Starting phenix.real_space_refine on Tue Mar 26 00:31:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ixh_9747/03_2024/6ixh_9747.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ixh_9747/03_2024/6ixh_9747.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/6ixh_9747/03_2024/6ixh_9747.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ixh_9747/03_2024/6ixh_9747.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ixh_9747/03_2024/6ixh_9747.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ixh_9747/03_2024/6ixh_9747.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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 200 5.16 5 C 33115 2.51 5 N 9115 2.21 5 O 9850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 34": "OE1" <-> "OE2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "B GLU 34": "OE1" <-> "OE2" Residue "B ASP 61": "OD1" <-> "OD2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B ASP 135": "OD1" <-> "OD2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "C ASP 97": "OD1" <-> "OD2" Residue "C ASP 135": "OD1" <-> "OD2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D ASP 61": "OD1" <-> "OD2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "D ASP 135": "OD1" <-> "OD2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E ASP 97": "OD1" <-> "OD2" Residue "F ASP 61": "OD1" <-> "OD2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F GLU 115": "OE1" <-> "OE2" Residue "F ASP 135": "OD1" <-> "OD2" Residue "G ASP 29": "OD1" <-> "OD2" Residue "G ASP 85": "OD1" <-> "OD2" Residue "G GLU 115": "OE1" <-> "OE2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "H ASP 61": "OD1" <-> "OD2" Residue "H GLU 115": "OE1" <-> "OE2" Residue "H ASP 135": "OD1" <-> "OD2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "I ASP 56": "OD1" <-> "OD2" Residue "I ASP 61": "OD1" <-> "OD2" Residue "I ASP 85": "OD1" <-> "OD2" Residue "I GLU 115": "OE1" <-> "OE2" Residue "J ASP 85": "OD1" <-> "OD2" Residue "J GLU 115": "OE1" <-> "OE2" Residue "K TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 56": "OD1" <-> "OD2" Residue "K ASP 79": "OD1" <-> "OD2" Residue "L TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 56": "OD1" <-> "OD2" Residue "L ASP 79": "OD1" <-> "OD2" Residue "M TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 56": "OD1" <-> "OD2" Residue "M ASP 79": "OD1" <-> "OD2" Residue "N TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 56": "OD1" <-> "OD2" Residue "N ASP 79": "OD1" <-> "OD2" Residue "O TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 56": "OD1" <-> "OD2" Residue "O ASP 79": "OD1" <-> "OD2" Residue "O ASP 135": "OD1" <-> "OD2" Residue "P GLU 616": "OE1" <-> "OE2" Residue "P ARG 673": "NH1" <-> "NH2" Residue "P TYR 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 916": "OD1" <-> "OD2" Residue "Q GLU 616": "OE1" <-> "OE2" Residue "Q ARG 673": "NH1" <-> "NH2" Residue "Q TYR 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 1040": "OD1" <-> "OD2" Residue "Q GLU 1085": "OE1" <-> "OE2" Residue "R ASP 607": "OD1" <-> "OD2" Residue "R GLU 616": "OE1" <-> "OE2" Residue "R GLU 628": "OE1" <-> "OE2" Residue "R ARG 673": "NH1" <-> "NH2" Residue "R ASP 709": "OD1" <-> "OD2" Residue "R ASP 829": "OD1" <-> "OD2" Residue "R TYR 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 607": "OD1" <-> "OD2" Residue "S GLU 616": "OE1" <-> "OE2" Residue "S GLU 628": "OE1" <-> "OE2" Residue "S ARG 673": "NH1" <-> "NH2" Residue "S ASP 709": "OD1" <-> "OD2" Residue "S TYR 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 616": "OE1" <-> "OE2" Residue "T ARG 673": "NH1" <-> "NH2" Residue "T ASP 677": "OD1" <-> "OD2" Residue "T ASP 709": "OD1" <-> "OD2" Residue "T TYR 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 1085": "OE1" <-> "OE2" Residue "U ASP 596": "OD1" <-> "OD2" Residue "U ASP 607": "OD1" <-> "OD2" Residue "U PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 835": "OD1" <-> "OD2" Residue "U PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 1040": "OD1" <-> "OD2" Residue "U ASP 1074": "OD1" <-> "OD2" Residue "V ASP 596": "OD1" <-> "OD2" Residue "V ASP 607": "OD1" <-> "OD2" Residue "V PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 699": "OD1" <-> "OD2" Residue "V ASP 777": "OD1" <-> "OD2" Residue "V ASP 835": "OD1" <-> "OD2" Residue "V ASP 916": "OD1" <-> "OD2" Residue "V PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 601": "OD1" <-> "OD2" Residue "W ASP 607": "OD1" <-> "OD2" Residue "W PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 702": "OE1" <-> "OE2" Residue "W ASP 709": "OD1" <-> "OD2" Residue "W ASP 777": "OD1" <-> "OD2" Residue "W ASP 835": "OD1" <-> "OD2" Residue "W GLU 873": "OE1" <-> "OE2" Residue "W GLU 964": "OE1" <-> "OE2" Residue "W GLU 1020": "OE1" <-> "OE2" Residue "X ASP 596": "OD1" <-> "OD2" Residue "X ASP 607": "OD1" <-> "OD2" Residue "X PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 702": "OE1" <-> "OE2" Residue "X ASP 835": "OD1" <-> "OD2" Residue "X ASP 916": "OD1" <-> "OD2" Residue "X GLU 964": "OE1" <-> "OE2" Residue "X GLU 1085": "OE1" <-> "OE2" Residue "Y ASP 601": "OD1" <-> "OD2" Residue "Y ASP 607": "OD1" <-> "OD2" Residue "Y PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 777": "OD1" <-> "OD2" Residue "Y ASP 835": "OD1" <-> "OD2" Residue "Y ASP 916": "OD1" <-> "OD2" Residue "Y GLU 964": "OE1" <-> "OE2" Residue "Y GLU 1020": "OE1" <-> "OE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 52280 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1020 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 127} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1020 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 127} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1020 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 127} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1020 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 127} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1020 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 127} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1006 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 125} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1006 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 125} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1006 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 125} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "I" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1006 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 125} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1006 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 125} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 924 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 924 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "M" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 924 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "N" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 924 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "O" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 924 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "P" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3771 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 460} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "Q" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3771 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 460} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3771 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 460} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "S" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3771 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 460} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "T" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3771 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 460} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "U" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3735 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "V" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3735 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "W" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3735 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "X" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3735 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "Y" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3735 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 27.26, per 1000 atoms: 0.52 Number of scatterers: 52280 At special positions: 0 Unit cell: (179.52, 178.2, 178.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 200 16.00 O 9850 8.00 N 9115 7.00 C 33115 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: 20.00 Conformation dependent library (CDL) restraints added in 9.6 seconds 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12680 Finding SS restraints... Secondary structure from input PDB file: 256 helices and 65 sheets defined 32.8% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.30 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 70 through 74 removed outlier: 4.211A pdb=" N ASN A 73 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 70 through 74 removed outlier: 4.227A pdb=" N ASN B 73 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'C' and resid 57 through 63 Processing helix chain 'C' and resid 70 through 74 removed outlier: 4.228A pdb=" N ASN C 73 " --> pdb=" O THR C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'D' and resid 57 through 63 Processing helix chain 'D' and resid 70 through 74 removed outlier: 4.204A pdb=" N ASN D 73 " --> pdb=" O THR D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'E' and resid 57 through 63 Processing helix chain 'E' and resid 70 through 74 removed outlier: 4.221A pdb=" N ASN E 73 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'F' and resid 57 through 62 Processing helix chain 'F' and resid 65 through 70 removed outlier: 3.782A pdb=" N PHE F 69 " --> pdb=" O TYR F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 80 Processing helix chain 'F' and resid 130 through 132 No H-bonds generated for 'chain 'F' and resid 130 through 132' Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 65 through 70 removed outlier: 3.782A pdb=" N PHE G 69 " --> pdb=" O TYR G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 80 Processing helix chain 'G' and resid 130 through 132 No H-bonds generated for 'chain 'G' and resid 130 through 132' Processing helix chain 'H' and resid 57 through 62 Processing helix chain 'H' and resid 65 through 70 removed outlier: 3.776A pdb=" N PHE H 69 " --> pdb=" O TYR H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 80 Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'I' and resid 57 through 62 Processing helix chain 'I' and resid 65 through 70 removed outlier: 3.763A pdb=" N PHE I 69 " --> pdb=" O TYR I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 80 Processing helix chain 'I' and resid 130 through 132 No H-bonds generated for 'chain 'I' and resid 130 through 132' Processing helix chain 'J' and resid 57 through 62 Processing helix chain 'J' and resid 65 through 70 removed outlier: 3.791A pdb=" N PHE J 69 " --> pdb=" O TYR J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 80 Processing helix chain 'J' and resid 130 through 132 No H-bonds generated for 'chain 'J' and resid 130 through 132' Processing helix chain 'K' and resid 64 through 69 removed outlier: 3.680A pdb=" N LEU K 68 " --> pdb=" O ASP K 64 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE K 69 " --> pdb=" O TYR K 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 64 through 69' Processing helix chain 'K' and resid 130 through 132 No H-bonds generated for 'chain 'K' and resid 130 through 132' Processing helix chain 'L' and resid 64 through 69 removed outlier: 3.659A pdb=" N LEU L 68 " --> pdb=" O ASP L 64 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE L 69 " --> pdb=" O TYR L 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 64 through 69' Processing helix chain 'L' and resid 130 through 132 No H-bonds generated for 'chain 'L' and resid 130 through 132' Processing helix chain 'M' and resid 64 through 69 removed outlier: 3.624A pdb=" N LEU M 68 " --> pdb=" O ASP M 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE M 69 " --> pdb=" O TYR M 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 64 through 69' Processing helix chain 'M' and resid 130 through 132 No H-bonds generated for 'chain 'M' and resid 130 through 132' Processing helix chain 'N' and resid 64 through 69 removed outlier: 3.650A pdb=" N LEU N 68 " --> pdb=" O ASP N 64 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE N 69 " --> pdb=" O TYR N 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 64 through 69' Processing helix chain 'N' and resid 130 through 132 No H-bonds generated for 'chain 'N' and resid 130 through 132' Processing helix chain 'O' and resid 64 through 69 removed outlier: 3.625A pdb=" N LEU O 68 " --> pdb=" O ASP O 64 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE O 69 " --> pdb=" O TYR O 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 64 through 69' Processing helix chain 'O' and resid 130 through 132 No H-bonds generated for 'chain 'O' and resid 130 through 132' Processing helix chain 'P' and resid 580 through 591 removed outlier: 3.987A pdb=" N ARG P 589 " --> pdb=" O LYS P 585 " (cutoff:3.500A) Processing helix chain 'P' and resid 623 through 629 Processing helix chain 'P' and resid 631 through 641 removed outlier: 3.832A pdb=" N ASP P 636 " --> pdb=" O LEU P 632 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL P 638 " --> pdb=" O SER P 634 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASN P 640 " --> pdb=" O ASP P 636 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU P 641 " --> pdb=" O THR P 637 " (cutoff:3.500A) Processing helix chain 'P' and resid 662 through 687 removed outlier: 4.159A pdb=" N GLN P 668 " --> pdb=" O GLU P 664 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR P 671 " --> pdb=" O ARG P 667 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ARG P 673 " --> pdb=" O ARG P 669 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP P 677 " --> pdb=" O ARG P 673 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN P 680 " --> pdb=" O ALA P 676 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA P 681 " --> pdb=" O ASP P 677 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN P 684 " --> pdb=" O ASN P 680 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE P 685 " --> pdb=" O ALA P 681 " (cutoff:3.500A) Processing helix chain 'P' and resid 697 through 708 removed outlier: 3.536A pdb=" N THR P 701 " --> pdb=" O LEU P 697 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA P 708 " --> pdb=" O LEU P 704 " (cutoff:3.500A) Processing helix chain 'P' and resid 716 through 725 removed outlier: 3.823A pdb=" N GLN P 725 " --> pdb=" O THR P 721 " (cutoff:3.500A) Processing helix chain 'P' and resid 769 through 776 removed outlier: 3.966A pdb=" N MET P 776 " --> pdb=" O VAL P 772 " (cutoff:3.500A) Processing helix chain 'P' and resid 795 through 800 Processing helix chain 'P' and resid 800 through 807 removed outlier: 3.725A pdb=" N ALA P 806 " --> pdb=" O LEU P 802 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY P 807 " --> pdb=" O GLN P 803 " (cutoff:3.500A) Processing helix chain 'P' and resid 810 through 824 removed outlier: 3.641A pdb=" N MET P 814 " --> pdb=" O ASP P 810 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU P 817 " --> pdb=" O ALA P 813 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR P 821 " --> pdb=" O LEU P 817 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU P 823 " --> pdb=" O ALA P 819 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN P 824 " --> pdb=" O GLN P 820 " (cutoff:3.500A) Processing helix chain 'P' and resid 833 through 844 removed outlier: 4.370A pdb=" N LEU P 839 " --> pdb=" O ASP P 835 " (cutoff:3.500A) Processing helix chain 'P' and resid 851 through 856 Processing helix chain 'P' and resid 857 through 875 removed outlier: 4.478A pdb=" N ALA P 863 " --> pdb=" O PRO P 859 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TRP P 864 " --> pdb=" O MET P 860 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN P 865 " --> pdb=" O GLU P 861 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR P 869 " --> pdb=" O GLN P 865 " (cutoff:3.500A) Proline residue: P 870 - end of helix removed outlier: 3.789A pdb=" N GLU P 873 " --> pdb=" O THR P 869 " (cutoff:3.500A) Processing helix chain 'P' and resid 883 through 888 Processing helix chain 'P' and resid 905 through 910 Processing helix chain 'P' and resid 920 through 928 removed outlier: 3.903A pdb=" N GLN P 925 " --> pdb=" O ALA P 921 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN P 926 " --> pdb=" O ARG P 922 " (cutoff:3.500A) Processing helix chain 'P' and resid 954 through 959 Processing helix chain 'P' and resid 1045 through 1053 removed outlier: 3.513A pdb=" N ARG P1049 " --> pdb=" O TRP P1045 " (cutoff:3.500A) Processing helix chain 'P' and resid 1088 through 1096 removed outlier: 3.577A pdb=" N LEU P1091 " --> pdb=" O GLU P1088 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU P1093 " --> pdb=" O PRO P1090 " (cutoff:3.500A) Processing helix chain 'Q' and resid 580 through 591 removed outlier: 4.054A pdb=" N ARG Q 589 " --> pdb=" O LYS Q 585 " (cutoff:3.500A) Processing helix chain 'Q' and resid 623 through 629 Processing helix chain 'Q' and resid 631 through 641 removed outlier: 3.837A pdb=" N ASP Q 636 " --> pdb=" O LEU Q 632 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL Q 638 " --> pdb=" O SER Q 634 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASN Q 640 " --> pdb=" O ASP Q 636 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU Q 641 " --> pdb=" O THR Q 637 " (cutoff:3.500A) Processing helix chain 'Q' and resid 662 through 687 removed outlier: 4.113A pdb=" N GLN Q 668 " --> pdb=" O GLU Q 664 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR Q 671 " --> pdb=" O ARG Q 667 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG Q 673 " --> pdb=" O ARG Q 669 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP Q 677 " --> pdb=" O ARG Q 673 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN Q 680 " --> pdb=" O ALA Q 676 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA Q 681 " --> pdb=" O ASP Q 677 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN Q 684 " --> pdb=" O ASN Q 680 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE Q 685 " --> pdb=" O ALA Q 681 " (cutoff:3.500A) Processing helix chain 'Q' and resid 697 through 708 removed outlier: 3.560A pdb=" N THR Q 701 " --> pdb=" O LEU Q 697 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA Q 708 " --> pdb=" O LEU Q 704 " (cutoff:3.500A) Processing helix chain 'Q' and resid 717 through 725 removed outlier: 3.875A pdb=" N GLN Q 725 " --> pdb=" O THR Q 721 " (cutoff:3.500A) Processing helix chain 'Q' and resid 769 through 776 removed outlier: 3.979A pdb=" N MET Q 776 " --> pdb=" O VAL Q 772 " (cutoff:3.500A) Processing helix chain 'Q' and resid 795 through 800 Processing helix chain 'Q' and resid 800 through 807 removed outlier: 3.628A pdb=" N GLN Q 804 " --> pdb=" O LEU Q 800 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA Q 806 " --> pdb=" O LEU Q 802 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY Q 807 " --> pdb=" O GLN Q 803 " (cutoff:3.500A) Processing helix chain 'Q' and resid 810 through 824 removed outlier: 3.594A pdb=" N MET Q 814 " --> pdb=" O ASP Q 810 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU Q 817 " --> pdb=" O ALA Q 813 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR Q 821 " --> pdb=" O LEU Q 817 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU Q 823 " --> pdb=" O ALA Q 819 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN Q 824 " --> pdb=" O GLN Q 820 " (cutoff:3.500A) Processing helix chain 'Q' and resid 833 through 844 removed outlier: 4.367A pdb=" N LEU Q 839 " --> pdb=" O ASP Q 835 " (cutoff:3.500A) Processing helix chain 'Q' and resid 851 through 856 Processing helix chain 'Q' and resid 857 through 867 removed outlier: 4.458A pdb=" N ALA Q 863 " --> pdb=" O PRO Q 859 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP Q 864 " --> pdb=" O MET Q 860 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN Q 865 " --> pdb=" O GLU Q 861 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN Q 866 " --> pdb=" O GLN Q 862 " (cutoff:3.500A) Processing helix chain 'Q' and resid 867 through 875 removed outlier: 3.903A pdb=" N ALA Q 871 " --> pdb=" O VAL Q 867 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU Q 873 " --> pdb=" O THR Q 869 " (cutoff:3.500A) Processing helix chain 'Q' and resid 883 through 888 Processing helix chain 'Q' and resid 905 through 910 Processing helix chain 'Q' and resid 920 through 928 removed outlier: 3.897A pdb=" N GLN Q 925 " --> pdb=" O ALA Q 921 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN Q 926 " --> pdb=" O ARG Q 922 " (cutoff:3.500A) Processing helix chain 'Q' and resid 954 through 959 Processing helix chain 'Q' and resid 1045 through 1053 removed outlier: 3.548A pdb=" N ARG Q1049 " --> pdb=" O TRP Q1045 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1088 through 1096 removed outlier: 4.011A pdb=" N LEU Q1093 " --> pdb=" O PRO Q1090 " (cutoff:3.500A) Processing helix chain 'R' and resid 580 through 591 removed outlier: 3.958A pdb=" N ARG R 589 " --> pdb=" O LYS R 585 " (cutoff:3.500A) Processing helix chain 'R' and resid 623 through 629 Processing helix chain 'R' and resid 631 through 640 removed outlier: 3.855A pdb=" N ASP R 636 " --> pdb=" O LEU R 632 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL R 638 " --> pdb=" O SER R 634 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN R 640 " --> pdb=" O ASP R 636 " (cutoff:3.500A) Processing helix chain 'R' and resid 662 through 687 removed outlier: 4.092A pdb=" N GLN R 668 " --> pdb=" O GLU R 664 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR R 671 " --> pdb=" O ARG R 667 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ARG R 673 " --> pdb=" O ARG R 669 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP R 677 " --> pdb=" O ARG R 673 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN R 680 " --> pdb=" O ALA R 676 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA R 681 " --> pdb=" O ASP R 677 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN R 684 " --> pdb=" O ASN R 680 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE R 685 " --> pdb=" O ALA R 681 " (cutoff:3.500A) Processing helix chain 'R' and resid 697 through 708 removed outlier: 3.780A pdb=" N ALA R 708 " --> pdb=" O LEU R 704 " (cutoff:3.500A) Processing helix chain 'R' and resid 716 through 724 Processing helix chain 'R' and resid 769 through 776 removed outlier: 3.967A pdb=" N MET R 776 " --> pdb=" O VAL R 772 " (cutoff:3.500A) Processing helix chain 'R' and resid 795 through 800 Processing helix chain 'R' and resid 800 through 807 removed outlier: 3.536A pdb=" N GLN R 804 " --> pdb=" O LEU R 800 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA R 806 " --> pdb=" O LEU R 802 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY R 807 " --> pdb=" O GLN R 803 " (cutoff:3.500A) Processing helix chain 'R' and resid 810 through 824 removed outlier: 3.582A pdb=" N MET R 814 " --> pdb=" O ASP R 810 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN R 816 " --> pdb=" O GLN R 812 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU R 817 " --> pdb=" O ALA R 813 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR R 821 " --> pdb=" O LEU R 817 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU R 823 " --> pdb=" O ALA R 819 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN R 824 " --> pdb=" O GLN R 820 " (cutoff:3.500A) Processing helix chain 'R' and resid 833 through 842 removed outlier: 4.323A pdb=" N LEU R 839 " --> pdb=" O ASP R 835 " (cutoff:3.500A) Processing helix chain 'R' and resid 851 through 856 Processing helix chain 'R' and resid 857 through 875 removed outlier: 4.535A pdb=" N ALA R 863 " --> pdb=" O PRO R 859 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TRP R 864 " --> pdb=" O MET R 860 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR R 869 " --> pdb=" O GLN R 865 " (cutoff:3.500A) Proline residue: R 870 - end of helix removed outlier: 3.763A pdb=" N GLU R 873 " --> pdb=" O THR R 869 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU R 875 " --> pdb=" O ALA R 871 " (cutoff:3.500A) Processing helix chain 'R' and resid 883 through 892 removed outlier: 4.335A pdb=" N ASN R 889 " --> pdb=" O ASP R 885 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER R 892 " --> pdb=" O ASN R 888 " (cutoff:3.500A) Processing helix chain 'R' and resid 905 through 910 Processing helix chain 'R' and resid 920 through 928 removed outlier: 3.881A pdb=" N GLN R 925 " --> pdb=" O ALA R 921 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASN R 926 " --> pdb=" O ARG R 922 " (cutoff:3.500A) Processing helix chain 'R' and resid 954 through 962 Processing helix chain 'R' and resid 964 through 969 Processing helix chain 'R' and resid 1045 through 1053 Processing helix chain 'R' and resid 1088 through 1096 removed outlier: 4.096A pdb=" N LEU R1093 " --> pdb=" O PRO R1090 " (cutoff:3.500A) Processing helix chain 'S' and resid 580 through 591 removed outlier: 4.070A pdb=" N ARG S 589 " --> pdb=" O LYS S 585 " (cutoff:3.500A) Processing helix chain 'S' and resid 623 through 629 Processing helix chain 'S' and resid 631 through 640 removed outlier: 3.873A pdb=" N ASP S 636 " --> pdb=" O LEU S 632 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL S 638 " --> pdb=" O SER S 634 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASN S 640 " --> pdb=" O ASP S 636 " (cutoff:3.500A) Processing helix chain 'S' and resid 662 through 687 removed outlier: 4.093A pdb=" N GLN S 668 " --> pdb=" O GLU S 664 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR S 671 " --> pdb=" O ARG S 667 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ARG S 673 " --> pdb=" O ARG S 669 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP S 677 " --> pdb=" O ARG S 673 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN S 680 " --> pdb=" O ALA S 676 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA S 681 " --> pdb=" O ASP S 677 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN S 684 " --> pdb=" O ASN S 680 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE S 685 " --> pdb=" O ALA S 681 " (cutoff:3.500A) Processing helix chain 'S' and resid 697 through 708 removed outlier: 3.734A pdb=" N ALA S 708 " --> pdb=" O LEU S 704 " (cutoff:3.500A) Processing helix chain 'S' and resid 717 through 725 removed outlier: 3.900A pdb=" N GLN S 725 " --> pdb=" O THR S 721 " (cutoff:3.500A) Processing helix chain 'S' and resid 769 through 776 removed outlier: 3.955A pdb=" N MET S 776 " --> pdb=" O VAL S 772 " (cutoff:3.500A) Processing helix chain 'S' and resid 795 through 800 Processing helix chain 'S' and resid 800 through 807 removed outlier: 3.740A pdb=" N ALA S 806 " --> pdb=" O LEU S 802 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY S 807 " --> pdb=" O GLN S 803 " (cutoff:3.500A) Processing helix chain 'S' and resid 810 through 824 removed outlier: 3.635A pdb=" N MET S 814 " --> pdb=" O ASP S 810 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN S 816 " --> pdb=" O GLN S 812 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU S 817 " --> pdb=" O ALA S 813 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR S 821 " --> pdb=" O LEU S 817 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU S 823 " --> pdb=" O ALA S 819 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN S 824 " --> pdb=" O GLN S 820 " (cutoff:3.500A) Processing helix chain 'S' and resid 833 through 843 removed outlier: 4.378A pdb=" N LEU S 839 " --> pdb=" O ASP S 835 " (cutoff:3.500A) Processing helix chain 'S' and resid 851 through 856 Processing helix chain 'S' and resid 857 through 867 removed outlier: 4.472A pdb=" N ALA S 863 " --> pdb=" O PRO S 859 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP S 864 " --> pdb=" O MET S 860 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN S 865 " --> pdb=" O GLU S 861 " (cutoff:3.500A) Processing helix chain 'S' and resid 867 through 875 removed outlier: 3.832A pdb=" N ALA S 871 " --> pdb=" O VAL S 867 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU S 873 " --> pdb=" O THR S 869 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU S 875 " --> pdb=" O ALA S 871 " (cutoff:3.500A) Processing helix chain 'S' and resid 883 through 891 removed outlier: 4.534A pdb=" N ASN S 889 " --> pdb=" O ASP S 885 " (cutoff:3.500A) Processing helix chain 'S' and resid 905 through 910 Processing helix chain 'S' and resid 920 through 928 removed outlier: 3.877A pdb=" N GLN S 925 " --> pdb=" O ALA S 921 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN S 926 " --> pdb=" O ARG S 922 " (cutoff:3.500A) Processing helix chain 'S' and resid 954 through 962 Processing helix chain 'S' and resid 1045 through 1053 Processing helix chain 'S' and resid 1088 through 1096 removed outlier: 3.750A pdb=" N LEU S1091 " --> pdb=" O GLU S1088 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU S1093 " --> pdb=" O PRO S1090 " (cutoff:3.500A) Processing helix chain 'T' and resid 580 through 591 removed outlier: 4.019A pdb=" N ARG T 589 " --> pdb=" O LYS T 585 " (cutoff:3.500A) Processing helix chain 'T' and resid 623 through 629 Processing helix chain 'T' and resid 631 through 639 removed outlier: 3.847A pdb=" N ASP T 636 " --> pdb=" O LEU T 632 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL T 638 " --> pdb=" O SER T 634 " (cutoff:3.500A) Processing helix chain 'T' and resid 662 through 687 removed outlier: 4.104A pdb=" N GLN T 668 " --> pdb=" O GLU T 664 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR T 671 " --> pdb=" O ARG T 667 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ARG T 673 " --> pdb=" O ARG T 669 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP T 677 " --> pdb=" O ARG T 673 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN T 680 " --> pdb=" O ALA T 676 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA T 681 " --> pdb=" O ASP T 677 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN T 684 " --> pdb=" O ASN T 680 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE T 685 " --> pdb=" O ALA T 681 " (cutoff:3.500A) Processing helix chain 'T' and resid 697 through 708 removed outlier: 3.690A pdb=" N ALA T 708 " --> pdb=" O LEU T 704 " (cutoff:3.500A) Processing helix chain 'T' and resid 717 through 725 removed outlier: 3.867A pdb=" N GLN T 725 " --> pdb=" O THR T 721 " (cutoff:3.500A) Processing helix chain 'T' and resid 769 through 776 removed outlier: 3.961A pdb=" N MET T 776 " --> pdb=" O VAL T 772 " (cutoff:3.500A) Processing helix chain 'T' and resid 795 through 800 Processing helix chain 'T' and resid 800 through 807 removed outlier: 3.646A pdb=" N GLN T 804 " --> pdb=" O LEU T 800 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA T 806 " --> pdb=" O LEU T 802 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY T 807 " --> pdb=" O GLN T 803 " (cutoff:3.500A) Processing helix chain 'T' and resid 810 through 820 removed outlier: 3.618A pdb=" N MET T 814 " --> pdb=" O ASP T 810 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU T 817 " --> pdb=" O ALA T 813 " (cutoff:3.500A) Processing helix chain 'T' and resid 833 through 842 removed outlier: 4.334A pdb=" N LEU T 839 " --> pdb=" O ASP T 835 " (cutoff:3.500A) Processing helix chain 'T' and resid 851 through 856 Processing helix chain 'T' and resid 857 through 875 removed outlier: 4.468A pdb=" N ALA T 863 " --> pdb=" O PRO T 859 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TRP T 864 " --> pdb=" O MET T 860 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN T 865 " --> pdb=" O GLU T 861 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR T 869 " --> pdb=" O GLN T 865 " (cutoff:3.500A) Proline residue: T 870 - end of helix removed outlier: 3.801A pdb=" N GLU T 873 " --> pdb=" O THR T 869 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU T 875 " --> pdb=" O ALA T 871 " (cutoff:3.500A) Processing helix chain 'T' and resid 883 through 892 removed outlier: 4.402A pdb=" N ASN T 889 " --> pdb=" O ASP T 885 " (cutoff:3.500A) Processing helix chain 'T' and resid 905 through 910 Processing helix chain 'T' and resid 920 through 928 removed outlier: 3.874A pdb=" N GLN T 925 " --> pdb=" O ALA T 921 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN T 926 " --> pdb=" O ARG T 922 " (cutoff:3.500A) Processing helix chain 'T' and resid 954 through 959 Processing helix chain 'T' and resid 1045 through 1053 Processing helix chain 'T' and resid 1073 through 1075 No H-bonds generated for 'chain 'T' and resid 1073 through 1075' Processing helix chain 'T' and resid 1088 through 1096 removed outlier: 4.056A pdb=" N LEU T1093 " --> pdb=" O PRO T1090 " (cutoff:3.500A) Processing helix chain 'U' and resid 581 through 591 removed outlier: 3.758A pdb=" N MET U 586 " --> pdb=" O LEU U 582 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU U 587 " --> pdb=" O TYR U 583 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA U 588 " --> pdb=" O GLN U 584 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL U 590 " --> pdb=" O MET U 586 " (cutoff:3.500A) Processing helix chain 'U' and resid 624 through 629 Processing helix chain 'U' and resid 631 through 641 removed outlier: 4.085A pdb=" N ASP U 636 " --> pdb=" O LEU U 632 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR U 637 " --> pdb=" O PRO U 633 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL U 638 " --> pdb=" O SER U 634 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN U 640 " --> pdb=" O ASP U 636 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU U 641 " --> pdb=" O THR U 637 " (cutoff:3.500A) Processing helix chain 'U' and resid 662 through 665 Processing helix chain 'U' and resid 666 through 671 Processing helix chain 'U' and resid 671 through 676 Processing helix chain 'U' and resid 679 through 687 Processing helix chain 'U' and resid 698 through 707 removed outlier: 3.509A pdb=" N LEU U 704 " --> pdb=" O VAL U 700 " (cutoff:3.500A) Processing helix chain 'U' and resid 716 through 725 removed outlier: 3.676A pdb=" N GLN U 725 " --> pdb=" O THR U 721 " (cutoff:3.500A) Processing helix chain 'U' and resid 726 through 728 No H-bonds generated for 'chain 'U' and resid 726 through 728' Processing helix chain 'U' and resid 787 through 806 removed outlier: 3.873A pdb=" N TYR U 791 " --> pdb=" O ASN U 787 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR U 793 " --> pdb=" O GLN U 789 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN U 797 " --> pdb=" O THR U 793 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL U 798 " --> pdb=" O ARG U 794 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN U 804 " --> pdb=" O LEU U 800 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE U 805 " --> pdb=" O ARG U 801 " (cutoff:3.500A) Processing helix chain 'U' and resid 815 through 820 Processing helix chain 'U' and resid 829 through 834 removed outlier: 3.579A pdb=" N THR U 833 " --> pdb=" O ASP U 829 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG U 834 " --> pdb=" O LEU U 830 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 829 through 834' Processing helix chain 'U' and resid 835 through 842 removed outlier: 3.696A pdb=" N ALA U 841 " --> pdb=" O GLY U 837 " (cutoff:3.500A) Processing helix chain 'U' and resid 851 through 856 Processing helix chain 'U' and resid 856 through 865 removed outlier: 3.646A pdb=" N MET U 860 " --> pdb=" O PHE U 856 " (cutoff:3.500A) Processing helix chain 'U' and resid 868 through 876 removed outlier: 4.085A pdb=" N SER U 874 " --> pdb=" O PRO U 870 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN U 876 " --> pdb=" O ALA U 872 " (cutoff:3.500A) Processing helix chain 'U' and resid 876 through 881 removed outlier: 3.654A pdb=" N THR U 881 " --> pdb=" O ALA U 877 " (cutoff:3.500A) Processing helix chain 'U' and resid 883 through 888 Processing helix chain 'U' and resid 905 through 913 Processing helix chain 'U' and resid 920 through 928 removed outlier: 3.641A pdb=" N GLN U 925 " --> pdb=" O ALA U 921 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASN U 926 " --> pdb=" O ARG U 922 " (cutoff:3.500A) Processing helix chain 'U' and resid 954 through 966 removed outlier: 3.692A pdb=" N ASN U 960 " --> pdb=" O LEU U 956 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU U 964 " --> pdb=" O ASN U 960 " (cutoff:3.500A) Processing helix chain 'U' and resid 1045 through 1053 removed outlier: 4.074A pdb=" N MET U1053 " --> pdb=" O ARG U1049 " (cutoff:3.500A) Processing helix chain 'U' and resid 1088 through 1097 removed outlier: 3.713A pdb=" N LEU U1091 " --> pdb=" O GLU U1088 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL U1092 " --> pdb=" O GLY U1089 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU U1093 " --> pdb=" O PRO U1090 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU U1096 " --> pdb=" O LEU U1093 " (cutoff:3.500A) Processing helix chain 'V' and resid 581 through 591 removed outlier: 3.508A pdb=" N LYS V 585 " --> pdb=" O MET V 581 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET V 586 " --> pdb=" O LEU V 582 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU V 587 " --> pdb=" O TYR V 583 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA V 588 " --> pdb=" O GLN V 584 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL V 590 " --> pdb=" O MET V 586 " (cutoff:3.500A) Processing helix chain 'V' and resid 624 through 629 Processing helix chain 'V' and resid 631 through 640 removed outlier: 4.028A pdb=" N ASP V 636 " --> pdb=" O LEU V 632 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR V 637 " --> pdb=" O PRO V 633 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL V 638 " --> pdb=" O SER V 634 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN V 640 " --> pdb=" O ASP V 636 " (cutoff:3.500A) Processing helix chain 'V' and resid 662 through 665 Processing helix chain 'V' and resid 666 through 687 removed outlier: 4.165A pdb=" N THR V 672 " --> pdb=" O GLN V 668 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP V 677 " --> pdb=" O ARG V 673 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY V 679 " --> pdb=" O PHE V 675 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN V 680 " --> pdb=" O ALA V 676 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA V 681 " --> pdb=" O ASP V 677 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP V 682 " --> pdb=" O PHE V 678 " (cutoff:3.500A) Processing helix chain 'V' and resid 698 through 707 Processing helix chain 'V' and resid 716 through 725 removed outlier: 3.775A pdb=" N GLN V 725 " --> pdb=" O THR V 721 " (cutoff:3.500A) Processing helix chain 'V' and resid 726 through 728 No H-bonds generated for 'chain 'V' and resid 726 through 728' Processing helix chain 'V' and resid 787 through 806 removed outlier: 3.822A pdb=" N TYR V 791 " --> pdb=" O ASN V 787 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR V 793 " --> pdb=" O GLN V 789 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN V 797 " --> pdb=" O THR V 793 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL V 798 " --> pdb=" O ARG V 794 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN V 804 " --> pdb=" O LEU V 800 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE V 805 " --> pdb=" O ARG V 801 " (cutoff:3.500A) Processing helix chain 'V' and resid 815 through 820 Processing helix chain 'V' and resid 829 through 842 removed outlier: 3.605A pdb=" N THR V 833 " --> pdb=" O ASP V 829 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG V 834 " --> pdb=" O LEU V 830 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASP V 835 " --> pdb=" O THR V 831 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY V 837 " --> pdb=" O THR V 833 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER V 838 " --> pdb=" O ARG V 834 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA V 841 " --> pdb=" O GLY V 837 " (cutoff:3.500A) Processing helix chain 'V' and resid 851 through 856 Processing helix chain 'V' and resid 856 through 865 removed outlier: 3.733A pdb=" N MET V 860 " --> pdb=" O PHE V 856 " (cutoff:3.500A) Processing helix chain 'V' and resid 868 through 876 removed outlier: 4.039A pdb=" N SER V 874 " --> pdb=" O PRO V 870 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN V 876 " --> pdb=" O ALA V 872 " (cutoff:3.500A) Processing helix chain 'V' and resid 876 through 881 removed outlier: 3.619A pdb=" N THR V 881 " --> pdb=" O ALA V 877 " (cutoff:3.500A) Processing helix chain 'V' and resid 883 through 888 Processing helix chain 'V' and resid 905 through 911 Processing helix chain 'V' and resid 920 through 928 removed outlier: 3.648A pdb=" N GLN V 925 " --> pdb=" O ALA V 921 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASN V 926 " --> pdb=" O ARG V 922 " (cutoff:3.500A) Processing helix chain 'V' and resid 954 through 966 removed outlier: 3.722A pdb=" N ASN V 960 " --> pdb=" O LEU V 956 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU V 964 " --> pdb=" O ASN V 960 " (cutoff:3.500A) Processing helix chain 'V' and resid 1045 through 1053 removed outlier: 4.000A pdb=" N MET V1053 " --> pdb=" O ARG V1049 " (cutoff:3.500A) Processing helix chain 'V' and resid 1088 through 1097 removed outlier: 3.689A pdb=" N LEU V1091 " --> pdb=" O GLU V1088 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL V1092 " --> pdb=" O GLY V1089 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU V1093 " --> pdb=" O PRO V1090 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU V1096 " --> pdb=" O LEU V1093 " (cutoff:3.500A) Processing helix chain 'W' and resid 581 through 591 removed outlier: 3.689A pdb=" N MET W 586 " --> pdb=" O LEU W 582 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU W 587 " --> pdb=" O TYR W 583 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA W 588 " --> pdb=" O GLN W 584 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL W 590 " --> pdb=" O MET W 586 " (cutoff:3.500A) Processing helix chain 'W' and resid 624 through 629 Processing helix chain 'W' and resid 631 through 641 removed outlier: 4.052A pdb=" N ASP W 636 " --> pdb=" O LEU W 632 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR W 637 " --> pdb=" O PRO W 633 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL W 638 " --> pdb=" O SER W 634 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN W 640 " --> pdb=" O ASP W 636 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU W 641 " --> pdb=" O THR W 637 " (cutoff:3.500A) Processing helix chain 'W' and resid 662 through 665 Processing helix chain 'W' and resid 666 through 687 removed outlier: 4.160A pdb=" N THR W 672 " --> pdb=" O GLN W 668 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP W 677 " --> pdb=" O ARG W 673 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY W 679 " --> pdb=" O PHE W 675 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN W 680 " --> pdb=" O ALA W 676 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA W 681 " --> pdb=" O ASP W 677 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP W 682 " --> pdb=" O PHE W 678 " (cutoff:3.500A) Processing helix chain 'W' and resid 698 through 707 Processing helix chain 'W' and resid 716 through 725 removed outlier: 3.718A pdb=" N GLN W 725 " --> pdb=" O THR W 721 " (cutoff:3.500A) Processing helix chain 'W' and resid 726 through 728 No H-bonds generated for 'chain 'W' and resid 726 through 728' Processing helix chain 'W' and resid 787 through 806 removed outlier: 3.882A pdb=" N TYR W 791 " --> pdb=" O ASN W 787 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR W 793 " --> pdb=" O GLN W 789 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN W 797 " --> pdb=" O THR W 793 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL W 798 " --> pdb=" O ARG W 794 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN W 804 " --> pdb=" O LEU W 800 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE W 805 " --> pdb=" O ARG W 801 " (cutoff:3.500A) Processing helix chain 'W' and resid 815 through 820 Processing helix chain 'W' and resid 829 through 834 removed outlier: 3.579A pdb=" N THR W 833 " --> pdb=" O ASP W 829 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG W 834 " --> pdb=" O LEU W 830 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 829 through 834' Processing helix chain 'W' and resid 835 through 842 removed outlier: 3.722A pdb=" N ALA W 841 " --> pdb=" O GLY W 837 " (cutoff:3.500A) Processing helix chain 'W' and resid 851 through 856 Processing helix chain 'W' and resid 856 through 865 removed outlier: 3.657A pdb=" N MET W 860 " --> pdb=" O PHE W 856 " (cutoff:3.500A) Processing helix chain 'W' and resid 868 through 876 removed outlier: 4.038A pdb=" N SER W 874 " --> pdb=" O PRO W 870 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN W 876 " --> pdb=" O ALA W 872 " (cutoff:3.500A) Processing helix chain 'W' and resid 876 through 881 removed outlier: 3.660A pdb=" N THR W 881 " --> pdb=" O ALA W 877 " (cutoff:3.500A) Processing helix chain 'W' and resid 883 through 888 Processing helix chain 'W' and resid 905 through 911 Processing helix chain 'W' and resid 920 through 928 removed outlier: 3.598A pdb=" N GLN W 925 " --> pdb=" O ALA W 921 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN W 926 " --> pdb=" O ARG W 922 " (cutoff:3.500A) Processing helix chain 'W' and resid 954 through 966 removed outlier: 3.712A pdb=" N ASN W 960 " --> pdb=" O LEU W 956 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU W 964 " --> pdb=" O ASN W 960 " (cutoff:3.500A) Processing helix chain 'W' and resid 1045 through 1053 removed outlier: 4.124A pdb=" N MET W1053 " --> pdb=" O ARG W1049 " (cutoff:3.500A) Processing helix chain 'W' and resid 1088 through 1097 removed outlier: 3.726A pdb=" N LEU W1091 " --> pdb=" O GLU W1088 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU W1093 " --> pdb=" O PRO W1090 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU W1096 " --> pdb=" O LEU W1093 " (cutoff:3.500A) Processing helix chain 'X' and resid 581 through 591 removed outlier: 3.763A pdb=" N MET X 586 " --> pdb=" O LEU X 582 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU X 587 " --> pdb=" O TYR X 583 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA X 588 " --> pdb=" O GLN X 584 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL X 590 " --> pdb=" O MET X 586 " (cutoff:3.500A) Processing helix chain 'X' and resid 624 through 629 Processing helix chain 'X' and resid 631 through 641 removed outlier: 4.076A pdb=" N ASP X 636 " --> pdb=" O LEU X 632 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR X 637 " --> pdb=" O PRO X 633 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL X 638 " --> pdb=" O SER X 634 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN X 640 " --> pdb=" O ASP X 636 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU X 641 " --> pdb=" O THR X 637 " (cutoff:3.500A) Processing helix chain 'X' and resid 662 through 665 Processing helix chain 'X' and resid 666 through 687 removed outlier: 4.142A pdb=" N THR X 672 " --> pdb=" O GLN X 668 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP X 677 " --> pdb=" O ARG X 673 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY X 679 " --> pdb=" O PHE X 675 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN X 680 " --> pdb=" O ALA X 676 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA X 681 " --> pdb=" O ASP X 677 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TRP X 682 " --> pdb=" O PHE X 678 " (cutoff:3.500A) Processing helix chain 'X' and resid 698 through 707 removed outlier: 3.502A pdb=" N LEU X 704 " --> pdb=" O VAL X 700 " (cutoff:3.500A) Processing helix chain 'X' and resid 716 through 725 removed outlier: 3.719A pdb=" N GLN X 725 " --> pdb=" O THR X 721 " (cutoff:3.500A) Processing helix chain 'X' and resid 726 through 728 No H-bonds generated for 'chain 'X' and resid 726 through 728' Processing helix chain 'X' and resid 787 through 806 removed outlier: 3.842A pdb=" N TYR X 791 " --> pdb=" O ASN X 787 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR X 793 " --> pdb=" O GLN X 789 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN X 797 " --> pdb=" O THR X 793 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL X 798 " --> pdb=" O ARG X 794 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN X 804 " --> pdb=" O LEU X 800 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE X 805 " --> pdb=" O ARG X 801 " (cutoff:3.500A) Processing helix chain 'X' and resid 815 through 820 Processing helix chain 'X' and resid 829 through 834 removed outlier: 3.579A pdb=" N THR X 833 " --> pdb=" O ASP X 829 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG X 834 " --> pdb=" O LEU X 830 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 829 through 834' Processing helix chain 'X' and resid 835 through 842 removed outlier: 3.755A pdb=" N ALA X 841 " --> pdb=" O GLY X 837 " (cutoff:3.500A) Processing helix chain 'X' and resid 851 through 856 Processing helix chain 'X' and resid 856 through 868 removed outlier: 3.578A pdb=" N MET X 860 " --> pdb=" O PHE X 856 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN X 866 " --> pdb=" O GLN X 862 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL X 867 " --> pdb=" O ALA X 863 " (cutoff:3.500A) Processing helix chain 'X' and resid 868 through 876 removed outlier: 4.017A pdb=" N SER X 874 " --> pdb=" O PRO X 870 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN X 876 " --> pdb=" O ALA X 872 " (cutoff:3.500A) Processing helix chain 'X' and resid 876 through 881 removed outlier: 3.643A pdb=" N THR X 881 " --> pdb=" O ALA X 877 " (cutoff:3.500A) Processing helix chain 'X' and resid 883 through 888 Processing helix chain 'X' and resid 905 through 911 Processing helix chain 'X' and resid 920 through 928 removed outlier: 3.668A pdb=" N GLN X 925 " --> pdb=" O ALA X 921 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN X 926 " --> pdb=" O ARG X 922 " (cutoff:3.500A) Processing helix chain 'X' and resid 954 through 966 removed outlier: 3.701A pdb=" N ASN X 960 " --> pdb=" O LEU X 956 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU X 964 " --> pdb=" O ASN X 960 " (cutoff:3.500A) Processing helix chain 'X' and resid 1045 through 1053 removed outlier: 4.108A pdb=" N MET X1053 " --> pdb=" O ARG X1049 " (cutoff:3.500A) Processing helix chain 'X' and resid 1088 through 1097 removed outlier: 3.752A pdb=" N LEU X1091 " --> pdb=" O GLU X1088 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL X1092 " --> pdb=" O GLY X1089 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU X1093 " --> pdb=" O PRO X1090 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU X1096 " --> pdb=" O LEU X1093 " (cutoff:3.500A) Processing helix chain 'Y' and resid 581 through 591 removed outlier: 3.759A pdb=" N MET Y 586 " --> pdb=" O LEU Y 582 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU Y 587 " --> pdb=" O TYR Y 583 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA Y 588 " --> pdb=" O GLN Y 584 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL Y 590 " --> pdb=" O MET Y 586 " (cutoff:3.500A) Processing helix chain 'Y' and resid 624 through 629 Processing helix chain 'Y' and resid 631 through 641 removed outlier: 4.049A pdb=" N ASP Y 636 " --> pdb=" O LEU Y 632 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR Y 637 " --> pdb=" O PRO Y 633 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL Y 638 " --> pdb=" O SER Y 634 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN Y 640 " --> pdb=" O ASP Y 636 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU Y 641 " --> pdb=" O THR Y 637 " (cutoff:3.500A) Processing helix chain 'Y' and resid 662 through 665 Processing helix chain 'Y' and resid 666 through 671 Processing helix chain 'Y' and resid 671 through 676 Processing helix chain 'Y' and resid 679 through 687 Processing helix chain 'Y' and resid 698 through 707 removed outlier: 3.514A pdb=" N LEU Y 704 " --> pdb=" O VAL Y 700 " (cutoff:3.500A) Processing helix chain 'Y' and resid 716 through 725 removed outlier: 3.796A pdb=" N GLN Y 725 " --> pdb=" O THR Y 721 " (cutoff:3.500A) Processing helix chain 'Y' and resid 726 through 728 No H-bonds generated for 'chain 'Y' and resid 726 through 728' Processing helix chain 'Y' and resid 787 through 806 removed outlier: 3.844A pdb=" N TYR Y 791 " --> pdb=" O ASN Y 787 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR Y 793 " --> pdb=" O GLN Y 789 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN Y 797 " --> pdb=" O THR Y 793 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL Y 798 " --> pdb=" O ARG Y 794 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN Y 804 " --> pdb=" O LEU Y 800 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE Y 805 " --> pdb=" O ARG Y 801 " (cutoff:3.500A) Processing helix chain 'Y' and resid 829 through 834 removed outlier: 3.659A pdb=" N THR Y 833 " --> pdb=" O ASP Y 829 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG Y 834 " --> pdb=" O LEU Y 830 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 829 through 834' Processing helix chain 'Y' and resid 835 through 842 removed outlier: 3.674A pdb=" N ALA Y 841 " --> pdb=" O GLY Y 837 " (cutoff:3.500A) Processing helix chain 'Y' and resid 851 through 856 Processing helix chain 'Y' and resid 856 through 865 removed outlier: 3.653A pdb=" N MET Y 860 " --> pdb=" O PHE Y 856 " (cutoff:3.500A) Processing helix chain 'Y' and resid 868 through 876 removed outlier: 3.916A pdb=" N SER Y 874 " --> pdb=" O PRO Y 870 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN Y 876 " --> pdb=" O ALA Y 872 " (cutoff:3.500A) Processing helix chain 'Y' and resid 876 through 881 removed outlier: 3.595A pdb=" N THR Y 881 " --> pdb=" O ALA Y 877 " (cutoff:3.500A) Processing helix chain 'Y' and resid 883 through 888 Processing helix chain 'Y' and resid 905 through 911 Processing helix chain 'Y' and resid 920 through 928 removed outlier: 3.639A pdb=" N GLN Y 925 " --> pdb=" O ALA Y 921 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN Y 926 " --> pdb=" O ARG Y 922 " (cutoff:3.500A) Processing helix chain 'Y' and resid 954 through 966 removed outlier: 3.747A pdb=" N ASN Y 960 " --> pdb=" O LEU Y 956 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU Y 964 " --> pdb=" O ASN Y 960 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1045 through 1053 removed outlier: 4.104A pdb=" N MET Y1053 " --> pdb=" O ARG Y1049 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1088 through 1097 removed outlier: 3.755A pdb=" N LEU Y1091 " --> pdb=" O GLU Y1088 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL Y1092 " --> pdb=" O GLY Y1089 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU Y1093 " --> pdb=" O PRO Y1090 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU Y1096 " --> pdb=" O LEU Y1093 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 96 removed outlier: 3.640A pdb=" N ASP A 29 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 31 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY A 144 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA A 35 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 88 Processing sheet with id=AA3, first strand: chain 'B' and resid 93 through 96 removed outlier: 3.630A pdb=" N ASP B 29 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 31 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY B 144 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA B 35 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 88 removed outlier: 4.710A pdb=" N VAL B 48 " --> pdb=" O MET B 112 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.693A pdb=" N ASP C 29 " --> pdb=" O ARG C 138 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 31 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLY C 144 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA C 35 " --> pdb=" O GLY C 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 88 removed outlier: 4.709A pdb=" N VAL C 48 " --> pdb=" O MET C 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 93 through 96 removed outlier: 3.676A pdb=" N ASP D 29 " --> pdb=" O ARG D 138 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 31 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY D 144 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA D 35 " --> pdb=" O GLY D 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 84 through 88 Processing sheet with id=AA9, first strand: chain 'E' and resid 93 through 96 removed outlier: 3.637A pdb=" N ASP E 29 " --> pdb=" O ARG E 138 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG E 31 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLY E 144 " --> pdb=" O ARG E 33 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA E 35 " --> pdb=" O GLY E 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 84 through 88 removed outlier: 4.765A pdb=" N VAL E 48 " --> pdb=" O MET E 112 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 93 through 99 removed outlier: 3.669A pdb=" N ARG F 138 " --> pdb=" O HIS F 27 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL F 142 " --> pdb=" O ARG F 31 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY F 144 " --> pdb=" O ARG F 33 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ALA F 35 " --> pdb=" O GLY F 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 82 through 88 removed outlier: 3.633A pdb=" N ALA F 82 " --> pdb=" O GLN F 53 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL F 47 " --> pdb=" O LEU F 88 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 93 through 99 removed outlier: 3.652A pdb=" N ARG G 138 " --> pdb=" O HIS G 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 142 " --> pdb=" O ARG G 31 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLY G 144 " --> pdb=" O ARG G 33 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA G 35 " --> pdb=" O GLY G 144 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 82 through 88 removed outlier: 3.807A pdb=" N ALA G 82 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL G 47 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE G 106 " --> pdb=" O LEU G 54 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 93 through 99 removed outlier: 3.644A pdb=" N ARG H 138 " --> pdb=" O HIS H 27 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL H 142 " --> pdb=" O ARG H 31 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY H 144 " --> pdb=" O ARG H 33 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA H 35 " --> pdb=" O GLY H 144 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 82 through 88 removed outlier: 3.567A pdb=" N ALA H 82 " --> pdb=" O GLN H 53 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL H 47 " --> pdb=" O LEU H 88 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 93 through 99 removed outlier: 3.670A pdb=" N ARG I 138 " --> pdb=" O HIS I 27 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL I 142 " --> pdb=" O ARG I 31 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY I 144 " --> pdb=" O ARG I 33 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ALA I 35 " --> pdb=" O GLY I 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 82 through 88 removed outlier: 3.591A pdb=" N ALA I 82 " --> pdb=" O GLN I 53 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL I 47 " --> pdb=" O LEU I 88 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE I 106 " --> pdb=" O LEU I 54 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 93 through 99 removed outlier: 3.673A pdb=" N ARG J 138 " --> pdb=" O HIS J 27 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL J 142 " --> pdb=" O ARG J 31 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLY J 144 " --> pdb=" O ARG J 33 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALA J 35 " --> pdb=" O GLY J 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 82 through 88 removed outlier: 3.645A pdb=" N ALA J 82 " --> pdb=" O GLN J 53 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL J 47 " --> pdb=" O LEU J 88 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE J 106 " --> pdb=" O LEU J 54 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 93 through 96 removed outlier: 6.988A pdb=" N GLY K 144 " --> pdb=" O ARG K 33 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA K 35 " --> pdb=" O GLY K 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 83 through 88 removed outlier: 3.585A pdb=" N VAL K 47 " --> pdb=" O LEU K 88 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 93 through 96 removed outlier: 7.027A pdb=" N GLY L 144 " --> pdb=" O ARG L 33 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ALA L 35 " --> pdb=" O GLY L 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 83 through 88 Processing sheet with id=AC7, first strand: chain 'M' and resid 93 through 96 removed outlier: 7.080A pdb=" N GLY M 144 " --> pdb=" O ARG M 33 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ALA M 35 " --> pdb=" O GLY M 144 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 83 through 88 Processing sheet with id=AC9, first strand: chain 'N' and resid 94 through 96 removed outlier: 7.019A pdb=" N GLY N 144 " --> pdb=" O ARG N 33 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA N 35 " --> pdb=" O GLY N 144 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 83 through 88 Processing sheet with id=AD2, first strand: chain 'O' and resid 94 through 96 removed outlier: 7.044A pdb=" N GLY O 144 " --> pdb=" O ARG O 33 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ALA O 35 " --> pdb=" O GLY O 144 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 83 through 88 Processing sheet with id=AD4, first strand: chain 'P' and resid 932 through 935 Processing sheet with id=AD5, first strand: chain 'P' and resid 1011 through 1012 removed outlier: 4.711A pdb=" N GLY P1065 " --> pdb=" O ALA P1059 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA P1059 " --> pdb=" O GLY P1065 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 1011 through 1012 Processing sheet with id=AD7, first strand: chain 'P' and resid 1000 through 1003 removed outlier: 3.521A pdb=" N GLN P 991 " --> pdb=" O VAL P1029 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA P1024 " --> pdb=" O ASP P1040 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP P1040 " --> pdb=" O ALA P1024 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU P1026 " --> pdb=" O TYR P1038 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP P1028 " --> pdb=" O ARG P1036 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG P1036 " --> pdb=" O TRP P1028 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 932 through 935 Processing sheet with id=AD9, first strand: chain 'Q' and resid 1011 through 1012 removed outlier: 4.679A pdb=" N GLY Q1065 " --> pdb=" O ALA Q1059 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA Q1059 " --> pdb=" O GLY Q1065 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS Q1057 " --> pdb=" O SER Q1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 1011 through 1012 Processing sheet with id=AE2, first strand: chain 'Q' and resid 1002 through 1003 removed outlier: 6.582A pdb=" N ALA Q1024 " --> pdb=" O ASP Q1040 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP Q1040 " --> pdb=" O ALA Q1024 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU Q1026 " --> pdb=" O TYR Q1038 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP Q1028 " --> pdb=" O ARG Q1036 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG Q1036 " --> pdb=" O TRP Q1028 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 932 through 935 Processing sheet with id=AE4, first strand: chain 'R' and resid 1011 through 1012 removed outlier: 4.771A pdb=" N GLY R1065 " --> pdb=" O ALA R1059 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA R1059 " --> pdb=" O GLY R1065 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 1011 through 1012 Processing sheet with id=AE6, first strand: chain 'R' and resid 1000 through 1003 removed outlier: 3.504A pdb=" N GLN R 991 " --> pdb=" O VAL R1029 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA R1024 " --> pdb=" O ASP R1040 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP R1040 " --> pdb=" O ALA R1024 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU R1026 " --> pdb=" O TYR R1038 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP R1028 " --> pdb=" O ARG R1036 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG R1036 " --> pdb=" O TRP R1028 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 932 through 935 Processing sheet with id=AE8, first strand: chain 'S' and resid 1011 through 1012 removed outlier: 4.725A pdb=" N GLY S1065 " --> pdb=" O ALA S1059 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA S1059 " --> pdb=" O GLY S1065 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS S1057 " --> pdb=" O SER S1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 1011 through 1012 Processing sheet with id=AF1, first strand: chain 'S' and resid 1002 through 1003 removed outlier: 6.561A pdb=" N ALA S1024 " --> pdb=" O ASP S1040 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP S1040 " --> pdb=" O ALA S1024 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU S1026 " --> pdb=" O TYR S1038 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP S1028 " --> pdb=" O ARG S1036 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 932 through 935 Processing sheet with id=AF3, first strand: chain 'T' and resid 1011 through 1012 removed outlier: 4.782A pdb=" N GLY T1065 " --> pdb=" O ALA T1059 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA T1059 " --> pdb=" O GLY T1065 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS T1057 " --> pdb=" O SER T1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'T' and resid 1011 through 1012 Processing sheet with id=AF5, first strand: chain 'T' and resid 1000 through 1003 removed outlier: 6.604A pdb=" N ALA T1024 " --> pdb=" O ASP T1040 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASP T1040 " --> pdb=" O ALA T1024 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU T1026 " --> pdb=" O TYR T1038 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP T1028 " --> pdb=" O ARG T1036 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG T1036 " --> pdb=" O TRP T1028 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 932 through 935 Processing sheet with id=AF7, first strand: chain 'U' and resid 1011 through 1012 removed outlier: 3.605A pdb=" N LYS U1057 " --> pdb=" O SER U1067 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER U1069 " --> pdb=" O ARG U1055 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG U1055 " --> pdb=" O SER U1069 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'U' and resid 1000 through 1003 removed outlier: 6.538A pdb=" N ALA U1024 " --> pdb=" O ASP U1040 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP U1040 " --> pdb=" O ALA U1024 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU U1026 " --> pdb=" O TYR U1038 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 932 through 935 Processing sheet with id=AG1, first strand: chain 'V' and resid 1011 through 1012 removed outlier: 3.502A pdb=" N ARG V1083 " --> pdb=" O GLU V 980 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS V1057 " --> pdb=" O SER V1067 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER V1069 " --> pdb=" O ARG V1055 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG V1055 " --> pdb=" O SER V1069 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 999 through 1003 removed outlier: 6.415A pdb=" N ALA V1024 " --> pdb=" O ASP V1040 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP V1040 " --> pdb=" O ALA V1024 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU V1026 " --> pdb=" O TYR V1038 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 932 through 935 Processing sheet with id=AG4, first strand: chain 'W' and resid 1011 through 1012 removed outlier: 3.688A pdb=" N LYS W1057 " --> pdb=" O SER W1067 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER W1069 " --> pdb=" O ARG W1055 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG W1055 " --> pdb=" O SER W1069 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'W' and resid 999 through 1003 removed outlier: 6.389A pdb=" N VAL W1029 " --> pdb=" O MET W 990 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR W 992 " --> pdb=" O SER W1027 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER W1027 " --> pdb=" O THR W 992 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU W 994 " --> pdb=" O SER W1025 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER W1025 " --> pdb=" O LEU W 994 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR W 996 " --> pdb=" O GLY W1023 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY W1023 " --> pdb=" O THR W 996 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA W1024 " --> pdb=" O ASP W1040 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP W1040 " --> pdb=" O ALA W1024 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU W1026 " --> pdb=" O TYR W1038 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 932 through 935 Processing sheet with id=AG7, first strand: chain 'X' and resid 1011 through 1012 removed outlier: 3.606A pdb=" N LYS X1057 " --> pdb=" O SER X1067 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER X1069 " --> pdb=" O ARG X1055 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG X1055 " --> pdb=" O SER X1069 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'X' and resid 999 through 1003 removed outlier: 6.381A pdb=" N VAL X1029 " --> pdb=" O MET X 990 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR X 992 " --> pdb=" O SER X1027 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER X1027 " --> pdb=" O THR X 992 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU X 994 " --> pdb=" O SER X1025 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER X1025 " --> pdb=" O LEU X 994 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR X 996 " --> pdb=" O GLY X1023 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY X1023 " --> pdb=" O THR X 996 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA X1024 " --> pdb=" O ASP X1040 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASP X1040 " --> pdb=" O ALA X1024 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU X1026 " --> pdb=" O TYR X1038 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Y' and resid 932 through 935 Processing sheet with id=AH1, first strand: chain 'Y' and resid 1011 through 1012 removed outlier: 3.655A pdb=" N LYS Y1057 " --> pdb=" O SER Y1067 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER Y1069 " --> pdb=" O ARG Y1055 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG Y1055 " --> pdb=" O SER Y1069 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Y' and resid 999 through 1003 removed outlier: 6.516A pdb=" N ALA Y1024 " --> pdb=" O ASP Y1040 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP Y1040 " --> pdb=" O ALA Y1024 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU Y1026 " --> pdb=" O TYR Y1038 " (cutoff:3.500A) 1559 hydrogen bonds defined for protein. 4269 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: 20.71 Time building geometry restraints manager: 21.70 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: 16788 1.33 - 1.45: 10015 1.45 - 1.58: 26132 1.58 - 1.70: 0 1.70 - 1.82: 390 Bond restraints: 53325 Sorted by residual: bond pdb=" C GLN S 846 " pdb=" N GLU S 847 " ideal model delta sigma weight residual 1.332 1.300 0.032 1.40e-02 5.10e+03 5.34e+00 bond pdb=" CA THR S1084 " pdb=" CB THR S1084 " ideal model delta sigma weight residual 1.533 1.499 0.035 1.51e-02 4.39e+03 5.31e+00 bond pdb=" C LEU E 88 " pdb=" N GLN E 89 " ideal model delta sigma weight residual 1.331 1.266 0.065 2.83e-02 1.25e+03 5.28e+00 bond pdb=" CB THR R1084 " pdb=" CG2 THR R1084 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.81e+00 bond pdb=" CB TRP T1045 " pdb=" CG TRP T1045 " ideal model delta sigma weight residual 1.498 1.430 0.068 3.10e-02 1.04e+03 4.80e+00 ... (remaining 53320 not shown) Histogram of bond angle deviations from ideal: 97.58 - 104.88: 1077 104.88 - 112.18: 26569 112.18 - 119.48: 18694 119.48 - 126.79: 25352 126.79 - 134.09: 973 Bond angle restraints: 72665 Sorted by residual: angle pdb=" N ILE G 23 " pdb=" CA ILE G 23 " pdb=" C ILE G 23 " ideal model delta sigma weight residual 112.83 103.87 8.96 9.90e-01 1.02e+00 8.18e+01 angle pdb=" CA VAL Q 828 " pdb=" C VAL Q 828 " pdb=" N ASP Q 829 " ideal model delta sigma weight residual 116.86 124.16 -7.30 1.14e+00 7.69e-01 4.10e+01 angle pdb=" C ALA W 813 " pdb=" N MET W 814 " pdb=" CA MET W 814 " ideal model delta sigma weight residual 121.54 133.37 -11.83 1.91e+00 2.74e-01 3.84e+01 angle pdb=" C ALA X 813 " pdb=" N MET X 814 " pdb=" CA MET X 814 " ideal model delta sigma weight residual 121.54 133.33 -11.79 1.91e+00 2.74e-01 3.81e+01 angle pdb=" C ALA U 813 " pdb=" N MET U 814 " pdb=" CA MET U 814 " ideal model delta sigma weight residual 121.54 133.28 -11.74 1.91e+00 2.74e-01 3.78e+01 ... (remaining 72660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 27991 17.91 - 35.82: 3136 35.82 - 53.73: 561 53.73 - 71.64: 97 71.64 - 89.55: 20 Dihedral angle restraints: 31805 sinusoidal: 12255 harmonic: 19550 Sorted by residual: dihedral pdb=" CA MET V 785 " pdb=" C MET V 785 " pdb=" N LEU V 786 " pdb=" CA LEU V 786 " ideal model delta harmonic sigma weight residual 180.00 131.30 48.70 0 5.00e+00 4.00e-02 9.49e+01 dihedral pdb=" CA MET X 785 " pdb=" C MET X 785 " pdb=" N LEU X 786 " pdb=" CA LEU X 786 " ideal model delta harmonic sigma weight residual 180.00 131.56 48.44 0 5.00e+00 4.00e-02 9.39e+01 dihedral pdb=" CA MET U 785 " pdb=" C MET U 785 " pdb=" N LEU U 786 " pdb=" CA LEU U 786 " ideal model delta harmonic sigma weight residual 180.00 131.59 48.41 0 5.00e+00 4.00e-02 9.37e+01 ... (remaining 31802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 5466 0.054 - 0.108: 2279 0.108 - 0.162: 520 0.162 - 0.217: 134 0.217 - 0.271: 26 Chirality restraints: 8425 Sorted by residual: chirality pdb=" CA THR W 869 " pdb=" N THR W 869 " pdb=" C THR W 869 " pdb=" CB THR W 869 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA THR X 869 " pdb=" N THR X 869 " pdb=" C THR X 869 " pdb=" CB THR X 869 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB VAL Q 867 " pdb=" CA VAL Q 867 " pdb=" CG1 VAL Q 867 " pdb=" CG2 VAL Q 867 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 8422 not shown) Planarity restraints: 9415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 23 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ILE A 23 " -0.059 2.00e-02 2.50e+03 pdb=" O ILE A 23 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS A 24 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 23 " -0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C ILE E 23 " 0.058 2.00e-02 2.50e+03 pdb=" O ILE E 23 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS E 24 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 23 " 0.016 2.00e-02 2.50e+03 3.31e-02 1.09e+01 pdb=" C ILE B 23 " -0.057 2.00e-02 2.50e+03 pdb=" O ILE B 23 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS B 24 " 0.019 2.00e-02 2.50e+03 ... (remaining 9412 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 10733 2.76 - 3.30: 47003 3.30 - 3.83: 84035 3.83 - 4.37: 95711 4.37 - 4.90: 163808 Nonbonded interactions: 401290 Sorted by model distance: nonbonded pdb=" O ASP U 942 " pdb=" OG1 THR U 946 " model vdw 2.228 2.440 nonbonded pdb=" O ASP V 942 " pdb=" OG1 THR V 946 " model vdw 2.232 2.440 nonbonded pdb=" O ASP W 942 " pdb=" OG1 THR W 946 " model vdw 2.239 2.440 nonbonded pdb=" O GLY Q 850 " pdb=" OG1 THR Q 854 " model vdw 2.251 2.440 nonbonded pdb=" O ASP T 942 " pdb=" OG1 THR T 946 " model vdw 2.252 2.440 ... (remaining 401285 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 72 or resid 80 through 152)) selection = (chain 'B' and (resid 23 through 72 or resid 80 through 152)) selection = (chain 'C' and (resid 23 through 72 or resid 80 through 152)) selection = (chain 'D' and (resid 23 through 72 or resid 80 through 152)) selection = (chain 'E' and (resid 23 through 72 or resid 80 through 152)) selection = (chain 'F' and (resid 23 through 72 or resid 80 through 152)) selection = (chain 'G' and (resid 23 through 72 or resid 80 through 152)) selection = (chain 'H' and (resid 23 through 72 or resid 80 through 152)) selection = (chain 'I' and (resid 23 through 72 or resid 80 through 152)) selection = (chain 'J' and (resid 23 through 72 or resid 80 through 152)) selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = (chain 'P' and (resid 577 through 946 or (resid 947 and (name N or name CA or na \ me C or name O or name CB )) or resid 948 through 1107)) selection = (chain 'Q' and (resid 577 through 946 or (resid 947 and (name N or name CA or na \ me C or name O or name CB )) or resid 948 through 1107)) selection = (chain 'R' and (resid 577 through 946 or (resid 947 and (name N or name CA or na \ me C or name O or name CB )) or resid 948 through 1107)) selection = (chain 'S' and (resid 577 through 946 or (resid 947 and (name N or name CA or na \ me C or name O or name CB )) or resid 948 through 1107)) selection = (chain 'T' and (resid 577 through 946 or (resid 947 and (name N or name CA or na \ me C or name O or name CB )) or resid 948 through 1107)) selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.16 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: 2.330 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: 0.040 Extract box with map and model: 11.180 Check model and map are aligned: 0.810 Set scattering table: 0.440 Process input model: 131.850 Find NCS groups from input model: 4.100 Set up NCS constraints: 0.220 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 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 : 0.010 0.097 53325 Z= 0.644 Angle : 1.109 12.600 72665 Z= 0.604 Chirality : 0.063 0.271 8425 Planarity : 0.007 0.071 9415 Dihedral : 15.285 89.547 19125 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.57 % Favored : 92.03 % Rotamer: Outliers : 0.60 % Allowed : 10.37 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.89 (0.08), residues: 6685 helix: -4.60 (0.05), residues: 2125 sheet: -1.77 (0.12), residues: 1415 loop : -2.87 (0.09), residues: 3145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP Q 887 HIS 0.006 0.002 HIS R 933 PHE 0.029 0.003 PHE R 613 TYR 0.016 0.002 TYR P1080 ARG 0.008 0.001 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1371 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1338 time to evaluate : 5.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.8308 (m-80) cc_final: 0.8071 (m-80) REVERT: A 141 GLU cc_start: 0.6950 (tp30) cc_final: 0.6739 (tp30) REVERT: B 31 ARG cc_start: 0.8143 (mtt180) cc_final: 0.7915 (ttm110) REVERT: B 53 GLN cc_start: 0.8177 (mt0) cc_final: 0.7842 (mm110) REVERT: B 66 GLN cc_start: 0.8934 (tp40) cc_final: 0.8639 (mp10) REVERT: B 141 GLU cc_start: 0.7014 (tp30) cc_final: 0.6643 (tp30) REVERT: C 31 ARG cc_start: 0.8016 (mtt180) cc_final: 0.7534 (ttm-80) REVERT: C 53 GLN cc_start: 0.8605 (mt0) cc_final: 0.8211 (mm-40) REVERT: C 140 ILE cc_start: 0.9264 (mt) cc_final: 0.9058 (mm) REVERT: D 31 ARG cc_start: 0.7860 (mtt180) cc_final: 0.7435 (ttm-80) REVERT: D 52 TYR cc_start: 0.7703 (m-80) cc_final: 0.7036 (m-80) REVERT: D 53 GLN cc_start: 0.8254 (mt0) cc_final: 0.7900 (mm110) REVERT: E 31 ARG cc_start: 0.8155 (mtt180) cc_final: 0.7729 (ttm-80) REVERT: E 74 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8248 (mp0) REVERT: F 50 ARG cc_start: 0.9006 (ttm170) cc_final: 0.8706 (ttm170) REVERT: F 53 GLN cc_start: 0.8241 (mt0) cc_final: 0.7939 (mt0) REVERT: F 135 ASP cc_start: 0.7926 (p0) cc_final: 0.7716 (p0) REVERT: G 34 GLU cc_start: 0.8020 (mp0) cc_final: 0.7532 (mp0) REVERT: G 50 ARG cc_start: 0.9035 (ttm170) cc_final: 0.8814 (ttm170) REVERT: G 53 GLN cc_start: 0.8294 (mt0) cc_final: 0.8052 (mt0) REVERT: G 76 LEU cc_start: 0.8374 (tp) cc_final: 0.7689 (tt) REVERT: G 84 LYS cc_start: 0.8742 (tptm) cc_final: 0.8523 (tttm) REVERT: G 106 PHE cc_start: 0.8683 (m-80) cc_final: 0.8070 (m-80) REVERT: G 112 MET cc_start: 0.9171 (mtp) cc_final: 0.8885 (mtm) REVERT: H 21 ARG cc_start: 0.7246 (mmt90) cc_final: 0.5869 (mpp-170) REVERT: H 22 GLN cc_start: 0.7098 (mp10) cc_final: 0.5947 (pt0) REVERT: H 30 ILE cc_start: 0.9280 (mt) cc_final: 0.9001 (mm) REVERT: H 106 PHE cc_start: 0.8667 (m-80) cc_final: 0.8410 (m-80) REVERT: H 112 MET cc_start: 0.9241 (mtp) cc_final: 0.9027 (mtm) REVERT: I 21 ARG cc_start: 0.6785 (mmt90) cc_final: 0.5931 (mpp-170) REVERT: I 22 GLN cc_start: 0.7118 (mp10) cc_final: 0.6108 (pt0) REVERT: I 30 ILE cc_start: 0.9207 (mt) cc_final: 0.8987 (mm) REVERT: I 48 VAL cc_start: 0.9025 (t) cc_final: 0.8520 (t) REVERT: I 50 ARG cc_start: 0.8888 (ttm170) cc_final: 0.8608 (ttm170) REVERT: I 53 GLN cc_start: 0.7901 (mt0) cc_final: 0.7373 (mt0) REVERT: I 65 TYR cc_start: 0.8978 (t80) cc_final: 0.8732 (t80) REVERT: I 98 MET cc_start: 0.8723 (ptm) cc_final: 0.8389 (ptm) REVERT: J 21 ARG cc_start: 0.7187 (mmt90) cc_final: 0.5866 (mpp-170) REVERT: J 30 ILE cc_start: 0.9257 (mt) cc_final: 0.8964 (mm) REVERT: J 53 GLN cc_start: 0.8294 (mt0) cc_final: 0.7995 (mt0) REVERT: K 31 ARG cc_start: 0.8470 (mtt180) cc_final: 0.7877 (mmm160) REVERT: K 50 ARG cc_start: 0.8859 (ttm-80) cc_final: 0.8432 (ttm110) REVERT: K 52 TYR cc_start: 0.6769 (m-80) cc_final: 0.6381 (m-80) REVERT: K 79 ASP cc_start: 0.6651 (t70) cc_final: 0.6079 (t0) REVERT: K 84 LYS cc_start: 0.8643 (tptm) cc_final: 0.8351 (tppp) REVERT: L 31 ARG cc_start: 0.8604 (mtt180) cc_final: 0.8130 (mmm160) REVERT: L 50 ARG cc_start: 0.8820 (ttm170) cc_final: 0.8492 (ttm-80) REVERT: L 52 TYR cc_start: 0.6901 (m-80) cc_final: 0.6247 (m-80) REVERT: L 79 ASP cc_start: 0.6763 (t70) cc_final: 0.6182 (t0) REVERT: L 113 PHE cc_start: 0.8413 (m-80) cc_final: 0.8018 (m-10) REVERT: M 31 ARG cc_start: 0.8496 (mtt180) cc_final: 0.8126 (mmm160) REVERT: M 50 ARG cc_start: 0.8785 (ttm170) cc_final: 0.8525 (ttm-80) REVERT: M 113 PHE cc_start: 0.8331 (m-80) cc_final: 0.8080 (m-80) REVERT: N 31 ARG cc_start: 0.8520 (mtt180) cc_final: 0.7868 (mmm160) REVERT: N 50 ARG cc_start: 0.8770 (ttm170) cc_final: 0.8484 (mtt-85) REVERT: N 52 TYR cc_start: 0.6807 (m-80) cc_final: 0.6473 (m-80) REVERT: N 113 PHE cc_start: 0.8345 (m-80) cc_final: 0.7973 (m-80) REVERT: O 27 HIS cc_start: 0.8529 (m-70) cc_final: 0.8323 (m90) REVERT: O 31 ARG cc_start: 0.8438 (mtt180) cc_final: 0.8053 (mmm160) REVERT: O 50 ARG cc_start: 0.8903 (ttm170) cc_final: 0.8603 (ttm110) REVERT: O 52 TYR cc_start: 0.6427 (m-80) cc_final: 0.5943 (m-80) REVERT: O 79 ASP cc_start: 0.7013 (t70) cc_final: 0.6294 (t0) REVERT: P 581 MET cc_start: 0.8832 (ttm) cc_final: 0.8567 (ttm) REVERT: P 616 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7295 (tm-30) REVERT: Q 697 LEU cc_start: 0.9591 (tp) cc_final: 0.9385 (tp) REVERT: Q 773 LEU cc_start: 0.9496 (mm) cc_final: 0.9237 (mp) REVERT: Q 995 ILE cc_start: 0.9523 (mt) cc_final: 0.9098 (tt) REVERT: R 583 TYR cc_start: 0.8989 (t80) cc_final: 0.8532 (t80) REVERT: R 616 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7319 (tm-30) REVERT: R 667 ARG cc_start: 0.8914 (mtm110) cc_final: 0.8645 (mtp85) REVERT: R 814 MET cc_start: 0.8866 (mtm) cc_final: 0.8433 (mtt) REVERT: R 995 ILE cc_start: 0.9553 (mt) cc_final: 0.9214 (tt) REVERT: R 1103 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8029 (mm-30) REVERT: S 583 TYR cc_start: 0.9034 (t80) cc_final: 0.8788 (t80) REVERT: S 613 PHE cc_start: 0.8228 (p90) cc_final: 0.8014 (p90) REVERT: S 693 LYS cc_start: 0.9334 (tptm) cc_final: 0.9115 (tptm) REVERT: S 1004 VAL cc_start: 0.9581 (m) cc_final: 0.9346 (p) REVERT: T 583 TYR cc_start: 0.9053 (t80) cc_final: 0.8653 (t80) REVERT: T 712 GLN cc_start: 0.8507 (pt0) cc_final: 0.8244 (tm-30) REVERT: T 773 LEU cc_start: 0.9565 (mm) cc_final: 0.9302 (mt) REVERT: T 846 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7391 (tm-30) REVERT: T 895 TYR cc_start: 0.9276 (t80) cc_final: 0.8905 (t80) REVERT: T 957 LYS cc_start: 0.9255 (tttp) cc_final: 0.9042 (tttp) REVERT: T 962 LEU cc_start: 0.9612 (mt) cc_final: 0.9337 (mt) REVERT: T 995 ILE cc_start: 0.9543 (mt) cc_final: 0.9159 (tt) REVERT: U 635 ILE cc_start: 0.7067 (pt) cc_final: 0.6717 (pt) REVERT: U 957 LYS cc_start: 0.9221 (tppt) cc_final: 0.8927 (tppt) REVERT: U 998 ASN cc_start: 0.8693 (t0) cc_final: 0.8421 (t0) REVERT: U 1011 LYS cc_start: 0.9401 (tttm) cc_final: 0.8935 (ttmt) REVERT: V 784 ASP cc_start: 0.8337 (t0) cc_final: 0.7875 (t0) REVERT: V 805 ILE cc_start: 0.8834 (mm) cc_final: 0.8621 (mm) REVERT: V 957 LYS cc_start: 0.9272 (tppt) cc_final: 0.9043 (tppt) REVERT: W 635 ILE cc_start: 0.7286 (pt) cc_final: 0.6935 (pt) REVERT: W 719 MET cc_start: 0.9232 (mmm) cc_final: 0.8858 (mmm) REVERT: W 805 ILE cc_start: 0.8812 (mm) cc_final: 0.8604 (mm) REVERT: W 978 HIS cc_start: 0.8810 (m90) cc_final: 0.8041 (m90) REVERT: W 998 ASN cc_start: 0.8728 (t0) cc_final: 0.8481 (t0) REVERT: W 1074 ASP cc_start: 0.7881 (m-30) cc_final: 0.7569 (t70) REVERT: X 635 ILE cc_start: 0.7332 (pt) cc_final: 0.6860 (pt) REVERT: X 720 ASN cc_start: 0.8985 (m110) cc_final: 0.8706 (m-40) REVERT: X 792 LEU cc_start: 0.9342 (mm) cc_final: 0.8891 (mm) REVERT: X 998 ASN cc_start: 0.8693 (t0) cc_final: 0.8464 (t0) REVERT: X 1011 LYS cc_start: 0.9389 (tttm) cc_final: 0.9140 (ttmt) REVERT: Y 581 MET cc_start: 0.6271 (ptt) cc_final: 0.5538 (pmm) REVERT: Y 635 ILE cc_start: 0.7503 (pt) cc_final: 0.7118 (pt) REVERT: Y 720 ASN cc_start: 0.8918 (m110) cc_final: 0.8629 (m110) REVERT: Y 784 ASP cc_start: 0.8381 (t0) cc_final: 0.8120 (t0) REVERT: Y 998 ASN cc_start: 0.8641 (t0) cc_final: 0.8328 (t0) outliers start: 33 outliers final: 16 residues processed: 1369 average time/residue: 0.6837 time to fit residues: 1525.6024 Evaluate side-chains 1027 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1011 time to evaluate : 6.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain P residue 1035 THR Chi-restraints excluded: chain P residue 1074 ASP Chi-restraints excluded: chain Q residue 608 VAL Chi-restraints excluded: chain Q residue 913 LEU Chi-restraints excluded: chain Q residue 1074 ASP Chi-restraints excluded: chain R residue 913 LEU Chi-restraints excluded: chain R residue 1074 ASP Chi-restraints excluded: chain S residue 1035 THR Chi-restraints excluded: chain S residue 1074 ASP Chi-restraints excluded: chain T residue 606 THR Chi-restraints excluded: chain T residue 1074 ASP Chi-restraints excluded: chain X residue 869 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 670 random chunks: chunk 565 optimal weight: 0.1980 chunk 507 optimal weight: 0.5980 chunk 281 optimal weight: 4.9990 chunk 173 optimal weight: 9.9990 chunk 342 optimal weight: 0.8980 chunk 271 optimal weight: 0.5980 chunk 525 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 319 optimal weight: 0.7980 chunk 390 optimal weight: 0.8980 chunk 608 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 ASN G 121 ASN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN I 121 ASN J 121 ASN K 53 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 GLN L 118 GLN M 53 GLN M 118 GLN N 53 GLN N 89 GLN N 118 GLN ** O 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 576 GLN P 680 ASN P 684 ASN P 816 GLN P 862 GLN P 866 GLN P 999 GLN ** Q 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 680 ASN Q 684 ASN Q 781 ASN Q 803 GLN ** Q 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 862 GLN Q 866 GLN Q 914 ASN Q 978 HIS Q1073 GLN R 684 ASN R 781 ASN R 803 GLN R 862 GLN R 866 GLN R 914 ASN R 978 HIS R 999 GLN R1073 GLN S 680 ASN S 684 ASN ** S 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 781 ASN S 862 GLN S 866 GLN S 914 ASN S 999 GLN S1073 GLN ** T 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 684 ASN ** T 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 781 ASN T 862 GLN T 866 GLN T 914 ASN T 999 GLN T1073 GLN U 720 ASN U 779 GLN U 820 GLN U 862 GLN U 978 HIS U1079 ASN V 584 GLN V 779 GLN V 820 GLN V 862 GLN V 978 HIS V1079 ASN W 779 GLN W 820 GLN W 862 GLN W 978 HIS W1079 ASN X 720 ASN X 779 GLN X 820 GLN X 862 GLN X 933 HIS X1079 ASN Y 779 GLN Y 820 GLN Y 862 GLN Y 978 HIS Y1079 ASN Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 53325 Z= 0.190 Angle : 0.720 11.759 72665 Z= 0.372 Chirality : 0.044 0.182 8425 Planarity : 0.005 0.049 9415 Dihedral : 6.544 44.471 7278 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.25 % Favored : 93.67 % Rotamer: Outliers : 2.58 % Allowed : 17.56 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.09), residues: 6685 helix: -3.66 (0.07), residues: 2245 sheet: -1.27 (0.13), residues: 1375 loop : -2.57 (0.10), residues: 3065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Q 887 HIS 0.004 0.000 HIS U 690 PHE 0.025 0.001 PHE L 60 TYR 0.036 0.002 TYR Q 895 ARG 0.006 0.000 ARG I 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1308 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1166 time to evaluate : 5.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.8353 (m-80) cc_final: 0.8022 (m-80) REVERT: A 131 GLU cc_start: 0.8670 (mp0) cc_final: 0.8462 (mp0) REVERT: B 31 ARG cc_start: 0.7694 (mtt180) cc_final: 0.7211 (mtm110) REVERT: B 33 ARG cc_start: 0.8565 (mtp85) cc_final: 0.8059 (ttm110) REVERT: B 106 PHE cc_start: 0.8232 (m-10) cc_final: 0.7829 (m-10) REVERT: B 131 GLU cc_start: 0.8759 (mp0) cc_final: 0.8540 (mp0) REVERT: C 31 ARG cc_start: 0.7512 (mtt180) cc_final: 0.7141 (ttm-80) REVERT: C 74 GLU cc_start: 0.9125 (mp0) cc_final: 0.8351 (mp0) REVERT: D 33 ARG cc_start: 0.8585 (mtp85) cc_final: 0.8372 (ttm110) REVERT: D 52 TYR cc_start: 0.7375 (m-80) cc_final: 0.6793 (m-80) REVERT: E 31 ARG cc_start: 0.8168 (mtt180) cc_final: 0.7624 (ttm-80) REVERT: E 33 ARG cc_start: 0.8754 (mtp85) cc_final: 0.8519 (ttm110) REVERT: E 74 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8626 (mm-30) REVERT: E 106 PHE cc_start: 0.8240 (m-80) cc_final: 0.7969 (m-80) REVERT: E 140 ILE cc_start: 0.9003 (mm) cc_final: 0.8644 (tt) REVERT: F 106 PHE cc_start: 0.8546 (m-80) cc_final: 0.7886 (m-80) REVERT: G 34 GLU cc_start: 0.7863 (mp0) cc_final: 0.7356 (mp0) REVERT: G 65 TYR cc_start: 0.9062 (t80) cc_final: 0.8807 (t80) REVERT: G 106 PHE cc_start: 0.8568 (m-80) cc_final: 0.8162 (m-80) REVERT: G 120 LYS cc_start: 0.8325 (mttp) cc_final: 0.8071 (mttp) REVERT: H 21 ARG cc_start: 0.7216 (mmt90) cc_final: 0.5927 (mpp-170) REVERT: H 106 PHE cc_start: 0.8683 (m-80) cc_final: 0.8130 (m-80) REVERT: H 112 MET cc_start: 0.9074 (mtp) cc_final: 0.8827 (mtm) REVERT: I 21 ARG cc_start: 0.6721 (mmt90) cc_final: 0.5813 (mpp-170) REVERT: I 30 ILE cc_start: 0.9345 (mt) cc_final: 0.9103 (mm) REVERT: I 34 GLU cc_start: 0.7795 (mp0) cc_final: 0.7517 (mp0) REVERT: I 53 GLN cc_start: 0.8063 (mt0) cc_final: 0.7780 (mt0) REVERT: I 65 TYR cc_start: 0.9063 (t80) cc_final: 0.8732 (t80) REVERT: I 98 MET cc_start: 0.8574 (ptm) cc_final: 0.8238 (ptm) REVERT: J 21 ARG cc_start: 0.7191 (mmt90) cc_final: 0.5956 (mpp-170) REVERT: J 34 GLU cc_start: 0.7636 (mp0) cc_final: 0.7428 (mp0) REVERT: J 53 GLN cc_start: 0.7975 (mt0) cc_final: 0.7580 (mt0) REVERT: J 98 MET cc_start: 0.8615 (ptm) cc_final: 0.8028 (ptm) REVERT: K 31 ARG cc_start: 0.8440 (mtt180) cc_final: 0.7811 (mmm160) REVERT: K 50 ARG cc_start: 0.8733 (ttm-80) cc_final: 0.8040 (ttm110) REVERT: K 113 PHE cc_start: 0.8587 (m-80) cc_final: 0.8183 (m-80) REVERT: L 31 ARG cc_start: 0.8664 (mtt180) cc_final: 0.8080 (mmm160) REVERT: L 45 LEU cc_start: 0.7904 (mt) cc_final: 0.7661 (mm) REVERT: L 50 ARG cc_start: 0.8785 (ttm170) cc_final: 0.8116 (ttm110) REVERT: L 113 PHE cc_start: 0.8384 (m-80) cc_final: 0.7989 (m-10) REVERT: M 31 ARG cc_start: 0.8475 (mtt180) cc_final: 0.8087 (mmm160) REVERT: M 113 PHE cc_start: 0.8335 (m-80) cc_final: 0.8108 (m-80) REVERT: N 31 ARG cc_start: 0.8409 (mtt180) cc_final: 0.7911 (mmm160) REVERT: N 66 GLN cc_start: 0.8524 (mm110) cc_final: 0.8303 (mm110) REVERT: N 113 PHE cc_start: 0.8256 (m-80) cc_final: 0.7891 (m-80) REVERT: O 31 ARG cc_start: 0.8388 (mtt180) cc_final: 0.8083 (mmm160) REVERT: O 50 ARG cc_start: 0.8819 (ttm170) cc_final: 0.8586 (ttm-80) REVERT: P 581 MET cc_start: 0.8644 (ttm) cc_final: 0.8422 (ttm) REVERT: P 616 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7276 (tm-30) REVERT: P 667 ARG cc_start: 0.8726 (mtm110) cc_final: 0.8412 (mtp85) REVERT: P 785 MET cc_start: 0.7835 (mmp) cc_final: 0.7295 (mmm) REVERT: P 804 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8309 (mm-40) REVERT: P 829 ASP cc_start: 0.7451 (p0) cc_final: 0.7204 (p0) REVERT: P 878 ARG cc_start: 0.8384 (ttm170) cc_final: 0.7766 (ttp80) REVERT: P 995 ILE cc_start: 0.9441 (mt) cc_final: 0.9002 (tt) REVERT: P 1077 MET cc_start: 0.8933 (mmt) cc_final: 0.8500 (mmp) REVERT: Q 583 TYR cc_start: 0.8812 (t80) cc_final: 0.8488 (t80) REVERT: Q 697 LEU cc_start: 0.9571 (tp) cc_final: 0.9366 (tp) REVERT: Q 709 ASP cc_start: 0.8326 (t70) cc_final: 0.8026 (t70) REVERT: Q 895 TYR cc_start: 0.8811 (t80) cc_final: 0.8407 (t80) REVERT: Q 911 LYS cc_start: 0.9197 (mmmm) cc_final: 0.8887 (ttmm) REVERT: Q 995 ILE cc_start: 0.9447 (mt) cc_final: 0.9060 (tt) REVERT: Q 1052 GLU cc_start: 0.7927 (tt0) cc_final: 0.7526 (tt0) REVERT: R 616 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7371 (tm-30) REVERT: R 667 ARG cc_start: 0.8680 (mtm110) cc_final: 0.8386 (mtp85) REVERT: R 669 ARG cc_start: 0.8682 (ttm110) cc_final: 0.8390 (ttm110) REVERT: R 990 MET cc_start: 0.8289 (mtm) cc_final: 0.7924 (ttm) REVERT: R 995 ILE cc_start: 0.9453 (mt) cc_final: 0.9160 (tt) REVERT: S 995 ILE cc_start: 0.9520 (mt) cc_final: 0.9020 (tt) REVERT: T 667 ARG cc_start: 0.8785 (mtm110) cc_final: 0.8569 (mtp85) REVERT: T 722 LEU cc_start: 0.9690 (tp) cc_final: 0.9333 (tp) REVERT: T 773 LEU cc_start: 0.9538 (mm) cc_final: 0.9282 (mm) REVERT: T 895 TYR cc_start: 0.9200 (t80) cc_final: 0.8879 (t80) REVERT: T 957 LYS cc_start: 0.9281 (tttp) cc_final: 0.9049 (tttp) REVERT: T 1038 TYR cc_start: 0.9322 (t80) cc_final: 0.9095 (t80) REVERT: T 1052 GLU cc_start: 0.8310 (tt0) cc_final: 0.8058 (tt0) REVERT: U 611 LEU cc_start: 0.8665 (tp) cc_final: 0.8412 (tp) REVERT: U 998 ASN cc_start: 0.8668 (t0) cc_final: 0.8358 (t0) REVERT: U 1007 MET cc_start: 0.8785 (ttp) cc_final: 0.8519 (ttp) REVERT: V 586 MET cc_start: 0.6298 (mmm) cc_final: 0.5902 (mmm) REVERT: V 611 LEU cc_start: 0.8785 (tp) cc_final: 0.8535 (tp) REVERT: W 611 LEU cc_start: 0.8837 (tp) cc_final: 0.8598 (tp) REVERT: W 805 ILE cc_start: 0.8661 (mm) cc_final: 0.8329 (mm) REVERT: W 978 HIS cc_start: 0.8578 (m-70) cc_final: 0.7867 (m90) REVERT: W 990 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8649 (mtp) REVERT: W 998 ASN cc_start: 0.8611 (t0) cc_final: 0.8357 (t0) REVERT: W 1074 ASP cc_start: 0.7823 (m-30) cc_final: 0.7556 (t70) REVERT: W 1077 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7734 (mmm) REVERT: X 611 LEU cc_start: 0.8774 (tp) cc_final: 0.8438 (tp) REVERT: X 792 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9277 (mm) REVERT: X 911 LYS cc_start: 0.9408 (mtmm) cc_final: 0.9181 (ttmt) REVERT: X 998 ASN cc_start: 0.8506 (t0) cc_final: 0.8305 (t0) REVERT: X 1011 LYS cc_start: 0.9176 (tttm) cc_final: 0.8771 (ttmt) REVERT: Y 581 MET cc_start: 0.7027 (ptt) cc_final: 0.6230 (pmm) REVERT: Y 583 TYR cc_start: 0.5876 (t80) cc_final: 0.5484 (t80) REVERT: Y 784 ASP cc_start: 0.8150 (t0) cc_final: 0.7939 (t0) REVERT: Y 785 MET cc_start: 0.7759 (mmp) cc_final: 0.7494 (mmp) REVERT: Y 820 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8669 (tt0) REVERT: Y 957 LYS cc_start: 0.9072 (tppt) cc_final: 0.8686 (mmtm) REVERT: Y 998 ASN cc_start: 0.8535 (t0) cc_final: 0.8319 (t0) outliers start: 142 outliers final: 84 residues processed: 1262 average time/residue: 0.6232 time to fit residues: 1299.2576 Evaluate side-chains 1111 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1023 time to evaluate : 5.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain K residue 83 GLN Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 29 ASP Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain N residue 29 ASP Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 29 ASP Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain P residue 855 VAL Chi-restraints excluded: chain P residue 913 LEU Chi-restraints excluded: chain P residue 943 THR Chi-restraints excluded: chain P residue 946 THR Chi-restraints excluded: chain P residue 996 THR Chi-restraints excluded: chain P residue 1035 THR Chi-restraints excluded: chain P residue 1074 ASP Chi-restraints excluded: chain Q residue 608 VAL Chi-restraints excluded: chain Q residue 855 VAL Chi-restraints excluded: chain Q residue 913 LEU Chi-restraints excluded: chain Q residue 943 THR Chi-restraints excluded: chain Q residue 996 THR Chi-restraints excluded: chain Q residue 1074 ASP Chi-restraints excluded: chain R residue 608 VAL Chi-restraints excluded: chain R residue 773 LEU Chi-restraints excluded: chain R residue 855 VAL Chi-restraints excluded: chain R residue 913 LEU Chi-restraints excluded: chain R residue 946 THR Chi-restraints excluded: chain R residue 967 ASP Chi-restraints excluded: chain R residue 996 THR Chi-restraints excluded: chain R residue 1074 ASP Chi-restraints excluded: chain S residue 773 LEU Chi-restraints excluded: chain S residue 855 VAL Chi-restraints excluded: chain S residue 914 ASN Chi-restraints excluded: chain S residue 943 THR Chi-restraints excluded: chain S residue 946 THR Chi-restraints excluded: chain S residue 1035 THR Chi-restraints excluded: chain S residue 1074 ASP Chi-restraints excluded: chain T residue 606 THR Chi-restraints excluded: chain T residue 943 THR Chi-restraints excluded: chain T residue 946 THR Chi-restraints excluded: chain T residue 996 THR Chi-restraints excluded: chain T residue 1074 ASP Chi-restraints excluded: chain U residue 814 MET Chi-restraints excluded: chain U residue 829 ASP Chi-restraints excluded: chain V residue 720 ASN Chi-restraints excluded: chain V residue 776 MET Chi-restraints excluded: chain V residue 866 GLN Chi-restraints excluded: chain V residue 1007 MET Chi-restraints excluded: chain W residue 822 VAL Chi-restraints excluded: chain W residue 967 ASP Chi-restraints excluded: chain W residue 990 MET Chi-restraints excluded: chain W residue 1077 MET Chi-restraints excluded: chain W residue 1104 THR Chi-restraints excluded: chain X residue 690 HIS Chi-restraints excluded: chain X residue 792 LEU Chi-restraints excluded: chain X residue 869 THR Chi-restraints excluded: chain X residue 1074 ASP Chi-restraints excluded: chain X residue 1104 THR Chi-restraints excluded: chain Y residue 820 GLN Chi-restraints excluded: chain Y residue 829 ASP Chi-restraints excluded: chain Y residue 866 GLN Chi-restraints excluded: chain Y residue 967 ASP Chi-restraints excluded: chain Y residue 996 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 670 random chunks: chunk 338 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 506 optimal weight: 3.9990 chunk 414 optimal weight: 2.9990 chunk 167 optimal weight: 9.9990 chunk 609 optimal weight: 4.9990 chunk 658 optimal weight: 9.9990 chunk 542 optimal weight: 3.9990 chunk 604 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 488 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN ** M 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN P 816 GLN P1079 ASN Q 680 ASN Q 690 HIS Q 803 GLN Q 846 GLN ** R 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 576 GLN ** T 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T1005 ASN U 812 GLN V 820 GLN V 933 HIS W 933 HIS W1037 GLN X 778 ASN X 820 GLN Y 978 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 53325 Z= 0.448 Angle : 0.790 9.723 72665 Z= 0.401 Chirality : 0.047 0.187 8425 Planarity : 0.005 0.050 9415 Dihedral : 6.395 44.122 7278 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.20 % Favored : 92.64 % Rotamer: Outliers : 4.70 % Allowed : 20.75 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.09), residues: 6685 helix: -3.04 (0.09), residues: 2255 sheet: -1.01 (0.13), residues: 1360 loop : -2.29 (0.10), residues: 3070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP Q 887 HIS 0.003 0.001 HIS W 690 PHE 0.022 0.002 PHE L 60 TYR 0.042 0.002 TYR P 895 ARG 0.006 0.001 ARG I 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1285 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1027 time to evaluate : 6.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8683 (t0) cc_final: 0.8447 (t0) REVERT: A 106 PHE cc_start: 0.8469 (m-80) cc_final: 0.8039 (m-80) REVERT: B 106 PHE cc_start: 0.8191 (m-10) cc_final: 0.7747 (m-10) REVERT: C 31 ARG cc_start: 0.7696 (mtt180) cc_final: 0.7351 (ttm-80) REVERT: C 98 MET cc_start: 0.8411 (ppp) cc_final: 0.7652 (ppp) REVERT: D 29 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.6876 (p0) REVERT: D 33 ARG cc_start: 0.8696 (mtp85) cc_final: 0.8471 (ttm110) REVERT: D 140 ILE cc_start: 0.8924 (mm) cc_final: 0.8426 (tt) REVERT: E 29 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7102 (p0) REVERT: E 31 ARG cc_start: 0.8210 (mtt180) cc_final: 0.7677 (ttm-80) REVERT: E 33 ARG cc_start: 0.8745 (mtp85) cc_final: 0.8503 (ttm110) REVERT: E 106 PHE cc_start: 0.8343 (m-80) cc_final: 0.8077 (m-10) REVERT: E 140 ILE cc_start: 0.9034 (mm) cc_final: 0.8668 (tt) REVERT: F 21 ARG cc_start: 0.7164 (mmt90) cc_final: 0.5985 (mpp-170) REVERT: F 65 TYR cc_start: 0.9090 (t80) cc_final: 0.8788 (t80) REVERT: F 106 PHE cc_start: 0.8616 (m-80) cc_final: 0.8063 (m-80) REVERT: G 21 ARG cc_start: 0.7064 (mmt90) cc_final: 0.5781 (mpp-170) REVERT: G 65 TYR cc_start: 0.9105 (t80) cc_final: 0.8782 (t80) REVERT: G 106 PHE cc_start: 0.8660 (m-80) cc_final: 0.8360 (m-80) REVERT: H 21 ARG cc_start: 0.7312 (mmt90) cc_final: 0.6059 (mpp-170) REVERT: H 50 ARG cc_start: 0.8953 (ttm170) cc_final: 0.8401 (ttm170) REVERT: H 106 PHE cc_start: 0.8786 (m-80) cc_final: 0.8221 (m-80) REVERT: H 112 MET cc_start: 0.9146 (mtp) cc_final: 0.8833 (mtm) REVERT: I 21 ARG cc_start: 0.6760 (mmt90) cc_final: 0.5842 (mpp-170) REVERT: I 30 ILE cc_start: 0.9378 (mt) cc_final: 0.9150 (mm) REVERT: I 34 GLU cc_start: 0.7758 (mp0) cc_final: 0.7380 (mp0) REVERT: I 53 GLN cc_start: 0.8072 (mt0) cc_final: 0.7728 (mt0) REVERT: I 89 GLN cc_start: 0.7979 (tp40) cc_final: 0.7740 (tm-30) REVERT: I 98 MET cc_start: 0.8531 (ptm) cc_final: 0.8270 (ptm) REVERT: J 21 ARG cc_start: 0.7241 (mmt90) cc_final: 0.5989 (mpp-170) REVERT: J 34 GLU cc_start: 0.7675 (mp0) cc_final: 0.7068 (mp0) REVERT: J 53 GLN cc_start: 0.8210 (mt0) cc_final: 0.7513 (mt0) REVERT: J 65 TYR cc_start: 0.9237 (t80) cc_final: 0.8803 (t80) REVERT: J 98 MET cc_start: 0.8569 (ptm) cc_final: 0.7884 (ptm) REVERT: K 31 ARG cc_start: 0.8342 (mtt180) cc_final: 0.7791 (mmm160) REVERT: K 50 ARG cc_start: 0.8733 (ttm-80) cc_final: 0.8020 (ttm110) REVERT: L 31 ARG cc_start: 0.8607 (mtt180) cc_final: 0.8036 (mmm160) REVERT: L 45 LEU cc_start: 0.7976 (mt) cc_final: 0.7739 (mm) REVERT: L 113 PHE cc_start: 0.8553 (m-80) cc_final: 0.8267 (m-80) REVERT: M 31 ARG cc_start: 0.8463 (mtt180) cc_final: 0.8060 (mmm160) REVERT: M 50 ARG cc_start: 0.8793 (ttm-80) cc_final: 0.8149 (ttm110) REVERT: N 31 ARG cc_start: 0.8516 (mtt180) cc_final: 0.7904 (mmm160) REVERT: O 31 ARG cc_start: 0.8430 (mtt180) cc_final: 0.8079 (mmm160) REVERT: P 581 MET cc_start: 0.8696 (ttm) cc_final: 0.8479 (ttm) REVERT: P 616 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7455 (tm-30) REVERT: P 667 ARG cc_start: 0.8673 (mtm110) cc_final: 0.8328 (mtp85) REVERT: P 860 MET cc_start: 0.9231 (tpp) cc_final: 0.9009 (tpp) REVERT: P 916 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8145 (p0) REVERT: P 990 MET cc_start: 0.8395 (mtp) cc_final: 0.8125 (ttm) REVERT: P 995 ILE cc_start: 0.9487 (mt) cc_final: 0.9056 (tt) REVERT: P 1077 MET cc_start: 0.8853 (mmt) cc_final: 0.8345 (mmp) REVERT: Q 709 ASP cc_start: 0.8561 (t70) cc_final: 0.8217 (t70) REVERT: Q 911 LYS cc_start: 0.9356 (mmmm) cc_final: 0.9050 (ttmm) REVERT: R 586 MET cc_start: 0.9174 (mmm) cc_final: 0.8698 (mmm) REVERT: R 628 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: R 667 ARG cc_start: 0.8751 (mtm110) cc_final: 0.8419 (mtp85) REVERT: R 990 MET cc_start: 0.8341 (mtm) cc_final: 0.7875 (ttm) REVERT: R 995 ILE cc_start: 0.9473 (mt) cc_final: 0.9149 (tt) REVERT: S 585 LYS cc_start: 0.9185 (mmmt) cc_final: 0.8918 (pttm) REVERT: S 849 TYR cc_start: 0.8842 (t80) cc_final: 0.8544 (t80) REVERT: S 913 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9088 (pp) REVERT: T 773 LEU cc_start: 0.9557 (mm) cc_final: 0.9260 (mm) REVERT: T 860 MET cc_start: 0.9313 (mmm) cc_final: 0.9081 (tpp) REVERT: T 895 TYR cc_start: 0.9279 (t80) cc_final: 0.8979 (t80) REVERT: U 597 MET cc_start: 0.7780 (tpt) cc_final: 0.7316 (tpt) REVERT: U 998 ASN cc_start: 0.8730 (t0) cc_final: 0.8452 (t0) REVERT: U 1011 LYS cc_start: 0.9313 (ttmm) cc_final: 0.8953 (ttmt) REVERT: V 611 LEU cc_start: 0.8826 (tp) cc_final: 0.8544 (tp) REVERT: V 720 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7892 (p0) REVERT: W 805 ILE cc_start: 0.8913 (mm) cc_final: 0.8648 (mm) REVERT: W 990 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8653 (mtp) REVERT: W 998 ASN cc_start: 0.8689 (t0) cc_final: 0.8464 (t0) REVERT: X 611 LEU cc_start: 0.8752 (tp) cc_final: 0.8532 (tp) REVERT: X 911 LYS cc_start: 0.9485 (mtmm) cc_final: 0.9241 (ttmt) REVERT: Y 581 MET cc_start: 0.6888 (ptt) cc_final: 0.6212 (pmm) REVERT: Y 583 TYR cc_start: 0.6123 (t80) cc_final: 0.5665 (t80) REVERT: Y 784 ASP cc_start: 0.8149 (t0) cc_final: 0.7894 (t0) REVERT: Y 785 MET cc_start: 0.8019 (mmp) cc_final: 0.7690 (mmp) REVERT: Y 957 LYS cc_start: 0.9128 (tppt) cc_final: 0.8736 (mmtm) REVERT: Y 998 ASN cc_start: 0.8574 (t0) cc_final: 0.8320 (t0) outliers start: 258 outliers final: 178 residues processed: 1192 average time/residue: 0.6184 time to fit residues: 1222.9260 Evaluate side-chains 1151 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 966 time to evaluate : 6.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 84 LYS Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 106 PHE Chi-restraints excluded: chain K residue 135 ASP Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 29 ASP Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain M residue 135 ASP Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 29 ASP Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 106 PHE Chi-restraints excluded: chain P residue 608 VAL Chi-restraints excluded: chain P residue 618 VAL Chi-restraints excluded: chain P residue 705 THR Chi-restraints excluded: chain P residue 798 VAL Chi-restraints excluded: chain P residue 855 VAL Chi-restraints excluded: chain P residue 867 VAL Chi-restraints excluded: chain P residue 875 LEU Chi-restraints excluded: chain P residue 913 LEU Chi-restraints excluded: chain P residue 915 THR Chi-restraints excluded: chain P residue 916 ASP Chi-restraints excluded: chain P residue 943 THR Chi-restraints excluded: chain P residue 946 THR Chi-restraints excluded: chain P residue 996 THR Chi-restraints excluded: chain P residue 1035 THR Chi-restraints excluded: chain P residue 1074 ASP Chi-restraints excluded: chain Q residue 608 VAL Chi-restraints excluded: chain Q residue 787 ASN Chi-restraints excluded: chain Q residue 803 GLN Chi-restraints excluded: chain Q residue 817 LEU Chi-restraints excluded: chain Q residue 855 VAL Chi-restraints excluded: chain Q residue 875 LEU Chi-restraints excluded: chain Q residue 913 LEU Chi-restraints excluded: chain Q residue 943 THR Chi-restraints excluded: chain Q residue 946 THR Chi-restraints excluded: chain Q residue 996 THR Chi-restraints excluded: chain Q residue 1002 ILE Chi-restraints excluded: chain Q residue 1051 LEU Chi-restraints excluded: chain Q residue 1052 GLU Chi-restraints excluded: chain Q residue 1074 ASP Chi-restraints excluded: chain Q residue 1092 VAL Chi-restraints excluded: chain R residue 608 VAL Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 628 GLU Chi-restraints excluded: chain R residue 689 LEU Chi-restraints excluded: chain R residue 705 THR Chi-restraints excluded: chain R residue 817 LEU Chi-restraints excluded: chain R residue 855 VAL Chi-restraints excluded: chain R residue 875 LEU Chi-restraints excluded: chain R residue 913 LEU Chi-restraints excluded: chain R residue 940 VAL Chi-restraints excluded: chain R residue 943 THR Chi-restraints excluded: chain R residue 946 THR Chi-restraints excluded: chain R residue 996 THR Chi-restraints excluded: chain R residue 1074 ASP Chi-restraints excluded: chain R residue 1092 VAL Chi-restraints excluded: chain S residue 618 VAL Chi-restraints excluded: chain S residue 724 VAL Chi-restraints excluded: chain S residue 773 LEU Chi-restraints excluded: chain S residue 817 LEU Chi-restraints excluded: chain S residue 855 VAL Chi-restraints excluded: chain S residue 875 LEU Chi-restraints excluded: chain S residue 913 LEU Chi-restraints excluded: chain S residue 940 VAL Chi-restraints excluded: chain S residue 943 THR Chi-restraints excluded: chain S residue 946 THR Chi-restraints excluded: chain S residue 1035 THR Chi-restraints excluded: chain S residue 1074 ASP Chi-restraints excluded: chain S residue 1092 VAL Chi-restraints excluded: chain T residue 606 THR Chi-restraints excluded: chain T residue 817 LEU Chi-restraints excluded: chain T residue 855 VAL Chi-restraints excluded: chain T residue 875 LEU Chi-restraints excluded: chain T residue 933 HIS Chi-restraints excluded: chain T residue 943 THR Chi-restraints excluded: chain T residue 946 THR Chi-restraints excluded: chain T residue 996 THR Chi-restraints excluded: chain T residue 1002 ILE Chi-restraints excluded: chain T residue 1074 ASP Chi-restraints excluded: chain T residue 1092 VAL Chi-restraints excluded: chain U residue 781 ASN Chi-restraints excluded: chain U residue 814 MET Chi-restraints excluded: chain U residue 829 ASP Chi-restraints excluded: chain U residue 857 VAL Chi-restraints excluded: chain U residue 905 SER Chi-restraints excluded: chain U residue 915 THR Chi-restraints excluded: chain U residue 967 ASP Chi-restraints excluded: chain U residue 996 THR Chi-restraints excluded: chain U residue 1104 THR Chi-restraints excluded: chain V residue 716 VAL Chi-restraints excluded: chain V residue 720 ASN Chi-restraints excluded: chain V residue 776 MET Chi-restraints excluded: chain V residue 781 ASN Chi-restraints excluded: chain V residue 820 GLN Chi-restraints excluded: chain V residue 855 VAL Chi-restraints excluded: chain V residue 866 GLN Chi-restraints excluded: chain V residue 867 VAL Chi-restraints excluded: chain V residue 1007 MET Chi-restraints excluded: chain V residue 1104 THR Chi-restraints excluded: chain W residue 615 ASP Chi-restraints excluded: chain W residue 822 VAL Chi-restraints excluded: chain W residue 847 GLU Chi-restraints excluded: chain W residue 855 VAL Chi-restraints excluded: chain W residue 869 THR Chi-restraints excluded: chain W residue 990 MET Chi-restraints excluded: chain W residue 996 THR Chi-restraints excluded: chain W residue 1104 THR Chi-restraints excluded: chain X residue 631 VAL Chi-restraints excluded: chain X residue 690 HIS Chi-restraints excluded: chain X residue 820 GLN Chi-restraints excluded: chain X residue 867 VAL Chi-restraints excluded: chain X residue 869 THR Chi-restraints excluded: chain X residue 946 THR Chi-restraints excluded: chain X residue 967 ASP Chi-restraints excluded: chain X residue 1074 ASP Chi-restraints excluded: chain X residue 1104 THR Chi-restraints excluded: chain Y residue 706 LEU Chi-restraints excluded: chain Y residue 829 ASP Chi-restraints excluded: chain Y residue 847 GLU Chi-restraints excluded: chain Y residue 855 VAL Chi-restraints excluded: chain Y residue 866 GLN Chi-restraints excluded: chain Y residue 967 ASP Chi-restraints excluded: chain Y residue 1002 ILE Chi-restraints excluded: chain Y residue 1104 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 670 random chunks: chunk 602 optimal weight: 1.9990 chunk 458 optimal weight: 0.8980 chunk 316 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 290 optimal weight: 3.9990 chunk 409 optimal weight: 0.7980 chunk 611 optimal weight: 0.7980 chunk 647 optimal weight: 0.7980 chunk 319 optimal weight: 0.9980 chunk 579 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 83 GLN ** M 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 816 GLN ** Q 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 816 GLN Q 999 GLN R 866 GLN ** S 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 576 GLN ** T 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 778 ASN T 787 ASN X 820 GLN Y 779 GLN Y 978 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 53325 Z= 0.185 Angle : 0.661 10.866 72665 Z= 0.337 Chirality : 0.044 0.172 8425 Planarity : 0.004 0.041 9415 Dihedral : 5.865 53.852 7278 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.01 % Favored : 93.91 % Rotamer: Outliers : 3.89 % Allowed : 22.18 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.09), residues: 6685 helix: -2.72 (0.09), residues: 2265 sheet: -0.83 (0.13), residues: 1365 loop : -2.07 (0.11), residues: 3055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP U 848 HIS 0.003 0.000 HIS W 690 PHE 0.022 0.001 PHE L 60 TYR 0.048 0.001 TYR P 895 ARG 0.007 0.000 ARG W 922 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1320 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1106 time to evaluate : 6.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8809 (mtp85) cc_final: 0.8555 (ttm110) REVERT: A 52 TYR cc_start: 0.7663 (m-80) cc_final: 0.7397 (m-80) REVERT: A 106 PHE cc_start: 0.8445 (m-80) cc_final: 0.7978 (m-80) REVERT: A 131 GLU cc_start: 0.8733 (mp0) cc_final: 0.8530 (mp0) REVERT: B 106 PHE cc_start: 0.8116 (m-80) cc_final: 0.7796 (m-80) REVERT: C 31 ARG cc_start: 0.7501 (mtt180) cc_final: 0.6972 (ttm-80) REVERT: C 74 GLU cc_start: 0.9109 (mp0) cc_final: 0.8862 (mp0) REVERT: C 98 MET cc_start: 0.8203 (ppp) cc_final: 0.7748 (ppp) REVERT: C 140 ILE cc_start: 0.8867 (mm) cc_final: 0.8149 (tt) REVERT: D 29 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7095 (p0) REVERT: D 131 GLU cc_start: 0.8695 (mp0) cc_final: 0.8127 (pm20) REVERT: D 140 ILE cc_start: 0.8833 (mm) cc_final: 0.8370 (tt) REVERT: E 29 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.6665 (p0) REVERT: E 31 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7512 (ttm-80) REVERT: E 33 ARG cc_start: 0.8689 (mtp85) cc_final: 0.8472 (ttm110) REVERT: E 106 PHE cc_start: 0.8328 (m-80) cc_final: 0.8080 (m-10) REVERT: E 140 ILE cc_start: 0.8962 (mm) cc_final: 0.8604 (tt) REVERT: F 21 ARG cc_start: 0.7080 (mmt90) cc_final: 0.5913 (mpp-170) REVERT: F 53 GLN cc_start: 0.8302 (mt0) cc_final: 0.8085 (mt0) REVERT: F 65 TYR cc_start: 0.9069 (t80) cc_final: 0.8798 (t80) REVERT: F 106 PHE cc_start: 0.8525 (m-80) cc_final: 0.8076 (m-80) REVERT: G 21 ARG cc_start: 0.6896 (mmt90) cc_final: 0.5620 (mpp-170) REVERT: G 65 TYR cc_start: 0.9023 (t80) cc_final: 0.8787 (t80) REVERT: G 76 LEU cc_start: 0.7965 (tp) cc_final: 0.7438 (tt) REVERT: G 120 LYS cc_start: 0.8363 (mttp) cc_final: 0.8136 (mttp) REVERT: H 21 ARG cc_start: 0.7277 (mmt90) cc_final: 0.6055 (mpp-170) REVERT: H 50 ARG cc_start: 0.8843 (ttm170) cc_final: 0.8339 (ttm170) REVERT: H 106 PHE cc_start: 0.8732 (m-80) cc_final: 0.8230 (m-80) REVERT: H 112 MET cc_start: 0.9011 (mtp) cc_final: 0.8680 (mtm) REVERT: I 21 ARG cc_start: 0.6754 (mmt90) cc_final: 0.5889 (mpp-170) REVERT: I 30 ILE cc_start: 0.9405 (mt) cc_final: 0.9184 (mm) REVERT: I 34 GLU cc_start: 0.7893 (mp0) cc_final: 0.7452 (mp0) REVERT: I 98 MET cc_start: 0.8450 (ptm) cc_final: 0.8195 (ptm) REVERT: J 21 ARG cc_start: 0.7071 (mmt90) cc_final: 0.5836 (mpp-170) REVERT: J 34 GLU cc_start: 0.7895 (mp0) cc_final: 0.7175 (mp0) REVERT: J 65 TYR cc_start: 0.9195 (t80) cc_final: 0.8775 (t80) REVERT: K 31 ARG cc_start: 0.8342 (mtt180) cc_final: 0.7787 (mmm160) REVERT: K 50 ARG cc_start: 0.8847 (ttm-80) cc_final: 0.8634 (ttm110) REVERT: K 113 PHE cc_start: 0.8632 (m-80) cc_final: 0.8274 (m-80) REVERT: L 45 LEU cc_start: 0.7952 (mt) cc_final: 0.7726 (mm) REVERT: L 50 ARG cc_start: 0.8923 (mtp85) cc_final: 0.8679 (mtp85) REVERT: L 56 ASP cc_start: 0.7167 (t0) cc_final: 0.6960 (p0) REVERT: L 85 ASP cc_start: 0.7808 (m-30) cc_final: 0.7357 (m-30) REVERT: L 113 PHE cc_start: 0.8566 (m-80) cc_final: 0.8209 (m-10) REVERT: L 147 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7467 (mp) REVERT: M 31 ARG cc_start: 0.8424 (mtt180) cc_final: 0.8057 (mmm160) REVERT: M 50 ARG cc_start: 0.8753 (ttm-80) cc_final: 0.8235 (ttm110) REVERT: M 113 PHE cc_start: 0.8326 (m-80) cc_final: 0.8069 (m-80) REVERT: N 113 PHE cc_start: 0.8406 (m-80) cc_final: 0.8024 (m-80) REVERT: N 131 GLU cc_start: 0.8771 (tp30) cc_final: 0.7975 (tp30) REVERT: O 31 ARG cc_start: 0.8380 (mtt180) cc_final: 0.7998 (mmm160) REVERT: P 616 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7384 (tm-30) REVERT: P 990 MET cc_start: 0.8309 (mtp) cc_final: 0.8022 (ttm) REVERT: P 995 ILE cc_start: 0.9440 (mt) cc_final: 0.8987 (tt) REVERT: P 1077 MET cc_start: 0.8866 (mmt) cc_final: 0.8312 (mmp) REVERT: P 1081 THR cc_start: 0.9637 (m) cc_final: 0.9184 (p) REVERT: Q 706 LEU cc_start: 0.9313 (tp) cc_final: 0.9055 (tt) REVERT: Q 709 ASP cc_start: 0.8284 (t70) cc_final: 0.7971 (t70) REVERT: Q 911 LYS cc_start: 0.9219 (mmmm) cc_final: 0.8935 (ttmm) REVERT: Q 995 ILE cc_start: 0.9442 (mt) cc_final: 0.8935 (tt) REVERT: R 616 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7637 (tm-30) REVERT: R 667 ARG cc_start: 0.8740 (mtm110) cc_final: 0.8438 (mtp85) REVERT: R 990 MET cc_start: 0.8300 (mtm) cc_final: 0.7933 (ttm) REVERT: R 995 ILE cc_start: 0.9438 (mt) cc_final: 0.9079 (tt) REVERT: R 1081 THR cc_start: 0.9570 (m) cc_final: 0.9117 (p) REVERT: S 621 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8719 (ppp) REVERT: S 849 TYR cc_start: 0.8622 (t80) cc_final: 0.7877 (t80) REVERT: S 913 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9087 (pp) REVERT: S 1006 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8245 (pt0) REVERT: S 1081 THR cc_start: 0.9659 (m) cc_final: 0.9234 (p) REVERT: T 773 LEU cc_start: 0.9511 (mm) cc_final: 0.9302 (mt) REVERT: T 804 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8137 (tp40) REVERT: T 895 TYR cc_start: 0.9238 (t80) cc_final: 0.8908 (t80) REVERT: T 1052 GLU cc_start: 0.8379 (tt0) cc_final: 0.8168 (tt0) REVERT: U 597 MET cc_start: 0.7726 (tpt) cc_final: 0.7066 (tpt) REVERT: U 601 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7463 (p0) REVERT: U 691 LEU cc_start: 0.9442 (tt) cc_final: 0.9148 (tt) REVERT: U 703 GLN cc_start: 0.9125 (mt0) cc_final: 0.8925 (mt0) REVERT: U 820 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8575 (tt0) REVERT: U 998 ASN cc_start: 0.8704 (t0) cc_final: 0.8417 (t0) REVERT: V 611 LEU cc_start: 0.8763 (tp) cc_final: 0.8496 (tp) REVERT: V 990 MET cc_start: 0.9093 (mtp) cc_final: 0.8874 (mtm) REVERT: V 1011 LYS cc_start: 0.9351 (ttmm) cc_final: 0.9000 (tttp) REVERT: W 611 LEU cc_start: 0.8927 (tp) cc_final: 0.8674 (tp) REVERT: W 978 HIS cc_start: 0.8686 (m-70) cc_final: 0.7887 (m90) REVERT: W 990 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8714 (mtp) REVERT: X 611 LEU cc_start: 0.8770 (tp) cc_final: 0.8415 (tp) REVERT: X 691 LEU cc_start: 0.9441 (tt) cc_final: 0.9165 (tp) REVERT: X 786 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8856 (mm) REVERT: Y 581 MET cc_start: 0.6809 (ptt) cc_final: 0.6139 (pmm) REVERT: Y 583 TYR cc_start: 0.6073 (t80) cc_final: 0.5646 (t80) REVERT: Y 784 ASP cc_start: 0.8061 (t0) cc_final: 0.7857 (t0) REVERT: Y 785 MET cc_start: 0.7864 (mmp) cc_final: 0.7597 (mmp) REVERT: Y 957 LYS cc_start: 0.9021 (tppt) cc_final: 0.8685 (mmtm) REVERT: Y 998 ASN cc_start: 0.8445 (t0) cc_final: 0.8221 (t0) outliers start: 214 outliers final: 145 residues processed: 1254 average time/residue: 0.6040 time to fit residues: 1264.4119 Evaluate side-chains 1162 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1007 time to evaluate : 6.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 66 GLN Chi-restraints excluded: chain K residue 106 PHE Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 29 ASP Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 29 ASP Chi-restraints excluded: chain N residue 148 THR Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 29 ASP Chi-restraints excluded: chain P residue 671 THR Chi-restraints excluded: chain P residue 724 VAL Chi-restraints excluded: chain P residue 810 ASP Chi-restraints excluded: chain P residue 855 VAL Chi-restraints excluded: chain P residue 875 LEU Chi-restraints excluded: chain P residue 913 LEU Chi-restraints excluded: chain P residue 915 THR Chi-restraints excluded: chain P residue 940 VAL Chi-restraints excluded: chain P residue 946 THR Chi-restraints excluded: chain P residue 996 THR Chi-restraints excluded: chain P residue 1035 THR Chi-restraints excluded: chain P residue 1053 MET Chi-restraints excluded: chain P residue 1074 ASP Chi-restraints excluded: chain P residue 1092 VAL Chi-restraints excluded: chain Q residue 608 VAL Chi-restraints excluded: chain Q residue 618 VAL Chi-restraints excluded: chain Q residue 724 VAL Chi-restraints excluded: chain Q residue 787 ASN Chi-restraints excluded: chain Q residue 817 LEU Chi-restraints excluded: chain Q residue 855 VAL Chi-restraints excluded: chain Q residue 867 VAL Chi-restraints excluded: chain Q residue 875 LEU Chi-restraints excluded: chain Q residue 913 LEU Chi-restraints excluded: chain Q residue 946 THR Chi-restraints excluded: chain Q residue 972 THR Chi-restraints excluded: chain Q residue 996 THR Chi-restraints excluded: chain Q residue 1051 LEU Chi-restraints excluded: chain Q residue 1074 ASP Chi-restraints excluded: chain R residue 606 THR Chi-restraints excluded: chain R residue 608 VAL Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 628 GLU Chi-restraints excluded: chain R residue 671 THR Chi-restraints excluded: chain R residue 705 THR Chi-restraints excluded: chain R residue 773 LEU Chi-restraints excluded: chain R residue 817 LEU Chi-restraints excluded: chain R residue 855 VAL Chi-restraints excluded: chain R residue 940 VAL Chi-restraints excluded: chain R residue 943 THR Chi-restraints excluded: chain R residue 946 THR Chi-restraints excluded: chain R residue 996 THR Chi-restraints excluded: chain R residue 1074 ASP Chi-restraints excluded: chain R residue 1092 VAL Chi-restraints excluded: chain S residue 621 MET Chi-restraints excluded: chain S residue 689 LEU Chi-restraints excluded: chain S residue 773 LEU Chi-restraints excluded: chain S residue 810 ASP Chi-restraints excluded: chain S residue 855 VAL Chi-restraints excluded: chain S residue 913 LEU Chi-restraints excluded: chain S residue 940 VAL Chi-restraints excluded: chain S residue 946 THR Chi-restraints excluded: chain S residue 1006 GLN Chi-restraints excluded: chain S residue 1035 THR Chi-restraints excluded: chain S residue 1074 ASP Chi-restraints excluded: chain S residue 1092 VAL Chi-restraints excluded: chain T residue 606 THR Chi-restraints excluded: chain T residue 724 VAL Chi-restraints excluded: chain T residue 817 LEU Chi-restraints excluded: chain T residue 946 THR Chi-restraints excluded: chain T residue 1006 GLN Chi-restraints excluded: chain T residue 1074 ASP Chi-restraints excluded: chain U residue 601 ASP Chi-restraints excluded: chain U residue 623 THR Chi-restraints excluded: chain U residue 784 ASP Chi-restraints excluded: chain U residue 814 MET Chi-restraints excluded: chain U residue 820 GLN Chi-restraints excluded: chain U residue 829 ASP Chi-restraints excluded: chain U residue 857 VAL Chi-restraints excluded: chain U residue 905 SER Chi-restraints excluded: chain U residue 967 ASP Chi-restraints excluded: chain U residue 996 THR Chi-restraints excluded: chain U residue 1009 VAL Chi-restraints excluded: chain V residue 631 VAL Chi-restraints excluded: chain V residue 713 SER Chi-restraints excluded: chain V residue 776 MET Chi-restraints excluded: chain V residue 822 VAL Chi-restraints excluded: chain V residue 829 ASP Chi-restraints excluded: chain V residue 855 VAL Chi-restraints excluded: chain V residue 866 GLN Chi-restraints excluded: chain V residue 1007 MET Chi-restraints excluded: chain W residue 615 ASP Chi-restraints excluded: chain W residue 822 VAL Chi-restraints excluded: chain W residue 855 VAL Chi-restraints excluded: chain W residue 869 THR Chi-restraints excluded: chain W residue 990 MET Chi-restraints excluded: chain W residue 996 THR Chi-restraints excluded: chain W residue 1009 VAL Chi-restraints excluded: chain X residue 690 HIS Chi-restraints excluded: chain X residue 786 LEU Chi-restraints excluded: chain X residue 800 LEU Chi-restraints excluded: chain X residue 822 VAL Chi-restraints excluded: chain X residue 857 VAL Chi-restraints excluded: chain X residue 867 VAL Chi-restraints excluded: chain X residue 869 THR Chi-restraints excluded: chain X residue 946 THR Chi-restraints excluded: chain X residue 957 LYS Chi-restraints excluded: chain X residue 967 ASP Chi-restraints excluded: chain X residue 996 THR Chi-restraints excluded: chain X residue 1074 ASP Chi-restraints excluded: chain Y residue 623 THR Chi-restraints excluded: chain Y residue 706 LEU Chi-restraints excluded: chain Y residue 829 ASP Chi-restraints excluded: chain Y residue 855 VAL Chi-restraints excluded: chain Y residue 857 VAL Chi-restraints excluded: chain Y residue 866 GLN Chi-restraints excluded: chain Y residue 967 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 670 random chunks: chunk 539 optimal weight: 0.0570 chunk 367 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 482 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 552 optimal weight: 3.9990 chunk 447 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 330 optimal weight: 5.9990 chunk 581 optimal weight: 0.0020 chunk 163 optimal weight: 9.9990 overall best weight: 0.8310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 83 GLN ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN ** P 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 803 GLN Q 804 GLN ** S 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 816 GLN ** V 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 779 GLN X 820 GLN Y 978 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 53325 Z= 0.184 Angle : 0.654 11.784 72665 Z= 0.329 Chirality : 0.043 0.181 8425 Planarity : 0.004 0.037 9415 Dihedral : 5.465 42.786 7276 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.25 % Favored : 93.67 % Rotamer: Outliers : 4.60 % Allowed : 22.88 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.10), residues: 6685 helix: -2.37 (0.10), residues: 2255 sheet: -0.46 (0.14), residues: 1310 loop : -1.87 (0.11), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 864 HIS 0.004 0.000 HIS Y 690 PHE 0.022 0.001 PHE L 60 TYR 0.053 0.001 TYR P 895 ARG 0.008 0.000 ARG X 589 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1340 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1087 time to evaluate : 5.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.7530 (m-80) cc_final: 0.7262 (m-80) REVERT: A 74 GLU cc_start: 0.8766 (mp0) cc_final: 0.8396 (mp0) REVERT: A 106 PHE cc_start: 0.8414 (m-80) cc_final: 0.7934 (m-80) REVERT: A 131 GLU cc_start: 0.8673 (mp0) cc_final: 0.8467 (mp0) REVERT: B 24 LYS cc_start: 0.8770 (ttpt) cc_final: 0.8520 (ptpp) REVERT: B 106 PHE cc_start: 0.8157 (m-80) cc_final: 0.7875 (m-80) REVERT: C 31 ARG cc_start: 0.7397 (mtt180) cc_final: 0.6629 (mtm110) REVERT: C 74 GLU cc_start: 0.9132 (mp0) cc_final: 0.8894 (mp0) REVERT: C 98 MET cc_start: 0.8099 (ppp) cc_final: 0.7769 (ppp) REVERT: D 29 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7879 (p0) REVERT: D 131 GLU cc_start: 0.8558 (mp0) cc_final: 0.8049 (pm20) REVERT: D 140 ILE cc_start: 0.8809 (mm) cc_final: 0.8331 (tt) REVERT: E 29 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.6926 (p0) REVERT: E 31 ARG cc_start: 0.7736 (mtt180) cc_final: 0.7487 (ttm-80) REVERT: E 33 ARG cc_start: 0.8701 (mtp85) cc_final: 0.8491 (ttm110) REVERT: E 131 GLU cc_start: 0.8683 (mp0) cc_final: 0.8265 (pm20) REVERT: E 140 ILE cc_start: 0.8922 (mm) cc_final: 0.8569 (tt) REVERT: F 33 ARG cc_start: 0.7491 (mmm-85) cc_final: 0.7251 (mmm-85) REVERT: F 65 TYR cc_start: 0.9053 (t80) cc_final: 0.8759 (t80) REVERT: F 89 GLN cc_start: 0.8166 (tp40) cc_final: 0.7845 (tm-30) REVERT: F 106 PHE cc_start: 0.8447 (m-80) cc_final: 0.7911 (m-80) REVERT: G 21 ARG cc_start: 0.7061 (mmt90) cc_final: 0.5798 (mpp-170) REVERT: G 65 TYR cc_start: 0.8949 (t80) cc_final: 0.8721 (t80) REVERT: G 76 LEU cc_start: 0.8063 (tp) cc_final: 0.7524 (tt) REVERT: G 106 PHE cc_start: 0.8456 (m-80) cc_final: 0.8084 (m-80) REVERT: G 120 LYS cc_start: 0.8368 (mttp) cc_final: 0.8155 (mttp) REVERT: H 21 ARG cc_start: 0.7292 (mmt90) cc_final: 0.6136 (mpp-170) REVERT: H 50 ARG cc_start: 0.8857 (ttm170) cc_final: 0.8384 (ttm170) REVERT: H 106 PHE cc_start: 0.8735 (m-80) cc_final: 0.7897 (m-80) REVERT: H 112 MET cc_start: 0.8981 (mtp) cc_final: 0.8700 (mtm) REVERT: I 21 ARG cc_start: 0.6969 (mmt90) cc_final: 0.5935 (mpp-170) REVERT: I 30 ILE cc_start: 0.9399 (mt) cc_final: 0.9185 (mm) REVERT: I 53 GLN cc_start: 0.8031 (mt0) cc_final: 0.7583 (mt0) REVERT: I 112 MET cc_start: 0.9028 (mtp) cc_final: 0.8801 (mtp) REVERT: J 34 GLU cc_start: 0.7857 (mp0) cc_final: 0.7229 (mp0) REVERT: J 65 TYR cc_start: 0.9180 (t80) cc_final: 0.8754 (t80) REVERT: J 84 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8351 (ttpp) REVERT: K 50 ARG cc_start: 0.8843 (ttm-80) cc_final: 0.8101 (ttm110) REVERT: K 113 PHE cc_start: 0.8686 (m-80) cc_final: 0.8287 (m-80) REVERT: L 31 ARG cc_start: 0.8416 (ptp-170) cc_final: 0.7770 (ptp-110) REVERT: L 45 LEU cc_start: 0.7894 (mt) cc_final: 0.7694 (mm) REVERT: L 66 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8643 (mm110) REVERT: L 113 PHE cc_start: 0.8559 (m-80) cc_final: 0.8223 (m-10) REVERT: M 31 ARG cc_start: 0.8378 (mtt180) cc_final: 0.8002 (mmm160) REVERT: M 50 ARG cc_start: 0.8795 (ttm-80) cc_final: 0.8161 (ttm110) REVERT: M 113 PHE cc_start: 0.8405 (m-80) cc_final: 0.8126 (m-80) REVERT: N 113 PHE cc_start: 0.8392 (m-80) cc_final: 0.8075 (m-80) REVERT: N 131 GLU cc_start: 0.8792 (tp30) cc_final: 0.8029 (tp30) REVERT: O 31 ARG cc_start: 0.8341 (mtt180) cc_final: 0.7975 (mmm160) REVERT: P 616 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7431 (tm-30) REVERT: P 669 ARG cc_start: 0.8695 (ttm110) cc_final: 0.8168 (mtm-85) REVERT: P 995 ILE cc_start: 0.9450 (mt) cc_final: 0.8969 (tt) REVERT: P 1081 THR cc_start: 0.9631 (m) cc_final: 0.9175 (p) REVERT: Q 585 LYS cc_start: 0.9245 (mmmt) cc_final: 0.9015 (pttm) REVERT: Q 706 LEU cc_start: 0.9346 (tp) cc_final: 0.9026 (tt) REVERT: Q 709 ASP cc_start: 0.8097 (t70) cc_final: 0.7794 (t70) REVERT: Q 911 LYS cc_start: 0.9195 (mmmm) cc_final: 0.8951 (ttmm) REVERT: Q 995 ILE cc_start: 0.9438 (mt) cc_final: 0.8924 (tt) REVERT: R 583 TYR cc_start: 0.8869 (t80) cc_final: 0.8573 (t80) REVERT: R 616 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7527 (tm-30) REVERT: R 667 ARG cc_start: 0.8778 (mtm110) cc_final: 0.8483 (mtp85) REVERT: R 962 LEU cc_start: 0.9590 (mt) cc_final: 0.9389 (tp) REVERT: R 990 MET cc_start: 0.8295 (mtm) cc_final: 0.7953 (ttm) REVERT: R 995 ILE cc_start: 0.9427 (mt) cc_final: 0.9052 (tt) REVERT: R 1081 THR cc_start: 0.9568 (m) cc_final: 0.9120 (p) REVERT: S 584 GLN cc_start: 0.9232 (mm-40) cc_final: 0.9030 (mm110) REVERT: S 585 LYS cc_start: 0.9181 (mmmt) cc_final: 0.8895 (pttm) REVERT: S 913 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9103 (pp) REVERT: S 1006 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8203 (pt0) REVERT: S 1081 THR cc_start: 0.9673 (m) cc_final: 0.9238 (p) REVERT: T 583 TYR cc_start: 0.8987 (t80) cc_final: 0.8691 (t80) REVERT: T 616 GLU cc_start: 0.8198 (tt0) cc_final: 0.7701 (tm-30) REVERT: T 773 LEU cc_start: 0.9405 (mm) cc_final: 0.9046 (mp) REVERT: T 804 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8184 (tp40) REVERT: T 895 TYR cc_start: 0.9265 (t80) cc_final: 0.8944 (t80) REVERT: U 597 MET cc_start: 0.7690 (tpt) cc_final: 0.6838 (tpt) REVERT: U 601 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7458 (p0) REVERT: U 820 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8602 (tt0) REVERT: U 998 ASN cc_start: 0.8662 (t0) cc_final: 0.8365 (t0) REVERT: V 611 LEU cc_start: 0.8792 (tp) cc_final: 0.8546 (tp) REVERT: V 680 ASN cc_start: 0.8725 (t0) cc_final: 0.8476 (m-40) REVERT: V 814 MET cc_start: 0.8185 (ttp) cc_final: 0.7969 (tmm) REVERT: V 990 MET cc_start: 0.9036 (mtp) cc_final: 0.8809 (mtm) REVERT: W 586 MET cc_start: 0.7826 (mpp) cc_final: 0.7559 (mpp) REVERT: W 611 LEU cc_start: 0.8953 (tp) cc_final: 0.8701 (tp) REVERT: W 814 MET cc_start: 0.8692 (tpp) cc_final: 0.8414 (tpp) REVERT: W 978 HIS cc_start: 0.8700 (m-70) cc_final: 0.7922 (m90) REVERT: W 990 MET cc_start: 0.9059 (mtp) cc_final: 0.8778 (mtp) REVERT: W 1011 LYS cc_start: 0.9239 (tttp) cc_final: 0.8888 (tttt) REVERT: W 1037 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8059 (pm20) REVERT: X 597 MET cc_start: 0.7469 (tpt) cc_final: 0.7150 (tpt) REVERT: X 611 LEU cc_start: 0.8927 (tp) cc_final: 0.8608 (tp) REVERT: X 786 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8534 (mm) REVERT: X 805 ILE cc_start: 0.8959 (mm) cc_final: 0.8493 (mm) REVERT: X 990 MET cc_start: 0.8540 (mtp) cc_final: 0.8106 (ptp) REVERT: Y 581 MET cc_start: 0.6487 (ptt) cc_final: 0.5829 (pmm) REVERT: Y 583 TYR cc_start: 0.5967 (t80) cc_final: 0.5495 (t80) REVERT: Y 785 MET cc_start: 0.7848 (mmp) cc_final: 0.7584 (mmp) REVERT: Y 957 LYS cc_start: 0.8963 (tppt) cc_final: 0.8650 (mmtm) outliers start: 253 outliers final: 170 residues processed: 1269 average time/residue: 0.5841 time to fit residues: 1240.9681 Evaluate side-chains 1204 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1025 time to evaluate : 5.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 84 LYS Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 106 PHE Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 87 TRP Chi-restraints excluded: chain L residue 106 PHE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain O residue 29 ASP Chi-restraints excluded: chain O residue 57 ASN Chi-restraints excluded: chain O residue 106 PHE Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 148 THR Chi-restraints excluded: chain P residue 618 VAL Chi-restraints excluded: chain P residue 671 THR Chi-restraints excluded: chain P residue 689 LEU Chi-restraints excluded: chain P residue 810 ASP Chi-restraints excluded: chain P residue 855 VAL Chi-restraints excluded: chain P residue 875 LEU Chi-restraints excluded: chain P residue 913 LEU Chi-restraints excluded: chain P residue 915 THR Chi-restraints excluded: chain P residue 940 VAL Chi-restraints excluded: chain P residue 946 THR Chi-restraints excluded: chain P residue 996 THR Chi-restraints excluded: chain P residue 1035 THR Chi-restraints excluded: chain P residue 1053 MET Chi-restraints excluded: chain P residue 1074 ASP Chi-restraints excluded: chain P residue 1092 VAL Chi-restraints excluded: chain Q residue 608 VAL Chi-restraints excluded: chain Q residue 618 VAL Chi-restraints excluded: chain Q residue 671 THR Chi-restraints excluded: chain Q residue 724 VAL Chi-restraints excluded: chain Q residue 787 ASN Chi-restraints excluded: chain Q residue 817 LEU Chi-restraints excluded: chain Q residue 855 VAL Chi-restraints excluded: chain Q residue 869 THR Chi-restraints excluded: chain Q residue 875 LEU Chi-restraints excluded: chain Q residue 913 LEU Chi-restraints excluded: chain Q residue 943 THR Chi-restraints excluded: chain Q residue 946 THR Chi-restraints excluded: chain Q residue 972 THR Chi-restraints excluded: chain Q residue 996 THR Chi-restraints excluded: chain Q residue 1014 THR Chi-restraints excluded: chain Q residue 1051 LEU Chi-restraints excluded: chain Q residue 1074 ASP Chi-restraints excluded: chain R residue 606 THR Chi-restraints excluded: chain R residue 608 VAL Chi-restraints excluded: chain R residue 628 GLU Chi-restraints excluded: chain R residue 705 THR Chi-restraints excluded: chain R residue 773 LEU Chi-restraints excluded: chain R residue 817 LEU Chi-restraints excluded: chain R residue 855 VAL Chi-restraints excluded: chain R residue 867 VAL Chi-restraints excluded: chain R residue 913 LEU Chi-restraints excluded: chain R residue 940 VAL Chi-restraints excluded: chain R residue 943 THR Chi-restraints excluded: chain R residue 946 THR Chi-restraints excluded: chain R residue 996 THR Chi-restraints excluded: chain R residue 997 ASP Chi-restraints excluded: chain R residue 1074 ASP Chi-restraints excluded: chain R residue 1092 VAL Chi-restraints excluded: chain S residue 671 THR Chi-restraints excluded: chain S residue 773 LEU Chi-restraints excluded: chain S residue 855 VAL Chi-restraints excluded: chain S residue 875 LEU Chi-restraints excluded: chain S residue 913 LEU Chi-restraints excluded: chain S residue 943 THR Chi-restraints excluded: chain S residue 946 THR Chi-restraints excluded: chain S residue 1006 GLN Chi-restraints excluded: chain S residue 1035 THR Chi-restraints excluded: chain S residue 1074 ASP Chi-restraints excluded: chain T residue 606 THR Chi-restraints excluded: chain T residue 618 VAL Chi-restraints excluded: chain T residue 724 VAL Chi-restraints excluded: chain T residue 817 LEU Chi-restraints excluded: chain T residue 875 LEU Chi-restraints excluded: chain T residue 933 HIS Chi-restraints excluded: chain T residue 943 THR Chi-restraints excluded: chain T residue 946 THR Chi-restraints excluded: chain T residue 996 THR Chi-restraints excluded: chain T residue 997 ASP Chi-restraints excluded: chain T residue 1004 VAL Chi-restraints excluded: chain T residue 1006 GLN Chi-restraints excluded: chain T residue 1074 ASP Chi-restraints excluded: chain T residue 1092 VAL Chi-restraints excluded: chain U residue 601 ASP Chi-restraints excluded: chain U residue 690 HIS Chi-restraints excluded: chain U residue 776 MET Chi-restraints excluded: chain U residue 820 GLN Chi-restraints excluded: chain U residue 829 ASP Chi-restraints excluded: chain U residue 857 VAL Chi-restraints excluded: chain U residue 905 SER Chi-restraints excluded: chain U residue 915 THR Chi-restraints excluded: chain U residue 967 ASP Chi-restraints excluded: chain U residue 996 THR Chi-restraints excluded: chain V residue 618 VAL Chi-restraints excluded: chain V residue 631 VAL Chi-restraints excluded: chain V residue 713 SER Chi-restraints excluded: chain V residue 776 MET Chi-restraints excluded: chain V residue 780 ASN Chi-restraints excluded: chain V residue 822 VAL Chi-restraints excluded: chain V residue 855 VAL Chi-restraints excluded: chain V residue 867 VAL Chi-restraints excluded: chain V residue 1029 VAL Chi-restraints excluded: chain V residue 1104 THR Chi-restraints excluded: chain W residue 615 ASP Chi-restraints excluded: chain W residue 713 SER Chi-restraints excluded: chain W residue 796 THR Chi-restraints excluded: chain W residue 822 VAL Chi-restraints excluded: chain W residue 855 VAL Chi-restraints excluded: chain W residue 869 THR Chi-restraints excluded: chain W residue 967 ASP Chi-restraints excluded: chain W residue 996 THR Chi-restraints excluded: chain W residue 1009 VAL Chi-restraints excluded: chain W residue 1037 GLN Chi-restraints excluded: chain W residue 1104 THR Chi-restraints excluded: chain X residue 631 VAL Chi-restraints excluded: chain X residue 786 LEU Chi-restraints excluded: chain X residue 820 GLN Chi-restraints excluded: chain X residue 822 VAL Chi-restraints excluded: chain X residue 867 VAL Chi-restraints excluded: chain X residue 869 THR Chi-restraints excluded: chain X residue 946 THR Chi-restraints excluded: chain X residue 957 LYS Chi-restraints excluded: chain X residue 967 ASP Chi-restraints excluded: chain X residue 1074 ASP Chi-restraints excluded: chain X residue 1104 THR Chi-restraints excluded: chain Y residue 623 THR Chi-restraints excluded: chain Y residue 661 VAL Chi-restraints excluded: chain Y residue 822 VAL Chi-restraints excluded: chain Y residue 829 ASP Chi-restraints excluded: chain Y residue 847 GLU Chi-restraints excluded: chain Y residue 855 VAL Chi-restraints excluded: chain Y residue 866 GLN Chi-restraints excluded: chain Y residue 967 ASP Chi-restraints excluded: chain Y residue 971 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 670 random chunks: chunk 217 optimal weight: 1.9990 chunk 583 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 380 optimal weight: 0.4980 chunk 159 optimal weight: 6.9990 chunk 648 optimal weight: 2.9990 chunk 538 optimal weight: 7.9990 chunk 300 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 340 optimal weight: 0.9980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** J 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 83 GLN ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 GLN P 576 GLN ** P 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1005 ASN S 576 GLN ** S 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 914 ASN ** T 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 820 GLN ** V 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 820 GLN Y 978 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 53325 Z= 0.223 Angle : 0.661 12.148 72665 Z= 0.332 Chirality : 0.044 0.214 8425 Planarity : 0.004 0.045 9415 Dihedral : 5.390 43.460 7276 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 4.60 % Allowed : 23.46 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.10), residues: 6685 helix: -2.24 (0.10), residues: 2325 sheet: -0.48 (0.14), residues: 1360 loop : -1.73 (0.11), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Q1028 HIS 0.003 0.000 HIS Y 690 PHE 0.022 0.001 PHE O 60 TYR 0.044 0.002 TYR P 895 ARG 0.007 0.000 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1303 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1050 time to evaluate : 5.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.7516 (m-80) cc_final: 0.7268 (m-80) REVERT: A 106 PHE cc_start: 0.8420 (m-80) cc_final: 0.7930 (m-80) REVERT: A 131 GLU cc_start: 0.8683 (mp0) cc_final: 0.8463 (mp0) REVERT: A 141 GLU cc_start: 0.7900 (tp30) cc_final: 0.7685 (tm-30) REVERT: B 33 ARG cc_start: 0.8492 (mtp85) cc_final: 0.8286 (ttm110) REVERT: B 106 PHE cc_start: 0.8156 (m-80) cc_final: 0.7916 (m-80) REVERT: C 74 GLU cc_start: 0.9124 (mp0) cc_final: 0.8885 (mp0) REVERT: C 98 MET cc_start: 0.8098 (ppp) cc_final: 0.7834 (ppp) REVERT: D 131 GLU cc_start: 0.8552 (mp0) cc_final: 0.8068 (pm20) REVERT: D 140 ILE cc_start: 0.8794 (mm) cc_final: 0.8327 (tt) REVERT: E 29 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.6922 (p0) REVERT: E 31 ARG cc_start: 0.7726 (mtt180) cc_final: 0.7498 (ttm-80) REVERT: E 74 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7942 (mp0) REVERT: E 131 GLU cc_start: 0.8582 (mp0) cc_final: 0.8224 (pm20) REVERT: E 140 ILE cc_start: 0.8919 (mm) cc_final: 0.8560 (tt) REVERT: F 33 ARG cc_start: 0.7469 (mmm-85) cc_final: 0.7153 (mmm-85) REVERT: F 65 TYR cc_start: 0.9050 (t80) cc_final: 0.8652 (t80) REVERT: F 106 PHE cc_start: 0.8422 (m-80) cc_final: 0.7862 (m-80) REVERT: G 21 ARG cc_start: 0.7035 (mmt90) cc_final: 0.5790 (mpp-170) REVERT: G 53 GLN cc_start: 0.8393 (mt0) cc_final: 0.8120 (mt0) REVERT: G 65 TYR cc_start: 0.8899 (t80) cc_final: 0.8676 (t80) REVERT: G 76 LEU cc_start: 0.8025 (tp) cc_final: 0.7525 (tt) REVERT: G 106 PHE cc_start: 0.8460 (m-80) cc_final: 0.8121 (m-80) REVERT: G 120 LYS cc_start: 0.8419 (mttp) cc_final: 0.8145 (mttp) REVERT: H 34 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7514 (tp30) REVERT: H 50 ARG cc_start: 0.8853 (ttm170) cc_final: 0.8425 (ttm170) REVERT: H 61 ASP cc_start: 0.8571 (m-30) cc_final: 0.8266 (t0) REVERT: H 65 TYR cc_start: 0.8885 (t80) cc_final: 0.8278 (t80) REVERT: H 106 PHE cc_start: 0.8747 (m-80) cc_final: 0.7933 (m-80) REVERT: H 112 MET cc_start: 0.8984 (mtp) cc_final: 0.8769 (mtm) REVERT: I 21 ARG cc_start: 0.7058 (mmt90) cc_final: 0.5963 (mpp-170) REVERT: I 30 ILE cc_start: 0.9411 (mt) cc_final: 0.9181 (mm) REVERT: I 65 TYR cc_start: 0.9010 (t80) cc_final: 0.8446 (t80) REVERT: J 34 GLU cc_start: 0.7874 (mp0) cc_final: 0.7239 (mp0) REVERT: J 65 TYR cc_start: 0.9197 (t80) cc_final: 0.8747 (t80) REVERT: J 84 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8339 (ttpt) REVERT: J 98 MET cc_start: 0.8310 (ptp) cc_final: 0.7984 (ptm) REVERT: K 28 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7655 (mm) REVERT: K 56 ASP cc_start: 0.6665 (p0) cc_final: 0.6406 (p0) REVERT: K 57 ASN cc_start: 0.7756 (p0) cc_final: 0.7463 (p0) REVERT: K 79 ASP cc_start: 0.6475 (t0) cc_final: 0.4836 (m-30) REVERT: K 113 PHE cc_start: 0.8698 (m-80) cc_final: 0.8278 (m-80) REVERT: K 120 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8819 (mmtm) REVERT: L 45 LEU cc_start: 0.7894 (mt) cc_final: 0.7692 (mm) REVERT: L 52 TYR cc_start: 0.6712 (m-80) cc_final: 0.6420 (m-80) REVERT: L 113 PHE cc_start: 0.8578 (m-80) cc_final: 0.8216 (m-10) REVERT: M 31 ARG cc_start: 0.8375 (mtt180) cc_final: 0.7992 (mmm160) REVERT: M 50 ARG cc_start: 0.8845 (ttm-80) cc_final: 0.8030 (ttm110) REVERT: M 83 GLN cc_start: 0.8799 (mt0) cc_final: 0.8532 (mm110) REVERT: M 113 PHE cc_start: 0.8426 (m-80) cc_final: 0.8145 (m-80) REVERT: N 113 PHE cc_start: 0.8438 (m-80) cc_final: 0.8050 (m-80) REVERT: N 131 GLU cc_start: 0.8786 (tp30) cc_final: 0.7983 (tp30) REVERT: O 31 ARG cc_start: 0.8330 (mtt180) cc_final: 0.7964 (mmm160) REVERT: P 616 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7450 (tm-30) REVERT: P 785 MET cc_start: 0.7684 (mmp) cc_final: 0.7461 (mmp) REVERT: P 990 MET cc_start: 0.8200 (ttm) cc_final: 0.7856 (ttm) REVERT: P 1077 MET cc_start: 0.8703 (mmt) cc_final: 0.8381 (mmp) REVERT: P 1081 THR cc_start: 0.9636 (m) cc_final: 0.9186 (p) REVERT: Q 585 LYS cc_start: 0.9195 (mmmt) cc_final: 0.8965 (pttm) REVERT: Q 706 LEU cc_start: 0.9352 (tp) cc_final: 0.9002 (tt) REVERT: Q 709 ASP cc_start: 0.8251 (t70) cc_final: 0.7956 (t70) REVERT: Q 911 LYS cc_start: 0.9187 (mmmm) cc_final: 0.8907 (ttmm) REVERT: R 583 TYR cc_start: 0.8886 (t80) cc_final: 0.8510 (t80) REVERT: R 616 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7528 (tm-30) REVERT: R 667 ARG cc_start: 0.8801 (mtm110) cc_final: 0.8522 (mtp85) REVERT: R 990 MET cc_start: 0.8286 (mtm) cc_final: 0.7937 (ttm) REVERT: R 995 ILE cc_start: 0.9435 (mt) cc_final: 0.9005 (tt) REVERT: R 1081 THR cc_start: 0.9574 (m) cc_final: 0.9130 (p) REVERT: S 584 GLN cc_start: 0.9232 (mm-40) cc_final: 0.9026 (mm110) REVERT: S 585 LYS cc_start: 0.9156 (mmmt) cc_final: 0.8897 (pttm) REVERT: S 616 GLU cc_start: 0.8227 (tt0) cc_final: 0.7511 (tm-30) REVERT: S 801 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8229 (tpp80) REVERT: S 913 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9199 (pp) REVERT: S 1006 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8284 (pt0) REVERT: S 1081 THR cc_start: 0.9672 (m) cc_final: 0.9213 (p) REVERT: T 583 TYR cc_start: 0.8985 (t80) cc_final: 0.8726 (t80) REVERT: T 616 GLU cc_start: 0.8216 (tt0) cc_final: 0.7717 (tt0) REVERT: T 773 LEU cc_start: 0.9400 (mm) cc_final: 0.9079 (mp) REVERT: T 804 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8226 (tp40) REVERT: T 895 TYR cc_start: 0.9251 (t80) cc_final: 0.8957 (t80) REVERT: U 597 MET cc_start: 0.7715 (tpt) cc_final: 0.6840 (tpt) REVERT: U 601 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7551 (p0) REVERT: U 820 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8598 (tt0) REVERT: U 998 ASN cc_start: 0.8673 (t0) cc_final: 0.8381 (t0) REVERT: V 680 ASN cc_start: 0.8731 (t0) cc_final: 0.8476 (m-40) REVERT: V 990 MET cc_start: 0.9002 (mtp) cc_final: 0.8772 (mtm) REVERT: V 1011 LYS cc_start: 0.9348 (tttp) cc_final: 0.9124 (tttp) REVERT: W 586 MET cc_start: 0.7849 (mpp) cc_final: 0.7326 (mpp) REVERT: W 611 LEU cc_start: 0.8922 (tp) cc_final: 0.8653 (tp) REVERT: W 814 MET cc_start: 0.8572 (tpp) cc_final: 0.8292 (tpp) REVERT: W 990 MET cc_start: 0.9052 (mtp) cc_final: 0.8713 (mtp) REVERT: W 1011 LYS cc_start: 0.9240 (tttp) cc_final: 0.8869 (tttt) REVERT: X 597 MET cc_start: 0.7397 (tpt) cc_final: 0.6975 (tpt) REVERT: X 611 LEU cc_start: 0.8922 (tp) cc_final: 0.8675 (tp) REVERT: X 805 ILE cc_start: 0.8973 (mm) cc_final: 0.8498 (mm) REVERT: Y 581 MET cc_start: 0.6501 (ptt) cc_final: 0.5826 (pmm) REVERT: Y 583 TYR cc_start: 0.6060 (t80) cc_final: 0.5585 (t80) REVERT: Y 785 MET cc_start: 0.7650 (mmp) cc_final: 0.7334 (mmp) REVERT: Y 805 ILE cc_start: 0.8886 (mm) cc_final: 0.8668 (mm) REVERT: Y 815 MET cc_start: 0.8347 (mmm) cc_final: 0.7994 (mpp) REVERT: Y 957 LYS cc_start: 0.9009 (tppt) cc_final: 0.8714 (mmtm) REVERT: Y 967 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8437 (t0) REVERT: Y 1007 MET cc_start: 0.8869 (ptm) cc_final: 0.8623 (ptt) outliers start: 253 outliers final: 202 residues processed: 1234 average time/residue: 0.5465 time to fit residues: 1133.7086 Evaluate side-chains 1223 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1013 time to evaluate : 4.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 84 LYS Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 66 GLN Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 87 TRP Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 29 ASP Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 148 THR Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 29 ASP Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 57 ASN Chi-restraints excluded: chain O residue 87 TRP Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 148 THR Chi-restraints excluded: chain P residue 671 THR Chi-restraints excluded: chain P residue 689 LEU Chi-restraints excluded: chain P residue 705 THR Chi-restraints excluded: chain P residue 810 ASP Chi-restraints excluded: chain P residue 855 VAL Chi-restraints excluded: chain P residue 875 LEU Chi-restraints excluded: chain P residue 913 LEU Chi-restraints excluded: chain P residue 915 THR Chi-restraints excluded: chain P residue 933 HIS Chi-restraints excluded: chain P residue 940 VAL Chi-restraints excluded: chain P residue 943 THR Chi-restraints excluded: chain P residue 946 THR Chi-restraints excluded: chain P residue 996 THR Chi-restraints excluded: chain P residue 1035 THR Chi-restraints excluded: chain P residue 1053 MET Chi-restraints excluded: chain P residue 1074 ASP Chi-restraints excluded: chain P residue 1092 VAL Chi-restraints excluded: chain Q residue 608 VAL Chi-restraints excluded: chain Q residue 618 VAL Chi-restraints excluded: chain Q residue 671 THR Chi-restraints excluded: chain Q residue 724 VAL Chi-restraints excluded: chain Q residue 787 ASN Chi-restraints excluded: chain Q residue 817 LEU Chi-restraints excluded: chain Q residue 855 VAL Chi-restraints excluded: chain Q residue 869 THR Chi-restraints excluded: chain Q residue 875 LEU Chi-restraints excluded: chain Q residue 913 LEU Chi-restraints excluded: chain Q residue 943 THR Chi-restraints excluded: chain Q residue 946 THR Chi-restraints excluded: chain Q residue 972 THR Chi-restraints excluded: chain Q residue 996 THR Chi-restraints excluded: chain Q residue 1014 THR Chi-restraints excluded: chain Q residue 1051 LEU Chi-restraints excluded: chain Q residue 1074 ASP Chi-restraints excluded: chain Q residue 1092 VAL Chi-restraints excluded: chain R residue 606 THR Chi-restraints excluded: chain R residue 608 VAL Chi-restraints excluded: chain R residue 628 GLU Chi-restraints excluded: chain R residue 671 THR Chi-restraints excluded: chain R residue 705 THR Chi-restraints excluded: chain R residue 724 VAL Chi-restraints excluded: chain R residue 773 LEU Chi-restraints excluded: chain R residue 798 VAL Chi-restraints excluded: chain R residue 817 LEU Chi-restraints excluded: chain R residue 855 VAL Chi-restraints excluded: chain R residue 875 LEU Chi-restraints excluded: chain R residue 913 LEU Chi-restraints excluded: chain R residue 940 VAL Chi-restraints excluded: chain R residue 943 THR Chi-restraints excluded: chain R residue 946 THR Chi-restraints excluded: chain R residue 996 THR Chi-restraints excluded: chain R residue 997 ASP Chi-restraints excluded: chain R residue 1074 ASP Chi-restraints excluded: chain R residue 1092 VAL Chi-restraints excluded: chain R residue 1094 LEU Chi-restraints excluded: chain S residue 671 THR Chi-restraints excluded: chain S residue 773 LEU Chi-restraints excluded: chain S residue 810 ASP Chi-restraints excluded: chain S residue 830 LEU Chi-restraints excluded: chain S residue 855 VAL Chi-restraints excluded: chain S residue 867 VAL Chi-restraints excluded: chain S residue 875 LEU Chi-restraints excluded: chain S residue 913 LEU Chi-restraints excluded: chain S residue 914 ASN Chi-restraints excluded: chain S residue 943 THR Chi-restraints excluded: chain S residue 946 THR Chi-restraints excluded: chain S residue 972 THR Chi-restraints excluded: chain S residue 1006 GLN Chi-restraints excluded: chain S residue 1035 THR Chi-restraints excluded: chain S residue 1074 ASP Chi-restraints excluded: chain S residue 1092 VAL Chi-restraints excluded: chain T residue 606 THR Chi-restraints excluded: chain T residue 618 VAL Chi-restraints excluded: chain T residue 623 THR Chi-restraints excluded: chain T residue 724 VAL Chi-restraints excluded: chain T residue 810 ASP Chi-restraints excluded: chain T residue 817 LEU Chi-restraints excluded: chain T residue 875 LEU Chi-restraints excluded: chain T residue 933 HIS Chi-restraints excluded: chain T residue 943 THR Chi-restraints excluded: chain T residue 946 THR Chi-restraints excluded: chain T residue 967 ASP Chi-restraints excluded: chain T residue 996 THR Chi-restraints excluded: chain T residue 997 ASP Chi-restraints excluded: chain T residue 1006 GLN Chi-restraints excluded: chain T residue 1074 ASP Chi-restraints excluded: chain T residue 1092 VAL Chi-restraints excluded: chain U residue 601 ASP Chi-restraints excluded: chain U residue 623 THR Chi-restraints excluded: chain U residue 690 HIS Chi-restraints excluded: chain U residue 780 ASN Chi-restraints excluded: chain U residue 820 GLN Chi-restraints excluded: chain U residue 829 ASP Chi-restraints excluded: chain U residue 857 VAL Chi-restraints excluded: chain U residue 905 SER Chi-restraints excluded: chain U residue 915 THR Chi-restraints excluded: chain U residue 996 THR Chi-restraints excluded: chain V residue 618 VAL Chi-restraints excluded: chain V residue 631 VAL Chi-restraints excluded: chain V residue 713 SER Chi-restraints excluded: chain V residue 718 LEU Chi-restraints excluded: chain V residue 776 MET Chi-restraints excluded: chain V residue 780 ASN Chi-restraints excluded: chain V residue 796 THR Chi-restraints excluded: chain V residue 822 VAL Chi-restraints excluded: chain V residue 829 ASP Chi-restraints excluded: chain V residue 855 VAL Chi-restraints excluded: chain V residue 867 VAL Chi-restraints excluded: chain V residue 1029 VAL Chi-restraints excluded: chain V residue 1104 THR Chi-restraints excluded: chain W residue 615 ASP Chi-restraints excluded: chain W residue 618 VAL Chi-restraints excluded: chain W residue 631 VAL Chi-restraints excluded: chain W residue 713 SER Chi-restraints excluded: chain W residue 822 VAL Chi-restraints excluded: chain W residue 855 VAL Chi-restraints excluded: chain W residue 869 THR Chi-restraints excluded: chain W residue 967 ASP Chi-restraints excluded: chain W residue 996 THR Chi-restraints excluded: chain W residue 1104 THR Chi-restraints excluded: chain X residue 631 VAL Chi-restraints excluded: chain X residue 710 VAL Chi-restraints excluded: chain X residue 716 VAL Chi-restraints excluded: chain X residue 820 GLN Chi-restraints excluded: chain X residue 822 VAL Chi-restraints excluded: chain X residue 855 VAL Chi-restraints excluded: chain X residue 857 VAL Chi-restraints excluded: chain X residue 867 VAL Chi-restraints excluded: chain X residue 946 THR Chi-restraints excluded: chain X residue 957 LYS Chi-restraints excluded: chain X residue 967 ASP Chi-restraints excluded: chain X residue 1053 MET Chi-restraints excluded: chain X residue 1074 ASP Chi-restraints excluded: chain X residue 1104 THR Chi-restraints excluded: chain Y residue 623 THR Chi-restraints excluded: chain Y residue 661 VAL Chi-restraints excluded: chain Y residue 822 VAL Chi-restraints excluded: chain Y residue 829 ASP Chi-restraints excluded: chain Y residue 847 GLU Chi-restraints excluded: chain Y residue 855 VAL Chi-restraints excluded: chain Y residue 857 VAL Chi-restraints excluded: chain Y residue 866 GLN Chi-restraints excluded: chain Y residue 967 ASP Chi-restraints excluded: chain Y residue 971 THR Chi-restraints excluded: chain Y residue 1104 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 670 random chunks: chunk 624 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 369 optimal weight: 1.9990 chunk 473 optimal weight: 0.8980 chunk 366 optimal weight: 0.2980 chunk 545 optimal weight: 3.9990 chunk 361 optimal weight: 1.9990 chunk 645 optimal weight: 0.2980 chunk 404 optimal weight: 0.7980 chunk 393 optimal weight: 0.7980 chunk 298 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN I 89 GLN J 53 GLN ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN ** L 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 GLN ** P 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 978 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 53325 Z= 0.169 Angle : 0.658 12.321 72665 Z= 0.327 Chirality : 0.043 0.211 8425 Planarity : 0.004 0.070 9415 Dihedral : 5.187 42.177 7275 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.79 % Rotamer: Outliers : 4.08 % Allowed : 24.57 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.10), residues: 6685 helix: -2.01 (0.10), residues: 2285 sheet: -0.21 (0.14), residues: 1325 loop : -1.65 (0.11), residues: 3075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 87 HIS 0.004 0.000 HIS X 690 PHE 0.023 0.001 PHE L 60 TYR 0.028 0.001 TYR E 65 ARG 0.011 0.000 ARG E 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1298 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1074 time to evaluate : 5.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7336 (ptt90) cc_final: 0.6984 (ptt90) REVERT: A 52 TYR cc_start: 0.7453 (m-80) cc_final: 0.7215 (m-80) REVERT: A 74 GLU cc_start: 0.8761 (mp0) cc_final: 0.8402 (mp0) REVERT: A 106 PHE cc_start: 0.8351 (m-80) cc_final: 0.7886 (m-80) REVERT: A 131 GLU cc_start: 0.8650 (mp0) cc_final: 0.8436 (mp0) REVERT: B 33 ARG cc_start: 0.8502 (mtp85) cc_final: 0.8264 (ttm110) REVERT: B 52 TYR cc_start: 0.7050 (m-80) cc_final: 0.6683 (m-80) REVERT: B 74 GLU cc_start: 0.8774 (mp0) cc_final: 0.8312 (mp0) REVERT: B 106 PHE cc_start: 0.8189 (m-80) cc_final: 0.7938 (m-80) REVERT: C 74 GLU cc_start: 0.9082 (mp0) cc_final: 0.8602 (mp0) REVERT: C 98 MET cc_start: 0.8055 (ppp) cc_final: 0.7822 (ppp) REVERT: D 33 ARG cc_start: 0.8479 (mtp85) cc_final: 0.8079 (mtm110) REVERT: D 131 GLU cc_start: 0.8460 (mp0) cc_final: 0.8079 (pm20) REVERT: E 29 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7720 (p0) REVERT: E 74 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8003 (mp0) REVERT: E 106 PHE cc_start: 0.8218 (m-10) cc_final: 0.7991 (m-10) REVERT: E 131 GLU cc_start: 0.8560 (mp0) cc_final: 0.8054 (pm20) REVERT: E 140 ILE cc_start: 0.8843 (mm) cc_final: 0.8491 (tt) REVERT: F 33 ARG cc_start: 0.7308 (mmm-85) cc_final: 0.7035 (mmm-85) REVERT: F 65 TYR cc_start: 0.8972 (t80) cc_final: 0.8196 (t80) REVERT: F 106 PHE cc_start: 0.8373 (m-80) cc_final: 0.7851 (m-80) REVERT: G 21 ARG cc_start: 0.6988 (mmt90) cc_final: 0.5777 (mpp-170) REVERT: G 52 TYR cc_start: 0.8971 (m-80) cc_final: 0.8730 (m-10) REVERT: G 65 TYR cc_start: 0.8894 (t80) cc_final: 0.8659 (t80) REVERT: G 76 LEU cc_start: 0.7967 (tp) cc_final: 0.7480 (tt) REVERT: G 106 PHE cc_start: 0.8463 (m-80) cc_final: 0.8174 (m-80) REVERT: G 120 LYS cc_start: 0.8364 (mttp) cc_final: 0.8104 (mttp) REVERT: H 50 ARG cc_start: 0.8813 (ttm170) cc_final: 0.8428 (ttm170) REVERT: H 61 ASP cc_start: 0.8548 (m-30) cc_final: 0.8273 (t0) REVERT: H 65 TYR cc_start: 0.8874 (t80) cc_final: 0.8279 (t80) REVERT: H 106 PHE cc_start: 0.8701 (m-80) cc_final: 0.7955 (m-80) REVERT: H 112 MET cc_start: 0.8887 (mtp) cc_final: 0.8645 (mtm) REVERT: I 21 ARG cc_start: 0.6965 (mmt90) cc_final: 0.5808 (mpp-170) REVERT: I 30 ILE cc_start: 0.9398 (mt) cc_final: 0.9171 (mm) REVERT: I 65 TYR cc_start: 0.9034 (t80) cc_final: 0.8486 (t80) REVERT: I 76 LEU cc_start: 0.8039 (tp) cc_final: 0.7472 (tt) REVERT: J 34 GLU cc_start: 0.7821 (mp0) cc_final: 0.7277 (mp0) REVERT: J 53 GLN cc_start: 0.8059 (mt0) cc_final: 0.7794 (mt0) REVERT: J 84 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8279 (ttpt) REVERT: J 87 TRP cc_start: 0.9283 (OUTLIER) cc_final: 0.8944 (m-90) REVERT: K 28 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7653 (mm) REVERT: K 50 ARG cc_start: 0.8659 (ttm-80) cc_final: 0.7756 (ttm110) REVERT: K 56 ASP cc_start: 0.6518 (p0) cc_final: 0.6305 (p0) REVERT: K 57 ASN cc_start: 0.7670 (p0) cc_final: 0.7401 (p0) REVERT: K 79 ASP cc_start: 0.6430 (t0) cc_final: 0.5028 (m-30) REVERT: K 83 GLN cc_start: 0.8204 (tp-100) cc_final: 0.7526 (mm-40) REVERT: K 113 PHE cc_start: 0.8678 (m-80) cc_final: 0.8258 (m-80) REVERT: K 120 LYS cc_start: 0.9075 (mmmm) cc_final: 0.8831 (mmtm) REVERT: L 45 LEU cc_start: 0.7879 (mt) cc_final: 0.7668 (mm) REVERT: L 66 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8546 (mm-40) REVERT: L 113 PHE cc_start: 0.8541 (m-80) cc_final: 0.8175 (m-10) REVERT: M 50 ARG cc_start: 0.8867 (ttm-80) cc_final: 0.8006 (ttm110) REVERT: M 113 PHE cc_start: 0.8459 (m-80) cc_final: 0.8078 (m-80) REVERT: N 113 PHE cc_start: 0.8406 (m-80) cc_final: 0.8010 (m-80) REVERT: N 131 GLU cc_start: 0.8732 (tp30) cc_final: 0.8024 (tp30) REVERT: O 85 ASP cc_start: 0.7435 (m-30) cc_final: 0.7192 (m-30) REVERT: P 616 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7444 (tm-30) REVERT: P 990 MET cc_start: 0.8123 (ttm) cc_final: 0.7609 (ttm) REVERT: P 1077 MET cc_start: 0.8664 (mmt) cc_final: 0.8406 (mmp) REVERT: P 1081 THR cc_start: 0.9644 (m) cc_final: 0.9167 (p) REVERT: Q 709 ASP cc_start: 0.8190 (t70) cc_final: 0.7918 (t70) REVERT: Q 883 VAL cc_start: 0.9742 (t) cc_final: 0.9526 (p) REVERT: Q 911 LYS cc_start: 0.9145 (mmmm) cc_final: 0.8899 (ttmm) REVERT: R 583 TYR cc_start: 0.8892 (t80) cc_final: 0.8041 (t80) REVERT: R 586 MET cc_start: 0.9261 (mmm) cc_final: 0.8980 (mmm) REVERT: R 616 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7527 (tm-30) REVERT: R 667 ARG cc_start: 0.8797 (mtm110) cc_final: 0.8561 (mtp85) REVERT: R 677 ASP cc_start: 0.8355 (t70) cc_final: 0.8047 (t0) REVERT: R 699 ASP cc_start: 0.8438 (m-30) cc_final: 0.8195 (m-30) REVERT: R 867 VAL cc_start: 0.9258 (p) cc_final: 0.8967 (p) REVERT: R 990 MET cc_start: 0.8250 (mtm) cc_final: 0.7921 (ttm) REVERT: R 1081 THR cc_start: 0.9550 (m) cc_final: 0.9094 (p) REVERT: S 585 LYS cc_start: 0.9113 (mmmt) cc_final: 0.8870 (pttm) REVERT: S 616 GLU cc_start: 0.8216 (tt0) cc_final: 0.7547 (tm-30) REVERT: S 801 ARG cc_start: 0.8486 (tpp80) cc_final: 0.8152 (tpp80) REVERT: S 866 GLN cc_start: 0.9246 (tp40) cc_final: 0.8988 (tp-100) REVERT: S 913 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9164 (pp) REVERT: S 962 LEU cc_start: 0.9638 (mt) cc_final: 0.9326 (tp) REVERT: S 1006 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8341 (pt0) REVERT: S 1081 THR cc_start: 0.9680 (m) cc_final: 0.9257 (p) REVERT: T 583 TYR cc_start: 0.8955 (t80) cc_final: 0.8568 (t80) REVERT: T 587 LEU cc_start: 0.9275 (mt) cc_final: 0.9019 (mm) REVERT: T 616 GLU cc_start: 0.8153 (tt0) cc_final: 0.7667 (tt0) REVERT: T 638 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.8411 (p) REVERT: T 804 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8277 (tp40) REVERT: T 895 TYR cc_start: 0.9239 (t80) cc_final: 0.8779 (t80) REVERT: T 913 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9160 (pp) REVERT: T 1052 GLU cc_start: 0.8211 (tt0) cc_final: 0.7980 (tt0) REVERT: U 597 MET cc_start: 0.7662 (tpt) cc_final: 0.6790 (tpt) REVERT: U 601 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7632 (p0) REVERT: U 998 ASN cc_start: 0.8632 (t0) cc_final: 0.8336 (t0) REVERT: V 680 ASN cc_start: 0.8700 (t0) cc_final: 0.8446 (m-40) REVERT: V 805 ILE cc_start: 0.8788 (mm) cc_final: 0.8406 (mm) REVERT: V 990 MET cc_start: 0.8994 (mtp) cc_final: 0.8752 (mtm) REVERT: V 1011 LYS cc_start: 0.9347 (tttp) cc_final: 0.9108 (tttp) REVERT: W 611 LEU cc_start: 0.8902 (tp) cc_final: 0.8653 (tp) REVERT: W 680 ASN cc_start: 0.8632 (t0) cc_final: 0.8365 (m-40) REVERT: W 814 MET cc_start: 0.8540 (tpp) cc_final: 0.8291 (tpp) REVERT: W 978 HIS cc_start: 0.8685 (m-70) cc_final: 0.7918 (m90) REVERT: W 990 MET cc_start: 0.8976 (mtp) cc_final: 0.8643 (mtp) REVERT: W 1011 LYS cc_start: 0.9226 (tttp) cc_final: 0.8874 (tttt) REVERT: W 1037 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8083 (pm20) REVERT: X 597 MET cc_start: 0.7365 (tpt) cc_final: 0.6534 (tpt) REVERT: X 601 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8375 (p0) REVERT: X 611 LEU cc_start: 0.9017 (tp) cc_final: 0.8689 (tp) REVERT: X 785 MET cc_start: 0.7899 (mmp) cc_final: 0.7498 (mmp) REVERT: X 805 ILE cc_start: 0.8915 (mm) cc_final: 0.8471 (mm) REVERT: Y 581 MET cc_start: 0.6498 (ptt) cc_final: 0.5818 (pmm) REVERT: Y 583 TYR cc_start: 0.6084 (t80) cc_final: 0.5613 (t80) REVERT: Y 785 MET cc_start: 0.7634 (mmp) cc_final: 0.7410 (mmp) REVERT: Y 815 MET cc_start: 0.8398 (mmm) cc_final: 0.8116 (mpp) REVERT: Y 946 THR cc_start: 0.6991 (OUTLIER) cc_final: 0.6783 (p) REVERT: Y 957 LYS cc_start: 0.8933 (tppt) cc_final: 0.8658 (mmtm) REVERT: Y 967 ASP cc_start: 0.8621 (m-30) cc_final: 0.8400 (t0) outliers start: 224 outliers final: 165 residues processed: 1237 average time/residue: 0.5134 time to fit residues: 1066.0421 Evaluate side-chains 1204 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1026 time to evaluate : 4.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 84 LYS Chi-restraints excluded: chain J residue 87 TRP Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 66 GLN Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain L residue 87 TRP Chi-restraints excluded: chain M residue 29 ASP Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 148 THR Chi-restraints excluded: chain O residue 29 ASP Chi-restraints excluded: chain O residue 87 TRP Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 148 THR Chi-restraints excluded: chain P residue 618 VAL Chi-restraints excluded: chain P residue 671 THR Chi-restraints excluded: chain P residue 810 ASP Chi-restraints excluded: chain P residue 855 VAL Chi-restraints excluded: chain P residue 875 LEU Chi-restraints excluded: chain P residue 913 LEU Chi-restraints excluded: chain P residue 915 THR Chi-restraints excluded: chain P residue 933 HIS Chi-restraints excluded: chain P residue 946 THR Chi-restraints excluded: chain P residue 950 THR Chi-restraints excluded: chain P residue 996 THR Chi-restraints excluded: chain P residue 1035 THR Chi-restraints excluded: chain P residue 1074 ASP Chi-restraints excluded: chain Q residue 608 VAL Chi-restraints excluded: chain Q residue 618 VAL Chi-restraints excluded: chain Q residue 671 THR Chi-restraints excluded: chain Q residue 724 VAL Chi-restraints excluded: chain Q residue 787 ASN Chi-restraints excluded: chain Q residue 817 LEU Chi-restraints excluded: chain Q residue 855 VAL Chi-restraints excluded: chain Q residue 869 THR Chi-restraints excluded: chain Q residue 875 LEU Chi-restraints excluded: chain Q residue 879 TRP Chi-restraints excluded: chain Q residue 913 LEU Chi-restraints excluded: chain Q residue 943 THR Chi-restraints excluded: chain Q residue 946 THR Chi-restraints excluded: chain Q residue 972 THR Chi-restraints excluded: chain Q residue 996 THR Chi-restraints excluded: chain Q residue 1014 THR Chi-restraints excluded: chain Q residue 1051 LEU Chi-restraints excluded: chain Q residue 1074 ASP Chi-restraints excluded: chain Q residue 1092 VAL Chi-restraints excluded: chain R residue 606 THR Chi-restraints excluded: chain R residue 608 VAL Chi-restraints excluded: chain R residue 671 THR Chi-restraints excluded: chain R residue 705 THR Chi-restraints excluded: chain R residue 724 VAL Chi-restraints excluded: chain R residue 773 LEU Chi-restraints excluded: chain R residue 798 VAL Chi-restraints excluded: chain R residue 817 LEU Chi-restraints excluded: chain R residue 855 VAL Chi-restraints excluded: chain R residue 875 LEU Chi-restraints excluded: chain R residue 913 LEU Chi-restraints excluded: chain R residue 940 VAL Chi-restraints excluded: chain R residue 943 THR Chi-restraints excluded: chain R residue 946 THR Chi-restraints excluded: chain R residue 996 THR Chi-restraints excluded: chain R residue 1074 ASP Chi-restraints excluded: chain R residue 1092 VAL Chi-restraints excluded: chain S residue 855 VAL Chi-restraints excluded: chain S residue 875 LEU Chi-restraints excluded: chain S residue 913 LEU Chi-restraints excluded: chain S residue 943 THR Chi-restraints excluded: chain S residue 946 THR Chi-restraints excluded: chain S residue 972 THR Chi-restraints excluded: chain S residue 1006 GLN Chi-restraints excluded: chain S residue 1035 THR Chi-restraints excluded: chain S residue 1074 ASP Chi-restraints excluded: chain S residue 1092 VAL Chi-restraints excluded: chain T residue 606 THR Chi-restraints excluded: chain T residue 618 VAL Chi-restraints excluded: chain T residue 638 VAL Chi-restraints excluded: chain T residue 875 LEU Chi-restraints excluded: chain T residue 913 LEU Chi-restraints excluded: chain T residue 933 HIS Chi-restraints excluded: chain T residue 943 THR Chi-restraints excluded: chain T residue 946 THR Chi-restraints excluded: chain T residue 967 ASP Chi-restraints excluded: chain T residue 996 THR Chi-restraints excluded: chain T residue 1004 VAL Chi-restraints excluded: chain T residue 1006 GLN Chi-restraints excluded: chain T residue 1074 ASP Chi-restraints excluded: chain T residue 1092 VAL Chi-restraints excluded: chain U residue 601 ASP Chi-restraints excluded: chain U residue 773 LEU Chi-restraints excluded: chain U residue 776 MET Chi-restraints excluded: chain U residue 780 ASN Chi-restraints excluded: chain U residue 829 ASP Chi-restraints excluded: chain U residue 857 VAL Chi-restraints excluded: chain U residue 905 SER Chi-restraints excluded: chain U residue 996 THR Chi-restraints excluded: chain U residue 1077 MET Chi-restraints excluded: chain V residue 618 VAL Chi-restraints excluded: chain V residue 631 VAL Chi-restraints excluded: chain V residue 713 SER Chi-restraints excluded: chain V residue 776 MET Chi-restraints excluded: chain V residue 780 ASN Chi-restraints excluded: chain V residue 822 VAL Chi-restraints excluded: chain V residue 829 ASP Chi-restraints excluded: chain V residue 855 VAL Chi-restraints excluded: chain V residue 867 VAL Chi-restraints excluded: chain V residue 1029 VAL Chi-restraints excluded: chain W residue 615 ASP Chi-restraints excluded: chain W residue 618 VAL Chi-restraints excluded: chain W residue 623 THR Chi-restraints excluded: chain W residue 631 VAL Chi-restraints excluded: chain W residue 713 SER Chi-restraints excluded: chain W residue 796 THR Chi-restraints excluded: chain W residue 822 VAL Chi-restraints excluded: chain W residue 855 VAL Chi-restraints excluded: chain W residue 869 THR Chi-restraints excluded: chain W residue 1037 GLN Chi-restraints excluded: chain X residue 601 ASP Chi-restraints excluded: chain X residue 631 VAL Chi-restraints excluded: chain X residue 710 VAL Chi-restraints excluded: chain X residue 716 VAL Chi-restraints excluded: chain X residue 822 VAL Chi-restraints excluded: chain X residue 855 VAL Chi-restraints excluded: chain X residue 857 VAL Chi-restraints excluded: chain X residue 867 VAL Chi-restraints excluded: chain X residue 957 LYS Chi-restraints excluded: chain Y residue 623 THR Chi-restraints excluded: chain Y residue 661 VAL Chi-restraints excluded: chain Y residue 786 LEU Chi-restraints excluded: chain Y residue 814 MET Chi-restraints excluded: chain Y residue 822 VAL Chi-restraints excluded: chain Y residue 829 ASP Chi-restraints excluded: chain Y residue 855 VAL Chi-restraints excluded: chain Y residue 857 VAL Chi-restraints excluded: chain Y residue 866 GLN Chi-restraints excluded: chain Y residue 946 THR Chi-restraints excluded: chain Y residue 971 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 670 random chunks: chunk 399 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 385 optimal weight: 4.9990 chunk 194 optimal weight: 0.2980 chunk 126 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 410 optimal weight: 0.9980 chunk 439 optimal weight: 3.9990 chunk 319 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 507 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN ** H 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 816 GLN ** R 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1005 ASN S 576 GLN S 584 GLN ** S 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 803 GLN S 914 ASN T 680 ASN ** T 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 816 GLN ** V 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 846 GLN X 690 HIS ** X 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 998 ASN ** X1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 978 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 53325 Z= 0.216 Angle : 0.678 13.672 72665 Z= 0.335 Chirality : 0.044 0.195 8425 Planarity : 0.004 0.050 9415 Dihedral : 5.162 41.675 7275 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.31 % Favored : 93.60 % Rotamer: Outliers : 4.37 % Allowed : 24.90 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.10), residues: 6685 helix: -1.89 (0.10), residues: 2295 sheet: -0.23 (0.14), residues: 1335 loop : -1.55 (0.11), residues: 3055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Y 848 HIS 0.004 0.000 HIS X 690 PHE 0.025 0.001 PHE L 60 TYR 0.031 0.001 TYR D 65 ARG 0.006 0.000 ARG R 919 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1272 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1032 time to evaluate : 5.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7375 (ptt90) cc_final: 0.6963 (ptt90) REVERT: A 74 GLU cc_start: 0.8748 (mp0) cc_final: 0.8397 (mp0) REVERT: A 106 PHE cc_start: 0.8369 (m-80) cc_final: 0.7886 (m-80) REVERT: A 131 GLU cc_start: 0.8624 (mp0) cc_final: 0.8410 (mp0) REVERT: B 33 ARG cc_start: 0.8584 (mtp85) cc_final: 0.8360 (ttm110) REVERT: B 52 TYR cc_start: 0.7015 (m-80) cc_final: 0.6692 (m-80) REVERT: B 74 GLU cc_start: 0.8767 (mp0) cc_final: 0.8562 (mp0) REVERT: B 106 PHE cc_start: 0.8200 (m-80) cc_final: 0.7952 (m-80) REVERT: C 74 GLU cc_start: 0.8937 (mp0) cc_final: 0.8705 (mp0) REVERT: D 31 ARG cc_start: 0.8269 (ttp80) cc_final: 0.7285 (ptt90) REVERT: D 33 ARG cc_start: 0.8559 (mtp85) cc_final: 0.8119 (mtm110) REVERT: D 131 GLU cc_start: 0.8463 (mp0) cc_final: 0.8249 (pm20) REVERT: E 29 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7037 (p0) REVERT: E 74 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7994 (mp0) REVERT: E 106 PHE cc_start: 0.8137 (m-10) cc_final: 0.7920 (m-10) REVERT: E 131 GLU cc_start: 0.8541 (mp0) cc_final: 0.8042 (pm20) REVERT: E 140 ILE cc_start: 0.8848 (mm) cc_final: 0.8501 (tt) REVERT: F 33 ARG cc_start: 0.7301 (mmm-85) cc_final: 0.6998 (mmm-85) REVERT: F 65 TYR cc_start: 0.8822 (t80) cc_final: 0.8113 (t80) REVERT: F 106 PHE cc_start: 0.8421 (m-80) cc_final: 0.7902 (m-80) REVERT: G 21 ARG cc_start: 0.6966 (mmt90) cc_final: 0.5771 (mpp-170) REVERT: G 65 TYR cc_start: 0.8955 (t80) cc_final: 0.8740 (t80) REVERT: G 76 LEU cc_start: 0.7954 (tp) cc_final: 0.7509 (tt) REVERT: G 106 PHE cc_start: 0.8459 (m-80) cc_final: 0.8183 (m-80) REVERT: H 61 ASP cc_start: 0.8574 (m-30) cc_final: 0.8296 (t0) REVERT: H 65 TYR cc_start: 0.8909 (t80) cc_final: 0.8341 (t80) REVERT: H 106 PHE cc_start: 0.8709 (m-80) cc_final: 0.7989 (m-80) REVERT: I 30 ILE cc_start: 0.9395 (mt) cc_final: 0.9173 (mm) REVERT: J 87 TRP cc_start: 0.9285 (OUTLIER) cc_final: 0.8973 (m-90) REVERT: K 28 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7663 (mm) REVERT: K 50 ARG cc_start: 0.8670 (ttm-80) cc_final: 0.7747 (ttm110) REVERT: K 56 ASP cc_start: 0.6621 (p0) cc_final: 0.6418 (p0) REVERT: K 79 ASP cc_start: 0.6471 (t0) cc_final: 0.5062 (m-30) REVERT: K 83 GLN cc_start: 0.7977 (tp-100) cc_final: 0.7337 (mm-40) REVERT: K 113 PHE cc_start: 0.8655 (m-80) cc_final: 0.8292 (m-80) REVERT: K 120 LYS cc_start: 0.9062 (mmmm) cc_final: 0.8820 (mmtm) REVERT: L 45 LEU cc_start: 0.7987 (mt) cc_final: 0.7731 (mm) REVERT: L 66 GLN cc_start: 0.8900 (tp40) cc_final: 0.8603 (mm110) REVERT: L 85 ASP cc_start: 0.8317 (m-30) cc_final: 0.8056 (m-30) REVERT: L 113 PHE cc_start: 0.8584 (m-80) cc_final: 0.8160 (m-10) REVERT: M 50 ARG cc_start: 0.8770 (ttm-80) cc_final: 0.8175 (ttm110) REVERT: M 113 PHE cc_start: 0.8443 (m-80) cc_final: 0.8081 (m-80) REVERT: N 112 MET cc_start: 0.7465 (mtm) cc_final: 0.7046 (mtm) REVERT: N 113 PHE cc_start: 0.8319 (m-80) cc_final: 0.7852 (m-80) REVERT: N 131 GLU cc_start: 0.8793 (tp30) cc_final: 0.8039 (tp30) REVERT: O 129 ARG cc_start: 0.4840 (mmm-85) cc_final: 0.4634 (mmm160) REVERT: P 616 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7451 (tm-30) REVERT: P 990 MET cc_start: 0.8052 (ttm) cc_final: 0.7485 (ttm) REVERT: P 1077 MET cc_start: 0.8705 (mmt) cc_final: 0.8401 (mmp) REVERT: P 1081 THR cc_start: 0.9660 (m) cc_final: 0.9183 (p) REVERT: Q 709 ASP cc_start: 0.8274 (t70) cc_final: 0.7987 (t70) REVERT: Q 773 LEU cc_start: 0.9369 (mm) cc_final: 0.9167 (mt) REVERT: Q 911 LYS cc_start: 0.9149 (mmmm) cc_final: 0.8914 (ttmm) REVERT: Q 1081 THR cc_start: 0.9528 (m) cc_final: 0.9109 (p) REVERT: R 583 TYR cc_start: 0.8919 (t80) cc_final: 0.8602 (t80) REVERT: R 616 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7539 (tm-30) REVERT: R 667 ARG cc_start: 0.8803 (mtm110) cc_final: 0.8596 (mtp85) REVERT: R 677 ASP cc_start: 0.8369 (t70) cc_final: 0.8086 (t0) REVERT: R 990 MET cc_start: 0.8268 (mtm) cc_final: 0.7896 (ttm) REVERT: R 1081 THR cc_start: 0.9559 (m) cc_final: 0.9105 (p) REVERT: S 585 LYS cc_start: 0.9095 (mmmt) cc_final: 0.8836 (pttm) REVERT: S 616 GLU cc_start: 0.8233 (tt0) cc_final: 0.7533 (tm-30) REVERT: S 785 MET cc_start: 0.8099 (mmp) cc_final: 0.7835 (mmp) REVERT: S 801 ARG cc_start: 0.8505 (tpp80) cc_final: 0.8139 (tpp80) REVERT: S 803 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8750 (mm-40) REVERT: S 866 GLN cc_start: 0.9257 (tp40) cc_final: 0.8383 (tp40) REVERT: S 913 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9242 (pp) REVERT: S 1006 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8250 (pt0) REVERT: S 1081 THR cc_start: 0.9682 (m) cc_final: 0.9249 (p) REVERT: T 583 TYR cc_start: 0.8947 (t80) cc_final: 0.8704 (t80) REVERT: T 586 MET cc_start: 0.9028 (mmm) cc_final: 0.8685 (mmt) REVERT: T 616 GLU cc_start: 0.8186 (tt0) cc_final: 0.7692 (tt0) REVERT: T 773 LEU cc_start: 0.9266 (mp) cc_final: 0.9056 (mp) REVERT: T 895 TYR cc_start: 0.9246 (t80) cc_final: 0.8818 (t80) REVERT: T 913 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9184 (pp) REVERT: T 957 LYS cc_start: 0.9123 (tttp) cc_final: 0.8841 (tttt) REVERT: T 1052 GLU cc_start: 0.8205 (tt0) cc_final: 0.7995 (tt0) REVERT: U 597 MET cc_start: 0.7666 (tpt) cc_final: 0.7001 (tpt) REVERT: U 814 MET cc_start: 0.8822 (tpp) cc_final: 0.8323 (tpp) REVERT: U 990 MET cc_start: 0.8794 (mtp) cc_final: 0.8548 (mtp) REVERT: U 998 ASN cc_start: 0.8642 (t0) cc_final: 0.8348 (t0) REVERT: V 680 ASN cc_start: 0.8689 (t0) cc_final: 0.8477 (m-40) REVERT: V 805 ILE cc_start: 0.8751 (mm) cc_final: 0.8516 (mm) REVERT: V 1011 LYS cc_start: 0.9352 (tttp) cc_final: 0.9118 (tttp) REVERT: W 680 ASN cc_start: 0.8644 (t0) cc_final: 0.8378 (m-40) REVERT: W 816 GLN cc_start: 0.8975 (pt0) cc_final: 0.8387 (pm20) REVERT: W 913 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9319 (pp) REVERT: W 990 MET cc_start: 0.8989 (mtp) cc_final: 0.8702 (mtp) REVERT: W 1011 LYS cc_start: 0.9236 (tttp) cc_final: 0.8853 (tttt) REVERT: W 1037 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8094 (pm20) REVERT: X 597 MET cc_start: 0.7331 (tpt) cc_final: 0.6492 (tpt) REVERT: X 601 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8361 (p0) REVERT: X 611 LEU cc_start: 0.8968 (tp) cc_final: 0.8589 (tp) REVERT: X 805 ILE cc_start: 0.8974 (mm) cc_final: 0.8521 (mm) REVERT: Y 581 MET cc_start: 0.6511 (ptt) cc_final: 0.5818 (pmm) REVERT: Y 785 MET cc_start: 0.7501 (mmp) cc_final: 0.7281 (mmp) REVERT: Y 815 MET cc_start: 0.8430 (mmm) cc_final: 0.8198 (mtm) REVERT: Y 946 THR cc_start: 0.6988 (OUTLIER) cc_final: 0.6786 (p) REVERT: Y 957 LYS cc_start: 0.8975 (tppt) cc_final: 0.8695 (mmtm) REVERT: Y 967 ASP cc_start: 0.8631 (m-30) cc_final: 0.8423 (t0) REVERT: Y 990 MET cc_start: 0.8661 (mtp) cc_final: 0.8351 (mtp) outliers start: 240 outliers final: 197 residues processed: 1213 average time/residue: 0.4798 time to fit residues: 981.6100 Evaluate side-chains 1208 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1000 time to evaluate : 4.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 84 LYS Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 87 TRP Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 66 GLN Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 148 THR Chi-restraints excluded: chain O residue 57 ASN Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 148 THR Chi-restraints excluded: chain P residue 618 VAL Chi-restraints excluded: chain P residue 671 THR Chi-restraints excluded: chain P residue 705 THR Chi-restraints excluded: chain P residue 810 ASP Chi-restraints excluded: chain P residue 855 VAL Chi-restraints excluded: chain P residue 875 LEU Chi-restraints excluded: chain P residue 913 LEU Chi-restraints excluded: chain P residue 915 THR Chi-restraints excluded: chain P residue 933 HIS Chi-restraints excluded: chain P residue 943 THR Chi-restraints excluded: chain P residue 946 THR Chi-restraints excluded: chain P residue 950 THR Chi-restraints excluded: chain P residue 996 THR Chi-restraints excluded: chain P residue 1035 THR Chi-restraints excluded: chain P residue 1074 ASP Chi-restraints excluded: chain P residue 1092 VAL Chi-restraints excluded: chain Q residue 608 VAL Chi-restraints excluded: chain Q residue 618 VAL Chi-restraints excluded: chain Q residue 671 THR Chi-restraints excluded: chain Q residue 724 VAL Chi-restraints excluded: chain Q residue 787 ASN Chi-restraints excluded: chain Q residue 817 LEU Chi-restraints excluded: chain Q residue 855 VAL Chi-restraints excluded: chain Q residue 869 THR Chi-restraints excluded: chain Q residue 875 LEU Chi-restraints excluded: chain Q residue 879 TRP Chi-restraints excluded: chain Q residue 913 LEU Chi-restraints excluded: chain Q residue 943 THR Chi-restraints excluded: chain Q residue 946 THR Chi-restraints excluded: chain Q residue 972 THR Chi-restraints excluded: chain Q residue 996 THR Chi-restraints excluded: chain Q residue 1014 THR Chi-restraints excluded: chain Q residue 1051 LEU Chi-restraints excluded: chain Q residue 1074 ASP Chi-restraints excluded: chain Q residue 1092 VAL Chi-restraints excluded: chain R residue 606 THR Chi-restraints excluded: chain R residue 608 VAL Chi-restraints excluded: chain R residue 623 THR Chi-restraints excluded: chain R residue 671 THR Chi-restraints excluded: chain R residue 705 THR Chi-restraints excluded: chain R residue 724 VAL Chi-restraints excluded: chain R residue 773 LEU Chi-restraints excluded: chain R residue 798 VAL Chi-restraints excluded: chain R residue 817 LEU Chi-restraints excluded: chain R residue 855 VAL Chi-restraints excluded: chain R residue 875 LEU Chi-restraints excluded: chain R residue 913 LEU Chi-restraints excluded: chain R residue 940 VAL Chi-restraints excluded: chain R residue 943 THR Chi-restraints excluded: chain R residue 946 THR Chi-restraints excluded: chain R residue 950 THR Chi-restraints excluded: chain R residue 996 THR Chi-restraints excluded: chain R residue 1074 ASP Chi-restraints excluded: chain R residue 1092 VAL Chi-restraints excluded: chain R residue 1094 LEU Chi-restraints excluded: chain S residue 671 THR Chi-restraints excluded: chain S residue 803 GLN Chi-restraints excluded: chain S residue 810 ASP Chi-restraints excluded: chain S residue 855 VAL Chi-restraints excluded: chain S residue 875 LEU Chi-restraints excluded: chain S residue 913 LEU Chi-restraints excluded: chain S residue 914 ASN Chi-restraints excluded: chain S residue 943 THR Chi-restraints excluded: chain S residue 946 THR Chi-restraints excluded: chain S residue 972 THR Chi-restraints excluded: chain S residue 1006 GLN Chi-restraints excluded: chain S residue 1035 THR Chi-restraints excluded: chain S residue 1074 ASP Chi-restraints excluded: chain T residue 606 THR Chi-restraints excluded: chain T residue 608 VAL Chi-restraints excluded: chain T residue 618 VAL Chi-restraints excluded: chain T residue 671 THR Chi-restraints excluded: chain T residue 810 ASP Chi-restraints excluded: chain T residue 817 LEU Chi-restraints excluded: chain T residue 875 LEU Chi-restraints excluded: chain T residue 913 LEU Chi-restraints excluded: chain T residue 933 HIS Chi-restraints excluded: chain T residue 943 THR Chi-restraints excluded: chain T residue 946 THR Chi-restraints excluded: chain T residue 950 THR Chi-restraints excluded: chain T residue 967 ASP Chi-restraints excluded: chain T residue 996 THR Chi-restraints excluded: chain T residue 997 ASP Chi-restraints excluded: chain T residue 1004 VAL Chi-restraints excluded: chain T residue 1006 GLN Chi-restraints excluded: chain T residue 1074 ASP Chi-restraints excluded: chain T residue 1092 VAL Chi-restraints excluded: chain T residue 1094 LEU Chi-restraints excluded: chain U residue 601 ASP Chi-restraints excluded: chain U residue 776 MET Chi-restraints excluded: chain U residue 780 ASN Chi-restraints excluded: chain U residue 822 VAL Chi-restraints excluded: chain U residue 857 VAL Chi-restraints excluded: chain U residue 905 SER Chi-restraints excluded: chain U residue 915 THR Chi-restraints excluded: chain U residue 996 THR Chi-restraints excluded: chain U residue 1077 MET Chi-restraints excluded: chain U residue 1104 THR Chi-restraints excluded: chain V residue 618 VAL Chi-restraints excluded: chain V residue 710 VAL Chi-restraints excluded: chain V residue 713 SER Chi-restraints excluded: chain V residue 776 MET Chi-restraints excluded: chain V residue 780 ASN Chi-restraints excluded: chain V residue 796 THR Chi-restraints excluded: chain V residue 822 VAL Chi-restraints excluded: chain V residue 829 ASP Chi-restraints excluded: chain V residue 855 VAL Chi-restraints excluded: chain V residue 857 VAL Chi-restraints excluded: chain V residue 867 VAL Chi-restraints excluded: chain V residue 1029 VAL Chi-restraints excluded: chain V residue 1104 THR Chi-restraints excluded: chain W residue 602 MET Chi-restraints excluded: chain W residue 615 ASP Chi-restraints excluded: chain W residue 618 VAL Chi-restraints excluded: chain W residue 623 THR Chi-restraints excluded: chain W residue 631 VAL Chi-restraints excluded: chain W residue 713 SER Chi-restraints excluded: chain W residue 796 THR Chi-restraints excluded: chain W residue 822 VAL Chi-restraints excluded: chain W residue 855 VAL Chi-restraints excluded: chain W residue 869 THR Chi-restraints excluded: chain W residue 913 LEU Chi-restraints excluded: chain W residue 967 ASP Chi-restraints excluded: chain W residue 1037 GLN Chi-restraints excluded: chain X residue 601 ASP Chi-restraints excluded: chain X residue 631 VAL Chi-restraints excluded: chain X residue 710 VAL Chi-restraints excluded: chain X residue 716 VAL Chi-restraints excluded: chain X residue 822 VAL Chi-restraints excluded: chain X residue 846 GLN Chi-restraints excluded: chain X residue 855 VAL Chi-restraints excluded: chain X residue 857 VAL Chi-restraints excluded: chain X residue 867 VAL Chi-restraints excluded: chain X residue 957 LYS Chi-restraints excluded: chain X residue 1053 MET Chi-restraints excluded: chain X residue 1074 ASP Chi-restraints excluded: chain Y residue 623 THR Chi-restraints excluded: chain Y residue 814 MET Chi-restraints excluded: chain Y residue 822 VAL Chi-restraints excluded: chain Y residue 829 ASP Chi-restraints excluded: chain Y residue 855 VAL Chi-restraints excluded: chain Y residue 857 VAL Chi-restraints excluded: chain Y residue 866 GLN Chi-restraints excluded: chain Y residue 946 THR Chi-restraints excluded: chain Y residue 971 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 670 random chunks: chunk 587 optimal weight: 5.9990 chunk 618 optimal weight: 4.9990 chunk 564 optimal weight: 1.9990 chunk 601 optimal weight: 0.9990 chunk 362 optimal weight: 2.9990 chunk 262 optimal weight: 0.9980 chunk 472 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 chunk 543 optimal weight: 0.7980 chunk 569 optimal weight: 0.9990 chunk 599 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN I 89 GLN ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN L 83 GLN ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 914 ASN T 680 ASN ** T 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 998 ASN X1005 ASN Y 978 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 53325 Z= 0.195 Angle : 0.686 14.841 72665 Z= 0.337 Chirality : 0.044 0.193 8425 Planarity : 0.004 0.045 9415 Dihedral : 5.111 41.199 7275 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.12 % Favored : 93.79 % Rotamer: Outliers : 4.11 % Allowed : 25.40 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.10), residues: 6685 helix: -1.79 (0.10), residues: 2295 sheet: -0.11 (0.15), residues: 1300 loop : -1.48 (0.11), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 87 HIS 0.004 0.000 HIS Y 690 PHE 0.028 0.001 PHE K 60 TYR 0.027 0.001 TYR E 65 ARG 0.005 0.000 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1267 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1041 time to evaluate : 4.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7433 (ptt90) cc_final: 0.6978 (ptt90) REVERT: A 74 GLU cc_start: 0.8807 (mp0) cc_final: 0.8459 (mp0) REVERT: A 106 PHE cc_start: 0.8333 (m-80) cc_final: 0.7859 (m-80) REVERT: A 131 GLU cc_start: 0.8577 (mp0) cc_final: 0.8337 (mp0) REVERT: B 33 ARG cc_start: 0.8577 (mtp85) cc_final: 0.8353 (ttm110) REVERT: B 52 TYR cc_start: 0.6926 (m-80) cc_final: 0.6624 (m-80) REVERT: B 106 PHE cc_start: 0.8187 (m-80) cc_final: 0.7950 (m-80) REVERT: C 33 ARG cc_start: 0.8272 (ttm110) cc_final: 0.7909 (mtm110) REVERT: C 74 GLU cc_start: 0.8931 (mp0) cc_final: 0.8697 (mp0) REVERT: C 141 GLU cc_start: 0.7551 (tp30) cc_final: 0.7162 (tp30) REVERT: D 31 ARG cc_start: 0.8270 (ttp80) cc_final: 0.7592 (ptt90) REVERT: D 33 ARG cc_start: 0.8540 (mtp85) cc_final: 0.8140 (mtm110) REVERT: D 131 GLU cc_start: 0.8451 (mp0) cc_final: 0.8249 (pm20) REVERT: E 29 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7624 (p0) REVERT: E 33 ARG cc_start: 0.8567 (mtm-85) cc_final: 0.8212 (mtm-85) REVERT: E 74 GLU cc_start: 0.8577 (mm-30) cc_final: 0.7979 (mp0) REVERT: E 106 PHE cc_start: 0.8116 (m-10) cc_final: 0.7897 (m-10) REVERT: E 131 GLU cc_start: 0.8527 (mp0) cc_final: 0.8047 (pm20) REVERT: E 140 ILE cc_start: 0.8742 (mm) cc_final: 0.8465 (tt) REVERT: F 33 ARG cc_start: 0.7273 (mmm-85) cc_final: 0.6975 (mmm-85) REVERT: F 65 TYR cc_start: 0.8739 (t80) cc_final: 0.8093 (t80) REVERT: F 106 PHE cc_start: 0.8496 (m-80) cc_final: 0.7932 (m-80) REVERT: G 52 TYR cc_start: 0.8978 (m-80) cc_final: 0.8534 (m-10) REVERT: G 106 PHE cc_start: 0.8387 (m-80) cc_final: 0.7945 (m-80) REVERT: H 61 ASP cc_start: 0.8562 (m-30) cc_final: 0.8256 (t0) REVERT: H 65 TYR cc_start: 0.8879 (t80) cc_final: 0.8285 (t80) REVERT: I 30 ILE cc_start: 0.9429 (mt) cc_final: 0.9200 (mm) REVERT: J 53 GLN cc_start: 0.8327 (mt0) cc_final: 0.8091 (mt0) REVERT: K 28 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7690 (mm) REVERT: K 50 ARG cc_start: 0.8675 (ttm-80) cc_final: 0.7751 (ttm110) REVERT: K 79 ASP cc_start: 0.6338 (t70) cc_final: 0.5035 (m-30) REVERT: K 83 GLN cc_start: 0.7987 (tp-100) cc_final: 0.7336 (mm-40) REVERT: K 113 PHE cc_start: 0.8669 (m-80) cc_final: 0.8256 (m-80) REVERT: L 45 LEU cc_start: 0.7895 (mt) cc_final: 0.7662 (mm) REVERT: L 66 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8593 (mm-40) REVERT: L 113 PHE cc_start: 0.8627 (m-80) cc_final: 0.8209 (m-10) REVERT: M 50 ARG cc_start: 0.8788 (ttm-80) cc_final: 0.8185 (ttm110) REVERT: M 113 PHE cc_start: 0.8438 (m-80) cc_final: 0.8078 (m-80) REVERT: N 112 MET cc_start: 0.7647 (mtm) cc_final: 0.7082 (mtm) REVERT: N 113 PHE cc_start: 0.8381 (m-80) cc_final: 0.7912 (m-80) REVERT: N 131 GLU cc_start: 0.8796 (tp30) cc_final: 0.8047 (tp30) REVERT: O 50 ARG cc_start: 0.8670 (mtp85) cc_final: 0.8432 (mtt90) REVERT: P 576 GLN cc_start: 0.7366 (mp10) cc_final: 0.7039 (mp10) REVERT: P 815 MET cc_start: 0.8746 (tpp) cc_final: 0.8348 (mmm) REVERT: P 990 MET cc_start: 0.8007 (ttm) cc_final: 0.7403 (ttm) REVERT: P 1077 MET cc_start: 0.8771 (mmt) cc_final: 0.8481 (mmp) REVERT: P 1081 THR cc_start: 0.9655 (m) cc_final: 0.9183 (p) REVERT: Q 585 LYS cc_start: 0.9277 (mmmt) cc_final: 0.8997 (pttm) REVERT: Q 693 LYS cc_start: 0.9201 (tptp) cc_final: 0.8970 (tttm) REVERT: Q 709 ASP cc_start: 0.8277 (t70) cc_final: 0.8009 (t70) REVERT: Q 869 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.9036 (m) REVERT: Q 911 LYS cc_start: 0.9128 (mmmm) cc_final: 0.8891 (ttmm) REVERT: Q 1081 THR cc_start: 0.9518 (m) cc_final: 0.9087 (p) REVERT: R 583 TYR cc_start: 0.8868 (t80) cc_final: 0.8508 (t80) REVERT: R 616 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7507 (tm-30) REVERT: R 677 ASP cc_start: 0.8239 (t70) cc_final: 0.8010 (t0) REVERT: R 699 ASP cc_start: 0.8449 (m-30) cc_final: 0.8236 (m-30) REVERT: R 990 MET cc_start: 0.8291 (mtm) cc_final: 0.7902 (ttm) REVERT: R 1081 THR cc_start: 0.9550 (m) cc_final: 0.9098 (p) REVERT: S 616 GLU cc_start: 0.8219 (tt0) cc_final: 0.7523 (tm-30) REVERT: S 866 GLN cc_start: 0.9184 (tp40) cc_final: 0.8326 (tp40) REVERT: S 913 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9196 (pp) REVERT: S 1006 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8231 (pt0) REVERT: S 1081 THR cc_start: 0.9672 (m) cc_final: 0.9238 (p) REVERT: T 586 MET cc_start: 0.9020 (mmm) cc_final: 0.8635 (mmt) REVERT: T 616 GLU cc_start: 0.8108 (tt0) cc_final: 0.7752 (tt0) REVERT: T 895 TYR cc_start: 0.9253 (t80) cc_final: 0.8756 (t80) REVERT: T 913 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9149 (pp) REVERT: T 957 LYS cc_start: 0.9100 (tttp) cc_final: 0.8818 (tttt) REVERT: T 1052 GLU cc_start: 0.8176 (tt0) cc_final: 0.7962 (tt0) REVERT: U 597 MET cc_start: 0.7638 (tpt) cc_final: 0.6978 (tpt) REVERT: U 706 LEU cc_start: 0.8747 (mp) cc_final: 0.8540 (tt) REVERT: U 816 GLN cc_start: 0.8946 (pt0) cc_final: 0.8507 (pm20) REVERT: U 978 HIS cc_start: 0.8581 (m-70) cc_final: 0.7787 (m90) REVERT: U 990 MET cc_start: 0.8818 (mtp) cc_final: 0.8577 (mtp) REVERT: U 998 ASN cc_start: 0.8634 (t0) cc_final: 0.8326 (t0) REVERT: V 680 ASN cc_start: 0.8680 (t0) cc_final: 0.8480 (m-40) REVERT: V 805 ILE cc_start: 0.8779 (mm) cc_final: 0.8503 (mm) REVERT: V 978 HIS cc_start: 0.8549 (m-70) cc_final: 0.7869 (m170) REVERT: V 1011 LYS cc_start: 0.9361 (tttp) cc_final: 0.9129 (tttp) REVERT: W 680 ASN cc_start: 0.8646 (t0) cc_final: 0.8410 (m-40) REVERT: W 816 GLN cc_start: 0.8946 (pt0) cc_final: 0.8349 (pm20) REVERT: W 913 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9295 (pp) REVERT: W 978 HIS cc_start: 0.8691 (m-70) cc_final: 0.7904 (m90) REVERT: W 990 MET cc_start: 0.8993 (mtp) cc_final: 0.8707 (mtp) REVERT: W 1011 LYS cc_start: 0.9247 (tttp) cc_final: 0.8857 (tttt) REVERT: W 1037 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8091 (pm20) REVERT: X 597 MET cc_start: 0.7288 (tpt) cc_final: 0.6449 (tpt) REVERT: X 601 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8349 (p0) REVERT: X 611 LEU cc_start: 0.8718 (tp) cc_final: 0.8434 (tp) REVERT: X 720 ASN cc_start: 0.8571 (m-40) cc_final: 0.8203 (p0) REVERT: X 805 ILE cc_start: 0.8959 (mm) cc_final: 0.8514 (mm) REVERT: Y 581 MET cc_start: 0.6507 (ptt) cc_final: 0.5791 (pmm) REVERT: Y 583 TYR cc_start: 0.5923 (t80) cc_final: 0.5579 (t80) REVERT: Y 785 MET cc_start: 0.7722 (mmp) cc_final: 0.7471 (mmp) REVERT: Y 957 LYS cc_start: 0.8962 (tppt) cc_final: 0.8687 (mmtm) REVERT: Y 967 ASP cc_start: 0.8617 (m-30) cc_final: 0.8410 (t0) REVERT: Y 990 MET cc_start: 0.8751 (mtp) cc_final: 0.8355 (mtp) outliers start: 226 outliers final: 198 residues processed: 1206 average time/residue: 0.4891 time to fit residues: 999.5989 Evaluate side-chains 1214 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1006 time to evaluate : 4.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 84 LYS Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 66 GLN Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain L residue 87 TRP Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 148 THR Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 57 ASN Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 148 THR Chi-restraints excluded: chain P residue 618 VAL Chi-restraints excluded: chain P residue 671 THR Chi-restraints excluded: chain P residue 705 THR Chi-restraints excluded: chain P residue 810 ASP Chi-restraints excluded: chain P residue 855 VAL Chi-restraints excluded: chain P residue 875 LEU Chi-restraints excluded: chain P residue 913 LEU Chi-restraints excluded: chain P residue 915 THR Chi-restraints excluded: chain P residue 933 HIS Chi-restraints excluded: chain P residue 943 THR Chi-restraints excluded: chain P residue 946 THR Chi-restraints excluded: chain P residue 950 THR Chi-restraints excluded: chain P residue 996 THR Chi-restraints excluded: chain P residue 1074 ASP Chi-restraints excluded: chain P residue 1092 VAL Chi-restraints excluded: chain Q residue 608 VAL Chi-restraints excluded: chain Q residue 618 VAL Chi-restraints excluded: chain Q residue 671 THR Chi-restraints excluded: chain Q residue 724 VAL Chi-restraints excluded: chain Q residue 787 ASN Chi-restraints excluded: chain Q residue 817 LEU Chi-restraints excluded: chain Q residue 855 VAL Chi-restraints excluded: chain Q residue 869 THR Chi-restraints excluded: chain Q residue 875 LEU Chi-restraints excluded: chain Q residue 879 TRP Chi-restraints excluded: chain Q residue 913 LEU Chi-restraints excluded: chain Q residue 943 THR Chi-restraints excluded: chain Q residue 946 THR Chi-restraints excluded: chain Q residue 972 THR Chi-restraints excluded: chain Q residue 996 THR Chi-restraints excluded: chain Q residue 1014 THR Chi-restraints excluded: chain Q residue 1051 LEU Chi-restraints excluded: chain Q residue 1074 ASP Chi-restraints excluded: chain Q residue 1092 VAL Chi-restraints excluded: chain R residue 606 THR Chi-restraints excluded: chain R residue 608 VAL Chi-restraints excluded: chain R residue 705 THR Chi-restraints excluded: chain R residue 724 VAL Chi-restraints excluded: chain R residue 773 LEU Chi-restraints excluded: chain R residue 798 VAL Chi-restraints excluded: chain R residue 817 LEU Chi-restraints excluded: chain R residue 855 VAL Chi-restraints excluded: chain R residue 875 LEU Chi-restraints excluded: chain R residue 913 LEU Chi-restraints excluded: chain R residue 940 VAL Chi-restraints excluded: chain R residue 943 THR Chi-restraints excluded: chain R residue 946 THR Chi-restraints excluded: chain R residue 950 THR Chi-restraints excluded: chain R residue 996 THR Chi-restraints excluded: chain R residue 1074 ASP Chi-restraints excluded: chain R residue 1092 VAL Chi-restraints excluded: chain R residue 1094 LEU Chi-restraints excluded: chain S residue 671 THR Chi-restraints excluded: chain S residue 855 VAL Chi-restraints excluded: chain S residue 875 LEU Chi-restraints excluded: chain S residue 913 LEU Chi-restraints excluded: chain S residue 943 THR Chi-restraints excluded: chain S residue 946 THR Chi-restraints excluded: chain S residue 972 THR Chi-restraints excluded: chain S residue 1006 GLN Chi-restraints excluded: chain S residue 1035 THR Chi-restraints excluded: chain S residue 1074 ASP Chi-restraints excluded: chain T residue 606 THR Chi-restraints excluded: chain T residue 608 VAL Chi-restraints excluded: chain T residue 618 VAL Chi-restraints excluded: chain T residue 623 THR Chi-restraints excluded: chain T residue 671 THR Chi-restraints excluded: chain T residue 810 ASP Chi-restraints excluded: chain T residue 817 LEU Chi-restraints excluded: chain T residue 875 LEU Chi-restraints excluded: chain T residue 913 LEU Chi-restraints excluded: chain T residue 933 HIS Chi-restraints excluded: chain T residue 943 THR Chi-restraints excluded: chain T residue 946 THR Chi-restraints excluded: chain T residue 950 THR Chi-restraints excluded: chain T residue 996 THR Chi-restraints excluded: chain T residue 997 ASP Chi-restraints excluded: chain T residue 1004 VAL Chi-restraints excluded: chain T residue 1006 GLN Chi-restraints excluded: chain T residue 1074 ASP Chi-restraints excluded: chain T residue 1092 VAL Chi-restraints excluded: chain T residue 1094 LEU Chi-restraints excluded: chain U residue 601 ASP Chi-restraints excluded: chain U residue 776 MET Chi-restraints excluded: chain U residue 780 ASN Chi-restraints excluded: chain U residue 822 VAL Chi-restraints excluded: chain U residue 857 VAL Chi-restraints excluded: chain U residue 905 SER Chi-restraints excluded: chain U residue 915 THR Chi-restraints excluded: chain U residue 996 THR Chi-restraints excluded: chain U residue 1077 MET Chi-restraints excluded: chain U residue 1104 THR Chi-restraints excluded: chain V residue 618 VAL Chi-restraints excluded: chain V residue 710 VAL Chi-restraints excluded: chain V residue 713 SER Chi-restraints excluded: chain V residue 776 MET Chi-restraints excluded: chain V residue 780 ASN Chi-restraints excluded: chain V residue 796 THR Chi-restraints excluded: chain V residue 822 VAL Chi-restraints excluded: chain V residue 829 ASP Chi-restraints excluded: chain V residue 855 VAL Chi-restraints excluded: chain V residue 857 VAL Chi-restraints excluded: chain V residue 867 VAL Chi-restraints excluded: chain V residue 1029 VAL Chi-restraints excluded: chain V residue 1104 THR Chi-restraints excluded: chain W residue 602 MET Chi-restraints excluded: chain W residue 615 ASP Chi-restraints excluded: chain W residue 618 VAL Chi-restraints excluded: chain W residue 623 THR Chi-restraints excluded: chain W residue 631 VAL Chi-restraints excluded: chain W residue 713 SER Chi-restraints excluded: chain W residue 796 THR Chi-restraints excluded: chain W residue 822 VAL Chi-restraints excluded: chain W residue 855 VAL Chi-restraints excluded: chain W residue 869 THR Chi-restraints excluded: chain W residue 913 LEU Chi-restraints excluded: chain W residue 967 ASP Chi-restraints excluded: chain W residue 1037 GLN Chi-restraints excluded: chain X residue 601 ASP Chi-restraints excluded: chain X residue 631 VAL Chi-restraints excluded: chain X residue 710 VAL Chi-restraints excluded: chain X residue 716 VAL Chi-restraints excluded: chain X residue 822 VAL Chi-restraints excluded: chain X residue 846 GLN Chi-restraints excluded: chain X residue 855 VAL Chi-restraints excluded: chain X residue 857 VAL Chi-restraints excluded: chain X residue 867 VAL Chi-restraints excluded: chain X residue 957 LYS Chi-restraints excluded: chain X residue 1053 MET Chi-restraints excluded: chain X residue 1074 ASP Chi-restraints excluded: chain Y residue 623 THR Chi-restraints excluded: chain Y residue 631 VAL Chi-restraints excluded: chain Y residue 814 MET Chi-restraints excluded: chain Y residue 822 VAL Chi-restraints excluded: chain Y residue 829 ASP Chi-restraints excluded: chain Y residue 855 VAL Chi-restraints excluded: chain Y residue 857 VAL Chi-restraints excluded: chain Y residue 866 GLN Chi-restraints excluded: chain Y residue 971 THR Chi-restraints excluded: chain Y residue 1104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 670 random chunks: chunk 395 optimal weight: 4.9990 chunk 636 optimal weight: 0.0060 chunk 388 optimal weight: 5.9990 chunk 301 optimal weight: 5.9990 chunk 442 optimal weight: 1.9990 chunk 667 optimal weight: 9.9990 chunk 614 optimal weight: 0.9980 chunk 531 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 410 optimal weight: 0.5980 chunk 325 optimal weight: 0.6980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 GLN ** L 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 914 ASN ** T 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 720 ASN X 998 ASN Y 978 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 53325 Z= 0.176 Angle : 0.687 16.832 72665 Z= 0.335 Chirality : 0.044 0.206 8425 Planarity : 0.004 0.039 9415 Dihedral : 5.010 41.095 7274 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.95 % Favored : 93.96 % Rotamer: Outliers : 3.89 % Allowed : 25.70 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.10), residues: 6685 helix: -1.62 (0.11), residues: 2255 sheet: -0.06 (0.15), residues: 1300 loop : -1.48 (0.11), residues: 3130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 87 HIS 0.004 0.000 HIS Y 690 PHE 0.026 0.001 PHE K 60 TYR 0.047 0.001 TYR L 65 ARG 0.006 0.000 ARG G 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1275 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1061 time to evaluate : 4.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7382 (ptt90) cc_final: 0.6882 (ptt90) REVERT: A 74 GLU cc_start: 0.8838 (mp0) cc_final: 0.8465 (mp0) REVERT: A 106 PHE cc_start: 0.8319 (m-80) cc_final: 0.7873 (m-80) REVERT: A 131 GLU cc_start: 0.8562 (mp0) cc_final: 0.8321 (mp0) REVERT: B 52 TYR cc_start: 0.6785 (m-80) cc_final: 0.6491 (m-80) REVERT: B 106 PHE cc_start: 0.8171 (m-80) cc_final: 0.7949 (m-80) REVERT: C 33 ARG cc_start: 0.8333 (ttm110) cc_final: 0.7970 (mtm110) REVERT: C 74 GLU cc_start: 0.8925 (mp0) cc_final: 0.8472 (mp0) REVERT: C 98 MET cc_start: 0.8242 (ppp) cc_final: 0.7786 (ppp) REVERT: C 141 GLU cc_start: 0.7562 (tp30) cc_final: 0.6713 (tp30) REVERT: D 33 ARG cc_start: 0.8643 (mtp85) cc_final: 0.8019 (mtm110) REVERT: D 141 GLU cc_start: 0.8016 (tp30) cc_final: 0.7749 (tm-30) REVERT: E 29 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7283 (p0) REVERT: E 33 ARG cc_start: 0.8626 (mtm-85) cc_final: 0.8157 (mtm-85) REVERT: E 74 GLU cc_start: 0.8557 (mm-30) cc_final: 0.7942 (mp0) REVERT: E 106 PHE cc_start: 0.8083 (m-10) cc_final: 0.7846 (m-10) REVERT: E 131 GLU cc_start: 0.8484 (mp0) cc_final: 0.8044 (pm20) REVERT: E 140 ILE cc_start: 0.8694 (mm) cc_final: 0.8359 (tt) REVERT: F 33 ARG cc_start: 0.7125 (mmm-85) cc_final: 0.6845 (mmm-85) REVERT: F 65 TYR cc_start: 0.8846 (t80) cc_final: 0.8123 (t80) REVERT: F 76 LEU cc_start: 0.8042 (tp) cc_final: 0.7359 (tt) REVERT: F 106 PHE cc_start: 0.8454 (m-80) cc_final: 0.7958 (m-80) REVERT: G 76 LEU cc_start: 0.7893 (tp) cc_final: 0.7436 (tt) REVERT: G 106 PHE cc_start: 0.8339 (m-80) cc_final: 0.7951 (m-80) REVERT: G 120 LYS cc_start: 0.8336 (mttp) cc_final: 0.8038 (mttp) REVERT: H 61 ASP cc_start: 0.8548 (m-30) cc_final: 0.8261 (t0) REVERT: H 65 TYR cc_start: 0.8947 (t80) cc_final: 0.8420 (t80) REVERT: H 106 PHE cc_start: 0.8482 (m-80) cc_final: 0.8065 (m-80) REVERT: I 30 ILE cc_start: 0.9429 (mt) cc_final: 0.9191 (mm) REVERT: I 65 TYR cc_start: 0.8889 (t80) cc_final: 0.8087 (t80) REVERT: J 65 TYR cc_start: 0.9147 (t80) cc_final: 0.8197 (t80) REVERT: J 87 TRP cc_start: 0.9130 (m-90) cc_final: 0.8874 (m-90) REVERT: K 28 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7702 (mm) REVERT: K 50 ARG cc_start: 0.8751 (ttm-80) cc_final: 0.7788 (ttm110) REVERT: K 56 ASP cc_start: 0.6988 (p0) cc_final: 0.6593 (t0) REVERT: K 79 ASP cc_start: 0.6523 (t70) cc_final: 0.5192 (m-30) REVERT: K 83 GLN cc_start: 0.7879 (tp-100) cc_final: 0.7190 (mm110) REVERT: K 113 PHE cc_start: 0.8673 (m-80) cc_final: 0.8341 (m-80) REVERT: K 120 LYS cc_start: 0.9076 (mmmm) cc_final: 0.8834 (mmtm) REVERT: L 45 LEU cc_start: 0.7825 (mt) cc_final: 0.7606 (mm) REVERT: L 50 ARG cc_start: 0.8889 (mmm-85) cc_final: 0.8288 (mmm-85) REVERT: L 66 GLN cc_start: 0.8901 (tp40) cc_final: 0.8619 (mm110) REVERT: L 85 ASP cc_start: 0.8020 (m-30) cc_final: 0.7352 (m-30) REVERT: L 113 PHE cc_start: 0.8646 (m-80) cc_final: 0.8231 (m-10) REVERT: M 50 ARG cc_start: 0.8797 (ttm-80) cc_final: 0.8180 (ttm110) REVERT: M 113 PHE cc_start: 0.8438 (m-80) cc_final: 0.8086 (m-80) REVERT: N 31 ARG cc_start: 0.7106 (ptp-110) cc_final: 0.6622 (ptp-170) REVERT: N 112 MET cc_start: 0.7358 (mtm) cc_final: 0.7019 (mtm) REVERT: N 113 PHE cc_start: 0.8389 (m-80) cc_final: 0.7893 (m-80) REVERT: N 131 GLU cc_start: 0.8833 (tp30) cc_final: 0.8124 (tp30) REVERT: O 50 ARG cc_start: 0.8707 (mtp85) cc_final: 0.8445 (mtt90) REVERT: O 129 ARG cc_start: 0.4814 (mmm160) cc_final: 0.4505 (mmm160) REVERT: P 576 GLN cc_start: 0.7351 (mp10) cc_final: 0.6996 (mp10) REVERT: P 815 MET cc_start: 0.8673 (tpp) cc_final: 0.8299 (mmm) REVERT: P 990 MET cc_start: 0.8034 (ttm) cc_final: 0.7445 (ttm) REVERT: P 1077 MET cc_start: 0.8760 (mmt) cc_final: 0.8469 (mmp) REVERT: P 1081 THR cc_start: 0.9641 (m) cc_final: 0.9166 (p) REVERT: Q 693 LYS cc_start: 0.9124 (tptp) cc_final: 0.8890 (tttm) REVERT: Q 773 LEU cc_start: 0.9289 (mt) cc_final: 0.9059 (mp) REVERT: Q 883 VAL cc_start: 0.9739 (t) cc_final: 0.9523 (p) REVERT: Q 911 LYS cc_start: 0.9113 (mmmm) cc_final: 0.8888 (ttmm) REVERT: Q 1081 THR cc_start: 0.9512 (m) cc_final: 0.9057 (p) REVERT: R 583 TYR cc_start: 0.8870 (t80) cc_final: 0.8537 (t80) REVERT: R 677 ASP cc_start: 0.8200 (t70) cc_final: 0.7998 (t0) REVERT: R 699 ASP cc_start: 0.8408 (m-30) cc_final: 0.8155 (m-30) REVERT: R 990 MET cc_start: 0.8304 (mtm) cc_final: 0.7887 (ttm) REVERT: R 1081 THR cc_start: 0.9538 (m) cc_final: 0.9083 (p) REVERT: S 616 GLU cc_start: 0.8203 (tt0) cc_final: 0.7505 (tm-30) REVERT: S 913 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9237 (pp) REVERT: S 1006 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8366 (pt0) REVERT: S 1081 THR cc_start: 0.9662 (m) cc_final: 0.9227 (p) REVERT: T 586 MET cc_start: 0.9051 (mmm) cc_final: 0.8674 (mmt) REVERT: T 616 GLU cc_start: 0.8073 (tt0) cc_final: 0.7736 (tt0) REVERT: T 895 TYR cc_start: 0.9260 (t80) cc_final: 0.8793 (t80) REVERT: T 913 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9083 (pp) REVERT: U 597 MET cc_start: 0.7571 (tpt) cc_final: 0.6908 (tpt) REVERT: U 814 MET cc_start: 0.8669 (tpp) cc_final: 0.8355 (tpp) REVERT: U 816 GLN cc_start: 0.8869 (pt0) cc_final: 0.8481 (pm20) REVERT: U 978 HIS cc_start: 0.8565 (m-70) cc_final: 0.7681 (m90) REVERT: U 990 MET cc_start: 0.8826 (mtp) cc_final: 0.8590 (mtp) REVERT: U 998 ASN cc_start: 0.8605 (t0) cc_final: 0.8291 (t0) REVERT: V 680 ASN cc_start: 0.8672 (t0) cc_final: 0.8469 (m-40) REVERT: V 805 ILE cc_start: 0.8736 (mm) cc_final: 0.8479 (mm) REVERT: V 978 HIS cc_start: 0.8474 (m-70) cc_final: 0.7740 (m-70) REVERT: W 611 LEU cc_start: 0.8981 (tp) cc_final: 0.8716 (tp) REVERT: W 680 ASN cc_start: 0.8646 (t0) cc_final: 0.8414 (m-40) REVERT: W 816 GLN cc_start: 0.8918 (pt0) cc_final: 0.8363 (pm20) REVERT: W 913 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9296 (pp) REVERT: W 978 HIS cc_start: 0.8680 (m-70) cc_final: 0.7932 (m90) REVERT: W 990 MET cc_start: 0.8980 (mtp) cc_final: 0.8666 (mtp) REVERT: W 1011 LYS cc_start: 0.9247 (tttp) cc_final: 0.8864 (tttt) REVERT: W 1037 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8057 (pm20) REVERT: X 597 MET cc_start: 0.7160 (tpt) cc_final: 0.6291 (tpt) REVERT: X 601 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8322 (p0) REVERT: X 720 ASN cc_start: 0.8585 (m110) cc_final: 0.8232 (p0) REVERT: X 776 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7824 (ptm) REVERT: X 805 ILE cc_start: 0.8922 (mm) cc_final: 0.8505 (mm) REVERT: Y 581 MET cc_start: 0.6244 (ptt) cc_final: 0.5631 (pmm) REVERT: Y 583 TYR cc_start: 0.6170 (t80) cc_final: 0.5867 (t80) REVERT: Y 957 LYS cc_start: 0.8939 (tppt) cc_final: 0.8672 (mmtm) REVERT: Y 967 ASP cc_start: 0.8574 (m-30) cc_final: 0.8356 (t0) REVERT: Y 990 MET cc_start: 0.8888 (mtp) cc_final: 0.8662 (mtp) outliers start: 214 outliers final: 187 residues processed: 1215 average time/residue: 0.4368 time to fit residues: 894.5269 Evaluate side-chains 1218 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1022 time to evaluate : 4.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 84 LYS Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 87 TRP Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 148 THR Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain O residue 57 ASN Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 148 THR Chi-restraints excluded: chain P residue 671 THR Chi-restraints excluded: chain P residue 705 THR Chi-restraints excluded: chain P residue 773 LEU Chi-restraints excluded: chain P residue 810 ASP Chi-restraints excluded: chain P residue 855 VAL Chi-restraints excluded: chain P residue 875 LEU Chi-restraints excluded: chain P residue 913 LEU Chi-restraints excluded: chain P residue 915 THR Chi-restraints excluded: chain P residue 933 HIS Chi-restraints excluded: chain P residue 943 THR Chi-restraints excluded: chain P residue 946 THR Chi-restraints excluded: chain P residue 950 THR Chi-restraints excluded: chain P residue 996 THR Chi-restraints excluded: chain P residue 1074 ASP Chi-restraints excluded: chain P residue 1092 VAL Chi-restraints excluded: chain Q residue 608 VAL Chi-restraints excluded: chain Q residue 618 VAL Chi-restraints excluded: chain Q residue 671 THR Chi-restraints excluded: chain Q residue 817 LEU Chi-restraints excluded: chain Q residue 855 VAL Chi-restraints excluded: chain Q residue 875 LEU Chi-restraints excluded: chain Q residue 879 TRP Chi-restraints excluded: chain Q residue 913 LEU Chi-restraints excluded: chain Q residue 943 THR Chi-restraints excluded: chain Q residue 946 THR Chi-restraints excluded: chain Q residue 972 THR Chi-restraints excluded: chain Q residue 996 THR Chi-restraints excluded: chain Q residue 1014 THR Chi-restraints excluded: chain Q residue 1051 LEU Chi-restraints excluded: chain Q residue 1074 ASP Chi-restraints excluded: chain Q residue 1092 VAL Chi-restraints excluded: chain R residue 606 THR Chi-restraints excluded: chain R residue 608 VAL Chi-restraints excluded: chain R residue 623 THR Chi-restraints excluded: chain R residue 705 THR Chi-restraints excluded: chain R residue 724 VAL Chi-restraints excluded: chain R residue 773 LEU Chi-restraints excluded: chain R residue 798 VAL Chi-restraints excluded: chain R residue 817 LEU Chi-restraints excluded: chain R residue 855 VAL Chi-restraints excluded: chain R residue 875 LEU Chi-restraints excluded: chain R residue 913 LEU Chi-restraints excluded: chain R residue 940 VAL Chi-restraints excluded: chain R residue 943 THR Chi-restraints excluded: chain R residue 946 THR Chi-restraints excluded: chain R residue 996 THR Chi-restraints excluded: chain R residue 1074 ASP Chi-restraints excluded: chain R residue 1092 VAL Chi-restraints excluded: chain R residue 1094 LEU Chi-restraints excluded: chain S residue 623 THR Chi-restraints excluded: chain S residue 855 VAL Chi-restraints excluded: chain S residue 875 LEU Chi-restraints excluded: chain S residue 913 LEU Chi-restraints excluded: chain S residue 914 ASN Chi-restraints excluded: chain S residue 943 THR Chi-restraints excluded: chain S residue 946 THR Chi-restraints excluded: chain S residue 1006 GLN Chi-restraints excluded: chain S residue 1035 THR Chi-restraints excluded: chain S residue 1074 ASP Chi-restraints excluded: chain T residue 606 THR Chi-restraints excluded: chain T residue 608 VAL Chi-restraints excluded: chain T residue 618 VAL Chi-restraints excluded: chain T residue 623 THR Chi-restraints excluded: chain T residue 671 THR Chi-restraints excluded: chain T residue 691 LEU Chi-restraints excluded: chain T residue 810 ASP Chi-restraints excluded: chain T residue 817 LEU Chi-restraints excluded: chain T residue 875 LEU Chi-restraints excluded: chain T residue 913 LEU Chi-restraints excluded: chain T residue 933 HIS Chi-restraints excluded: chain T residue 943 THR Chi-restraints excluded: chain T residue 946 THR Chi-restraints excluded: chain T residue 950 THR Chi-restraints excluded: chain T residue 996 THR Chi-restraints excluded: chain T residue 997 ASP Chi-restraints excluded: chain T residue 1004 VAL Chi-restraints excluded: chain T residue 1074 ASP Chi-restraints excluded: chain T residue 1092 VAL Chi-restraints excluded: chain T residue 1094 LEU Chi-restraints excluded: chain U residue 601 ASP Chi-restraints excluded: chain U residue 776 MET Chi-restraints excluded: chain U residue 822 VAL Chi-restraints excluded: chain U residue 857 VAL Chi-restraints excluded: chain U residue 905 SER Chi-restraints excluded: chain U residue 915 THR Chi-restraints excluded: chain U residue 996 THR Chi-restraints excluded: chain U residue 1077 MET Chi-restraints excluded: chain U residue 1104 THR Chi-restraints excluded: chain V residue 618 VAL Chi-restraints excluded: chain V residue 704 LEU Chi-restraints excluded: chain V residue 710 VAL Chi-restraints excluded: chain V residue 713 SER Chi-restraints excluded: chain V residue 776 MET Chi-restraints excluded: chain V residue 780 ASN Chi-restraints excluded: chain V residue 781 ASN Chi-restraints excluded: chain V residue 796 THR Chi-restraints excluded: chain V residue 822 VAL Chi-restraints excluded: chain V residue 829 ASP Chi-restraints excluded: chain V residue 855 VAL Chi-restraints excluded: chain V residue 857 VAL Chi-restraints excluded: chain V residue 1029 VAL Chi-restraints excluded: chain V residue 1104 THR Chi-restraints excluded: chain W residue 618 VAL Chi-restraints excluded: chain W residue 623 THR Chi-restraints excluded: chain W residue 631 VAL Chi-restraints excluded: chain W residue 713 SER Chi-restraints excluded: chain W residue 796 THR Chi-restraints excluded: chain W residue 822 VAL Chi-restraints excluded: chain W residue 855 VAL Chi-restraints excluded: chain W residue 869 THR Chi-restraints excluded: chain W residue 913 LEU Chi-restraints excluded: chain W residue 967 ASP Chi-restraints excluded: chain W residue 1037 GLN Chi-restraints excluded: chain X residue 601 ASP Chi-restraints excluded: chain X residue 631 VAL Chi-restraints excluded: chain X residue 710 VAL Chi-restraints excluded: chain X residue 776 MET Chi-restraints excluded: chain X residue 822 VAL Chi-restraints excluded: chain X residue 846 GLN Chi-restraints excluded: chain X residue 855 VAL Chi-restraints excluded: chain X residue 857 VAL Chi-restraints excluded: chain X residue 867 VAL Chi-restraints excluded: chain X residue 957 LYS Chi-restraints excluded: chain X residue 967 ASP Chi-restraints excluded: chain Y residue 623 THR Chi-restraints excluded: chain Y residue 631 VAL Chi-restraints excluded: chain Y residue 814 MET Chi-restraints excluded: chain Y residue 822 VAL Chi-restraints excluded: chain Y residue 855 VAL Chi-restraints excluded: chain Y residue 857 VAL Chi-restraints excluded: chain Y residue 866 GLN Chi-restraints excluded: chain Y residue 971 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 670 random chunks: chunk 422 optimal weight: 5.9990 chunk 566 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 490 optimal weight: 0.3980 chunk 78 optimal weight: 0.0030 chunk 147 optimal weight: 9.9990 chunk 532 optimal weight: 9.9990 chunk 222 optimal weight: 4.9990 chunk 546 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 overall best weight: 3.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN ** L 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 HIS ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 978 HIS Q 803 GLN ** R 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1079 ASN S 803 GLN S 914 ASN ** T 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 978 HIS T1079 ASN ** V 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 779 GLN ** V 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 812 GLN W 998 ASN ** X 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 998 ASN ** Y 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 820 GLN Y 978 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.106776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.076198 restraints weight = 114839.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.075810 restraints weight = 65212.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.076200 restraints weight = 59841.785| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 53325 Z= 0.487 Angle : 0.839 16.630 72665 Z= 0.413 Chirality : 0.049 0.248 8425 Planarity : 0.005 0.042 9415 Dihedral : 5.600 43.532 7274 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.49 % Favored : 92.40 % Rotamer: Outliers : 4.40 % Allowed : 25.70 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.10), residues: 6685 helix: -1.88 (0.10), residues: 2350 sheet: -0.21 (0.14), residues: 1290 loop : -1.56 (0.11), residues: 3045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP O 87 HIS 0.003 0.001 HIS P 978 PHE 0.026 0.002 PHE K 60 TYR 0.043 0.002 TYR U 895 ARG 0.010 0.001 ARG C 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15688.49 seconds wall clock time: 276 minutes 1.74 seconds (16561.74 seconds total)