785 (m110) cc_final: 0.7564 (m110) REVERT: A 122 MET cc_start: 0.8903 (mmm) cc_final: 0.8622 (mmm) REVERT: A 225 LYS cc_start: 0.8470 (tptt) cc_final: 0.8116 (tptt) REVERT: A 396 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7918 (tt) REVERT: B 122 MET cc_start: 0.7816 (mpp) cc_final: 0.7505 (mtt) REVERT: B 137 LYS cc_start: 0.7285 (ttmt) cc_final: 0.6330 (tptt) REVERT: C 110 ASP cc_start: 0.6474 (OUTLIER) cc_final: 0.5869 (p0) REVERT: C 344 GLU cc_start: 0.7189 (tp30) cc_final: 0.6734 (tp30) REVERT: C 570 TRP cc_start: 0.2415 (m100) cc_final: 0.1928 (t60) REVERT: D 164 LEU cc_start: 0.6628 (tp) cc_final: 0.6323 (tp) REVERT: D 480 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.8005 (tm-30) REVERT: E 124 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7390 (tp) REVERT: E 373 MET cc_start: 0.7970 (mmp) cc_final: 0.7500 (mmp) REVERT: E 379 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.8081 (p) REVERT: E 520 GLN cc_start: 0.8308 (tt0) cc_final: 0.8005 (tt0) REVERT: F 314 MET cc_start: 0.6089 (mmt) cc_final: 0.5805 (mmp) REVERT: F 529 ASN cc_start: 0.8561 (m-40) cc_final: 0.8288 (t0) REVERT: H 519 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7488 (mm-30) REVERT: I 101 ASN cc_start: 0.6556 (t0) cc_final: 0.6269 (m-40) REVERT: J 325 MET cc_start: 0.7889 (mtm) cc_final: 0.7436 (ttm) REVERT: J 364 GLU cc_start: 0.6679 (tt0) cc_final: 0.6451 (mt-10) REVERT: J 509 ARG cc_start: 0.6381 (tpt90) cc_final: 0.5942 (ttt-90) REVERT: K 13 MET cc_start: 0.6353 (mmt) cc_final: 0.4883 (ttp) REVERT: K 101 ASN cc_start: 0.6472 (t0) cc_final: 0.6251 (m-40) REVERT: K 112 THR cc_start: 0.6952 (m) cc_final: 0.6588 (p) REVERT: K 146 SER cc_start: 0.6698 (m) cc_final: 0.6313 (p) REVERT: K 150 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6493 (mm-30) REVERT: K 216 ASN cc_start: 0.7271 (t0) cc_final: 0.6510 (m-40) REVERT: L 325 MET cc_start: 0.7912 (mtm) cc_final: 0.7175 (ttp) REVERT: L 332 ARG cc_start: 0.7211 (mtt-85) cc_final: 0.6273 (mtt180) REVERT: M 307 LYS cc_start: 0.7757 (mtpt) cc_final: 0.7279 (mtmm) REVERT: M 325 MET cc_start: 0.8163 (mtm) cc_final: 0.7705 (ttm) REVERT: M 338 ASP cc_start: 0.7194 (p0) cc_final: 0.6812 (p0) REVERT: M 424 ASP cc_start: 0.7401 (p0) cc_final: 0.6907 (p0) REVERT: N 325 MET cc_start: 0.7776 (mtm) cc_final: 0.7230 (ttt) REVERT: N 364 GLU cc_start: 0.7864 (tt0) cc_final: 0.7253 (pt0) REVERT: N 399 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7608 (tt) REVERT: O 26 ARG cc_start: 0.7370 (ttp80) cc_final: 0.6659 (ppt170) REVERT: O 156 MET cc_start: 0.5378 (mtm) cc_final: 0.5059 (mtm) REVERT: O 214 ASP cc_start: 0.7064 (t0) cc_final: 0.6706 (t0) REVERT: P 325 MET cc_start: 0.7391 (mtm) cc_final: 0.6841 (ttp) REVERT: P 345 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7587 (mm) REVERT: P 432 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: Q 70 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6584 (mm-30) REVERT: Q 113 GLU cc_start: 0.7646 (tp30) cc_final: 0.7095 (tm-30) REVERT: Q 146 SER cc_start: 0.6722 (m) cc_final: 0.6324 (p) REVERT: R 325 MET cc_start: 0.7310 (mtm) cc_final: 0.6810 (ttp) REVERT: R 430 ASN cc_start: 0.8053 (t0) cc_final: 0.7565 (m-40) REVERT: S 519 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7090 (tm-30) REVERT: T 52 LYS cc_start: 0.7165 (mtpt) cc_final: 0.6613 (mtmm) REVERT: T 67 LYS cc_start: 0.7703 (tttt) cc_final: 0.7484 (tttt) REVERT: T 113 GLU cc_start: 0.7364 (tp30) cc_final: 0.7025 (tm-30) REVERT: T 121 GLU cc_start: 0.6889 (tt0) cc_final: 0.6209 (mm-30) REVERT: T 151 PRO cc_start: 0.8230 (Cg_endo) cc_final: 0.7986 (Cg_exo) REVERT: T 214 ASP cc_start: 0.6277 (t0) cc_final: 0.6000 (t0) REVERT: T 216 ASN cc_start: 0.7611 (t0) cc_final: 0.7295 (m110) REVERT: U 314 MET cc_start: 0.8158 (ttm) cc_final: 0.7725 (ttm) REVERT: U 401 LEU cc_start: 0.7399 (mt) cc_final: 0.6903 (mt) REVERT: U 509 ARG cc_start: 0.6307 (tpt170) cc_final: 0.6041 (ttp80) REVERT: V 325 MET cc_start: 0.7840 (ttp) cc_final: 0.6618 (mmt) REVERT: V 401 LEU cc_start: 0.7296 (tp) cc_final: 0.6968 (mt) REVERT: V 509 ARG cc_start: 0.6271 (OUTLIER) cc_final: 0.5600 (ttt180) REVERT: V 519 GLU cc_start: 0.7220 (tt0) cc_final: 0.6917 (mt-10) REVERT: W 307 LYS cc_start: 0.7305 (mtpt) cc_final: 0.6576 (mttt) REVERT: W 325 MET cc_start: 0.8058 (ttp) cc_final: 0.7689 (ttm) REVERT: W 364 GLU cc_start: 0.7097 (tt0) cc_final: 0.6584 (pt0) REVERT: W 388 ARG cc_start: 0.6899 (ttt180) cc_final: 0.6207 (ttm110) REVERT: X 52 LYS cc_start: 0.7659 (mtpt) cc_final: 0.7312 (mtmm) REVERT: X 130 TYR cc_start: 0.7473 (t80) cc_final: 0.6072 (t80) REVERT: X 156 MET cc_start: 0.4834 (mtm) cc_final: 0.4485 (mtm) REVERT: X 179 ASP cc_start: 0.6662 (m-30) cc_final: 0.6140 (t0) REVERT: X 216 ASN cc_start: 0.7584 (t0) cc_final: 0.7055 (t0) REVERT: Y 324 ASN cc_start: 0.7507 (m-40) cc_final: 0.7089 (t0) REVERT: Y 325 MET cc_start: 0.7862 (mtm) cc_final: 0.7209 (ttm) REVERT: Y 509 ARG cc_start: 0.7137 (tpt90) cc_final: 0.6440 (ttp80) REVERT: Z 44 GLU cc_start: 0.6545 (pt0) cc_final: 0.6214 (pt0) REVERT: Z 113 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6672 (tm-30) REVERT: Z 143 TYR cc_start: 0.5430 (p90) cc_final: 0.4739 (p90) REVERT: Z 152 HIS cc_start: 0.7242 (m-70) cc_final: 0.6662 (m-70) REVERT: Z 156 MET cc_start: 0.6834 (mtm) cc_final: 0.6417 (mtm) REVERT: Z 216 ASN cc_start: 0.8386 (t0) cc_final: 0.8006 (m-40) REVERT: a 325 MET cc_start: 0.7316 (mtm) cc_final: 0.6744 (ttm) REVERT: b 339 ASP cc_start: 0.8089 (t0) cc_final: 0.7669 (m-30) REVERT: d 13 MET cc_start: 0.5280 (ttp) cc_final: 0.4845 (ttm) REVERT: d 101 ASN cc_start: 0.7231 (t0) cc_final: 0.6903 (m-40) REVERT: d 189 ARG cc_start: 0.5695 (ttm-80) cc_final: 0.5125 (mtm-85) REVERT: d 234 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6928 (pt) REVERT: f 15 GLU cc_start: 0.7644 (tt0) cc_final: 0.7277 (tp30) REVERT: f 44 GLU cc_start: 0.7138 (pt0) cc_final: 0.6882 (pt0) REVERT: f 52 LYS cc_start: 0.6545 (OUTLIER) cc_final: 0.6068 (mtpt) REVERT: f 69 ASN cc_start: 0.6823 (p0) cc_final: 0.6358 (m-40) REVERT: f 101 ASN cc_start: 0.6972 (t0) cc_final: 0.6459 (m-40) REVERT: f 112 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7961 (p) outliers start: 131 outliers final: 94 residues processed: 827 average time/residue: 0.6595 time to fit residues: 925.7574 Evaluate side-chains 826 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 717 time to evaluate : 6.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 22 LYS Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 6 residue 179 ASP Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 474 CYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain J residue 434 GLU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 412 SER Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain P residue 345 ILE Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 409 ILE Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 149 ASP Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 13 MET Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 523 optimal weight: 3.9990 chunk 843 optimal weight: 0.3980 chunk 514 optimal weight: 0.8980 chunk 400 optimal weight: 4.9990 chunk 586 optimal weight: 0.2980 chunk 884 optimal weight: 0.8980 chunk 814 optimal weight: 1.9990 chunk 704 optimal weight: 0.1980 chunk 73 optimal weight: 2.9990 chunk 544 optimal weight: 2.9990 chunk 431 optimal weight: 8.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 174 ASN 2 45 ASN B 446 GLN B 546 HIS C 263 GLN ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 ASN ** F 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 GLN G 5 GLN I 174 ASN ** L 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 165 ASN U 322 GLN V 322 GLN X 98 GLN X 114 GLN Y 396 GLN Z 101 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 69957 Z= 0.132 Angle : 0.485 9.477 94694 Z= 0.253 Chirality : 0.041 0.178 10759 Planarity : 0.003 0.045 12440 Dihedral : 5.066 76.597 10190 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.41 % Allowed : 15.29 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.09), residues: 8881 helix: 2.63 (0.09), residues: 3496 sheet: 0.75 (0.12), residues: 2001 loop : -0.07 (0.11), residues: 3384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 187 HIS 0.005 0.001 HIS C 460 PHE 0.029 0.001 PHE T 111 TYR 0.018 0.001 TYR 6 118 ARG 0.010 0.000 ARG X 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 749 time to evaluate : 6.088 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: 0 67 LYS cc_start: 0.6804 (tttm) cc_final: 0.6595 (tttm) REVERT: 0 156 MET cc_start: 0.7488 (mtm) cc_final: 0.7058 (mtm) REVERT: 2 44 GLU cc_start: 0.7732 (tt0) cc_final: 0.7394 (tm-30) REVERT: 2 110 ILE cc_start: 0.7990 (mt) cc_final: 0.7714 (tp) REVERT: 2 135 ARG cc_start: 0.7992 (tpp80) cc_final: 0.7252 (mtm110) REVERT: 2 205 VAL cc_start: 0.5882 (m) cc_final: 0.5618 (p) REVERT: 2 234 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6999 (pt) REVERT: 4 45 ASN cc_start: 0.7721 (t0) cc_final: 0.7394 (t0) REVERT: 4 225 ILE cc_start: 0.8376 (mt) cc_final: 0.7925 (mm) REVERT: 6 44 GLU cc_start: 0.7514 (tt0) cc_final: 0.6917 (tm-30) REVERT: 6 51 GLN cc_start: 0.6853 (mm-40) cc_final: 0.6398 (mm-40) REVERT: 6 113 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6521 (tt0) REVERT: 6 233 LEU cc_start: 0.7720 (mp) cc_final: 0.7486 (mt) REVERT: 8 73 ASN cc_start: 0.7287 (m110) cc_final: 0.7033 (m110) REVERT: 8 113 GLU cc_start: 0.7600 (mm-30) cc_final: 0.6902 (tt0) REVERT: 8 174 ASN cc_start: 0.7876 (m110) cc_final: 0.7645 (m110) REVERT: A 122 MET cc_start: 0.8917 (mmm) cc_final: 0.8609 (mmm) REVERT: A 396 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7918 (tt) REVERT: C 344 GLU cc_start: 0.7071 (tp30) cc_final: 0.6619 (tp30) REVERT: C 570 TRP cc_start: 0.2388 (m100) cc_final: 0.1905 (t60) REVERT: D 164 LEU cc_start: 0.6551 (tp) cc_final: 0.6246 (tp) REVERT: D 480 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: E 124 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7324 (tp) REVERT: E 373 MET cc_start: 0.7897 (mmp) cc_final: 0.7452 (mmp) REVERT: E 379 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.8062 (p) REVERT: E 520 GLN cc_start: 0.8187 (tt0) cc_final: 0.7862 (tt0) REVERT: F 297 CYS cc_start: 0.8949 (m) cc_final: 0.8504 (m) REVERT: F 314 MET cc_start: 0.6273 (mmt) cc_final: 0.5948 (mmp) REVERT: F 529 ASN cc_start: 0.8583 (m-40) cc_final: 0.8228 (t0) REVERT: H 519 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7442 (mm-30) REVERT: I 101 ASN cc_start: 0.6457 (t0) cc_final: 0.6211 (m-40) REVERT: J 325 MET cc_start: 0.7957 (mtm) cc_final: 0.7472 (ttm) REVERT: J 364 GLU cc_start: 0.6602 (tt0) cc_final: 0.6276 (mt-10) REVERT: J 430 ASN cc_start: 0.7319 (t0) cc_final: 0.6520 (t0) REVERT: J 509 ARG cc_start: 0.6240 (tpt90) cc_final: 0.5905 (ttt180) REVERT: K 13 MET cc_start: 0.6329 (mmt) cc_final: 0.4805 (ttp) REVERT: K 14 ARG cc_start: 0.4802 (tpm170) cc_final: 0.4341 (tpm170) REVERT: K 112 THR cc_start: 0.6762 (m) cc_final: 0.6456 (p) REVERT: K 146 SER cc_start: 0.7118 (m) cc_final: 0.6705 (p) REVERT: K 150 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6202 (mm-30) REVERT: K 216 ASN cc_start: 0.7284 (t0) cc_final: 0.6533 (m-40) REVERT: L 325 MET cc_start: 0.7905 (mtm) cc_final: 0.7140 (ttp) REVERT: L 332 ARG cc_start: 0.7144 (mtt-85) cc_final: 0.6276 (mtt180) REVERT: M 307 LYS cc_start: 0.7637 (mtpt) cc_final: 0.7325 (mtmm) REVERT: M 325 MET cc_start: 0.8000 (mtm) cc_final: 0.7719 (ttm) REVERT: M 338 ASP cc_start: 0.7101 (p0) cc_final: 0.6690 (p0) REVERT: M 424 ASP cc_start: 0.7308 (p0) cc_final: 0.6803 (p0) REVERT: N 325 MET cc_start: 0.7851 (mtm) cc_final: 0.7283 (ttt) REVERT: N 364 GLU cc_start: 0.7852 (tt0) cc_final: 0.7156 (pt0) REVERT: N 399 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7574 (tt) REVERT: O 26 ARG cc_start: 0.7335 (ttp80) cc_final: 0.6643 (ppt170) REVERT: O 156 MET cc_start: 0.5775 (mtm) cc_final: 0.5464 (mtm) REVERT: P 325 MET cc_start: 0.7444 (mtm) cc_final: 0.6845 (ttp) REVERT: P 345 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7544 (mm) REVERT: P 432 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6380 (mp0) REVERT: Q 70 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6545 (mm-30) REVERT: Q 113 GLU cc_start: 0.7361 (tp30) cc_final: 0.6826 (tm-30) REVERT: Q 146 SER cc_start: 0.6735 (m) cc_final: 0.6331 (p) REVERT: R 325 MET cc_start: 0.7344 (mtm) cc_final: 0.6899 (ttp) REVERT: R 430 ASN cc_start: 0.8078 (t0) cc_final: 0.7558 (m-40) REVERT: S 519 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7097 (tm-30) REVERT: T 52 LYS cc_start: 0.7204 (mtpt) cc_final: 0.6560 (mtmm) REVERT: T 67 LYS cc_start: 0.7626 (tttt) cc_final: 0.7392 (tttt) REVERT: T 113 GLU cc_start: 0.7334 (tp30) cc_final: 0.6990 (tm-30) REVERT: T 121 GLU cc_start: 0.6754 (tt0) cc_final: 0.6135 (mm-30) REVERT: T 214 ASP cc_start: 0.6181 (t0) cc_final: 0.5912 (t0) REVERT: U 401 LEU cc_start: 0.7739 (mt) cc_final: 0.7325 (mt) REVERT: U 509 ARG cc_start: 0.6226 (tpt170) cc_final: 0.5973 (ttm170) REVERT: V 325 MET cc_start: 0.7816 (ttp) cc_final: 0.6585 (mmt) REVERT: V 401 LEU cc_start: 0.7333 (tp) cc_final: 0.6938 (mt) REVERT: V 509 ARG cc_start: 0.6181 (OUTLIER) cc_final: 0.5686 (ttt180) REVERT: V 519 GLU cc_start: 0.7170 (tt0) cc_final: 0.6742 (mm-30) REVERT: W 307 LYS cc_start: 0.7254 (mtpt) cc_final: 0.6513 (mttt) REVERT: W 364 GLU cc_start: 0.6988 (tt0) cc_final: 0.6477 (pt0) REVERT: W 388 ARG cc_start: 0.6913 (ttt180) cc_final: 0.6179 (ttm110) REVERT: X 52 LYS cc_start: 0.7653 (mtpt) cc_final: 0.7343 (mtmm) REVERT: X 80 GLN cc_start: 0.7263 (tp40) cc_final: 0.6669 (tp40) REVERT: X 130 TYR cc_start: 0.7578 (t80) cc_final: 0.6138 (t80) REVERT: X 133 THR cc_start: 0.8273 (m) cc_final: 0.8008 (p) REVERT: X 156 MET cc_start: 0.5053 (mtm) cc_final: 0.4702 (mtm) REVERT: X 179 ASP cc_start: 0.6617 (m-30) cc_final: 0.6114 (t0) REVERT: X 209 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5876 (mt-10) REVERT: X 216 ASN cc_start: 0.7521 (t0) cc_final: 0.7022 (t0) REVERT: Y 324 ASN cc_start: 0.7526 (m-40) cc_final: 0.7131 (t0) REVERT: Y 325 MET cc_start: 0.7810 (mtm) cc_final: 0.7270 (ttm) REVERT: Y 509 ARG cc_start: 0.7103 (tpt90) cc_final: 0.6366 (ttp80) REVERT: Z 44 GLU cc_start: 0.6482 (pt0) cc_final: 0.6032 (pt0) REVERT: Z 52 LYS cc_start: 0.7477 (mtpt) cc_final: 0.7050 (mttp) REVERT: Z 113 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6672 (tm-30) REVERT: Z 143 TYR cc_start: 0.5321 (p90) cc_final: 0.4618 (p90) REVERT: Z 150 GLU cc_start: 0.7951 (mp0) cc_final: 0.7612 (mp0) REVERT: Z 152 HIS cc_start: 0.7216 (m-70) cc_final: 0.6682 (m-70) REVERT: Z 156 MET cc_start: 0.6955 (mtm) cc_final: 0.6752 (mtm) REVERT: Z 216 ASN cc_start: 0.8355 (t0) cc_final: 0.7978 (m-40) REVERT: a 325 MET cc_start: 0.7566 (mtm) cc_final: 0.7032 (ttm) REVERT: b 339 ASP cc_start: 0.8043 (t0) cc_final: 0.7581 (m-30) REVERT: d 13 MET cc_start: 0.4985 (ttp) cc_final: 0.4547 (ttm) REVERT: d 101 ASN cc_start: 0.7199 (t0) cc_final: 0.6917 (m-40) REVERT: d 189 ARG cc_start: 0.5723 (ttm-80) cc_final: 0.5261 (mtm-85) REVERT: f 15 GLU cc_start: 0.7847 (tt0) cc_final: 0.7406 (tp30) REVERT: f 101 ASN cc_start: 0.6807 (t0) cc_final: 0.6376 (m-40) REVERT: f 112 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.7985 (p) outliers start: 99 outliers final: 68 residues processed: 820 average time/residue: 0.6668 time to fit residues: 920.2130 Evaluate side-chains 805 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 725 time to evaluate : 6.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 22 LYS Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 474 CYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 412 SER Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain P residue 345 ILE Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 149 ASP Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 209 GLU Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 559 optimal weight: 10.0000 chunk 750 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 649 optimal weight: 0.0970 chunk 104 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 705 optimal weight: 2.9990 chunk 295 optimal weight: 0.0020 chunk 724 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 129 optimal weight: 0.0570 overall best weight: 1.0308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 174 ASN 2 45 ASN B 546 HIS ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN ** F 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 GLN G 5 GLN I 174 ASN ** P 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 GLN V 322 GLN X 114 GLN Z 101 ASN ** Z 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.121080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.087711 restraints weight = 111209.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.086052 restraints weight = 217571.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.086311 restraints weight = 222815.580| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 69957 Z= 0.165 Angle : 0.499 9.075 94694 Z= 0.259 Chirality : 0.042 0.174 10759 Planarity : 0.004 0.043 12440 Dihedral : 5.061 73.382 10190 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.35 % Allowed : 15.19 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.09), residues: 8881 helix: 2.65 (0.09), residues: 3497 sheet: 0.74 (0.12), residues: 2007 loop : -0.05 (0.11), residues: 3377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 570 HIS 0.005 0.001 HIS C 460 PHE 0.028 0.002 PHE f 71 TYR 0.022 0.001 TYR 6 118 ARG 0.007 0.000 ARG X 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16253.04 seconds wall clock time: 285 minutes 33.81 seconds (17133.81 seconds total)