Starting phenix.real_space_refine (version: dev) on Thu Dec 22 09:39:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu3_10586/12_2022/6tu3_10586.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu3_10586/12_2022/6tu3_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_10586/12_2022/6tu3_10586.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu3_10586/12_2022/6tu3_10586.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu3_10586/12_2022/6tu3_10586.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu3_10586/12_2022/6tu3_10586.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 25.26, per 1000 atoms: 0.54 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: 18.97 Conformation dependent library (CDL) restraints added in 7.5 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: 2.85 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: 19.89 Time building geometry restraints manager: 20.57 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 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. 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: 4.290 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: 0.030 Extract box with map and model: 17.600 Check model and map are aligned: 0.610 Convert atoms to be neutral: 0.340 Process input model: 117.380 Find NCS groups from input model: 4.710 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 8.29 % 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 *********************** 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 : 5.418 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 outliers start: 405 outliers final: 197 residues processed: 1476 average time/residue: 1.5083 time to fit residues: 2762.5247 Evaluate side-chains 1097 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 900 time to evaluate : 5.372 Switching outliers to nearest non-outliers outliers start: 197 outliers final: 168 residues processed: 32 average time/residue: 0.5941 time to fit residues: 37.6050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 510 optimal weight: 9.9990 chunk 457 optimal weight: 1.9990 chunk 254 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 308 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 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: 3.7990 ------------------------------------------------------------------------------- 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 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 ASN H 110 GLN 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: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 47846 Z= 0.407 Angle : 0.756 10.437 64732 Z= 0.412 Chirality : 0.049 0.174 7368 Planarity : 0.006 0.069 8314 Dihedral : 5.087 27.643 6740 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer Outliers : 8.86 % 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: -1.53 (0.10), residues: 6102 helix: 0.79 (0.11), residues: 2202 sheet: -1.39 (0.13), residues: 1428 loop : -2.46 (0.11), residues: 2472 *********************** 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 1371 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 433 poor density : 938 time to evaluate : 5.662 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 outliers start: 433 outliers final: 270 residues processed: 1252 average time/residue: 1.4562 time to fit residues: 2293.8199 Evaluate side-chains 1152 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 882 time to evaluate : 5.542 Switching outliers to nearest non-outliers outliers start: 270 outliers final: 226 residues processed: 47 average time/residue: 0.6833 time to fit residues: 56.5221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 304 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 456 optimal weight: 0.8980 chunk 373 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 549 optimal weight: 9.9990 chunk 593 optimal weight: 6.9990 chunk 489 optimal weight: 9.9990 chunk 544 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 440 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 K 132 HIS K 193 ASN L 29 GLN L 119 ASN M 151 ASN Y 61 GLN 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 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 GLN V 181 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 47846 Z= 0.227 Angle : 0.616 8.932 64732 Z= 0.336 Chirality : 0.044 0.160 7368 Planarity : 0.005 0.069 8314 Dihedral : 4.696 24.737 6740 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 8.51 % 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: -0.83 (0.10), residues: 6102 helix: 1.43 (0.11), residues: 2204 sheet: -0.91 (0.13), residues: 1430 loop : -2.20 (0.11), residues: 2468 *********************** 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 1344 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 416 poor density : 928 time to evaluate : 5.822 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 outliers start: 416 outliers final: 263 residues processed: 1242 average time/residue: 1.4254 time to fit residues: 2238.7652 Evaluate side-chains 1118 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 855 time to evaluate : 5.442 Switching outliers to nearest non-outliers outliers start: 263 outliers final: 222 residues processed: 42 average time/residue: 0.6552 time to fit residues: 50.5829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 542 optimal weight: 4.9990 chunk 413 optimal weight: 5.9990 chunk 285 optimal weight: 0.0670 chunk 60 optimal weight: 0.9980 chunk 262 optimal weight: 0.6980 chunk 368 optimal weight: 6.9990 chunk 551 optimal weight: 2.9990 chunk 583 optimal weight: 10.0000 chunk 288 optimal weight: 7.9990 chunk 522 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 overall best weight: 1.1320 ------------------------------------------------------------------------------- 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 152 GLN F 90 GLN I 85 GLN J 80 GLN L 119 ASN X 80 GLN Y 61 GLN Y 132 HIS Y 193 ASN Z 9 GLN Z 119 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 Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 47846 Z= 0.178 Angle : 0.568 7.724 64732 Z= 0.308 Chirality : 0.043 0.171 7368 Planarity : 0.005 0.065 8314 Dihedral : 4.480 21.631 6740 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 7.57 % 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: -0.40 (0.11), residues: 6102 helix: 1.78 (0.11), residues: 2218 sheet: -0.62 (0.13), residues: 1448 loop : -2.03 (0.11), residues: 2436 *********************** 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 1254 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 370 poor density : 884 time to evaluate : 5.480 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 outliers start: 370 outliers final: 268 residues processed: 1161 average time/residue: 1.4328 time to fit residues: 2106.3177 Evaluate side-chains 1106 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 838 time to evaluate : 5.379 Switching outliers to nearest non-outliers outliers start: 268 outliers final: 226 residues processed: 42 average time/residue: 0.9417 time to fit residues: 62.5662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 486 optimal weight: 7.9990 chunk 331 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 434 optimal weight: 6.9990 chunk 240 optimal weight: 5.9990 chunk 498 optimal weight: 6.9990 chunk 403 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 298 optimal weight: 3.9990 chunk 524 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 204 GLN G 72 HIS ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 GLN L 119 ASN N 65 GLN T 90 GLN X 80 GLN Y 132 HIS Y 193 ASN Z 119 ASN W 85 GLN R 159 ASN R 175 ASN ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 152 GLN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.075 47846 Z= 0.467 Angle : 0.763 8.941 64732 Z= 0.416 Chirality : 0.051 0.185 7368 Planarity : 0.006 0.073 8314 Dihedral : 5.046 28.186 6740 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 8.65 % 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: -0.79 (0.10), residues: 6102 helix: 1.23 (0.11), residues: 2204 sheet: -0.62 (0.13), residues: 1446 loop : -2.12 (0.11), residues: 2452 *********************** 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 1291 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 423 poor density : 868 time to evaluate : 5.163 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 outliers start: 423 outliers final: 300 residues processed: 1185 average time/residue: 1.4060 time to fit residues: 2108.2374 Evaluate side-chains 1157 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 857 time to evaluate : 5.354 Switching outliers to nearest non-outliers outliers start: 300 outliers final: 250 residues processed: 50 average time/residue: 0.8501 time to fit residues: 68.4280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 196 optimal weight: 3.9990 chunk 525 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 342 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 584 optimal weight: 1.9990 chunk 485 optimal weight: 5.9990 chunk 270 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 chunk 306 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 193 GLN D 175 ASN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN J 80 GLN L 29 GLN L 119 ASN N 208 ASN T 90 GLN X 80 GLN Y 132 HIS Y 193 ASN Z 29 GLN Z 119 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 47846 Z= 0.184 Angle : 0.582 8.549 64732 Z= 0.316 Chirality : 0.043 0.164 7368 Planarity : 0.005 0.065 8314 Dihedral : 4.553 23.425 6740 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 7.28 % 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: -0.21 (0.11), residues: 6102 helix: 1.83 (0.11), residues: 2200 sheet: -0.40 (0.13), residues: 1462 loop : -1.87 (0.11), residues: 2440 *********************** 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 1249 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 893 time to evaluate : 5.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 356 outliers final: 258 residues processed: 1181 average time/residue: 1.4482 time to fit residues: 2185.4544 Evaluate side-chains 1120 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 862 time to evaluate : 5.767 Switching outliers to nearest non-outliers outliers start: 258 outliers final: 231 residues processed: 27 average time/residue: 0.6819 time to fit residues: 36.4188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 563 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 332 optimal weight: 4.9990 chunk 426 optimal weight: 6.9990 chunk 330 optimal weight: 0.9980 chunk 491 optimal weight: 5.9990 chunk 326 optimal weight: 3.9990 chunk 582 optimal weight: 4.9990 chunk 364 optimal weight: 0.9980 chunk 354 optimal weight: 0.8980 chunk 268 optimal weight: 0.6980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN B 168 ASN D 175 ASN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN J 80 GLN K 189 HIS L 119 ASN T 90 GLN X 80 GLN Y 193 ASN Z 9 GLN Z 119 ASN 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 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 47846 Z= 0.193 Angle : 0.582 9.385 64732 Z= 0.315 Chirality : 0.043 0.184 7368 Planarity : 0.005 0.064 8314 Dihedral : 4.449 21.861 6740 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 6.77 % 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: -0.07 (0.11), residues: 6102 helix: 1.93 (0.11), residues: 2210 sheet: -0.28 (0.13), residues: 1464 loop : -1.82 (0.11), residues: 2428 *********************** 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 1214 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 883 time to evaluate : 5.546 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 outliers start: 331 outliers final: 267 residues processed: 1156 average time/residue: 1.4416 time to fit residues: 2127.6278 Evaluate side-chains 1117 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 850 time to evaluate : 5.741 Switching outliers to nearest non-outliers outliers start: 267 outliers final: 238 residues processed: 30 average time/residue: 0.7490 time to fit residues: 41.0848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 360 optimal weight: 5.9990 chunk 232 optimal weight: 0.6980 chunk 347 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 114 optimal weight: 8.9990 chunk 112 optimal weight: 0.8980 chunk 370 optimal weight: 8.9990 chunk 396 optimal weight: 0.9990 chunk 287 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 457 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN D 175 ASN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN E 204 GLN E 225 ASN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 GLN J 80 GLN L 119 ASN ** T 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 GLN X 80 GLN Y 189 HIS Y 193 ASN 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 180 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 47846 Z= 0.200 Angle : 0.587 11.148 64732 Z= 0.317 Chirality : 0.043 0.158 7368 Planarity : 0.005 0.063 8314 Dihedral : 4.420 21.835 6740 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 6.57 % 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: -0.02 (0.11), residues: 6102 helix: 1.94 (0.11), residues: 2214 sheet: -0.23 (0.13), residues: 1462 loop : -1.78 (0.11), residues: 2426 *********************** 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 1192 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 871 time to evaluate : 5.450 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 outliers start: 321 outliers final: 268 residues processed: 1139 average time/residue: 1.3636 time to fit residues: 1979.5109 Evaluate side-chains 1124 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 856 time to evaluate : 4.925 Switching outliers to nearest non-outliers outliers start: 268 outliers final: 242 residues processed: 26 average time/residue: 0.6931 time to fit residues: 34.3615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 508 optimal weight: 30.0000 chunk 542 optimal weight: 5.9990 chunk 326 optimal weight: 3.9990 chunk 236 optimal weight: 6.9990 chunk 425 optimal weight: 0.9990 chunk 166 optimal weight: 7.9990 chunk 490 optimal weight: 0.5980 chunk 513 optimal weight: 0.9980 chunk 540 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN D 175 ASN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 GLN L 119 ASN ** T 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 GLN X 80 GLN Y 193 ASN Z 119 ASN R 175 ASN O 68 HIS ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 32 ASN ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 47846 Z= 0.203 Angle : 0.588 12.433 64732 Z= 0.317 Chirality : 0.044 0.190 7368 Planarity : 0.005 0.064 8314 Dihedral : 4.408 22.075 6740 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer Outliers : 6.14 % 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: 0.02 (0.11), residues: 6102 helix: 1.96 (0.11), residues: 2214 sheet: -0.22 (0.13), residues: 1466 loop : -1.73 (0.12), residues: 2422 *********************** 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 1163 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 863 time to evaluate : 5.452 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 outliers start: 300 outliers final: 260 residues processed: 1129 average time/residue: 1.4097 time to fit residues: 2018.5200 Evaluate side-chains 1102 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 842 time to evaluate : 5.271 Switching outliers to nearest non-outliers outliers start: 260 outliers final: 240 residues processed: 20 average time/residue: 0.8274 time to fit residues: 30.7928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 356 optimal weight: 2.9990 chunk 573 optimal weight: 0.6980 chunk 350 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 chunk 398 optimal weight: 1.9990 chunk 601 optimal weight: 3.9990 chunk 553 optimal weight: 10.0000 chunk 479 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 370 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN D 175 ASN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 ASN ** T 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 GLN X 80 GLN Y 193 ASN 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** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 47846 Z= 0.252 Angle : 0.626 12.866 64732 Z= 0.338 Chirality : 0.045 0.167 7368 Planarity : 0.005 0.066 8314 Dihedral : 4.529 22.920 6740 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 5.79 % 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: -0.07 (0.11), residues: 6102 helix: 1.85 (0.11), residues: 2210 sheet: -0.23 (0.13), residues: 1462 loop : -1.76 (0.11), residues: 2430 ********************** 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 1129 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 846 time to evaluate : 5.963 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 outliers start: 283 outliers final: 254 residues processed: 1103 average time/residue: 1.3920 time to fit residues: 1951.1273 Evaluate side-chains 1094 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 840 time to evaluate : 5.282 Switching outliers to nearest non-outliers outliers start: 254 outliers final: 241 residues processed: 13 average time/residue: 1.0454 time to fit residues: 25.5472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 380 optimal weight: 3.9990 chunk 510 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 441 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 479 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 492 optimal weight: 0.0050 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 overall best weight: 2.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 ASN D 175 ASN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 175 ASN ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 32 ASN ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.167543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.135549 restraints weight = 54834.266| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.69 r_work: 0.3406 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 47846 Z= 0.254 Angle : 0.631 13.719 64732 Z= 0.341 Chirality : 0.045 0.199 7368 Planarity : 0.005 0.065 8314 Dihedral : 4.556 23.169 6740 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 5.65 % 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: -0.10 (0.11), residues: 6102 helix: 1.81 (0.11), residues: 2208 sheet: -0.24 (0.13), residues: 1462 loop : -1.76 (0.11), residues: 2432 =============================================================================== Job complete usr+sys time: 27520.78 seconds wall clock time: 479 minutes 56.94 seconds (28796.94 seconds total)