Starting phenix.real_space_refine on Mon Mar 25 06:52:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu3_10586/03_2024/6tu3_10586.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu3_10586/03_2024/6tu3_10586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu3_10586/03_2024/6tu3_10586.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu3_10586/03_2024/6tu3_10586.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu3_10586/03_2024/6tu3_10586.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu3_10586/03_2024/6tu3_10586.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 288 5.16 5 C 29778 2.51 5 N 8094 2.21 5 O 8842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 88": "NH1" <-> "NH2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "B TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C ASP 82": "OD1" <-> "OD2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C GLU 232": "OE1" <-> "OE2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "D ASP 55": "OD1" <-> "OD2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D ASP 79": "OD1" <-> "OD2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D ASP 137": "OD1" <-> "OD2" Residue "D PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E GLU 183": "OE1" <-> "OE2" Residue "F TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 91": "OE1" <-> "OE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 228": "OD1" <-> "OD2" Residue "G ASP 17": "OD1" <-> "OD2" Residue "G ASP 89": "OD1" <-> "OD2" Residue "G GLU 175": "OE1" <-> "OE2" Residue "G GLU 192": "OE1" <-> "OE2" Residue "G PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 69": "OE1" <-> "OE2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H GLU 145": "OE1" <-> "OE2" Residue "H GLU 151": "OE1" <-> "OE2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "I ASP 10": "OD1" <-> "OD2" Residue "I ASP 53": "OD1" <-> "OD2" Residue "I TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 143": "NH1" <-> "NH2" Residue "I GLU 148": "OE1" <-> "OE2" Residue "I GLU 149": "OE1" <-> "OE2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "J ARG 25": "NH1" <-> "NH2" Residue "J ASP 37": "OD1" <-> "OD2" Residue "J ASP 46": "OD1" <-> "OD2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "J ARG 79": "NH1" <-> "NH2" Residue "J TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 105": "OE1" <-> "OE2" Residue "J ASP 158": "OD1" <-> "OD2" Residue "J GLU 190": "OE1" <-> "OE2" Residue "K ASP 18": "OD1" <-> "OD2" Residue "K GLU 49": "OE1" <-> "OE2" Residue "K ARG 86": "NH1" <-> "NH2" Residue "K ARG 153": "NH1" <-> "NH2" Residue "K GLU 165": "OE1" <-> "OE2" Residue "K ASP 184": "OD1" <-> "OD2" Residue "L GLU 36": "OE1" <-> "OE2" Residue "L GLU 72": "OE1" <-> "OE2" Residue "L TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 117": "OE1" <-> "OE2" Residue "L TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 150": "OE1" <-> "OE2" Residue "L ARG 158": "NH1" <-> "NH2" Residue "L GLU 181": "OE1" <-> "OE2" Residue "L ARG 186": "NH1" <-> "NH2" Residue "M GLU 31": "OE1" <-> "OE2" Residue "M ASP 48": "OD1" <-> "OD2" Residue "M ARG 99": "NH1" <-> "NH2" Residue "M GLU 111": "OE1" <-> "OE2" Residue "M GLU 116": "OE1" <-> "OE2" Residue "M ASP 133": "OD1" <-> "OD2" Residue "M ARG 173": "NH1" <-> "NH2" Residue "M GLU 184": "OE1" <-> "OE2" Residue "N PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 73": "OD1" <-> "OD2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N ARG 100": "NH1" <-> "NH2" Residue "N GLU 155": "OE1" <-> "OE2" Residue "N PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 90": "NH1" <-> "NH2" Residue "P TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 224": "OE1" <-> "OE2" Residue "T TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 91": "OE1" <-> "OE2" Residue "T ARG 101": "NH1" <-> "NH2" Residue "T TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 228": "OD1" <-> "OD2" Residue "X ARG 25": "NH1" <-> "NH2" Residue "X ASP 37": "OD1" <-> "OD2" Residue "X ASP 46": "OD1" <-> "OD2" Residue "X ARG 69": "NH1" <-> "NH2" Residue "X ARG 79": "NH1" <-> "NH2" Residue "X TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 105": "OE1" <-> "OE2" Residue "X ASP 158": "OD1" <-> "OD2" Residue "X GLU 190": "OE1" <-> "OE2" Residue "Y ASP 18": "OD1" <-> "OD2" Residue "Y GLU 49": "OE1" <-> "OE2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ARG 153": "NH1" <-> "NH2" Residue "Y GLU 165": "OE1" <-> "OE2" Residue "Y ASP 184": "OD1" <-> "OD2" Residue "Z GLU 36": "OE1" <-> "OE2" Residue "Z GLU 72": "OE1" <-> "OE2" Residue "Z TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 117": "OE1" <-> "OE2" Residue "Z TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 150": "OE1" <-> "OE2" Residue "Z ARG 158": "NH1" <-> "NH2" Residue "Z GLU 181": "OE1" <-> "OE2" Residue "Z ARG 186": "NH1" <-> "NH2" Residue "a GLU 31": "OE1" <-> "OE2" Residue "a ASP 48": "OD1" <-> "OD2" Residue "a ARG 99": "NH1" <-> "NH2" Residue "a GLU 111": "OE1" <-> "OE2" Residue "a GLU 116": "OE1" <-> "OE2" Residue "a ASP 133": "OD1" <-> "OD2" Residue "a ARG 173": "NH1" <-> "NH2" Residue "a GLU 184": "OE1" <-> "OE2" Residue "b PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 73": "OD1" <-> "OD2" Residue "b GLU 74": "OE1" <-> "OE2" Residue "b ARG 100": "NH1" <-> "NH2" Residue "b GLU 155": "OE1" <-> "OE2" Residue "b PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 10": "OD1" <-> "OD2" Residue "W ASP 53": "OD1" <-> "OD2" Residue "W TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 143": "NH1" <-> "NH2" Residue "W GLU 148": "OE1" <-> "OE2" Residue "W GLU 149": "OE1" <-> "OE2" Residue "W GLU 150": "OE1" <-> "OE2" Residue "R ASP 55": "OD1" <-> "OD2" Residue "R GLU 56": "OE1" <-> "OE2" Residue "R ASP 79": "OD1" <-> "OD2" Residue "R ASP 100": "OD1" <-> "OD2" Residue "R GLU 105": "OE1" <-> "OE2" Residue "R ASP 137": "OD1" <-> "OD2" Residue "R PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 163": "NH1" <-> "NH2" Residue "R GLU 173": "OE1" <-> "OE2" Residue "R GLU 207": "OE1" <-> "OE2" Residue "R ARG 213": "NH1" <-> "NH2" Residue "R TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 231": "OE1" <-> "OE2" Residue "O ARG 88": "NH1" <-> "NH2" Residue "O GLU 174": "OE1" <-> "OE2" Residue "U ASP 17": "OD1" <-> "OD2" Residue "U ASP 89": "OD1" <-> "OD2" Residue "U GLU 175": "OE1" <-> "OE2" Residue "U GLU 192": "OE1" <-> "OE2" Residue "U PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S ASP 90": "OD1" <-> "OD2" Residue "S GLU 105": "OE1" <-> "OE2" Residue "S GLU 183": "OE1" <-> "OE2" Residue "Q GLU 15": "OE1" <-> "OE2" Residue "Q GLU 70": "OE1" <-> "OE2" Residue "Q ASP 82": "OD1" <-> "OD2" Residue "Q GLU 209": "OE1" <-> "OE2" Residue "Q GLU 232": "OE1" <-> "OE2" Residue "Q GLU 244": "OE1" <-> "OE2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "V GLU 72": "OE1" <-> "OE2" Residue "V GLU 145": "OE1" <-> "OE2" Residue "V GLU 151": "OE1" <-> "OE2" Residue "V GLU 165": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 47002 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1789 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1765 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1902 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 241} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1778 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 224} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1743 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "F" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1787 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 224} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 40 Chain: "G" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1853 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1507 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1453 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1592 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "K" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1552 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 189} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1534 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 197} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "M" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1626 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 204} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "N" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1620 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 204} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "P" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1765 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "T" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1787 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 224} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 40 Chain: "X" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1592 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "Y" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1552 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 189} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "Z" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1534 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 197} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "a" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1626 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 204} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "b" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1620 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 204} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "W" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1453 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1778 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 224} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 36 Chain: "O" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1789 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "U" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1853 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "S" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1743 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "Q" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1902 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 241} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "V" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1507 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 22.35, per 1000 atoms: 0.48 Number of scatterers: 47002 At special positions: 0 Unit cell: (140.18, 184.04, 135.02, 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 288 16.00 O 8842 8.00 N 8094 7.00 C 29778 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: 14.89 Conformation dependent library (CDL) restraints added in 8.3 seconds 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11340 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 78 sheets defined 38.6% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.91 Creating SS restraints... Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.532A pdb=" N GLU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 83 through 106 removed outlier: 3.542A pdb=" N LYS A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 126 removed outlier: 3.694A pdb=" N VAL A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.647A pdb=" N LEU A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 189 Processing helix chain 'A' and resid 193 through 205 removed outlier: 4.130A pdb=" N THR A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL A 205 " --> pdb=" O CYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 57 through 61 removed outlier: 3.703A pdb=" N SER B 60 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 61 " --> pdb=" O GLU B 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 57 through 61' Processing helix chain 'B' and resid 78 through 101 removed outlier: 3.695A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 120 Processing helix chain 'B' and resid 165 through 177 removed outlier: 4.254A pdb=" N LYS B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.966A pdb=" N HIS B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 231 removed outlier: 3.751A pdb=" N ASP B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 30 removed outlier: 3.894A pdb=" N HIS C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 102 removed outlier: 3.697A pdb=" N VAL C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 121 removed outlier: 3.761A pdb=" N ILE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 177 removed outlier: 3.896A pdb=" N GLN C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 201 removed outlier: 3.809A pdb=" N LYS C 199 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 248 removed outlier: 3.704A pdb=" N GLU C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 27 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 76 through 99 removed outlier: 3.724A pdb=" N ILE D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 118 Processing helix chain 'D' and resid 164 through 176 removed outlier: 4.176A pdb=" N GLU D 170 " --> pdb=" O LYS D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 197 removed outlier: 4.139A pdb=" N LYS D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU D 197 " --> pdb=" O LYS D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 233 removed outlier: 3.591A pdb=" N TYR D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 30 removed outlier: 3.518A pdb=" N GLU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 removed outlier: 3.551A pdb=" N SER E 63 " --> pdb=" O GLU E 60 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE E 64 " --> pdb=" O PRO E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 60 through 64' Processing helix chain 'E' and resid 84 through 104 removed outlier: 4.232A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 Processing helix chain 'E' and resid 173 through 185 removed outlier: 4.496A pdb=" N SER E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 206 Processing helix chain 'E' and resid 232 through 241 Processing helix chain 'F' and resid 19 through 30 removed outlier: 3.631A pdb=" N VAL F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 100 removed outlier: 3.543A pdb=" N PHE F 87 " --> pdb=" O LEU F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 118 removed outlier: 3.973A pdb=" N ILE F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 122 removed outlier: 3.610A pdb=" N ARG F 122 " --> pdb=" O PRO F 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 119 through 122' Processing helix chain 'F' and resid 165 through 176 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 183 through 198 removed outlier: 3.997A pdb=" N THR F 198 " --> pdb=" O ALA F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 233 Processing helix chain 'G' and resid 20 through 32 removed outlier: 3.797A pdb=" N VAL G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 103 Processing helix chain 'G' and resid 107 through 121 Processing helix chain 'G' and resid 122 through 124 No H-bonds generated for 'chain 'G' and resid 122 through 124' Processing helix chain 'G' and resid 168 through 177 Processing helix chain 'G' and resid 185 through 201 removed outlier: 4.308A pdb=" N LYS G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU G 192 " --> pdb=" O ASP G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 244 Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 Processing helix chain 'H' and resid 131 through 134 Processing helix chain 'H' and resid 135 through 143 Processing helix chain 'H' and resid 148 through 165 Processing helix chain 'H' and resid 190 through 194 removed outlier: 3.665A pdb=" N ILE H 194 " --> pdb=" O GLY H 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 Processing helix chain 'I' and resid 130 through 142 removed outlier: 3.626A pdb=" N VAL I 137 " --> pdb=" O ALA I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 166 Processing helix chain 'J' and resid 55 through 78 Processing helix chain 'J' and resid 82 through 96 Processing helix chain 'J' and resid 141 through 153 removed outlier: 3.833A pdb=" N SER J 151 " --> pdb=" O GLY J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 175 removed outlier: 3.675A pdb=" N ASN J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 72 removed outlier: 3.508A pdb=" N TYR K 59 " --> pdb=" O GLN K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 90 Processing helix chain 'K' and resid 135 through 147 removed outlier: 4.808A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU K 143 " --> pdb=" O THR K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 171 Processing helix chain 'L' and resid 48 through 71 Processing helix chain 'L' and resid 75 through 89 removed outlier: 3.839A pdb=" N GLN L 89 " --> pdb=" O ASN L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 143 removed outlier: 3.652A pdb=" N GLY L 137 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG L 141 " --> pdb=" O GLY L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 167 Processing helix chain 'L' and resid 191 through 197 removed outlier: 3.800A pdb=" N ASP L 197 " --> pdb=" O ALA L 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 80 removed outlier: 3.567A pdb=" N LYS M 73 " --> pdb=" O GLU M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 99 removed outlier: 3.892A pdb=" N ARG M 99 " --> pdb=" O ILE M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 153 Proline residue: M 147 - end of helix Processing helix chain 'M' and resid 167 through 184 Processing helix chain 'N' and resid 57 through 77 removed outlier: 4.405A pdb=" N PHE N 77 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 102 removed outlier: 3.745A pdb=" N LYS N 102 " --> pdb=" O SER N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 146 Processing helix chain 'N' and resid 146 through 157 removed outlier: 4.044A pdb=" N LYS N 156 " --> pdb=" O GLU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 180 removed outlier: 3.806A pdb=" N VAL N 175 " --> pdb=" O ARG N 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 29 Processing helix chain 'P' and resid 57 through 61 removed outlier: 3.704A pdb=" N SER P 60 " --> pdb=" O ASP P 57 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL P 61 " --> pdb=" O GLU P 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 57 through 61' Processing helix chain 'P' and resid 78 through 101 removed outlier: 3.695A pdb=" N VAL P 84 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 120 Processing helix chain 'P' and resid 165 through 177 removed outlier: 4.254A pdb=" N LYS P 175 " --> pdb=" O THR P 171 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG P 176 " --> pdb=" O PHE P 172 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR P 177 " --> pdb=" O LEU P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 182 through 197 removed outlier: 3.967A pdb=" N HIS P 188 " --> pdb=" O GLU P 184 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR P 189 " --> pdb=" O ASP P 185 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER P 197 " --> pdb=" O THR P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 231 removed outlier: 3.751A pdb=" N ASP P 227 " --> pdb=" O THR P 223 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA P 231 " --> pdb=" O ASP P 227 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 30 removed outlier: 3.632A pdb=" N VAL T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 100 removed outlier: 3.543A pdb=" N PHE T 87 " --> pdb=" O LEU T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 118 removed outlier: 3.974A pdb=" N ILE T 118 " --> pdb=" O SER T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 119 through 122 removed outlier: 3.611A pdb=" N ARG T 122 " --> pdb=" O PRO T 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 119 through 122' Processing helix chain 'T' and resid 165 through 176 Processing helix chain 'T' and resid 177 through 179 No H-bonds generated for 'chain 'T' and resid 177 through 179' Processing helix chain 'T' and resid 183 through 198 removed outlier: 3.997A pdb=" N THR T 198 " --> pdb=" O ALA T 194 " (cutoff:3.500A) Processing helix chain 'T' and resid 229 through 233 Processing helix chain 'X' and resid 55 through 78 Processing helix chain 'X' and resid 82 through 96 Processing helix chain 'X' and resid 141 through 153 removed outlier: 3.833A pdb=" N SER X 151 " --> pdb=" O GLY X 147 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 175 removed outlier: 3.675A pdb=" N ASN X 172 " --> pdb=" O GLN X 168 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 72 removed outlier: 3.508A pdb=" N TYR Y 59 " --> pdb=" O GLN Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 90 Processing helix chain 'Y' and resid 135 through 147 removed outlier: 4.808A pdb=" N SER Y 141 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU Y 143 " --> pdb=" O THR Y 139 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 171 Processing helix chain 'Z' and resid 48 through 71 Processing helix chain 'Z' and resid 75 through 89 removed outlier: 3.839A pdb=" N GLN Z 89 " --> pdb=" O ASN Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 143 removed outlier: 3.651A pdb=" N GLY Z 137 " --> pdb=" O VAL Z 133 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL Z 138 " --> pdb=" O TYR Z 134 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG Z 141 " --> pdb=" O GLY Z 137 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 167 Processing helix chain 'Z' and resid 191 through 197 removed outlier: 3.800A pdb=" N ASP Z 197 " --> pdb=" O ALA Z 193 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 80 removed outlier: 3.567A pdb=" N LYS a 73 " --> pdb=" O GLU a 69 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 99 removed outlier: 3.892A pdb=" N ARG a 99 " --> pdb=" O ILE a 95 " (cutoff:3.500A) Processing helix chain 'a' and resid 141 through 153 Proline residue: a 147 - end of helix Processing helix chain 'a' and resid 167 through 184 Processing helix chain 'b' and resid 57 through 77 removed outlier: 4.405A pdb=" N PHE b 77 " --> pdb=" O ASP b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 102 removed outlier: 3.745A pdb=" N LYS b 102 " --> pdb=" O SER b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 141 through 146 Processing helix chain 'b' and resid 146 through 157 removed outlier: 4.045A pdb=" N LYS b 156 " --> pdb=" O GLU b 152 " (cutoff:3.500A) Processing helix chain 'b' and resid 161 through 180 removed outlier: 3.807A pdb=" N VAL b 175 " --> pdb=" O ARG b 171 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 90 Processing helix chain 'W' and resid 130 through 142 removed outlier: 3.625A pdb=" N VAL W 137 " --> pdb=" O ALA W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 166 Processing helix chain 'R' and resid 16 through 27 Processing helix chain 'R' and resid 55 through 59 Processing helix chain 'R' and resid 76 through 99 removed outlier: 3.724A pdb=" N ILE R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 118 Processing helix chain 'R' and resid 164 through 176 removed outlier: 4.176A pdb=" N GLU R 170 " --> pdb=" O LYS R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 197 removed outlier: 4.139A pdb=" N LYS R 189 " --> pdb=" O ASP R 185 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU R 197 " --> pdb=" O LYS R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 233 removed outlier: 3.592A pdb=" N TYR R 228 " --> pdb=" O GLU R 224 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL R 229 " --> pdb=" O ILE R 225 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA R 230 " --> pdb=" O GLU R 226 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 33 removed outlier: 3.532A pdb=" N GLU O 26 " --> pdb=" O LEU O 22 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE O 29 " --> pdb=" O VAL O 25 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS O 30 " --> pdb=" O GLU O 26 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN O 33 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 66 Processing helix chain 'O' and resid 83 through 106 removed outlier: 3.542A pdb=" N LYS O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 126 removed outlier: 3.693A pdb=" N VAL O 124 " --> pdb=" O ASP O 120 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR O 125 " --> pdb=" O ILE O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 181 removed outlier: 3.648A pdb=" N LEU O 179 " --> pdb=" O SER O 175 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS O 181 " --> pdb=" O SER O 177 " (cutoff:3.500A) Processing helix chain 'O' and resid 185 through 189 Processing helix chain 'O' and resid 193 through 205 removed outlier: 4.129A pdb=" N THR O 197 " --> pdb=" O GLN O 193 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL O 205 " --> pdb=" O CYS O 201 " (cutoff:3.500A) Processing helix chain 'O' and resid 231 through 242 Processing helix chain 'U' and resid 20 through 32 removed outlier: 3.797A pdb=" N VAL U 30 " --> pdb=" O ALA U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 103 Processing helix chain 'U' and resid 107 through 121 Processing helix chain 'U' and resid 122 through 124 No H-bonds generated for 'chain 'U' and resid 122 through 124' Processing helix chain 'U' and resid 168 through 177 Processing helix chain 'U' and resid 185 through 201 removed outlier: 4.308A pdb=" N LYS U 191 " --> pdb=" O ARG U 187 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU U 192 " --> pdb=" O ASP U 188 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 244 Processing helix chain 'S' and resid 21 through 30 removed outlier: 3.518A pdb=" N GLU S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 64 removed outlier: 3.552A pdb=" N SER S 63 " --> pdb=" O GLU S 60 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE S 64 " --> pdb=" O PRO S 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 60 through 64' Processing helix chain 'S' and resid 84 through 104 removed outlier: 4.233A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 118 Processing helix chain 'S' and resid 173 through 185 removed outlier: 4.496A pdb=" N SER S 179 " --> pdb=" O GLU S 175 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER S 180 " --> pdb=" O GLY S 176 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU S 183 " --> pdb=" O SER S 179 " (cutoff:3.500A) Processing helix chain 'S' and resid 190 through 206 Processing helix chain 'S' and resid 232 through 241 Processing helix chain 'Q' and resid 18 through 30 removed outlier: 3.895A pdb=" N HIS Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 102 removed outlier: 3.698A pdb=" N VAL Q 85 " --> pdb=" O SER Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 121 removed outlier: 3.761A pdb=" N ILE Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR Q 121 " --> pdb=" O ILE Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 177 removed outlier: 3.895A pdb=" N GLN Q 177 " --> pdb=" O SER Q 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 201 removed outlier: 3.809A pdb=" N LYS Q 199 " --> pdb=" O LYS Q 195 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET Q 201 " --> pdb=" O LEU Q 197 " (cutoff:3.500A) Processing helix chain 'Q' and resid 229 through 248 removed outlier: 3.705A pdb=" N GLU Q 248 " --> pdb=" O GLU Q 244 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 90 Processing helix chain 'V' and resid 131 through 134 Processing helix chain 'V' and resid 135 through 143 Processing helix chain 'V' and resid 148 through 165 Processing helix chain 'V' and resid 190 through 194 removed outlier: 3.666A pdb=" N ILE V 194 " --> pdb=" O GLY V 191 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 169 removed outlier: 6.166A pdb=" N THR A 38 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 53 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 73 removed outlier: 6.709A pdb=" N ILE A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N MET A 138 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 159 through 162 removed outlier: 3.689A pdb=" N SER B 34 " --> pdb=" O MET B 162 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B 42 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 208 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN B 213 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 216 " --> pdb=" O ASN B 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.508A pdb=" N GLY B 137 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN B 147 " --> pdb=" O PHE B 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.782A pdb=" N GLY C 42 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG C 226 " --> pdb=" O THR C 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 73 through 78 removed outlier: 3.645A pdb=" N LEU C 134 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY C 138 " --> pdb=" O GLN C 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 158 through 161 removed outlier: 3.620A pdb=" N VAL D 42 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 62 through 64 removed outlier: 3.716A pdb=" N MET D 71 " --> pdb=" O CYS D 63 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA D 131 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY D 135 " --> pdb=" O ARG D 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.388A pdb=" N ILE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.388A pdb=" N ILE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET E 156 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU E 153 " --> pdb=" O CYS E 165 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 158 through 159 removed outlier: 4.358A pdb=" N ILE F 212 " --> pdb=" O TYR F 224 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLY F 216 " --> pdb=" O GLU F 220 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLU F 220 " --> pdb=" O GLY F 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 65 Processing sheet with id=AB5, first strand: chain 'F' and resid 63 through 65 removed outlier: 3.890A pdb=" N LEU F 132 " --> pdb=" O THR F 147 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR F 147 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 162 through 163 removed outlier: 3.662A pdb=" N GLU G 212 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP G 215 " --> pdb=" O GLU G 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 66 through 70 removed outlier: 3.635A pdb=" N MET G 75 " --> pdb=" O PHE G 67 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY G 138 " --> pdb=" O GLY G 74 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR G 149 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER G 139 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR G 158 " --> pdb=" O MET G 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 125 through 129 removed outlier: 3.540A pdb=" N VAL H 12 " --> pdb=" O ILE H 179 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN H 187 " --> pdb=" O LEU H 176 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.667A pdb=" N THR H 22 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ILE H 26 " --> pdb=" O THR H 22 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 34 through 36 removed outlier: 3.597A pdb=" N GLY H 102 " --> pdb=" O GLN H 110 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL H 111 " --> pdb=" O GLN H 123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 124 through 128 removed outlier: 6.144A pdb=" N THR I 2 " --> pdb=" O ASP I 17 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY I 11 " --> pdb=" O TYR I 8 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE I 173 " --> pdb=" O PRO I 188 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 20 through 22 removed outlier: 6.802A pdb=" N ALA I 20 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL I 25 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.310A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.310A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP I 104 " --> pdb=" O GLY I 107 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 135 through 139 removed outlier: 5.980A pdb=" N ALA J 9 " --> pdb=" O ASP J 24 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL J 184 " --> pdb=" O LEU J 199 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 27 through 29 removed outlier: 7.088A pdb=" N PHE J 27 " --> pdb=" O VAL J 34 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 41 through 45 removed outlier: 6.252A pdb=" N LEU J 48 " --> pdb=" O MET J 44 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA J 53 " --> pdb=" O GLU J 105 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 129 through 132 removed outlier: 3.597A pdb=" N ARG K 181 " --> pdb=" O VAL K 15 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 129 through 132 removed outlier: 3.597A pdb=" N ARG K 181 " --> pdb=" O VAL K 15 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 35 through 39 removed outlier: 6.479A pdb=" N ILE K 42 " --> pdb=" O MET K 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET K 118 " --> pdb=" O LEU K 102 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 125 through 129 removed outlier: 3.642A pdb=" N GLY L 11 " --> pdb=" O PHE L 8 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL L 14 " --> pdb=" O TYR L 177 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU L 176 " --> pdb=" O VAL L 187 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY L 183 " --> pdb=" O ARG L 180 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 20 through 22 removed outlier: 6.999A pdb=" N ALA L 20 " --> pdb=" O ALA L 27 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR L 25 " --> pdb=" O ALA L 22 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 34 through 38 removed outlier: 3.578A pdb=" N ILE L 37 " --> pdb=" O LEU L 41 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU L 42 " --> pdb=" O CYS L 102 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N MET L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 135 through 139 removed outlier: 5.860A pdb=" N THR M 11 " --> pdb=" O ASP M 26 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP M 26 " --> pdb=" O THR M 11 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 29 through 31 removed outlier: 3.843A pdb=" N THR M 37 " --> pdb=" O LEU M 29 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU M 31 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE M 35 " --> pdb=" O GLU M 31 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 43 through 47 removed outlier: 6.569A pdb=" N THR M 50 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL M 121 " --> pdb=" O ASP M 133 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 7 through 8 removed outlier: 3.607A pdb=" N GLY N 55 " --> pdb=" O GLY N 8 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 136 through 138 removed outlier: 6.084A pdb=" N PHE N 187 " --> pdb=" O PRO N 202 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL N 189 " --> pdb=" O GLU N 200 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 28 through 29 Processing sheet with id=AE3, first strand: chain 'N' and resid 42 through 46 removed outlier: 6.607A pdb=" N THR N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 159 through 162 removed outlier: 3.688A pdb=" N SER P 34 " --> pdb=" O MET P 162 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY P 42 " --> pdb=" O ALA P 39 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU P 208 " --> pdb=" O THR P 47 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN P 213 " --> pdb=" O GLY P 216 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY P 216 " --> pdb=" O ASN P 213 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 65 through 66 removed outlier: 3.508A pdb=" N GLY P 137 " --> pdb=" O TYR P 144 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN P 147 " --> pdb=" O PHE P 155 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'T' and resid 158 through 159 removed outlier: 4.358A pdb=" N ILE T 212 " --> pdb=" O TYR T 224 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLY T 216 " --> pdb=" O GLU T 220 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLU T 220 " --> pdb=" O GLY T 216 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 63 through 65 Processing sheet with id=AE8, first strand: chain 'T' and resid 63 through 65 removed outlier: 3.890A pdb=" N LEU T 132 " --> pdb=" O THR T 147 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR T 147 " --> pdb=" O LEU T 132 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 135 through 139 removed outlier: 5.981A pdb=" N ALA X 9 " --> pdb=" O ASP X 24 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL X 184 " --> pdb=" O LEU X 199 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'X' and resid 27 through 29 removed outlier: 7.088A pdb=" N PHE X 27 " --> pdb=" O VAL X 34 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 41 through 45 removed outlier: 6.252A pdb=" N LEU X 48 " --> pdb=" O MET X 44 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA X 53 " --> pdb=" O GLU X 105 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 129 through 132 removed outlier: 3.597A pdb=" N ARG Y 181 " --> pdb=" O VAL Y 15 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Y' and resid 129 through 132 removed outlier: 3.597A pdb=" N ARG Y 181 " --> pdb=" O VAL Y 15 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 35 through 39 removed outlier: 6.479A pdb=" N ILE Y 42 " --> pdb=" O MET Y 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET Y 118 " --> pdb=" O LEU Y 102 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 125 through 129 removed outlier: 3.642A pdb=" N GLY Z 11 " --> pdb=" O PHE Z 8 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL Z 14 " --> pdb=" O TYR Z 177 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU Z 176 " --> pdb=" O VAL Z 187 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY Z 183 " --> pdb=" O ARG Z 180 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 20 through 22 removed outlier: 7.000A pdb=" N ALA Z 20 " --> pdb=" O ALA Z 27 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR Z 25 " --> pdb=" O ALA Z 22 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.578A pdb=" N ILE Z 37 " --> pdb=" O LEU Z 41 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU Z 42 " --> pdb=" O CYS Z 102 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N MET Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 135 through 139 removed outlier: 5.860A pdb=" N THR a 11 " --> pdb=" O ASP a 26 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP a 26 " --> pdb=" O THR a 11 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'a' and resid 29 through 31 removed outlier: 3.843A pdb=" N THR a 37 " --> pdb=" O LEU a 29 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU a 31 " --> pdb=" O ILE a 35 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ILE a 35 " --> pdb=" O GLU a 31 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 43 through 47 removed outlier: 6.568A pdb=" N THR a 50 " --> pdb=" O LEU a 46 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL a 121 " --> pdb=" O ASP a 133 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'b' and resid 7 through 8 removed outlier: 3.606A pdb=" N GLY b 55 " --> pdb=" O GLY b 8 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'b' and resid 136 through 138 removed outlier: 6.084A pdb=" N PHE b 187 " --> pdb=" O PRO b 202 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL b 189 " --> pdb=" O GLU b 200 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'b' and resid 28 through 29 Processing sheet with id=AG6, first strand: chain 'b' and resid 42 through 46 removed outlier: 6.607A pdb=" N THR b 49 " --> pdb=" O VAL b 45 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'W' and resid 124 through 128 removed outlier: 6.143A pdb=" N THR W 2 " --> pdb=" O ASP W 17 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY W 11 " --> pdb=" O TYR W 8 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE W 173 " --> pdb=" O PRO W 188 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'W' and resid 20 through 22 removed outlier: 6.801A pdb=" N ALA W 20 " --> pdb=" O ALA W 27 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL W 25 " --> pdb=" O GLU W 22 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.309A pdb=" N ILE W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.309A pdb=" N ILE W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP W 104 " --> pdb=" O GLY W 107 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'R' and resid 158 through 161 removed outlier: 3.621A pdb=" N VAL R 42 " --> pdb=" O VAL R 35 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'R' and resid 62 through 64 removed outlier: 3.716A pdb=" N MET R 71 " --> pdb=" O CYS R 63 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA R 131 " --> pdb=" O THR R 147 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY R 135 " --> pdb=" O ARG R 143 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 165 through 169 removed outlier: 6.166A pdb=" N THR O 38 " --> pdb=" O GLN O 53 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN O 53 " --> pdb=" O THR O 38 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 69 through 73 removed outlier: 6.709A pdb=" N ILE O 76 " --> pdb=" O ILE O 72 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET O 138 " --> pdb=" O CYS O 154 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'U' and resid 162 through 163 removed outlier: 3.662A pdb=" N GLU U 212 " --> pdb=" O VAL U 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP U 215 " --> pdb=" O GLU U 225 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'U' and resid 66 through 70 removed outlier: 3.634A pdb=" N MET U 75 " --> pdb=" O PHE U 67 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL U 73 " --> pdb=" O VAL U 69 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY U 138 " --> pdb=" O GLY U 74 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR U 149 " --> pdb=" O LEU U 137 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER U 139 " --> pdb=" O GLN U 147 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR U 158 " --> pdb=" O MET U 150 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'S' and resid 167 through 170 Processing sheet with id=AH9, first strand: chain 'S' and resid 67 through 71 removed outlier: 6.388A pdb=" N ILE S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'S' and resid 67 through 71 removed outlier: 6.388A pdb=" N ILE S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET S 156 " --> pdb=" O LEU S 141 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU S 153 " --> pdb=" O CYS S 165 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Q' and resid 161 through 164 removed outlier: 3.782A pdb=" N GLY Q 42 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG Q 226 " --> pdb=" O THR Q 215 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Q' and resid 73 through 78 removed outlier: 3.645A pdb=" N LEU Q 134 " --> pdb=" O SER Q 150 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY Q 138 " --> pdb=" O GLN Q 146 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'V' and resid 125 through 129 removed outlier: 3.540A pdb=" N VAL V 12 " --> pdb=" O ILE V 179 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN V 187 " --> pdb=" O LEU V 176 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.666A pdb=" N THR V 22 " --> pdb=" O ILE V 26 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ILE V 26 " --> pdb=" O THR V 22 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'V' and resid 34 through 36 removed outlier: 3.597A pdb=" N GLY V 102 " --> pdb=" O GLN V 110 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL V 111 " --> pdb=" O GLN V 123 " (cutoff:3.500A) 2556 hydrogen bonds defined for protein. 7302 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: 17.60 Time building geometry restraints manager: 16.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15325 1.34 - 1.46: 7244 1.46 - 1.57: 24809 1.57 - 1.69: 0 1.69 - 1.81: 468 Bond restraints: 47846 Sorted by residual: bond pdb=" CA ILE F 118 " pdb=" CB ILE F 118 " ideal model delta sigma weight residual 1.539 1.559 -0.020 5.40e-03 3.43e+04 1.34e+01 bond pdb=" CA ILE T 118 " pdb=" CB ILE T 118 " ideal model delta sigma weight residual 1.539 1.559 -0.020 5.40e-03 3.43e+04 1.34e+01 bond pdb=" C GLY I 128 " pdb=" O GLY I 128 " ideal model delta sigma weight residual 1.237 1.220 0.017 7.00e-03 2.04e+04 6.16e+00 bond pdb=" C GLY W 128 " pdb=" O GLY W 128 " ideal model delta sigma weight residual 1.237 1.220 0.017 7.00e-03 2.04e+04 5.91e+00 bond pdb=" CA ILE J 126 " pdb=" C ILE J 126 " ideal model delta sigma weight residual 1.519 1.545 -0.026 1.14e-02 7.69e+03 5.29e+00 ... (remaining 47841 not shown) Histogram of bond angle deviations from ideal: 98.90 - 105.94: 843 105.94 - 112.98: 25506 112.98 - 120.03: 16793 120.03 - 127.07: 21270 127.07 - 134.11: 320 Bond angle restraints: 64732 Sorted by residual: angle pdb=" C GLN D 215 " pdb=" N PRO D 216 " pdb=" CA PRO D 216 " ideal model delta sigma weight residual 119.90 128.37 -8.47 1.02e+00 9.61e-01 6.90e+01 angle pdb=" C GLN R 215 " pdb=" N PRO R 216 " pdb=" CA PRO R 216 " ideal model delta sigma weight residual 119.90 128.33 -8.43 1.02e+00 9.61e-01 6.82e+01 angle pdb=" N VAL F 66 " pdb=" CA VAL F 66 " pdb=" C VAL F 66 " ideal model delta sigma weight residual 111.90 105.78 6.12 8.10e-01 1.52e+00 5.72e+01 angle pdb=" N VAL T 66 " pdb=" CA VAL T 66 " pdb=" C VAL T 66 " ideal model delta sigma weight residual 111.90 105.81 6.09 8.10e-01 1.52e+00 5.65e+01 angle pdb=" N VAL L 187 " pdb=" CA VAL L 187 " pdb=" C VAL L 187 " ideal model delta sigma weight residual 111.45 118.03 -6.58 9.30e-01 1.16e+00 5.01e+01 ... (remaining 64727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 25317 17.99 - 35.98: 2631 35.98 - 53.98: 570 53.98 - 71.97: 182 71.97 - 89.96: 52 Dihedral angle restraints: 28752 sinusoidal: 10990 harmonic: 17762 Sorted by residual: dihedral pdb=" CA ASP O 58 " pdb=" C ASP O 58 " pdb=" N LYS O 59 " pdb=" CA LYS O 59 " ideal model delta harmonic sigma weight residual -180.00 -155.59 -24.41 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ASP A 58 " pdb=" C ASP A 58 " pdb=" N LYS A 59 " pdb=" CA LYS A 59 " ideal model delta harmonic sigma weight residual -180.00 -155.61 -24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA SER T 150 " pdb=" C SER T 150 " pdb=" N ALA T 151 " pdb=" CA ALA T 151 " ideal model delta harmonic sigma weight residual 180.00 -155.91 -24.09 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 28749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 5917 0.064 - 0.128: 1278 0.128 - 0.191: 128 0.191 - 0.255: 33 0.255 - 0.319: 12 Chirality restraints: 7368 Sorted by residual: chirality pdb=" CA LYS W 141 " pdb=" N LYS W 141 " pdb=" C LYS W 141 " pdb=" CB LYS W 141 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA LYS I 141 " pdb=" N LYS I 141 " pdb=" C LYS I 141 " pdb=" CB LYS I 141 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA LEU U 57 " pdb=" N LEU U 57 " pdb=" C LEU U 57 " pdb=" CB LEU U 57 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 7365 not shown) Planarity restraints: 8314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 210 " -0.021 2.00e-02 2.50e+03 2.39e-02 1.00e+01 pdb=" CG PHE A 210 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE A 210 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 210 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 210 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 210 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 210 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 210 " 0.021 2.00e-02 2.50e+03 2.38e-02 9.91e+00 pdb=" CG PHE O 210 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE O 210 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE O 210 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE O 210 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE O 210 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE O 210 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG F 101 " 0.044 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO F 102 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO F 102 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 102 " 0.037 5.00e-02 4.00e+02 ... (remaining 8311 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 21 1.99 - 2.72: 2861 2.72 - 3.45: 60917 3.45 - 4.17: 104001 4.17 - 4.90: 196269 Nonbonded interactions: 364069 Sorted by model distance: nonbonded pdb=" OE2 GLU P 204 " pdb=" C PRO P 222 " model vdw 1.264 3.270 nonbonded pdb=" OE2 GLU B 204 " pdb=" C PRO B 222 " model vdw 1.265 3.270 nonbonded pdb=" CB SER a 21 " pdb=" OE2 GLU a 111 " model vdw 1.590 3.440 nonbonded pdb=" CB SER M 21 " pdb=" OE2 GLU M 111 " model vdw 1.590 3.440 nonbonded pdb=" OD2 ASP R 139 " pdb=" OG1 THR R 141 " model vdw 1.612 2.440 ... (remaining 364064 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 6.820 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: 0.060 Extract box with map and model: 16.140 Check model and map are aligned: 0.610 Set scattering table: 0.410 Process input model: 109.670 Find NCS groups from input model: 4.010 Set up NCS constraints: 0.400 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:9.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 47846 Z= 0.363 Angle : 0.810 8.742 64732 Z= 0.510 Chirality : 0.054 0.319 7368 Planarity : 0.006 0.068 8314 Dihedral : 16.098 89.962 17412 Min Nonbonded Distance : 1.264 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 8.29 % Allowed : 16.92 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.10), residues: 6102 helix: 0.02 (0.10), residues: 2208 sheet: -2.34 (0.12), residues: 1464 loop : -2.87 (0.10), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 100 HIS 0.005 0.001 HIS S 31 PHE 0.056 0.002 PHE A 210 TYR 0.019 0.002 TYR M 97 ARG 0.004 0.000 ARG B 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1571 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 405 poor density : 1166 time to evaluate : 6.521 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: A 45 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7650 (ttmm) REVERT: A 226 LYS cc_start: 0.8521 (mttm) cc_final: 0.8298 (mttm) REVERT: F 26 MET cc_start: 0.7457 (mtm) cc_final: 0.7257 (mtm) REVERT: F 106 SER cc_start: 0.8342 (OUTLIER) cc_final: 0.8075 (p) REVERT: F 153 TYR cc_start: 0.8073 (p90) cc_final: 0.7785 (p90) REVERT: F 180 MET cc_start: 0.7161 (mmt) cc_final: 0.6865 (mmt) REVERT: H 92 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6689 (pm20) REVERT: H 104 ASP cc_start: 0.7573 (p0) cc_final: 0.7312 (p0) REVERT: H 120 MET cc_start: 0.6414 (ttp) cc_final: 0.6163 (ttp) REVERT: H 133 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8188 (p) REVERT: I 195 LYS cc_start: 0.5506 (OUTLIER) cc_final: 0.5043 (ttpt) REVERT: J 79 ARG cc_start: 0.8153 (ptt-90) cc_final: 0.7615 (ptt-90) REVERT: J 126 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7462 (mm) REVERT: J 182 MET cc_start: 0.7993 (mmt) cc_final: 0.7733 (mmm) REVERT: K 28 MET cc_start: 0.7873 (mtp) cc_final: 0.7658 (mtp) REVERT: K 29 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8501 (tttp) REVERT: K 31 ASP cc_start: 0.8114 (p0) cc_final: 0.7433 (p0) REVERT: L 88 TYR cc_start: 0.6311 (t80) cc_final: 0.5975 (t80) REVERT: L 117 GLU cc_start: 0.7400 (mp0) cc_final: 0.7149 (mp0) REVERT: M 107 TYR cc_start: 0.7835 (m-80) cc_final: 0.7591 (m-80) REVERT: N 186 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.7160 (ttp-110) REVERT: P 41 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.7756 (p0) REVERT: P 229 LEU cc_start: 0.8636 (mt) cc_final: 0.8303 (mp) REVERT: T 106 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.8050 (p) REVERT: T 153 TYR cc_start: 0.8093 (p90) cc_final: 0.7763 (p90) REVERT: T 230 SER cc_start: 0.8921 (OUTLIER) cc_final: 0.8656 (p) REVERT: X 79 ARG cc_start: 0.8066 (ptt-90) cc_final: 0.7741 (ptt-90) REVERT: X 126 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7602 (mm) REVERT: X 182 MET cc_start: 0.8099 (mmt) cc_final: 0.7839 (mmm) REVERT: Y 29 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7944 (tttp) REVERT: Y 31 ASP cc_start: 0.8183 (p0) cc_final: 0.7739 (p0) REVERT: Z 88 TYR cc_start: 0.6193 (t80) cc_final: 0.5911 (t80) REVERT: Z 117 GLU cc_start: 0.7413 (mp0) cc_final: 0.7170 (mp0) REVERT: a 107 TYR cc_start: 0.7918 (m-80) cc_final: 0.7689 (m-80) REVERT: b 186 ARG cc_start: 0.7449 (ttm-80) cc_final: 0.7071 (ttp-110) REVERT: W 84 LYS cc_start: 0.8365 (ptmt) cc_final: 0.8092 (pttt) REVERT: W 195 LYS cc_start: 0.5633 (OUTLIER) cc_final: 0.5424 (ttpt) REVERT: O 45 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7334 (mttt) REVERT: O 173 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7824 (p) REVERT: U 195 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8243 (ttmt) REVERT: V 92 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6697 (pm20) REVERT: V 104 ASP cc_start: 0.7714 (p0) cc_final: 0.7438 (p0) REVERT: V 133 SER cc_start: 0.8610 (OUTLIER) cc_final: 0.8188 (p) outliers start: 405 outliers final: 197 residues processed: 1476 average time/residue: 1.6381 time to fit residues: 2957.7278 Evaluate side-chains 1115 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 902 time to evaluate : 5.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 LYS Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 195 LYS Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 54 CYS Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 41 ASN Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 106 SER Chi-restraints excluded: chain T residue 177 SER Chi-restraints excluded: chain T residue 188 VAL Chi-restraints excluded: chain T residue 211 SER Chi-restraints excluded: chain T residue 230 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 88 SER Chi-restraints excluded: chain X residue 121 CYS Chi-restraints excluded: chain X residue 126 ILE Chi-restraints excluded: chain X residue 142 SER Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain X residue 198 THR Chi-restraints excluded: chain Y residue 29 LYS Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 105 ASP Chi-restraints excluded: chain Z residue 122 SER Chi-restraints excluded: chain Z residue 130 SER Chi-restraints excluded: chain Z residue 174 VAL Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 21 SER Chi-restraints excluded: chain a residue 34 SER Chi-restraints excluded: chain a residue 54 CYS Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain a residue 93 SER Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 84 SER Chi-restraints excluded: chain b residue 120 SER Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 195 LYS Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 141 THR Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 194 THR Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 205 VAL Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 193 VAL Chi-restraints excluded: chain U residue 195 LYS Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 226 ILE Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 62 SER Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 159 SER Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain V residue 24 SER Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 124 SER Chi-restraints excluded: chain V residue 133 SER Chi-restraints excluded: chain V residue 145 GLU Chi-restraints excluded: chain V residue 200 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 510 optimal weight: 10.0000 chunk 457 optimal weight: 1.9990 chunk 254 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 308 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 473 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 352 optimal weight: 6.9990 chunk 548 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN C 109 GLN C 167 ASN D 175 ASN E 182 GLN E 211 ASN F 4 ASN F 43 HIS F 53 GLN F 175 HIS H 71 ASN J 156 ASN K 63 ASN K 193 ASN L 9 GLN L 29 GLN L 119 ASN N 188 GLN P 188 HIS T 4 ASN T 43 HIS T 53 GLN X 156 ASN Y 61 GLN Y 63 ASN Y 174 ASN Y 193 ASN Z 9 GLN Z 29 GLN Z 119 ASN Z 191 ASN a 151 ASN a 157 ASN b 188 GLN R 23 GLN R 175 ASN O 24 GLN ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 GLN S 211 ASN Q 109 GLN Q 167 ASN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 47846 Z= 0.388 Angle : 0.742 10.713 64732 Z= 0.404 Chirality : 0.049 0.174 7368 Planarity : 0.006 0.069 8314 Dihedral : 8.381 88.711 7024 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 8.12 % Allowed : 23.28 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.10), residues: 6102 helix: 0.83 (0.11), residues: 2202 sheet: -1.38 (0.13), residues: 1424 loop : -2.43 (0.11), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E 100 HIS 0.010 0.001 HIS F 190 PHE 0.027 0.002 PHE W 36 TYR 0.024 0.002 TYR K 117 ARG 0.008 0.001 ARG G 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1333 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 397 poor density : 936 time to evaluate : 5.431 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: A 45 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7718 (ttmm) REVERT: A 78 CYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7955 (p) REVERT: C 28 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8270 (mp) REVERT: C 72 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7624 (mtt) REVERT: C 226 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6922 (ttt90) REVERT: D 46 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.8008 (tt0) REVERT: D 211 MET cc_start: 0.6718 (ttp) cc_final: 0.6455 (ttm) REVERT: D 218 LYS cc_start: 0.8027 (tmmt) cc_final: 0.7596 (tppt) REVERT: E 152 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7342 (mt0) REVERT: F 7 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7066 (p0) REVERT: F 188 VAL cc_start: 0.8889 (OUTLIER) cc_final: 0.8687 (m) REVERT: G 195 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8386 (tmmm) REVERT: H 92 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6817 (pm20) REVERT: H 104 ASP cc_start: 0.7642 (p0) cc_final: 0.7301 (p0) REVERT: H 133 SER cc_start: 0.8613 (OUTLIER) cc_final: 0.8178 (p) REVERT: I 91 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7238 (mt0) REVERT: J 79 ARG cc_start: 0.8165 (ptt-90) cc_final: 0.7743 (ptt-90) REVERT: J 182 MET cc_start: 0.8113 (mmt) cc_final: 0.7786 (mmm) REVERT: K 1 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6477 (tpt) REVERT: K 31 ASP cc_start: 0.8125 (p0) cc_final: 0.7372 (p0) REVERT: K 192 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: L 72 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7333 (pm20) REVERT: L 88 TYR cc_start: 0.6343 (t80) cc_final: 0.5938 (t80) REVERT: L 99 THR cc_start: 0.8792 (p) cc_final: 0.8564 (t) REVERT: L 117 GLU cc_start: 0.7432 (mp0) cc_final: 0.7194 (mp0) REVERT: M 107 TYR cc_start: 0.7770 (m-80) cc_final: 0.7546 (m-80) REVERT: N 112 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8105 (mt) REVERT: N 186 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.7270 (ttp-110) REVERT: P 101 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.6843 (mp10) REVERT: P 229 LEU cc_start: 0.8637 (mt) cc_final: 0.8344 (mp) REVERT: T 7 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7011 (p0) REVERT: T 178 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6950 (pm20) REVERT: X 79 ARG cc_start: 0.8173 (ptt-90) cc_final: 0.7785 (ptt-90) REVERT: X 182 MET cc_start: 0.8102 (mmt) cc_final: 0.7800 (mmm) REVERT: Y 28 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7203 (mtp) REVERT: Y 31 ASP cc_start: 0.8162 (p0) cc_final: 0.7563 (p0) REVERT: Z 72 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7345 (pm20) REVERT: Z 88 TYR cc_start: 0.6255 (t80) cc_final: 0.5856 (t80) REVERT: Z 99 THR cc_start: 0.8738 (p) cc_final: 0.8520 (t) REVERT: Z 117 GLU cc_start: 0.7448 (mp0) cc_final: 0.7207 (mp0) REVERT: a 100 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.5546 (tmt170) REVERT: a 107 TYR cc_start: 0.7904 (m-80) cc_final: 0.7672 (m-80) REVERT: b 186 ARG cc_start: 0.7557 (ttm-80) cc_final: 0.7213 (ttp-110) REVERT: W 84 LYS cc_start: 0.8365 (ptmt) cc_final: 0.8064 (pttt) REVERT: R 46 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7982 (tm-30) REVERT: O 45 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7667 (mptt) REVERT: O 88 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7278 (mmm160) REVERT: U 195 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8268 (ttmt) REVERT: S 105 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7655 (pt0) REVERT: Q 25 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.6458 (mpp) REVERT: Q 72 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7608 (mtt) REVERT: V 29 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8283 (ptt-90) REVERT: V 92 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6734 (pm20) REVERT: V 104 ASP cc_start: 0.7675 (p0) cc_final: 0.7358 (p0) REVERT: V 107 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: V 133 SER cc_start: 0.8629 (OUTLIER) cc_final: 0.8217 (p) outliers start: 397 outliers final: 231 residues processed: 1212 average time/residue: 1.5288 time to fit residues: 2296.9829 Evaluate side-chains 1136 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 873 time to evaluate : 5.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 192 GLU Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 79 ASP Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 101 GLN Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 148 SER Chi-restraints excluded: chain P residue 173 LEU Chi-restraints excluded: chain T residue 7 ASP Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 106 SER Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 177 SER Chi-restraints excluded: chain T residue 178 GLU Chi-restraints excluded: chain T residue 185 ASP Chi-restraints excluded: chain T residue 219 LEU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 104 THR Chi-restraints excluded: chain X residue 121 CYS Chi-restraints excluded: chain X residue 140 THR Chi-restraints excluded: chain X residue 142 SER Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain X residue 151 SER Chi-restraints excluded: chain X residue 198 THR Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 28 MET Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 190 ASN Chi-restraints excluded: chain Y residue 192 GLU Chi-restraints excluded: chain Y residue 195 THR Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 65 ILE Chi-restraints excluded: chain Z residue 72 GLU Chi-restraints excluded: chain Z residue 122 SER Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain Z residue 130 SER Chi-restraints excluded: chain Z residue 139 MET Chi-restraints excluded: chain Z residue 174 VAL Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 19 ASP Chi-restraints excluded: chain a residue 21 SER Chi-restraints excluded: chain a residue 34 SER Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain a residue 100 ARG Chi-restraints excluded: chain a residue 133 ASP Chi-restraints excluded: chain a residue 169 ASP Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 84 SER Chi-restraints excluded: chain b residue 120 SER Chi-restraints excluded: chain W residue 1 THR Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 112 SER Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 179 SER Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 43 ARG Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain O residue 115 CYS Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 194 THR Chi-restraints excluded: chain O residue 205 VAL Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 55 SER Chi-restraints excluded: chain U residue 71 ARG Chi-restraints excluded: chain U residue 195 LYS Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 226 ILE Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 105 GLU Chi-restraints excluded: chain S residue 134 SER Chi-restraints excluded: chain S residue 159 SER Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 184 VAL Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 184 MET Chi-restraints excluded: chain V residue 9 ASP Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 29 ARG Chi-restraints excluded: chain V residue 35 THR Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 107 GLU Chi-restraints excluded: chain V residue 124 SER Chi-restraints excluded: chain V residue 133 SER Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 200 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 304 optimal weight: 5.9990 chunk 170 optimal weight: 0.7980 chunk 456 optimal weight: 0.8980 chunk 373 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 chunk 549 optimal weight: 8.9990 chunk 593 optimal weight: 5.9990 chunk 489 optimal weight: 4.9990 chunk 544 optimal weight: 10.0000 chunk 187 optimal weight: 0.8980 chunk 440 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 HIS D 175 ASN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN F 90 GLN F 166 GLN K 101 ASN K 132 HIS L 29 GLN L 119 ASN M 151 ASN Y 61 GLN Y 101 ASN Y 193 ASN Z 9 GLN Z 29 GLN Z 119 ASN a 151 ASN R 175 ASN ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 GLN V 181 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 47846 Z= 0.163 Angle : 0.569 8.726 64732 Z= 0.309 Chirality : 0.043 0.185 7368 Planarity : 0.005 0.061 8314 Dihedral : 6.826 92.277 6915 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 6.04 % Allowed : 25.55 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.11), residues: 6102 helix: 1.61 (0.11), residues: 2212 sheet: -0.89 (0.13), residues: 1450 loop : -2.15 (0.11), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 100 HIS 0.006 0.001 HIS N 89 PHE 0.021 0.001 PHE I 36 TYR 0.015 0.001 TYR a 97 ARG 0.010 0.000 ARG U 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 936 time to evaluate : 5.987 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: A 239 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6894 (mt) REVERT: B 219 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7258 (ptt90) REVERT: D 46 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: D 211 MET cc_start: 0.6748 (ttp) cc_final: 0.6463 (ttm) REVERT: D 218 LYS cc_start: 0.7778 (tmmt) cc_final: 0.7486 (tppt) REVERT: E 152 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7272 (mt0) REVERT: F 153 TYR cc_start: 0.8090 (p90) cc_final: 0.7859 (p90) REVERT: G 195 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8379 (tmmm) REVERT: H 92 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6775 (pm20) REVERT: H 104 ASP cc_start: 0.7589 (p0) cc_final: 0.7291 (p0) REVERT: H 133 SER cc_start: 0.8639 (OUTLIER) cc_final: 0.8251 (p) REVERT: I 84 LYS cc_start: 0.8333 (ptmt) cc_final: 0.8024 (pttt) REVERT: J 79 ARG cc_start: 0.8099 (ptt-90) cc_final: 0.7548 (ptp90) REVERT: J 164 GLU cc_start: 0.7374 (mp0) cc_final: 0.7094 (mm-30) REVERT: J 182 MET cc_start: 0.7909 (mmt) cc_final: 0.7618 (mmm) REVERT: K 1 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.6376 (tpt) REVERT: K 41 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7862 (mmtp) REVERT: K 192 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6740 (tt0) REVERT: L 88 TYR cc_start: 0.6160 (t80) cc_final: 0.5805 (t80) REVERT: L 117 GLU cc_start: 0.7291 (mp0) cc_final: 0.7019 (mp0) REVERT: L 174 VAL cc_start: 0.7798 (OUTLIER) cc_final: 0.7551 (t) REVERT: N 186 ARG cc_start: 0.7360 (ttm-80) cc_final: 0.6996 (ttp-110) REVERT: P 229 LEU cc_start: 0.8601 (mt) cc_final: 0.8323 (mp) REVERT: T 122 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6639 (mtp85) REVERT: T 153 TYR cc_start: 0.7928 (p90) cc_final: 0.7694 (p90) REVERT: T 178 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6872 (pm20) REVERT: X 79 ARG cc_start: 0.8126 (ptt-90) cc_final: 0.7574 (ptp-170) REVERT: X 143 GLU cc_start: 0.6939 (mp0) cc_final: 0.6719 (mp0) REVERT: X 182 MET cc_start: 0.7890 (mmt) cc_final: 0.7604 (mmm) REVERT: Y 28 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7168 (mtp) REVERT: Y 31 ASP cc_start: 0.7969 (p0) cc_final: 0.7350 (p0) REVERT: Y 192 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6733 (tt0) REVERT: Z 88 TYR cc_start: 0.6093 (t80) cc_final: 0.5746 (t80) REVERT: Z 117 GLU cc_start: 0.7340 (mp0) cc_final: 0.7059 (mp0) REVERT: Z 174 VAL cc_start: 0.7842 (OUTLIER) cc_final: 0.7584 (t) REVERT: a 100 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.5291 (tmt170) REVERT: a 107 TYR cc_start: 0.7786 (m-80) cc_final: 0.7564 (m-80) REVERT: b 186 ARG cc_start: 0.7336 (ttm-80) cc_final: 0.6995 (ttp-110) REVERT: W 84 LYS cc_start: 0.8333 (ptmt) cc_final: 0.8047 (pttt) REVERT: R 71 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7452 (ptm) REVERT: O 45 LYS cc_start: 0.7728 (ttmm) cc_final: 0.7451 (mptt) REVERT: U 150 MET cc_start: 0.7416 (tmm) cc_final: 0.6963 (ttt) REVERT: Q 25 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.6372 (mpp) REVERT: V 92 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6717 (pm20) REVERT: V 104 ASP cc_start: 0.7659 (p0) cc_final: 0.7377 (p0) REVERT: V 133 SER cc_start: 0.8590 (OUTLIER) cc_final: 0.8290 (p) outliers start: 295 outliers final: 155 residues processed: 1150 average time/residue: 1.5890 time to fit residues: 2251.2267 Evaluate side-chains 1047 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 873 time to evaluate : 5.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 41 LYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 171 PHE Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 192 GLU Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 133 ASP Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 79 ASP Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 83 LEU Chi-restraints excluded: chain T residue 106 SER Chi-restraints excluded: chain T residue 122 ARG Chi-restraints excluded: chain T residue 156 CYS Chi-restraints excluded: chain T residue 177 SER Chi-restraints excluded: chain T residue 178 GLU Chi-restraints excluded: chain T residue 185 ASP Chi-restraints excluded: chain T residue 230 SER Chi-restraints excluded: chain X residue 4 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 28 MET Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 171 PHE Chi-restraints excluded: chain Y residue 190 ASN Chi-restraints excluded: chain Y residue 192 GLU Chi-restraints excluded: chain Y residue 195 THR Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 65 ILE Chi-restraints excluded: chain Z residue 97 MET Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain Z residue 139 MET Chi-restraints excluded: chain Z residue 174 VAL Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 21 SER Chi-restraints excluded: chain a residue 100 ARG Chi-restraints excluded: chain a residue 169 ASP Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 79 ASP Chi-restraints excluded: chain b residue 120 SER Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 112 SER Chi-restraints excluded: chain W residue 169 SER Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 115 CYS Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 194 THR Chi-restraints excluded: chain O residue 205 VAL Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 43 ASP Chi-restraints excluded: chain U residue 55 SER Chi-restraints excluded: chain U residue 71 ARG Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 134 SER Chi-restraints excluded: chain S residue 159 SER Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 184 MET Chi-restraints excluded: chain V residue 9 ASP Chi-restraints excluded: chain V residue 14 LEU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 124 SER Chi-restraints excluded: chain V residue 133 SER Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 200 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 542 optimal weight: 0.9990 chunk 413 optimal weight: 5.9990 chunk 285 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 262 optimal weight: 5.9990 chunk 368 optimal weight: 0.9990 chunk 551 optimal weight: 6.9990 chunk 583 optimal weight: 5.9990 chunk 288 optimal weight: 8.9990 chunk 522 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN F 90 GLN G 72 HIS J 80 GLN ** K 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 ASN T 90 GLN X 80 GLN Y 61 GLN Y 193 ASN Z 119 ASN R 175 ASN ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN U 72 HIS ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 181 GLN ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 47846 Z= 0.331 Angle : 0.668 7.824 64732 Z= 0.363 Chirality : 0.047 0.169 7368 Planarity : 0.005 0.068 8314 Dihedral : 6.437 87.018 6834 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 7.20 % Allowed : 25.04 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.10), residues: 6102 helix: 1.49 (0.11), residues: 2208 sheet: -0.68 (0.13), residues: 1442 loop : -2.12 (0.11), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 100 HIS 0.008 0.001 HIS T 65 PHE 0.027 0.002 PHE I 36 TYR 0.020 0.002 TYR K 117 ARG 0.009 0.001 ARG P 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 352 poor density : 889 time to evaluate : 4.947 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: A 45 LYS cc_start: 0.7871 (ttmm) cc_final: 0.7534 (mptt) REVERT: A 88 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7246 (mmm160) REVERT: A 239 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6797 (mt) REVERT: B 219 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7389 (ptt90) REVERT: C 72 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7558 (mtt) REVERT: C 226 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.7011 (ttt90) REVERT: D 46 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: D 211 MET cc_start: 0.6776 (ttp) cc_final: 0.6489 (ttm) REVERT: D 218 LYS cc_start: 0.7899 (tmmt) cc_final: 0.7637 (tppt) REVERT: E 152 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7380 (mt0) REVERT: E 234 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7170 (tt) REVERT: F 7 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7079 (p0) REVERT: F 61 LYS cc_start: 0.7608 (mtpt) cc_final: 0.7300 (ttmt) REVERT: G 195 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8372 (tmmm) REVERT: H 92 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6797 (pm20) REVERT: H 104 ASP cc_start: 0.7638 (p0) cc_final: 0.7347 (p0) REVERT: H 181 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6914 (tm-30) REVERT: H 186 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.6729 (mtp85) REVERT: I 63 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7790 (mp) REVERT: I 91 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7121 (mt0) REVERT: J 79 ARG cc_start: 0.8182 (ptt-90) cc_final: 0.7771 (ptt-90) REVERT: J 133 ASP cc_start: 0.7790 (t70) cc_final: 0.7553 (t70) REVERT: J 182 MET cc_start: 0.8040 (mmt) cc_final: 0.7725 (mmm) REVERT: K 1 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6583 (tpt) REVERT: K 31 ASP cc_start: 0.8138 (p0) cc_final: 0.7384 (p0) REVERT: K 41 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7766 (mmtp) REVERT: K 61 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: K 158 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6588 (mp0) REVERT: K 162 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7894 (ttmt) REVERT: K 192 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6850 (tt0) REVERT: L 72 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7239 (pm20) REVERT: L 117 GLU cc_start: 0.7353 (mp0) cc_final: 0.7097 (mp0) REVERT: L 186 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7408 (tmm-80) REVERT: M 100 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.5609 (tmt170) REVERT: N 112 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8101 (mt) REVERT: N 186 ARG cc_start: 0.7597 (ttm-80) cc_final: 0.7258 (ttp-110) REVERT: P 229 LEU cc_start: 0.8656 (mt) cc_final: 0.8346 (mp) REVERT: T 7 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7129 (p0) REVERT: T 122 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6773 (mtp85) REVERT: T 153 TYR cc_start: 0.8016 (p90) cc_final: 0.7786 (p90) REVERT: T 178 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6992 (pm20) REVERT: X 79 ARG cc_start: 0.8162 (ptt-90) cc_final: 0.7603 (ptp-170) REVERT: X 182 MET cc_start: 0.8018 (mmt) cc_final: 0.7707 (mmm) REVERT: Y 28 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7192 (mtp) REVERT: Y 31 ASP cc_start: 0.8136 (p0) cc_final: 0.7524 (p0) REVERT: Y 158 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6496 (mp0) REVERT: Y 192 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6711 (tt0) REVERT: Z 45 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.6776 (ttm) REVERT: Z 72 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7265 (pm20) REVERT: Z 88 TYR cc_start: 0.6160 (t80) cc_final: 0.5827 (t80) REVERT: Z 117 GLU cc_start: 0.7362 (mp0) cc_final: 0.7091 (mp0) REVERT: a 100 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.5576 (tmt170) REVERT: a 107 TYR cc_start: 0.7820 (m-80) cc_final: 0.7601 (m-80) REVERT: b 186 ARG cc_start: 0.7539 (ttm-80) cc_final: 0.7211 (ttp-110) REVERT: W 29 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8295 (mttt) REVERT: W 63 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7822 (mp) REVERT: W 84 LYS cc_start: 0.8427 (ptmt) cc_final: 0.8094 (pttt) REVERT: R 46 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: R 218 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7695 (tptp) REVERT: O 45 LYS cc_start: 0.7943 (ttmm) cc_final: 0.7651 (mptt) REVERT: U 232 ARG cc_start: 0.8430 (ttm110) cc_final: 0.8228 (ttm110) REVERT: S 152 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7253 (mt0) REVERT: Q 25 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.6477 (mpp) REVERT: Q 72 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7625 (mtt) REVERT: V 92 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6763 (pm20) REVERT: V 104 ASP cc_start: 0.7704 (p0) cc_final: 0.7407 (p0) REVERT: V 144 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.5771 (ppp80) outliers start: 352 outliers final: 208 residues processed: 1127 average time/residue: 1.5666 time to fit residues: 2176.8475 Evaluate side-chains 1097 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 848 time to evaluate : 5.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 186 ARG Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 3 MET Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 24 ASN Chi-restraints excluded: chain K residue 41 LYS Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 158 GLU Chi-restraints excluded: chain K residue 162 LYS Chi-restraints excluded: chain K residue 171 PHE Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 192 GLU Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 186 ARG Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 173 LEU Chi-restraints excluded: chain T residue 7 ASP Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 83 LEU Chi-restraints excluded: chain T residue 106 SER Chi-restraints excluded: chain T residue 122 ARG Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 156 CYS Chi-restraints excluded: chain T residue 178 GLU Chi-restraints excluded: chain T residue 230 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 140 THR Chi-restraints excluded: chain Y residue 2 GLU Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 24 ASN Chi-restraints excluded: chain Y residue 28 MET Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 158 GLU Chi-restraints excluded: chain Y residue 170 ARG Chi-restraints excluded: chain Y residue 171 PHE Chi-restraints excluded: chain Y residue 190 ASN Chi-restraints excluded: chain Y residue 192 GLU Chi-restraints excluded: chain Y residue 195 THR Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 45 MET Chi-restraints excluded: chain Z residue 65 ILE Chi-restraints excluded: chain Z residue 72 GLU Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 97 MET Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain Z residue 139 MET Chi-restraints excluded: chain Z residue 174 VAL Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 21 SER Chi-restraints excluded: chain a residue 100 ARG Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain a residue 169 ASP Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 120 SER Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 29 LYS Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 112 SER Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 179 SER Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 63 CYS Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 218 LYS Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain O residue 100 ASN Chi-restraints excluded: chain O residue 115 CYS Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 194 THR Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 205 VAL Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 43 ASP Chi-restraints excluded: chain U residue 55 SER Chi-restraints excluded: chain U residue 71 ARG Chi-restraints excluded: chain U residue 193 VAL Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 134 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 152 GLN Chi-restraints excluded: chain S residue 159 SER Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 184 VAL Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 184 MET Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain V residue 9 ASP Chi-restraints excluded: chain V residue 14 LEU Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 124 SER Chi-restraints excluded: chain V residue 144 ARG Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 200 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 486 optimal weight: 8.9990 chunk 331 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 434 optimal weight: 6.9990 chunk 240 optimal weight: 4.9990 chunk 498 optimal weight: 5.9990 chunk 403 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 298 optimal weight: 2.9990 chunk 524 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS D 175 ASN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 GLN ** K 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 ASN M 157 ASN N 65 GLN X 80 GLN Y 193 ASN Z 29 GLN Z 119 ASN R 175 ASN ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 181 GLN ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 47846 Z= 0.450 Angle : 0.755 9.204 64732 Z= 0.412 Chirality : 0.050 0.203 7368 Planarity : 0.006 0.072 8314 Dihedral : 6.655 86.194 6826 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 8.14 % Allowed : 24.75 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.10), residues: 6102 helix: 1.15 (0.11), residues: 2202 sheet: -0.60 (0.13), residues: 1446 loop : -2.17 (0.11), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP S 100 HIS 0.009 0.002 HIS T 65 PHE 0.028 0.003 PHE I 36 TYR 0.025 0.003 TYR a 97 ARG 0.011 0.001 ARG G 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 398 poor density : 870 time to evaluate : 6.078 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: A 88 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7507 (mmm160) REVERT: A 197 THR cc_start: 0.6830 (OUTLIER) cc_final: 0.6584 (p) REVERT: B 101 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.6891 (mp10) REVERT: B 219 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7424 (ptt90) REVERT: C 72 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7589 (mtt) REVERT: D 46 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: D 211 MET cc_start: 0.6827 (ttp) cc_final: 0.6547 (ttm) REVERT: D 218 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7705 (tptt) REVERT: E 234 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7202 (tt) REVERT: F 7 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7145 (p0) REVERT: F 61 LYS cc_start: 0.7595 (mtpt) cc_final: 0.7291 (ttmt) REVERT: F 122 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.6805 (mtp85) REVERT: G 195 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8376 (tmmm) REVERT: H 92 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6740 (pm20) REVERT: H 104 ASP cc_start: 0.7660 (p0) cc_final: 0.7413 (p0) REVERT: H 181 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7016 (tm-30) REVERT: I 63 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7763 (mp) REVERT: I 91 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7421 (mt0) REVERT: I 157 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: J 79 ARG cc_start: 0.8193 (ptt-90) cc_final: 0.7784 (ptt-90) REVERT: J 164 GLU cc_start: 0.7368 (mp0) cc_final: 0.7140 (mp0) REVERT: J 182 MET cc_start: 0.8032 (mmt) cc_final: 0.7686 (mmm) REVERT: K 1 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.6478 (tpt) REVERT: K 31 ASP cc_start: 0.8131 (p0) cc_final: 0.7411 (p0) REVERT: K 41 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7769 (mmtp) REVERT: K 61 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: K 158 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6443 (mp0) REVERT: K 162 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7939 (ttmt) REVERT: K 192 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6859 (tt0) REVERT: L 72 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7261 (pm20) REVERT: L 88 TYR cc_start: 0.6304 (t80) cc_final: 0.5914 (t80) REVERT: L 117 GLU cc_start: 0.7414 (mp0) cc_final: 0.7076 (mp0) REVERT: L 186 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7368 (tmm-80) REVERT: M 100 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.5676 (tmt170) REVERT: M 174 LEU cc_start: 0.8215 (tt) cc_final: 0.7971 (tm) REVERT: N 112 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8149 (mt) REVERT: P 229 LEU cc_start: 0.8716 (mt) cc_final: 0.8384 (mp) REVERT: T 7 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7142 (p0) REVERT: T 122 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6853 (mtp85) REVERT: T 178 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6986 (pm20) REVERT: X 79 ARG cc_start: 0.8170 (ptt-90) cc_final: 0.7796 (ptt-90) REVERT: X 182 MET cc_start: 0.8006 (mmt) cc_final: 0.7685 (mmm) REVERT: Y 28 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7265 (mtp) REVERT: Y 31 ASP cc_start: 0.8175 (p0) cc_final: 0.7649 (p0) REVERT: Y 41 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8205 (mttp) REVERT: Y 192 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6689 (tt0) REVERT: Z 72 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7264 (pm20) REVERT: Z 88 TYR cc_start: 0.6274 (t80) cc_final: 0.5966 (t80) REVERT: Z 117 GLU cc_start: 0.7409 (mp0) cc_final: 0.7060 (mp0) REVERT: Z 186 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7303 (tmm-80) REVERT: a 100 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.5704 (tmt170) REVERT: b 160 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7969 (mt) REVERT: b 186 ARG cc_start: 0.7538 (ttm-80) cc_final: 0.7204 (ttp-110) REVERT: W 63 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7806 (mp) REVERT: W 84 LYS cc_start: 0.8437 (ptmt) cc_final: 0.8099 (pttt) REVERT: R 46 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: R 71 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7404 (ptm) REVERT: R 218 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7814 (tptp) REVERT: O 45 LYS cc_start: 0.8090 (ttmm) cc_final: 0.7831 (mptt) REVERT: O 80 MET cc_start: 0.8466 (mmm) cc_final: 0.8184 (mmm) REVERT: U 27 MET cc_start: 0.7357 (mtt) cc_final: 0.7110 (mtt) REVERT: U 150 MET cc_start: 0.7475 (tmm) cc_final: 0.7061 (ttt) REVERT: S 152 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7195 (mt0) REVERT: Q 25 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.6492 (mpp) REVERT: Q 72 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7645 (mtt) REVERT: V 92 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6739 (pm20) REVERT: V 104 ASP cc_start: 0.7685 (p0) cc_final: 0.7381 (p0) outliers start: 398 outliers final: 247 residues processed: 1147 average time/residue: 1.5610 time to fit residues: 2214.6831 Evaluate side-chains 1136 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 847 time to evaluate : 5.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 29 ARG Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 157 GLU Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain J residue 3 MET Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 24 ASN Chi-restraints excluded: chain K residue 41 LYS Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 158 GLU Chi-restraints excluded: chain K residue 162 LYS Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 192 GLU Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 186 ARG Chi-restraints excluded: chain L residue 189 SER Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 47 ASP Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 79 ASP Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 173 LEU Chi-restraints excluded: chain T residue 7 ASP Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 83 LEU Chi-restraints excluded: chain T residue 106 SER Chi-restraints excluded: chain T residue 122 ARG Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 156 CYS Chi-restraints excluded: chain T residue 178 GLU Chi-restraints excluded: chain T residue 230 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 88 SER Chi-restraints excluded: chain X residue 104 THR Chi-restraints excluded: chain X residue 140 THR Chi-restraints excluded: chain X residue 174 VAL Chi-restraints excluded: chain X residue 198 THR Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 24 ASN Chi-restraints excluded: chain Y residue 28 MET Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 41 LYS Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 190 ASN Chi-restraints excluded: chain Y residue 192 GLU Chi-restraints excluded: chain Y residue 195 THR Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 65 ILE Chi-restraints excluded: chain Z residue 72 GLU Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 97 MET Chi-restraints excluded: chain Z residue 122 SER Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain Z residue 139 MET Chi-restraints excluded: chain Z residue 186 ARG Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 19 ASP Chi-restraints excluded: chain a residue 21 SER Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain a residue 100 ARG Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain a residue 169 ASP Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 79 ASP Chi-restraints excluded: chain b residue 120 SER Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 199 ILE Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 112 SER Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 179 SER Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 63 CYS Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 218 LYS Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain O residue 100 ASN Chi-restraints excluded: chain O residue 115 CYS Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 194 THR Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 55 SER Chi-restraints excluded: chain U residue 71 ARG Chi-restraints excluded: chain U residue 193 VAL Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 43 SER Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 134 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 152 GLN Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 184 VAL Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 48 GLU Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 173 SER Chi-restraints excluded: chain V residue 9 ASP Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 14 LEU Chi-restraints excluded: chain V residue 35 THR Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 124 SER Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain V residue 200 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 196 optimal weight: 2.9990 chunk 525 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 342 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 584 optimal weight: 0.9980 chunk 485 optimal weight: 6.9990 chunk 270 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 193 optimal weight: 0.5980 chunk 306 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN D 175 ASN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN K 189 HIS L 29 GLN L 119 ASN N 208 ASN ** T 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 132 HIS Y 193 ASN Z 29 GLN Z 119 ASN b 208 ASN R 175 ASN ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 181 GLN ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 47846 Z= 0.194 Angle : 0.592 9.077 64732 Z= 0.322 Chirality : 0.043 0.168 7368 Planarity : 0.005 0.064 8314 Dihedral : 6.172 88.835 6818 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 6.26 % Allowed : 27.13 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.11), residues: 6102 helix: 1.73 (0.11), residues: 2204 sheet: -0.42 (0.13), residues: 1456 loop : -1.96 (0.11), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 100 HIS 0.007 0.001 HIS T 65 PHE 0.020 0.001 PHE W 36 TYR 0.020 0.001 TYR a 97 ARG 0.010 0.000 ARG G 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 880 time to evaluate : 5.135 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: A 45 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7104 (mptt) REVERT: B 219 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7352 (ptt90) REVERT: D 211 MET cc_start: 0.6815 (ttp) cc_final: 0.6518 (ttm) REVERT: D 218 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7674 (tppt) REVERT: E 234 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7130 (tt) REVERT: F 61 LYS cc_start: 0.7571 (mtpt) cc_final: 0.7299 (ttmt) REVERT: F 122 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6642 (mtp85) REVERT: G 150 MET cc_start: 0.7429 (tmm) cc_final: 0.6944 (ttt) REVERT: H 92 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6793 (pm20) REVERT: H 181 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.6864 (tm-30) REVERT: I 63 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7765 (mp) REVERT: I 84 LYS cc_start: 0.8415 (ptmt) cc_final: 0.7951 (ptmm) REVERT: I 91 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7022 (mt0) REVERT: J 182 MET cc_start: 0.7871 (mmt) cc_final: 0.7564 (mmm) REVERT: K 1 MET cc_start: 0.6703 (OUTLIER) cc_final: 0.6324 (tpt) REVERT: K 31 ASP cc_start: 0.8055 (p0) cc_final: 0.7348 (p0) REVERT: K 41 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7637 (mmtp) REVERT: K 61 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: K 162 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7793 (ttmm) REVERT: K 192 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6660 (tt0) REVERT: L 88 TYR cc_start: 0.6222 (t80) cc_final: 0.5519 (t80) REVERT: L 117 GLU cc_start: 0.7295 (mp0) cc_final: 0.6979 (mp0) REVERT: L 174 VAL cc_start: 0.7868 (OUTLIER) cc_final: 0.7636 (t) REVERT: L 186 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7285 (tmm-80) REVERT: M 100 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.5469 (tmt170) REVERT: M 174 LEU cc_start: 0.8121 (tt) cc_final: 0.7903 (tm) REVERT: N 186 ARG cc_start: 0.7441 (ttm-80) cc_final: 0.7150 (ttp-110) REVERT: T 122 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6686 (mtp85) REVERT: T 178 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6934 (pm20) REVERT: X 79 ARG cc_start: 0.8124 (ptt-90) cc_final: 0.7570 (ptp-170) REVERT: X 182 MET cc_start: 0.7863 (mmt) cc_final: 0.7559 (mmm) REVERT: Y 28 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7156 (mtp) REVERT: Y 31 ASP cc_start: 0.8020 (p0) cc_final: 0.7423 (p0) REVERT: Y 41 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8163 (mttp) REVERT: Y 192 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6550 (tt0) REVERT: Z 88 TYR cc_start: 0.6161 (t80) cc_final: 0.5798 (t80) REVERT: Z 117 GLU cc_start: 0.7296 (mp0) cc_final: 0.6998 (mp0) REVERT: Z 174 VAL cc_start: 0.7901 (OUTLIER) cc_final: 0.7669 (t) REVERT: Z 186 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7257 (tmm-80) REVERT: a 100 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.5367 (tmt170) REVERT: b 74 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.5861 (mp0) REVERT: b 186 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.7146 (ttp-110) REVERT: W 63 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7788 (mp) REVERT: W 84 LYS cc_start: 0.8387 (ptmt) cc_final: 0.8066 (pttt) REVERT: R 46 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: R 218 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7681 (tptp) REVERT: O 45 LYS cc_start: 0.7932 (ttmm) cc_final: 0.7710 (mptt) REVERT: U 150 MET cc_start: 0.7459 (tmm) cc_final: 0.7007 (ttt) REVERT: S 152 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7225 (mt0) REVERT: Q 25 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.6441 (mpp) REVERT: V 92 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6744 (pm20) REVERT: V 104 ASP cc_start: 0.7695 (p0) cc_final: 0.7436 (p0) outliers start: 306 outliers final: 187 residues processed: 1084 average time/residue: 1.6044 time to fit residues: 2157.3475 Evaluate side-chains 1078 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 860 time to evaluate : 5.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 3 MET Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 24 ASN Chi-restraints excluded: chain K residue 41 LYS Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 162 LYS Chi-restraints excluded: chain K residue 171 PHE Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 192 GLU Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 186 ARG Chi-restraints excluded: chain L residue 189 SER Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain N residue 47 ASP Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 148 SER Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 83 LEU Chi-restraints excluded: chain T residue 122 ARG Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 134 ILE Chi-restraints excluded: chain T residue 156 CYS Chi-restraints excluded: chain T residue 178 GLU Chi-restraints excluded: chain T residue 195 LEU Chi-restraints excluded: chain T residue 230 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 88 SER Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 121 CYS Chi-restraints excluded: chain X residue 140 THR Chi-restraints excluded: chain X residue 170 MET Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 24 ASN Chi-restraints excluded: chain Y residue 28 MET Chi-restraints excluded: chain Y residue 41 LYS Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 171 PHE Chi-restraints excluded: chain Y residue 190 ASN Chi-restraints excluded: chain Y residue 192 GLU Chi-restraints excluded: chain Y residue 195 THR Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 65 ILE Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 97 MET Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain Z residue 139 MET Chi-restraints excluded: chain Z residue 174 VAL Chi-restraints excluded: chain Z residue 186 ARG Chi-restraints excluded: chain Z residue 189 SER Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 19 ASP Chi-restraints excluded: chain a residue 100 ARG Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain a residue 169 ASP Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 74 GLU Chi-restraints excluded: chain b residue 120 SER Chi-restraints excluded: chain b residue 199 ILE Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 112 SER Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 218 LYS Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 232 ILE Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain O residue 100 ASN Chi-restraints excluded: chain O residue 115 CYS Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 194 THR Chi-restraints excluded: chain O residue 205 VAL Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 55 SER Chi-restraints excluded: chain U residue 71 ARG Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 134 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 152 GLN Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 184 VAL Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 30 HIS Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain V residue 9 ASP Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 14 LEU Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 124 SER Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain V residue 200 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 563 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 332 optimal weight: 1.9990 chunk 426 optimal weight: 9.9990 chunk 330 optimal weight: 4.9990 chunk 491 optimal weight: 7.9990 chunk 326 optimal weight: 0.6980 chunk 582 optimal weight: 1.9990 chunk 364 optimal weight: 0.6980 chunk 354 optimal weight: 4.9990 chunk 268 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN D 175 ASN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN L 29 GLN L 119 ASN ** T 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 80 GLN Y 61 GLN Y 189 HIS Y 193 ASN Z 29 GLN Z 119 ASN W 85 GLN R 159 ASN R 175 ASN ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 32 ASN ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 181 GLN ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 47846 Z= 0.185 Angle : 0.573 9.975 64732 Z= 0.310 Chirality : 0.043 0.184 7368 Planarity : 0.005 0.062 8314 Dihedral : 5.755 87.417 6807 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.75 % Allowed : 27.72 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.11), residues: 6102 helix: 1.92 (0.11), residues: 2216 sheet: -0.25 (0.13), residues: 1462 loop : -1.86 (0.11), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 100 HIS 0.006 0.001 HIS T 65 PHE 0.021 0.001 PHE W 36 TYR 0.019 0.001 TYR a 97 ARG 0.012 0.000 ARG G 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 883 time to evaluate : 5.860 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: A 45 LYS cc_start: 0.7450 (mttp) cc_final: 0.7071 (mptt) REVERT: A 88 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7207 (mmm160) REVERT: A 202 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6382 (tt) REVERT: B 219 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7316 (ptt90) REVERT: D 211 MET cc_start: 0.6812 (ttp) cc_final: 0.6520 (ttm) REVERT: D 218 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7667 (tptt) REVERT: E 152 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7229 (mt0) REVERT: F 61 LYS cc_start: 0.7569 (mtpt) cc_final: 0.7334 (ttmt) REVERT: F 122 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6626 (mtp85) REVERT: G 150 MET cc_start: 0.7431 (tmm) cc_final: 0.6994 (ttt) REVERT: H 92 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6801 (pm20) REVERT: H 181 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6845 (tm-30) REVERT: I 63 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7785 (mp) REVERT: I 84 LYS cc_start: 0.8391 (ptmt) cc_final: 0.7943 (ptmm) REVERT: I 91 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.6945 (mt0) REVERT: J 79 ARG cc_start: 0.8128 (ptt-90) cc_final: 0.7505 (ptp-170) REVERT: J 182 MET cc_start: 0.7810 (mmt) cc_final: 0.7551 (mmm) REVERT: K 1 MET cc_start: 0.6665 (mmm) cc_final: 0.6294 (tpt) REVERT: K 31 ASP cc_start: 0.7964 (p0) cc_final: 0.7263 (p0) REVERT: K 192 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6551 (tt0) REVERT: L 88 TYR cc_start: 0.6115 (t80) cc_final: 0.5729 (t80) REVERT: L 117 GLU cc_start: 0.7262 (mp0) cc_final: 0.6941 (mp0) REVERT: L 174 VAL cc_start: 0.7860 (OUTLIER) cc_final: 0.7635 (t) REVERT: L 186 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7172 (tmm-80) REVERT: M 100 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.5479 (tmt170) REVERT: M 174 LEU cc_start: 0.8121 (tt) cc_final: 0.7919 (tm) REVERT: N 74 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.5803 (mp0) REVERT: N 186 ARG cc_start: 0.7452 (ttm-80) cc_final: 0.7145 (ttp-110) REVERT: T 122 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6670 (mtp85) REVERT: T 178 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6943 (pm20) REVERT: X 79 ARG cc_start: 0.8110 (ptt-90) cc_final: 0.7547 (ptp-170) REVERT: X 182 MET cc_start: 0.7787 (mmt) cc_final: 0.7531 (mmm) REVERT: Y 31 ASP cc_start: 0.8021 (p0) cc_final: 0.7468 (p0) REVERT: Y 192 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6445 (tt0) REVERT: Z 88 TYR cc_start: 0.6073 (t80) cc_final: 0.5729 (t80) REVERT: Z 117 GLU cc_start: 0.7278 (mp0) cc_final: 0.6951 (mp0) REVERT: Z 174 VAL cc_start: 0.7886 (OUTLIER) cc_final: 0.7660 (t) REVERT: Z 186 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7170 (tmm-80) REVERT: a 100 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.5406 (tmt170) REVERT: a 152 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.6952 (mp10) REVERT: b 74 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.5904 (mp0) REVERT: b 186 ARG cc_start: 0.7413 (ttm-80) cc_final: 0.7140 (ttp-110) REVERT: W 63 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7826 (mp) REVERT: W 84 LYS cc_start: 0.8403 (ptmt) cc_final: 0.8073 (pttt) REVERT: R 46 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: R 184 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7228 (p0) REVERT: R 218 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7723 (tptp) REVERT: U 150 MET cc_start: 0.7421 (tmm) cc_final: 0.6996 (ttt) REVERT: S 152 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7241 (mt0) REVERT: S 203 LYS cc_start: 0.8728 (ttmm) cc_final: 0.8389 (mtmm) REVERT: Q 25 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.6446 (mpp) REVERT: V 92 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6732 (pm20) REVERT: V 104 ASP cc_start: 0.7707 (p0) cc_final: 0.7424 (p0) outliers start: 281 outliers final: 189 residues processed: 1076 average time/residue: 1.5927 time to fit residues: 2122.8888 Evaluate side-chains 1070 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 852 time to evaluate : 5.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 227 ASP Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 3 MET Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 24 ASN Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 171 PHE Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 192 GLU Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 186 ARG Chi-restraints excluded: chain L residue 189 SER Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 47 ASP Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 148 SER Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 46 LEU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 83 LEU Chi-restraints excluded: chain T residue 122 ARG Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 156 CYS Chi-restraints excluded: chain T residue 178 GLU Chi-restraints excluded: chain T residue 195 LEU Chi-restraints excluded: chain T residue 230 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 88 SER Chi-restraints excluded: chain X residue 97 LYS Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 140 THR Chi-restraints excluded: chain X residue 170 MET Chi-restraints excluded: chain X residue 202 ARG Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 24 ASN Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 171 PHE Chi-restraints excluded: chain Y residue 190 ASN Chi-restraints excluded: chain Y residue 192 GLU Chi-restraints excluded: chain Y residue 195 THR Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 65 ILE Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 97 MET Chi-restraints excluded: chain Z residue 122 SER Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain Z residue 139 MET Chi-restraints excluded: chain Z residue 174 VAL Chi-restraints excluded: chain Z residue 186 ARG Chi-restraints excluded: chain a residue 19 ASP Chi-restraints excluded: chain a residue 100 ARG Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain a residue 152 GLN Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 74 GLU Chi-restraints excluded: chain b residue 120 SER Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 199 ILE Chi-restraints excluded: chain b residue 200 GLU Chi-restraints excluded: chain W residue 1 THR Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 112 SER Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 218 LYS Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 205 VAL Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 55 SER Chi-restraints excluded: chain U residue 71 ARG Chi-restraints excluded: chain U residue 136 MET Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 134 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 152 GLN Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 30 HIS Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain V residue 9 ASP Chi-restraints excluded: chain V residue 14 LEU Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 124 SER Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain V residue 200 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 360 optimal weight: 6.9990 chunk 232 optimal weight: 1.9990 chunk 347 optimal weight: 0.0060 chunk 175 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 370 optimal weight: 5.9990 chunk 396 optimal weight: 6.9990 chunk 287 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 457 optimal weight: 4.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN D 175 ASN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN I 85 GLN K 61 GLN L 29 GLN L 119 ASN ** T 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 GLN X 80 GLN Y 61 GLN Y 193 ASN Z 29 GLN Z 119 ASN R 175 ASN ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 32 ASN ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 181 GLN ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 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 : 0.002 0.039 47846 Z= 0.163 Angle : 0.547 11.913 64732 Z= 0.295 Chirality : 0.042 0.167 7368 Planarity : 0.004 0.058 8314 Dihedral : 5.395 87.522 6799 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.99 % Allowed : 28.68 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.11), residues: 6102 helix: 2.10 (0.11), residues: 2216 sheet: -0.14 (0.13), residues: 1464 loop : -1.75 (0.12), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 100 HIS 0.007 0.001 HIS T 65 PHE 0.020 0.001 PHE W 36 TYR 0.020 0.001 TYR T 137 ARG 0.013 0.000 ARG G 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 875 time to evaluate : 5.437 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: A 19 GLU cc_start: 0.7251 (mp0) cc_final: 0.7017 (mp0) REVERT: A 45 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7023 (mptt) REVERT: B 219 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7277 (ptt90) REVERT: C 57 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.6998 (m-30) REVERT: D 211 MET cc_start: 0.6802 (ttp) cc_final: 0.6508 (ttm) REVERT: D 218 LYS cc_start: 0.7926 (tmmt) cc_final: 0.7596 (tptt) REVERT: E 221 GLN cc_start: 0.7449 (pt0) cc_final: 0.7170 (mt0) REVERT: E 234 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7092 (tt) REVERT: F 61 LYS cc_start: 0.7612 (mtpt) cc_final: 0.7373 (ttmt) REVERT: F 122 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6629 (mtp85) REVERT: G 150 MET cc_start: 0.7459 (tmm) cc_final: 0.7048 (ttt) REVERT: H 92 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6787 (pm20) REVERT: H 181 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.6784 (tm-30) REVERT: I 63 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7773 (mp) REVERT: I 84 LYS cc_start: 0.8392 (ptmt) cc_final: 0.7969 (ptmm) REVERT: I 91 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6844 (mt0) REVERT: J 79 ARG cc_start: 0.8090 (ptt-90) cc_final: 0.7476 (ptp-170) REVERT: J 104 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8095 (m) REVERT: J 182 MET cc_start: 0.7738 (mmt) cc_final: 0.7515 (mmm) REVERT: K 1 MET cc_start: 0.6618 (OUTLIER) cc_final: 0.6260 (tpt) REVERT: K 31 ASP cc_start: 0.8023 (p0) cc_final: 0.7316 (p0) REVERT: K 162 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7753 (ttmm) REVERT: L 88 TYR cc_start: 0.6094 (t80) cc_final: 0.5721 (t80) REVERT: L 117 GLU cc_start: 0.7209 (mp0) cc_final: 0.6932 (mp0) REVERT: L 186 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7159 (tmm-80) REVERT: M 100 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.5535 (tmt170) REVERT: M 174 LEU cc_start: 0.8107 (tt) cc_final: 0.7879 (tm) REVERT: N 74 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.5957 (mp0) REVERT: N 186 ARG cc_start: 0.7420 (ttm-80) cc_final: 0.7128 (ttp-110) REVERT: T 122 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6607 (mtp85) REVERT: T 178 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.7018 (pm20) REVERT: X 79 ARG cc_start: 0.8078 (ptt-90) cc_final: 0.7523 (ptp-170) REVERT: X 182 MET cc_start: 0.7702 (mmt) cc_final: 0.7419 (mmm) REVERT: Y 31 ASP cc_start: 0.7951 (p0) cc_final: 0.7430 (p0) REVERT: Y 192 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6458 (tt0) REVERT: Z 88 TYR cc_start: 0.6064 (t80) cc_final: 0.5732 (t80) REVERT: Z 117 GLU cc_start: 0.7197 (mp0) cc_final: 0.6878 (mp0) REVERT: a 152 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.6901 (mp10) REVERT: b 74 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.5909 (mp0) REVERT: b 186 ARG cc_start: 0.7403 (ttm-80) cc_final: 0.7135 (ttp-110) REVERT: W 63 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7833 (mp) REVERT: W 84 LYS cc_start: 0.8390 (ptmt) cc_final: 0.8072 (pttt) REVERT: R 46 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: R 184 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7242 (p0) REVERT: R 218 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7700 (tptp) REVERT: O 88 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7464 (mmm160) REVERT: U 150 MET cc_start: 0.7411 (tmm) cc_final: 0.7016 (ttt) REVERT: S 152 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7246 (mt0) REVERT: Q 25 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.6370 (mpp) REVERT: V 92 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6736 (pm20) REVERT: V 104 ASP cc_start: 0.7688 (p0) cc_final: 0.7404 (p0) outliers start: 244 outliers final: 167 residues processed: 1047 average time/residue: 1.5848 time to fit residues: 2044.9566 Evaluate side-chains 1022 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 829 time to evaluate : 5.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 24 ASN Chi-restraints excluded: chain K residue 162 LYS Chi-restraints excluded: chain K residue 171 PHE Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 186 ARG Chi-restraints excluded: chain L residue 189 SER Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 47 ASP Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 148 SER Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 83 LEU Chi-restraints excluded: chain T residue 122 ARG Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 156 CYS Chi-restraints excluded: chain T residue 178 GLU Chi-restraints excluded: chain T residue 195 LEU Chi-restraints excluded: chain T residue 230 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 88 SER Chi-restraints excluded: chain X residue 97 LYS Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 121 CYS Chi-restraints excluded: chain X residue 140 THR Chi-restraints excluded: chain X residue 170 MET Chi-restraints excluded: chain X residue 202 ARG Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 24 ASN Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Y residue 170 ARG Chi-restraints excluded: chain Y residue 171 PHE Chi-restraints excluded: chain Y residue 190 ASN Chi-restraints excluded: chain Y residue 192 GLU Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 65 ILE Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 97 MET Chi-restraints excluded: chain Z residue 122 SER Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain Z residue 139 MET Chi-restraints excluded: chain Z residue 189 SER Chi-restraints excluded: chain a residue 19 ASP Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain a residue 152 GLN Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 74 GLU Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 199 ILE Chi-restraints excluded: chain b residue 200 GLU Chi-restraints excluded: chain W residue 1 THR Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 112 SER Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 218 LYS Chi-restraints excluded: chain R residue 232 ILE Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 55 SER Chi-restraints excluded: chain U residue 71 ARG Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 134 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 152 GLN Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 30 HIS Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain V residue 14 LEU Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 124 SER Chi-restraints excluded: chain V residue 169 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 529 optimal weight: 9.9990 chunk 557 optimal weight: 4.9990 chunk 508 optimal weight: 9.9990 chunk 542 optimal weight: 2.9990 chunk 326 optimal weight: 0.9980 chunk 236 optimal weight: 0.3980 chunk 425 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 chunk 490 optimal weight: 0.4980 chunk 513 optimal weight: 0.9980 chunk 540 optimal weight: 9.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN D 175 ASN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN E 204 GLN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN G 32 ASN H 53 GLN K 61 GLN L 119 ASN ** T 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 GLN X 80 GLN Y 61 GLN Y 193 ASN Z 119 ASN W 85 GLN R 175 ASN ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 32 ASN ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 GLN V 181 GLN ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 47846 Z= 0.180 Angle : 0.563 12.943 64732 Z= 0.303 Chirality : 0.043 0.192 7368 Planarity : 0.005 0.059 8314 Dihedral : 5.292 86.716 6789 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.93 % Allowed : 28.81 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.11), residues: 6102 helix: 2.13 (0.11), residues: 2208 sheet: -0.11 (0.13), residues: 1454 loop : -1.68 (0.12), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 100 HIS 0.007 0.001 HIS T 65 PHE 0.022 0.001 PHE W 36 TYR 0.023 0.001 TYR F 137 ARG 0.013 0.000 ARG G 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 854 time to evaluate : 5.377 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: A 19 GLU cc_start: 0.7254 (mp0) cc_final: 0.7024 (mp0) REVERT: A 45 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.7063 (mppt) REVERT: B 219 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7277 (ptt90) REVERT: D 211 MET cc_start: 0.6858 (ttp) cc_final: 0.6600 (ttm) REVERT: D 232 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8119 (mp) REVERT: E 152 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7264 (mt0) REVERT: E 234 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7097 (tt) REVERT: F 61 LYS cc_start: 0.7604 (mtpt) cc_final: 0.7367 (ttmt) REVERT: F 122 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6627 (mtp85) REVERT: G 150 MET cc_start: 0.7487 (tmm) cc_final: 0.7093 (ttt) REVERT: H 92 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6796 (pm20) REVERT: H 181 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: I 63 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7778 (mp) REVERT: I 84 LYS cc_start: 0.8412 (ptmt) cc_final: 0.7973 (ptmm) REVERT: I 91 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6890 (mt0) REVERT: J 79 ARG cc_start: 0.8102 (ptt-90) cc_final: 0.7483 (ptp-170) REVERT: J 104 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8096 (m) REVERT: J 182 MET cc_start: 0.7732 (mmt) cc_final: 0.7519 (mmm) REVERT: K 1 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6309 (tpt) REVERT: K 31 ASP cc_start: 0.7978 (p0) cc_final: 0.7304 (p0) REVERT: K 158 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.6220 (mp0) REVERT: K 162 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7837 (ttmt) REVERT: L 88 TYR cc_start: 0.6113 (t80) cc_final: 0.5719 (t80) REVERT: L 117 GLU cc_start: 0.7194 (mp0) cc_final: 0.6910 (mp0) REVERT: L 186 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7121 (tmm-80) REVERT: M 100 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.5466 (tmt170) REVERT: M 152 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.6620 (mp10) REVERT: M 174 LEU cc_start: 0.8092 (tt) cc_final: 0.7878 (tm) REVERT: N 74 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.5949 (mp0) REVERT: N 186 ARG cc_start: 0.7472 (ttm-80) cc_final: 0.7164 (ttp-110) REVERT: T 122 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6620 (mtp85) REVERT: T 178 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6982 (pm20) REVERT: X 79 ARG cc_start: 0.8097 (ptt-90) cc_final: 0.7525 (ptp-170) REVERT: X 182 MET cc_start: 0.7718 (mmt) cc_final: 0.7441 (mmm) REVERT: Y 31 ASP cc_start: 0.7979 (p0) cc_final: 0.7452 (p0) REVERT: Y 55 GLN cc_start: 0.7437 (tp40) cc_final: 0.7090 (mm-40) REVERT: Y 158 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.6171 (mp0) REVERT: Y 192 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6448 (tt0) REVERT: Z 88 TYR cc_start: 0.6078 (t80) cc_final: 0.5731 (t80) REVERT: Z 117 GLU cc_start: 0.7190 (mp0) cc_final: 0.6861 (mp0) REVERT: a 152 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6904 (mp10) REVERT: b 74 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.5899 (mp0) REVERT: b 186 ARG cc_start: 0.7429 (ttm-80) cc_final: 0.7157 (ttp-110) REVERT: W 29 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8087 (mttt) REVERT: W 63 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7809 (mp) REVERT: W 84 LYS cc_start: 0.8408 (ptmt) cc_final: 0.8075 (pttt) REVERT: R 46 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: R 184 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7279 (p0) REVERT: R 218 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7716 (tptp) REVERT: U 150 MET cc_start: 0.7414 (tmm) cc_final: 0.7039 (ttt) REVERT: U 213 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8330 (mt) REVERT: S 105 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7674 (pt0) REVERT: S 152 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7224 (mt0) REVERT: Q 25 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6416 (mpp) REVERT: V 92 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6780 (pm20) REVERT: V 104 ASP cc_start: 0.7702 (p0) cc_final: 0.7428 (p0) outliers start: 241 outliers final: 176 residues processed: 1021 average time/residue: 1.6204 time to fit residues: 2034.6858 Evaluate side-chains 1046 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 837 time to evaluate : 5.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 24 ASN Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 158 GLU Chi-restraints excluded: chain K residue 162 LYS Chi-restraints excluded: chain K residue 171 PHE Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 186 ARG Chi-restraints excluded: chain L residue 189 SER Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 152 GLN Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 47 ASP Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 148 SER Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 46 LEU Chi-restraints excluded: chain T residue 122 ARG Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 156 CYS Chi-restraints excluded: chain T residue 178 GLU Chi-restraints excluded: chain T residue 195 LEU Chi-restraints excluded: chain T residue 230 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 88 SER Chi-restraints excluded: chain X residue 97 LYS Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 121 CYS Chi-restraints excluded: chain X residue 140 THR Chi-restraints excluded: chain X residue 170 MET Chi-restraints excluded: chain X residue 202 ARG Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 24 ASN Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Y residue 158 GLU Chi-restraints excluded: chain Y residue 170 ARG Chi-restraints excluded: chain Y residue 171 PHE Chi-restraints excluded: chain Y residue 192 GLU Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 65 ILE Chi-restraints excluded: chain Z residue 72 GLU Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 97 MET Chi-restraints excluded: chain Z residue 122 SER Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain Z residue 139 MET Chi-restraints excluded: chain Z residue 189 SER Chi-restraints excluded: chain a residue 19 ASP Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain a residue 152 GLN Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 169 ASP Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 74 GLU Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 199 ILE Chi-restraints excluded: chain b residue 200 GLU Chi-restraints excluded: chain W residue 1 THR Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 29 LYS Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 112 SER Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 218 LYS Chi-restraints excluded: chain R residue 232 ILE Chi-restraints excluded: chain R residue 233 GLU Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 64 SER Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 71 ARG Chi-restraints excluded: chain U residue 213 LEU Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 105 GLU Chi-restraints excluded: chain S residue 134 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 152 GLN Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 184 VAL Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 30 HIS Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 124 SER Chi-restraints excluded: chain V residue 169 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 356 optimal weight: 0.7980 chunk 573 optimal weight: 0.3980 chunk 350 optimal weight: 0.0570 chunk 272 optimal weight: 0.9980 chunk 398 optimal weight: 0.9990 chunk 601 optimal weight: 0.9990 chunk 553 optimal weight: 9.9990 chunk 479 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 370 optimal weight: 3.9990 chunk 293 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN D 175 ASN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN E 204 GLN E 225 ASN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN G 32 ASN H 53 GLN K 61 GLN L 119 ASN ** T 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 GLN X 80 GLN Y 61 GLN Y 193 ASN Z 119 ASN R 23 GLN R 175 ASN ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 32 ASN ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 GLN V 181 GLN ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 47846 Z= 0.146 Angle : 0.532 13.950 64732 Z= 0.286 Chirality : 0.042 0.176 7368 Planarity : 0.004 0.057 8314 Dihedral : 5.112 87.416 6788 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.17 % Allowed : 29.56 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.11), residues: 6102 helix: 2.26 (0.11), residues: 2212 sheet: 0.03 (0.14), residues: 1464 loop : -1.57 (0.12), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 100 HIS 0.007 0.001 HIS T 65 PHE 0.019 0.001 PHE W 36 TYR 0.021 0.001 TYR T 137 ARG 0.014 0.000 ARG G 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 867 time to evaluate : 5.342 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: A 202 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6330 (tt) REVERT: A 228 ARG cc_start: 0.7039 (mtm110) cc_final: 0.6533 (mtm-85) REVERT: C 72 MET cc_start: 0.7937 (mtm) cc_final: 0.7553 (mtt) REVERT: D 232 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8096 (mp) REVERT: E 152 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7241 (mt0) REVERT: F 26 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.5485 (mpp) REVERT: F 61 LYS cc_start: 0.7565 (mtpt) cc_final: 0.7353 (ttmt) REVERT: F 122 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6610 (mtp85) REVERT: G 150 MET cc_start: 0.7434 (tmm) cc_final: 0.7077 (ttt) REVERT: H 92 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6787 (pm20) REVERT: H 104 ASP cc_start: 0.7669 (p0) cc_final: 0.7388 (p0) REVERT: H 181 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.6814 (tm-30) REVERT: I 63 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7815 (mp) REVERT: I 84 LYS cc_start: 0.8366 (ptmt) cc_final: 0.7959 (ptmm) REVERT: I 91 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6677 (tm-30) REVERT: J 79 ARG cc_start: 0.8005 (ptt-90) cc_final: 0.7400 (ptp-170) REVERT: J 182 MET cc_start: 0.7717 (mmt) cc_final: 0.7402 (mmm) REVERT: K 1 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.6361 (tpt) REVERT: K 31 ASP cc_start: 0.7950 (p0) cc_final: 0.7290 (p0) REVERT: K 162 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7821 (ttmt) REVERT: L 88 TYR cc_start: 0.6055 (t80) cc_final: 0.5690 (t80) REVERT: L 117 GLU cc_start: 0.7154 (mp0) cc_final: 0.6920 (mp0) REVERT: L 186 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7104 (tmm-80) REVERT: M 100 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.5473 (tmt170) REVERT: M 125 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8137 (p0) REVERT: M 152 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.6841 (mp10) REVERT: M 174 LEU cc_start: 0.8102 (tt) cc_final: 0.7889 (tm) REVERT: N 74 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6024 (mp0) REVERT: N 186 ARG cc_start: 0.7408 (ttm-80) cc_final: 0.7111 (ttp-110) REVERT: T 122 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6628 (mtp85) REVERT: X 79 ARG cc_start: 0.8023 (ptt-90) cc_final: 0.7470 (ptp-170) REVERT: X 182 MET cc_start: 0.7690 (mmt) cc_final: 0.7426 (mmm) REVERT: Y 31 ASP cc_start: 0.7914 (p0) cc_final: 0.7403 (p0) REVERT: Z 88 TYR cc_start: 0.6036 (t80) cc_final: 0.5715 (t80) REVERT: Z 117 GLU cc_start: 0.7141 (mp0) cc_final: 0.6861 (mp0) REVERT: b 74 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.5945 (mp0) REVERT: b 186 ARG cc_start: 0.7379 (ttm-80) cc_final: 0.7060 (ttp-110) REVERT: W 63 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7863 (mp) REVERT: W 84 LYS cc_start: 0.8390 (ptmt) cc_final: 0.8049 (pttt) REVERT: R 46 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: R 218 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7635 (tptp) REVERT: U 150 MET cc_start: 0.7394 (tmm) cc_final: 0.7034 (ttt) REVERT: U 213 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8274 (mt) REVERT: V 92 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6743 (pm20) REVERT: V 104 ASP cc_start: 0.7757 (p0) cc_final: 0.7499 (p0) outliers start: 204 outliers final: 136 residues processed: 1009 average time/residue: 1.6436 time to fit residues: 2039.0317 Evaluate side-chains 1003 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 845 time to evaluate : 5.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 24 ASN Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 162 LYS Chi-restraints excluded: chain K residue 171 PHE Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 186 ARG Chi-restraints excluded: chain L residue 189 SER Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain M residue 125 ASP Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 152 GLN Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 47 ASP Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 148 SER Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 122 ARG Chi-restraints excluded: chain T residue 156 CYS Chi-restraints excluded: chain T residue 195 LEU Chi-restraints excluded: chain T residue 230 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 88 SER Chi-restraints excluded: chain X residue 121 CYS Chi-restraints excluded: chain X residue 140 THR Chi-restraints excluded: chain X residue 170 MET Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 24 ASN Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Y residue 170 ARG Chi-restraints excluded: chain Y residue 171 PHE Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 65 ILE Chi-restraints excluded: chain Z residue 97 MET Chi-restraints excluded: chain Z residue 122 SER Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain Z residue 139 MET Chi-restraints excluded: chain Z residue 189 SER Chi-restraints excluded: chain a residue 19 ASP Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 74 GLU Chi-restraints excluded: chain b residue 200 GLU Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 112 SER Chi-restraints excluded: chain W residue 169 SER Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 218 LYS Chi-restraints excluded: chain R residue 232 ILE Chi-restraints excluded: chain R residue 233 GLU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 71 ARG Chi-restraints excluded: chain U residue 213 LEU Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 134 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 184 VAL Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain Q residue 30 HIS Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 93 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 380 optimal weight: 7.9990 chunk 510 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 441 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 479 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 492 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS B 168 ASN D 175 ASN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN E 221 GLN E 224 GLN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN G 32 ASN H 53 GLN K 61 GLN L 70 ASN L 119 ASN ** T 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 80 GLN Y 61 GLN Y 193 ASN Z 70 ASN Z 119 ASN R 23 GLN R 175 ASN O 150 GLN U 32 ASN ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 204 GLN S 225 ASN V 53 GLN V 181 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.166229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134866 restraints weight = 54959.176| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.69 r_work: 0.3375 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 47846 Z= 0.343 Angle : 0.675 13.719 64732 Z= 0.365 Chirality : 0.047 0.203 7368 Planarity : 0.006 0.066 8314 Dihedral : 5.498 85.606 6782 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.42 % Allowed : 29.34 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.11), residues: 6102 helix: 1.76 (0.11), residues: 2204 sheet: -0.15 (0.13), residues: 1444 loop : -1.75 (0.11), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 100 HIS 0.009 0.001 HIS T 65 PHE 0.029 0.002 PHE W 36 TYR 0.022 0.002 TYR T 137 ARG 0.014 0.001 ARG G 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28132.83 seconds wall clock time: 491 minutes 27.51 seconds (29487.51 seconds total)