Starting phenix.real_space_refine on Sat Feb 24 18:51:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rgq_4877/02_2024/6rgq_4877_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rgq_4877/02_2024/6rgq_4877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rgq_4877/02_2024/6rgq_4877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rgq_4877/02_2024/6rgq_4877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rgq_4877/02_2024/6rgq_4877_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rgq_4877/02_2024/6rgq_4877_neut.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.019 sd= 0.769 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 280 5.16 5 C 28992 2.51 5 N 8010 2.21 5 O 8058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 88": "NH1" <-> "NH2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "D PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "I TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 143": "NH1" <-> "NH2" Residue "J ARG 25": "NH1" <-> "NH2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "J ARG 79": "NH1" <-> "NH2" Residue "K ARG 86": "NH1" <-> "NH2" Residue "K ARG 153": "NH1" <-> "NH2" Residue "L PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 158": "NH1" <-> "NH2" Residue "L ARG 186": "NH1" <-> "NH2" Residue "M ARG 99": "NH1" <-> "NH2" Residue "M ARG 173": "NH1" <-> "NH2" Residue "N PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 100": "NH1" <-> "NH2" Residue "O ARG 88": "NH1" <-> "NH2" Residue "P ARG 90": "NH1" <-> "NH2" Residue "R PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 163": "NH1" <-> "NH2" Residue "R ARG 213": "NH1" <-> "NH2" Residue "T ARG 101": "NH1" <-> "NH2" Residue "W TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 143": "NH1" <-> "NH2" Residue "X ARG 25": "NH1" <-> "NH2" Residue "X ARG 69": "NH1" <-> "NH2" Residue "X ARG 79": "NH1" <-> "NH2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ARG 153": "NH1" <-> "NH2" Residue "Z PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 158": "NH1" <-> "NH2" Residue "Z ARG 186": "NH1" <-> "NH2" Residue "a ARG 99": "NH1" <-> "NH2" Residue "a ARG 173": "NH1" <-> "NH2" Residue "b PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 100": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 45340 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1734 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "B" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1662 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1786 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 241} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 18, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 109 Chain: "D" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1633 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 6, 'TRANS': 225} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "E" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1659 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 13, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 84 Chain: "F" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1704 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "G" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1760 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 77 Chain: "H" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1465 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "I" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1576 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "J" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1534 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "K" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1506 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "L" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1500 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 39 Chain: "M" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1583 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 205} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 55 Chain: "N" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1568 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 7, 'TRANS': 204} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "O" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1734 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "P" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1662 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 96 Chain: "Q" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1786 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 241} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 18, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 109 Chain: "R" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1633 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 6, 'TRANS': 225} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "S" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1659 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 13, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 84 Chain: "T" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1704 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "U" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1760 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 77 Chain: "V" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1465 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "W" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1576 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "X" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1534 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "Y" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1506 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "Z" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1500 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 39 Chain: "a" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1583 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 205} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 55 Chain: "b" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1568 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 7, 'TRANS': 204} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 67 Time building chain proxies: 22.11, per 1000 atoms: 0.49 Number of scatterers: 45340 At special positions: 0 Unit cell: (133.65, 179.01, 128.79, 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 280 16.00 O 8058 8.00 N 8010 7.00 C 28992 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: 17.58 Conformation dependent library (CDL) restraints added in 8.8 seconds 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11416 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 74 sheets defined 37.9% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.85 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 removed outlier: 3.679A pdb=" N ALA A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 36 removed outlier: 3.694A pdb=" N GLY A 35 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 106 removed outlier: 3.515A pdb=" N TRP A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 126 removed outlier: 3.712A pdb=" N VAL A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 180 removed outlier: 3.581A pdb=" N LEU A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 189 removed outlier: 4.408A pdb=" N ASP A 188 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP A 189 " --> pdb=" O LYS A 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 185 through 189' Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 194 through 207 removed outlier: 3.515A pdb=" N VAL A 205 " --> pdb=" O CYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 240 removed outlier: 3.617A pdb=" N HIS A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 removed outlier: 3.539A pdb=" N ALA B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 101 removed outlier: 3.604A pdb=" N ARG B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 99 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 120 Processing helix chain 'B' and resid 165 through 176 removed outlier: 3.623A pdb=" N LYS B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 4.103A pdb=" N HIS B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 230 removed outlier: 3.636A pdb=" N ASP B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 29 removed outlier: 3.646A pdb=" N GLU C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 27 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 102 removed outlier: 3.505A pdb=" N VAL C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 121 removed outlier: 3.501A pdb=" N ILE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 176 Processing helix chain 'C' and resid 185 through 200 removed outlier: 3.518A pdb=" N ALA C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS C 199 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 244 removed outlier: 3.717A pdb=" N LEU C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 248 removed outlier: 3.780A pdb=" N GLU C 248 " --> pdb=" O ALA C 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 245 through 248' Processing helix chain 'D' and resid 16 through 27 Processing helix chain 'D' and resid 56 through 59 removed outlier: 3.667A pdb=" N VAL D 59 " --> pdb=" O GLU D 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 59' Processing helix chain 'D' and resid 76 through 99 removed outlier: 3.601A pdb=" N ILE D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG D 95 " --> pdb=" O CYS D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 118 removed outlier: 3.551A pdb=" N ILE D 107 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 176 removed outlier: 3.591A pdb=" N GLU D 170 " --> pdb=" O LYS D 166 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.670A pdb=" N VAL D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU D 197 " --> pdb=" O LYS D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 231 removed outlier: 3.500A pdb=" N LYS D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TYR D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 32 removed outlier: 3.613A pdb=" N GLU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.553A pdb=" N ILE E 64 " --> pdb=" O PRO E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 81 through 104 removed outlier: 3.583A pdb=" N LYS E 86 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 117 Processing helix chain 'E' and resid 173 through 185 removed outlier: 6.309A pdb=" N SER E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 206 removed outlier: 3.546A pdb=" N LEU E 199 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE E 201 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU E 202 " --> pdb=" O SER E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.535A pdb=" N GLU E 235 " --> pdb=" O LYS E 231 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL E 237 " --> pdb=" O GLU E 233 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS E 239 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 30 removed outlier: 3.695A pdb=" N VAL F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 99 removed outlier: 3.625A pdb=" N PHE F 87 " --> pdb=" O LEU F 83 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER F 95 " --> pdb=" O GLU F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 117 Processing helix chain 'F' and resid 118 through 121 Processing helix chain 'F' and resid 165 through 176 removed outlier: 3.584A pdb=" N ARG F 174 " --> pdb=" O THR F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 182 removed outlier: 5.493A pdb=" N MET F 180 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU F 181 " --> pdb=" O GLU F 178 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS F 182 " --> pdb=" O PHE F 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 177 through 182' Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.501A pdb=" N LYS F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 27 Processing helix chain 'G' and resid 27 through 32 Processing helix chain 'G' and resid 80 through 103 removed outlier: 3.578A pdb=" N ARG G 99 " --> pdb=" O ALA G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 121 Processing helix chain 'G' and resid 168 through 178 removed outlier: 3.507A pdb=" N THR G 174 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS G 178 " --> pdb=" O THR G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 201 removed outlier: 4.105A pdb=" N LYS G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 228 through 242 removed outlier: 3.837A pdb=" N GLU G 234 " --> pdb=" O ASP G 230 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR G 238 " --> pdb=" O GLU G 234 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER G 242 " --> pdb=" O TYR G 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.535A pdb=" N ARG H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 134 removed outlier: 3.942A pdb=" N SER H 133 " --> pdb=" O SER H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 142 Processing helix chain 'H' and resid 148 through 167 removed outlier: 3.674A pdb=" N ARG H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 71 removed outlier: 4.185A pdb=" N LEU I 58 " --> pdb=" O MET I 54 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU I 68 " --> pdb=" O GLU I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.513A pdb=" N ARG I 89 " --> pdb=" O GLN I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 removed outlier: 3.868A pdb=" N VAL I 137 " --> pdb=" O ALA I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 164 Processing helix chain 'J' and resid 55 through 77 removed outlier: 3.620A pdb=" N ALA J 63 " --> pdb=" O VAL J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 97 removed outlier: 4.025A pdb=" N LYS J 97 " --> pdb=" O LEU J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 153 removed outlier: 3.602A pdb=" N GLY J 147 " --> pdb=" O GLU J 143 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER J 151 " --> pdb=" O GLY J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 175 removed outlier: 3.652A pdb=" N GLN J 168 " --> pdb=" O GLU J 164 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA J 173 " --> pdb=" O ALA J 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 56 Processing helix chain 'K' and resid 56 through 72 Processing helix chain 'K' and resid 76 through 90 removed outlier: 3.570A pdb=" N ASN K 87 " --> pdb=" O PHE K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 140 Processing helix chain 'K' and resid 142 through 147 removed outlier: 3.642A pdb=" N TYR K 147 " --> pdb=" O LEU K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 171 Processing helix chain 'L' and resid 48 through 71 removed outlier: 3.689A pdb=" N ARG L 57 " --> pdb=" O SER L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 89 removed outlier: 3.757A pdb=" N GLN L 89 " --> pdb=" O ASN L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 143 removed outlier: 3.884A pdb=" N GLY L 137 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 167 Processing helix chain 'L' and resid 191 through 199 removed outlier: 4.169A pdb=" N GLU L 197 " --> pdb=" O ALA L 193 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS L 198 " --> pdb=" O ASP L 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 80 removed outlier: 3.719A pdb=" N LYS M 73 " --> pdb=" O GLU M 69 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 99 removed outlier: 3.501A pdb=" N TYR M 97 " --> pdb=" O SER M 93 " (cutoff:3.500A) removed outlier: 3.698A 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 186 removed outlier: 3.695A pdb=" N VAL M 178 " --> pdb=" O LEU M 174 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG M 185 " --> pdb=" O SER M 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 78 removed outlier: 4.135A pdb=" N LEU N 77 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 102 removed outlier: 3.541A 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: 3.909A pdb=" N LYS N 156 " --> pdb=" O GLU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 180 removed outlier: 3.651A pdb=" N VAL N 175 " --> pdb=" O ARG N 171 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 31 removed outlier: 3.680A pdb=" N ALA O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE O 29 " --> pdb=" O VAL O 25 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS O 30 " --> pdb=" O GLU O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 36 removed outlier: 3.694A pdb=" N GLY O 35 " --> pdb=" O ILE O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 106 removed outlier: 3.515A pdb=" N TRP O 101 " --> pdb=" O GLU O 97 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 126 removed outlier: 3.712A pdb=" N VAL O 124 " --> pdb=" O ASP O 120 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR O 125 " --> pdb=" O ILE O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 180 removed outlier: 3.581A pdb=" N LEU O 179 " --> pdb=" O SER O 175 " (cutoff:3.500A) Processing helix chain 'O' and resid 185 through 189 removed outlier: 4.407A pdb=" N ASP O 188 " --> pdb=" O LYS O 185 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP O 189 " --> pdb=" O LYS O 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 185 through 189' Processing helix chain 'O' and resid 191 through 193 No H-bonds generated for 'chain 'O' and resid 191 through 193' Processing helix chain 'O' and resid 194 through 207 removed outlier: 3.516A pdb=" N VAL O 205 " --> pdb=" O CYS O 201 " (cutoff:3.500A) Processing helix chain 'O' and resid 231 through 240 removed outlier: 3.616A pdb=" N HIS O 238 " --> pdb=" O GLU O 234 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 29 removed outlier: 3.539A pdb=" N ALA P 26 " --> pdb=" O GLU P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 101 removed outlier: 3.604A pdb=" N ARG P 83 " --> pdb=" O GLY P 79 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL P 84 " --> pdb=" O PRO P 80 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL P 99 " --> pdb=" O GLN P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 120 Processing helix chain 'P' and resid 165 through 176 removed outlier: 3.623A pdb=" N LYS P 175 " --> pdb=" O THR P 171 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG P 176 " --> pdb=" O PHE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 182 through 196 removed outlier: 4.102A pdb=" N HIS P 188 " --> pdb=" O GLU P 184 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR P 189 " --> pdb=" O ASP P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 230 removed outlier: 3.636A pdb=" N ASP P 227 " --> pdb=" O THR P 223 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR P 228 " --> pdb=" O GLU P 224 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 29 removed outlier: 3.646A pdb=" N GLU Q 26 " --> pdb=" O GLU Q 22 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA Q 27 " --> pdb=" O TYR Q 23 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE Q 28 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 102 removed outlier: 3.505A pdb=" N VAL Q 85 " --> pdb=" O SER Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 121 removed outlier: 3.501A pdb=" N ILE Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR Q 121 " --> pdb=" O ILE Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 176 Processing helix chain 'Q' and resid 185 through 200 removed outlier: 3.517A pdb=" N ALA Q 191 " --> pdb=" O LYS Q 187 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS Q 199 " --> pdb=" O LYS Q 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 229 through 244 removed outlier: 3.717A pdb=" N LEU Q 236 " --> pdb=" O GLU Q 232 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU Q 243 " --> pdb=" O LYS Q 239 " (cutoff:3.500A) Processing helix chain 'Q' and resid 245 through 248 removed outlier: 3.780A pdb=" N GLU Q 248 " --> pdb=" O ALA Q 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 245 through 248' Processing helix chain 'R' and resid 16 through 27 Processing helix chain 'R' and resid 56 through 59 removed outlier: 3.667A pdb=" N VAL R 59 " --> pdb=" O GLU R 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 56 through 59' Processing helix chain 'R' and resid 76 through 99 removed outlier: 3.601A pdb=" N ILE R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG R 95 " --> pdb=" O CYS R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 118 removed outlier: 3.551A pdb=" N ILE R 107 " --> pdb=" O THR R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 176 removed outlier: 3.592A pdb=" N GLU R 170 " --> pdb=" O LYS R 166 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 197 removed outlier: 3.669A pdb=" N VAL R 191 " --> pdb=" O THR R 187 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU R 197 " --> pdb=" O LYS R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 231 removed outlier: 3.500A pdb=" N LYS R 227 " --> pdb=" O GLU R 223 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR R 228 " --> pdb=" O GLU R 224 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 32 removed outlier: 3.614A pdb=" N GLU S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE S 31 " --> pdb=" O ALA S 27 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS S 32 " --> pdb=" O ILE S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 64 removed outlier: 3.552A pdb=" N ILE S 64 " --> pdb=" O PRO S 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 61 through 64' Processing helix chain 'S' and resid 81 through 104 removed outlier: 3.583A pdb=" N LYS S 86 " --> pdb=" O ILE S 82 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 117 Processing helix chain 'S' and resid 173 through 185 removed outlier: 6.309A pdb=" N SER S 179 " --> pdb=" O GLU S 175 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER S 180 " --> pdb=" O GLY S 176 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU S 183 " --> pdb=" O SER S 179 " (cutoff:3.500A) Processing helix chain 'S' and resid 190 through 206 removed outlier: 3.547A pdb=" N LEU S 199 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE S 201 " --> pdb=" O SER S 197 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU S 202 " --> pdb=" O SER S 198 " (cutoff:3.500A) Processing helix chain 'S' and resid 230 through 241 removed outlier: 3.536A pdb=" N GLU S 235 " --> pdb=" O LYS S 231 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU S 236 " --> pdb=" O GLU S 232 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL S 237 " --> pdb=" O GLU S 233 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS S 239 " --> pdb=" O GLU S 235 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP S 240 " --> pdb=" O GLU S 236 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 30 removed outlier: 3.695A pdb=" N VAL T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 99 removed outlier: 3.625A pdb=" N PHE T 87 " --> pdb=" O LEU T 83 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER T 95 " --> pdb=" O GLU T 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 117 Processing helix chain 'T' and resid 118 through 121 Processing helix chain 'T' and resid 165 through 176 removed outlier: 3.583A pdb=" N ARG T 174 " --> pdb=" O THR T 170 " (cutoff:3.500A) Processing helix chain 'T' and resid 177 through 182 removed outlier: 5.494A pdb=" N MET T 180 " --> pdb=" O SER T 177 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU T 181 " --> pdb=" O GLU T 178 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS T 182 " --> pdb=" O PHE T 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 177 through 182' Processing helix chain 'T' and resid 183 through 197 removed outlier: 3.501A pdb=" N LYS T 189 " --> pdb=" O ASN T 185 " (cutoff:3.500A) Processing helix chain 'U' and resid 20 through 27 Processing helix chain 'U' and resid 27 through 32 Processing helix chain 'U' and resid 80 through 103 removed outlier: 3.577A pdb=" N ARG U 99 " --> pdb=" O ALA U 95 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 121 Processing helix chain 'U' and resid 168 through 178 removed outlier: 3.506A pdb=" N THR U 174 " --> pdb=" O GLN U 170 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU U 175 " --> pdb=" O ALA U 171 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS U 178 " --> pdb=" O THR U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 185 through 201 removed outlier: 4.105A pdb=" N LYS U 191 " --> pdb=" O ARG U 187 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS U 195 " --> pdb=" O LYS U 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 219 through 221 No H-bonds generated for 'chain 'U' and resid 219 through 221' Processing helix chain 'U' and resid 228 through 242 removed outlier: 3.837A pdb=" N GLU U 234 " --> pdb=" O ASP U 230 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR U 238 " --> pdb=" O GLU U 234 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER U 242 " --> pdb=" O TYR U 238 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 90 removed outlier: 3.534A pdb=" N ARG V 89 " --> pdb=" O GLU V 85 " (cutoff:3.500A) Processing helix chain 'V' and resid 129 through 134 removed outlier: 3.942A pdb=" N SER V 133 " --> pdb=" O SER V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 135 through 142 Processing helix chain 'V' and resid 148 through 167 removed outlier: 3.673A pdb=" N ARG V 166 " --> pdb=" O LEU V 162 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 71 removed outlier: 4.185A pdb=" N LEU W 58 " --> pdb=" O MET W 54 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU W 68 " --> pdb=" O GLU W 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 90 removed outlier: 3.513A pdb=" N ARG W 89 " --> pdb=" O GLN W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 142 removed outlier: 3.867A pdb=" N VAL W 137 " --> pdb=" O ALA W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 164 Processing helix chain 'X' and resid 55 through 77 removed outlier: 3.620A pdb=" N ALA X 63 " --> pdb=" O VAL X 59 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 97 removed outlier: 4.025A pdb=" N LYS X 97 " --> pdb=" O LEU X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 153 removed outlier: 3.602A pdb=" N GLY X 147 " --> pdb=" O GLU X 143 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER X 151 " --> pdb=" O GLY X 147 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 175 removed outlier: 3.652A pdb=" N GLN X 168 " --> pdb=" O GLU X 164 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN X 172 " --> pdb=" O GLN X 168 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA X 173 " --> pdb=" O ALA X 169 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 56 Processing helix chain 'Y' and resid 56 through 72 Processing helix chain 'Y' and resid 76 through 90 removed outlier: 3.571A pdb=" N ASN Y 87 " --> pdb=" O PHE Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 140 Processing helix chain 'Y' and resid 142 through 147 removed outlier: 3.642A pdb=" N TYR Y 147 " --> pdb=" O LEU Y 143 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 171 Processing helix chain 'Z' and resid 48 through 71 removed outlier: 3.687A pdb=" N ARG Z 57 " --> pdb=" O SER Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 75 through 89 removed outlier: 3.758A pdb=" N GLN Z 89 " --> pdb=" O ASN Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 143 removed outlier: 3.885A pdb=" N GLY Z 137 " --> pdb=" O VAL Z 133 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL Z 138 " --> pdb=" O TYR Z 134 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 167 Processing helix chain 'Z' and resid 191 through 199 removed outlier: 4.169A pdb=" N GLU Z 197 " --> pdb=" O ALA Z 193 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS Z 198 " --> pdb=" O ASP Z 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 80 removed outlier: 3.719A pdb=" N LYS a 73 " --> pdb=" O GLU a 69 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR a 75 " --> pdb=" O ARG a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 99 removed outlier: 3.501A pdb=" N TYR a 97 " --> pdb=" O SER a 93 " (cutoff:3.500A) removed outlier: 3.699A 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 186 removed outlier: 3.694A pdb=" N VAL a 178 " --> pdb=" O LEU a 174 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG a 185 " --> pdb=" O SER a 181 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 78 removed outlier: 4.135A pdb=" N LEU b 77 " --> pdb=" O ASP b 73 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY b 78 " --> pdb=" O GLU b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 102 removed outlier: 3.541A 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: 3.909A pdb=" N LYS b 156 " --> pdb=" O GLU b 152 " (cutoff:3.500A) Processing helix chain 'b' and resid 161 through 180 removed outlier: 3.650A pdb=" N VAL b 175 " --> pdb=" O ARG b 171 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 169 removed outlier: 6.077A pdb=" N THR A 38 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 71 removed outlier: 4.161A pdb=" N VAL A 151 " --> pdb=" O PHE A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 159 through 162 Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AA6, first strand: chain 'C' and resid 72 through 78 removed outlier: 4.177A pdb=" N LEU C 147 " --> pdb=" O TRP C 159 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY C 158 " --> pdb=" O ASP D 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AA8, first strand: chain 'D' and resid 69 through 75 removed outlier: 4.396A pdb=" N LEU D 144 " --> pdb=" O TRP D 156 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ALA D 155 " --> pdb=" O GLU E 60 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 167 through 170 removed outlier: 3.502A pdb=" N GLY E 45 " --> pdb=" O THR E 42 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.521A pdb=" N LEU E 141 " --> pdb=" O MET E 156 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU E 153 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN E 164 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 158 through 161 removed outlier: 3.694A pdb=" N ILE F 212 " --> pdb=" O TYR F 224 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 63 through 65 removed outlier: 4.058A pdb=" N ILE F 144 " --> pdb=" O CYS F 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 162 through 165 Processing sheet with id=AB5, first strand: chain 'G' and resid 66 through 68 Processing sheet with id=AB6, first strand: chain 'H' and resid 125 through 128 Processing sheet with id=AB7, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.835A pdb=" N THR H 20 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR H 25 " --> pdb=" O THR H 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.555A pdb=" N LEU H 34 " --> pdb=" O ARG H 45 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ARG H 45 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N CYS H 43 " --> pdb=" O PRO H 36 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE H 41 " --> pdb=" O HIS H 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 124 through 128 removed outlier: 6.370A pdb=" N THR I 2 " --> pdb=" O ASP I 17 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY I 11 " --> pdb=" O TYR I 8 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE I 173 " --> pdb=" O PRO I 188 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 20 through 21 removed outlier: 6.522A pdb=" N ALA I 20 " --> pdb=" O ALA I 27 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.489A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 112 through 113 Processing sheet with id=AC4, first strand: chain 'I' and resid 213 through 218 removed outlier: 4.120A pdb=" N VAL J 184 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ALA J 9 " --> pdb=" O ASP J 24 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 27 through 29 removed outlier: 7.040A pdb=" N PHE J 27 " --> pdb=" O VAL J 34 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 41 through 43 removed outlier: 4.633A pdb=" N ILE J 120 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR J 132 " --> pdb=" O ILE J 120 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 129 through 132 Processing sheet with id=AC8, first strand: chain 'K' and resid 35 through 37 Processing sheet with id=AC9, first strand: chain 'L' and resid 125 through 129 removed outlier: 3.668A pdb=" N GLY L 11 " --> pdb=" O PHE L 8 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU L 176 " --> pdb=" O VAL L 187 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 20 through 22 removed outlier: 6.279A pdb=" N ALA L 22 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ILE L 26 " --> pdb=" O ALA L 22 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.904A pdb=" N LEU L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR L 44 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N MET L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 135 through 139 removed outlier: 5.709A pdb=" N THR M 11 " --> pdb=" O ASP M 26 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 29 through 31 removed outlier: 6.699A pdb=" N LEU M 29 " --> pdb=" O HIS M 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 43 through 47 removed outlier: 6.636A pdb=" N THR M 50 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN M 108 " --> pdb=" O PHE M 124 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL M 121 " --> pdb=" O ASP M 133 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 7 through 8 Processing sheet with id=AD7, first strand: chain 'N' and resid 136 through 138 removed outlier: 3.629A pdb=" N GLY N 196 " --> pdb=" O THR N 193 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 136 through 138 Processing sheet with id=AD9, first strand: chain 'N' and resid 28 through 29 Processing sheet with id=AE1, first strand: chain 'N' and resid 42 through 46 removed outlier: 6.675A pdb=" N THR N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 165 through 169 removed outlier: 6.078A pdb=" N THR O 38 " --> pdb=" O GLN O 53 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 69 through 71 removed outlier: 4.162A pdb=" N VAL O 151 " --> pdb=" O PHE O 163 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 159 through 162 Processing sheet with id=AE5, first strand: chain 'P' and resid 64 through 66 Processing sheet with id=AE6, first strand: chain 'Q' and resid 161 through 164 Processing sheet with id=AE7, first strand: chain 'Q' and resid 72 through 78 removed outlier: 4.177A pdb=" N LEU Q 147 " --> pdb=" O TRP Q 159 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY Q 158 " --> pdb=" O ASP R 55 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 158 through 161 Processing sheet with id=AE9, first strand: chain 'R' and resid 69 through 75 removed outlier: 4.396A pdb=" N LEU R 144 " --> pdb=" O TRP R 156 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ALA R 155 " --> pdb=" O GLU S 60 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 167 through 170 removed outlier: 3.501A pdb=" N GLY S 45 " --> pdb=" O THR S 42 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 67 through 69 removed outlier: 3.522A pdb=" N LEU S 141 " --> pdb=" O MET S 156 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU S 153 " --> pdb=" O CYS S 165 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN S 164 " --> pdb=" O ALA T 58 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 158 through 161 removed outlier: 3.694A pdb=" N ILE T 212 " --> pdb=" O TYR T 224 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'T' and resid 63 through 65 removed outlier: 4.057A pdb=" N ILE T 144 " --> pdb=" O CYS T 156 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 162 through 165 Processing sheet with id=AF6, first strand: chain 'U' and resid 66 through 68 Processing sheet with id=AF7, first strand: chain 'V' and resid 125 through 128 Processing sheet with id=AF8, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.836A pdb=" N THR V 20 " --> pdb=" O ALA V 27 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR V 25 " --> pdb=" O THR V 22 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.556A pdb=" N LEU V 34 " --> pdb=" O ARG V 45 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ARG V 45 " --> pdb=" O LEU V 34 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N CYS V 43 " --> pdb=" O PRO V 36 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE V 41 " --> pdb=" O HIS V 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 124 through 128 removed outlier: 6.370A pdb=" N THR W 2 " --> pdb=" O ASP W 17 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY W 11 " --> pdb=" O TYR W 8 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE W 173 " --> pdb=" O PRO W 188 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 20 through 21 removed outlier: 6.522A pdb=" N ALA W 20 " --> pdb=" O ALA W 27 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.488A pdb=" N ILE W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 112 through 113 Processing sheet with id=AG5, first strand: chain 'W' and resid 213 through 218 removed outlier: 4.119A pdb=" N VAL X 184 " --> pdb=" O LEU X 199 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ALA X 9 " --> pdb=" O ASP X 24 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 27 through 29 removed outlier: 7.040A pdb=" N PHE X 27 " --> pdb=" O VAL X 34 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'X' and resid 41 through 43 removed outlier: 4.633A pdb=" N ILE X 120 " --> pdb=" O THR X 132 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR X 132 " --> pdb=" O ILE X 120 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 129 through 132 Processing sheet with id=AG9, first strand: chain 'Y' and resid 35 through 37 Processing sheet with id=AH1, first strand: chain 'Z' and resid 125 through 129 removed outlier: 3.668A pdb=" N GLY Z 11 " --> pdb=" O PHE Z 8 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU Z 176 " --> pdb=" O VAL Z 187 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 20 through 22 removed outlier: 6.280A pdb=" N ALA Z 22 " --> pdb=" O ILE Z 26 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ILE Z 26 " --> pdb=" O ALA Z 22 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.903A pdb=" N LEU Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR Z 44 " --> pdb=" O MET Z 100 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N MET Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'a' and resid 135 through 139 removed outlier: 5.709A pdb=" N THR a 11 " --> pdb=" O ASP a 26 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'a' and resid 29 through 31 removed outlier: 6.698A pdb=" N LEU a 29 " --> pdb=" O HIS a 36 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'a' and resid 43 through 47 removed outlier: 6.636A pdb=" N THR a 50 " --> pdb=" O LEU a 46 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN a 108 " --> pdb=" O PHE a 124 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL a 121 " --> pdb=" O ASP a 133 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'b' and resid 7 through 8 Processing sheet with id=AH8, first strand: chain 'b' and resid 136 through 138 removed outlier: 3.629A pdb=" N GLY b 196 " --> pdb=" O THR b 193 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'b' and resid 136 through 138 Processing sheet with id=AI1, first strand: chain 'b' and resid 28 through 29 Processing sheet with id=AI2, first strand: chain 'b' and resid 42 through 46 removed outlier: 6.674A pdb=" N THR b 49 " --> pdb=" O VAL b 45 " (cutoff:3.500A) 2516 hydrogen bonds defined for protein. 7224 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: 19.79 Time building geometry restraints manager: 18.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 7142 1.29 - 1.42: 11984 1.42 - 1.55: 26574 1.55 - 1.68: 20 1.68 - 1.81: 462 Bond restraints: 46182 Sorted by residual: bond pdb=" C TYR Z 25 " pdb=" O TYR Z 25 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.19e-02 7.06e+03 3.70e+01 bond pdb=" C TYR L 25 " pdb=" O TYR L 25 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.19e-02 7.06e+03 3.70e+01 bond pdb=" C ILE L 26 " pdb=" O ILE L 26 " ideal model delta sigma weight residual 1.236 1.165 0.071 1.19e-02 7.06e+03 3.56e+01 bond pdb=" C ILE Z 26 " pdb=" O ILE Z 26 " ideal model delta sigma weight residual 1.236 1.165 0.071 1.19e-02 7.06e+03 3.54e+01 bond pdb=" C ALA Z 20 " pdb=" O ALA Z 20 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.14e-02 7.69e+03 3.45e+01 ... (remaining 46177 not shown) Histogram of bond angle deviations from ideal: 93.70 - 101.83: 180 101.83 - 109.96: 9017 109.96 - 118.09: 25514 118.09 - 126.22: 27515 126.22 - 134.35: 482 Bond angle restraints: 62708 Sorted by residual: angle pdb=" C GLY I 170 " pdb=" N SER I 171 " pdb=" CA SER I 171 " ideal model delta sigma weight residual 121.54 134.35 -12.81 1.91e+00 2.74e-01 4.50e+01 angle pdb=" C GLY W 170 " pdb=" N SER W 171 " pdb=" CA SER W 171 " ideal model delta sigma weight residual 121.54 134.32 -12.78 1.91e+00 2.74e-01 4.47e+01 angle pdb=" CA SER W 38 " pdb=" C SER W 38 " pdb=" N PRO W 39 " ideal model delta sigma weight residual 117.68 121.39 -3.71 7.10e-01 1.98e+00 2.74e+01 angle pdb=" CA SER I 38 " pdb=" C SER I 38 " pdb=" N PRO I 39 " ideal model delta sigma weight residual 117.68 121.31 -3.63 7.10e-01 1.98e+00 2.61e+01 angle pdb=" N VAL A 183 " pdb=" CA VAL A 183 " pdb=" C VAL A 183 " ideal model delta sigma weight residual 111.91 107.47 4.44 8.90e-01 1.26e+00 2.49e+01 ... (remaining 62703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 26296 16.28 - 32.57: 901 32.57 - 48.85: 186 48.85 - 65.13: 17 65.13 - 81.41: 16 Dihedral angle restraints: 27416 sinusoidal: 9534 harmonic: 17882 Sorted by residual: dihedral pdb=" CA LYS A 185 " pdb=" C LYS A 185 " pdb=" N LYS A 186 " pdb=" CA LYS A 186 " ideal model delta harmonic sigma weight residual -180.00 -127.85 -52.15 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA LYS O 185 " pdb=" C LYS O 185 " pdb=" N LYS O 186 " pdb=" CA LYS O 186 " ideal model delta harmonic sigma weight residual 180.00 -127.90 -52.10 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA ASN K 24 " pdb=" C ASN K 24 " pdb=" N ILE K 25 " pdb=" CA ILE K 25 " ideal model delta harmonic sigma weight residual -180.00 -132.00 -48.00 0 5.00e+00 4.00e-02 9.22e+01 ... (remaining 27413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 5761 0.070 - 0.139: 1384 0.139 - 0.209: 168 0.209 - 0.279: 29 0.279 - 0.349: 4 Chirality restraints: 7346 Sorted by residual: chirality pdb=" CG LEU I 65 " pdb=" CB LEU I 65 " pdb=" CD1 LEU I 65 " pdb=" CD2 LEU I 65 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB ILE a 197 " pdb=" CA ILE a 197 " pdb=" CG1 ILE a 197 " pdb=" CG2 ILE a 197 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CG LEU W 65 " pdb=" CB LEU W 65 " pdb=" CD1 LEU W 65 " pdb=" CD2 LEU W 65 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 7343 not shown) Planarity restraints: 7974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL I 99 " 0.022 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C VAL I 99 " -0.078 2.00e-02 2.50e+03 pdb=" O VAL I 99 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU I 100 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL W 99 " 0.022 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C VAL W 99 " -0.078 2.00e-02 2.50e+03 pdb=" O VAL W 99 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU W 100 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU K 121 " 0.020 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C LEU K 121 " -0.071 2.00e-02 2.50e+03 pdb=" O LEU K 121 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA K 122 " 0.024 2.00e-02 2.50e+03 ... (remaining 7971 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 10841 2.78 - 3.31: 38426 3.31 - 3.84: 77922 3.84 - 4.37: 95030 4.37 - 4.90: 163292 Nonbonded interactions: 385511 Sorted by model distance: nonbonded pdb=" OD1 ASP a 60 " pdb=" OH TYR b 97 " model vdw 2.250 2.440 nonbonded pdb=" OD1 ASP M 60 " pdb=" OH TYR N 97 " model vdw 2.251 2.440 nonbonded pdb=" OD1 ASP Y 52 " pdb=" OH TYR Z 88 " model vdw 2.252 2.440 nonbonded pdb=" OD1 ASP K 52 " pdb=" OH TYR L 88 " model vdw 2.252 2.440 nonbonded pdb=" OG1 THR R 31 " pdb=" O ARG R 163 " model vdw 2.265 2.440 ... (remaining 385506 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 16.820 Check model and map are aligned: 0.680 Set scattering table: 0.410 Process input model: 114.290 Find NCS groups from input model: 4.920 Set up NCS constraints: 0.550 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 : 0.009 0.092 46182 Z= 0.623 Angle : 1.017 14.674 62708 Z= 0.549 Chirality : 0.061 0.349 7346 Planarity : 0.007 0.062 7974 Dihedral : 9.750 81.414 16000 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.92 % Favored : 95.02 % Rotamer: Outliers : 0.70 % Allowed : 2.48 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.09), residues: 6142 helix: -4.05 (0.05), residues: 2268 sheet: -1.47 (0.13), residues: 1514 loop : -1.98 (0.11), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.005 TRP U 215 HIS 0.014 0.003 HIS U 72 PHE 0.051 0.004 PHE W 138 TYR 0.056 0.005 TYR I 42 ARG 0.015 0.001 ARG R 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1718 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1688 time to evaluate : 4.906 Fit side-chains outliers start: 30 outliers final: 12 residues processed: 1706 average time/residue: 1.6420 time to fit residues: 3415.4892 Evaluate side-chains 1172 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1160 time to evaluate : 4.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain b residue 77 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 515 optimal weight: 0.7980 chunk 462 optimal weight: 0.9990 chunk 256 optimal weight: 0.6980 chunk 157 optimal weight: 0.8980 chunk 311 optimal weight: 0.1980 chunk 247 optimal weight: 1.9990 chunk 478 optimal weight: 0.9990 chunk 185 optimal weight: 0.6980 chunk 290 optimal weight: 0.6980 chunk 355 optimal weight: 2.9990 chunk 553 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 51 GLN B 95 GLN B 101 GLN B 108 GLN B 111 GLN B 188 HIS C 69 ASN C 146 GLN C 177 GLN C 230 GLN C 240 HIS D 23 GLN D 54 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 ASN E 225 ASN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN H 66 HIS H 110 GLN J 6 ASN J 17 ASN J 156 ASN K 63 ASN K 82 ASN K 101 ASN K 189 HIS L 62 GLN L 191 ASN M 8 ASN M 131 GLN O 24 GLN P 51 GLN P 95 GLN P 101 GLN ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN P 188 HIS Q 69 ASN Q 146 GLN Q 177 GLN Q 230 GLN Q 240 HIS R 23 GLN R 54 GLN ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 211 ASN S 225 ASN ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 32 ASN V 66 HIS V 110 GLN X 6 ASN X 17 ASN X 71 ASN X 156 ASN Y 63 ASN Y 82 ASN Y 101 ASN Z 62 GLN Z 191 ASN a 8 ASN a 131 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 46182 Z= 0.175 Angle : 0.617 9.036 62708 Z= 0.330 Chirality : 0.044 0.181 7346 Planarity : 0.005 0.067 7974 Dihedral : 5.717 45.932 6804 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.58 % Favored : 96.35 % Rotamer: Outliers : 4.76 % Allowed : 16.87 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.10 (0.10), residues: 6142 helix: -1.36 (0.09), residues: 2288 sheet: -1.04 (0.13), residues: 1524 loop : -1.41 (0.12), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP Z 104 HIS 0.010 0.001 HIS S 227 PHE 0.018 0.002 PHE A 191 TYR 0.021 0.001 TYR J 146 ARG 0.008 0.001 ARG X 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1508 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1305 time to evaluate : 5.078 Fit side-chains REVERT: A 30 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7906 (mmtp) REVERT: E 196 LYS cc_start: 0.8567 (tttp) cc_final: 0.8318 (tttp) REVERT: K 161 ARG cc_start: 0.7307 (ttm-80) cc_final: 0.7078 (mtt-85) REVERT: O 30 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7929 (mmtp) REVERT: S 196 LYS cc_start: 0.8574 (tttp) cc_final: 0.8331 (tttp) REVERT: Y 161 ARG cc_start: 0.7303 (ttm-80) cc_final: 0.7079 (mtt-85) outliers start: 203 outliers final: 66 residues processed: 1391 average time/residue: 1.4701 time to fit residues: 2551.5043 Evaluate side-chains 1258 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1190 time to evaluate : 4.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 97 LYS Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 30 LYS Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain P residue 224 GLU Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 190 THR Chi-restraints excluded: chain S residue 227 HIS Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 185 THR Chi-restraints excluded: chain U residue 206 ASP Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 175 LEU Chi-restraints excluded: chain X residue 97 LYS Chi-restraints excluded: chain X residue 108 ILE Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain Y residue 150 THR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain a residue 12 ILE Chi-restraints excluded: chain a residue 129 SER Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 191 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 307 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 461 optimal weight: 4.9990 chunk 377 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 554 optimal weight: 5.9990 chunk 599 optimal weight: 7.9990 chunk 494 optimal weight: 3.9990 chunk 550 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 445 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN B 122 GLN C 40 ASN C 69 ASN C 146 GLN C 177 GLN C 198 ASN D 116 GLN E 225 ASN F 20 HIS ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN H 123 GLN J 17 ASN J 39 GLN J 156 ASN J 168 GLN L 162 GLN M 8 ASN M 131 GLN M 157 ASN N 185 ASN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 108 GLN P 122 GLN Q 40 ASN Q 69 ASN Q 146 GLN Q 177 GLN Q 198 ASN R 92 GLN R 116 GLN S 118 ASN S 225 ASN T 20 HIS ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 180 GLN V 123 GLN X 17 ASN X 39 GLN X 156 ASN X 168 GLN Z 162 GLN a 8 ASN a 157 ASN b 185 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 46182 Z= 0.440 Angle : 0.657 9.063 62708 Z= 0.346 Chirality : 0.048 0.207 7346 Planarity : 0.005 0.054 7974 Dihedral : 5.436 44.993 6798 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.38 % Favored : 95.59 % Rotamer: Outliers : 6.28 % Allowed : 19.52 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.15 (0.10), residues: 6142 helix: -0.09 (0.10), residues: 2314 sheet: -0.87 (0.13), residues: 1514 loop : -1.20 (0.13), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 215 HIS 0.009 0.001 HIS E 227 PHE 0.018 0.002 PHE H 65 TYR 0.020 0.002 TYR Y 117 ARG 0.006 0.001 ARG P 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1437 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1169 time to evaluate : 5.019 Fit side-chains REVERT: A 30 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8033 (mmtp) REVERT: C 174 MET cc_start: 0.8133 (ttp) cc_final: 0.7868 (ttm) REVERT: D 124 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7710 (mtp180) REVERT: E 53 ARG cc_start: 0.8239 (mmm-85) cc_final: 0.8000 (mtm180) REVERT: K 38 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.6880 (mtm) REVERT: K 161 ARG cc_start: 0.7432 (ttm-80) cc_final: 0.7177 (mtt-85) REVERT: M 158 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6715 (mtt) REVERT: O 30 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8037 (mmtp) REVERT: Q 174 MET cc_start: 0.8108 (ttp) cc_final: 0.7834 (ttm) REVERT: R 124 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7703 (mtp180) REVERT: U 80 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8134 (mp) REVERT: Y 38 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.6869 (mmm) REVERT: Y 161 ARG cc_start: 0.7431 (ttm-80) cc_final: 0.7182 (mtt-85) REVERT: a 158 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6714 (mtt) outliers start: 268 outliers final: 133 residues processed: 1301 average time/residue: 1.5332 time to fit residues: 2480.3404 Evaluate side-chains 1267 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1125 time to evaluate : 5.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 93 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 29 LYS Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 105 GLU Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 158 MET Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 197 ILE Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 30 LYS Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 115 CYS Chi-restraints excluded: chain O residue 231 THR Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 148 SER Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain P residue 224 GLU Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 124 ARG Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 190 THR Chi-restraints excluded: chain S residue 227 HIS Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 165 SER Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 230 SER Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 93 GLU Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain U residue 185 THR Chi-restraints excluded: chain U residue 206 ASP Chi-restraints excluded: chain V residue 148 THR Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 29 LYS Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 175 LEU Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 105 GLU Chi-restraints excluded: chain X residue 108 ILE Chi-restraints excluded: chain X residue 122 SER Chi-restraints excluded: chain X residue 151 SER Chi-restraints excluded: chain Y residue 38 MET Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain Y residue 150 THR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 99 THR Chi-restraints excluded: chain Z residue 155 LEU Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 129 SER Chi-restraints excluded: chain a residue 158 MET Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 197 ILE Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 189 ILE Chi-restraints excluded: chain b residue 191 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 548 optimal weight: 0.8980 chunk 417 optimal weight: 0.0980 chunk 288 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 264 optimal weight: 0.9990 chunk 372 optimal weight: 6.9990 chunk 556 optimal weight: 0.9980 chunk 589 optimal weight: 0.0970 chunk 290 optimal weight: 0.7980 chunk 527 optimal weight: 1.9990 chunk 158 optimal weight: 0.2980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN B 87 HIS B 95 GLN B 122 GLN C 40 ASN C 177 GLN E 225 ASN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN G 32 ASN G 180 GLN H 123 GLN J 17 ASN J 39 GLN J 71 ASN J 156 ASN P 51 GLN P 87 HIS P 95 GLN P 122 GLN Q 40 ASN Q 177 GLN S 13 ASN S 225 ASN T 21 GLN T 166 GLN U 32 ASN U 180 GLN V 123 GLN X 17 ASN X 39 GLN X 156 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 46182 Z= 0.149 Angle : 0.553 8.185 62708 Z= 0.291 Chirality : 0.043 0.159 7346 Planarity : 0.004 0.047 7974 Dihedral : 5.064 42.301 6798 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 4.90 % Allowed : 20.83 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.11), residues: 6142 helix: 0.78 (0.11), residues: 2260 sheet: -0.68 (0.13), residues: 1514 loop : -0.96 (0.13), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 215 HIS 0.009 0.001 HIS E 227 PHE 0.015 0.001 PHE O 191 TYR 0.020 0.001 TYR F 171 ARG 0.006 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1451 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1242 time to evaluate : 5.358 Fit side-chains REVERT: A 30 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7895 (mmtp) REVERT: D 124 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7380 (mtp180) REVERT: K 161 ARG cc_start: 0.7312 (ttm-80) cc_final: 0.7074 (mtt-85) REVERT: M 158 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6610 (mtt) REVERT: O 30 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7894 (mmtp) REVERT: R 124 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7383 (mtp180) REVERT: Y 161 ARG cc_start: 0.7312 (ttm-80) cc_final: 0.7073 (mtt-85) REVERT: a 158 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6609 (mtt) outliers start: 209 outliers final: 83 residues processed: 1331 average time/residue: 1.5101 time to fit residues: 2510.0191 Evaluate side-chains 1268 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1179 time to evaluate : 5.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 130 TYR Chi-restraints excluded: chain M residue 158 MET Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 30 LYS Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 231 THR Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 148 SER Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 168 SER Chi-restraints excluded: chain R residue 124 ARG Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 190 THR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 185 THR Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 175 LEU Chi-restraints excluded: chain X residue 151 SER Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 155 LEU Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 12 ILE Chi-restraints excluded: chain a residue 129 SER Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 158 MET Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 22 ILE Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 189 ILE Chi-restraints excluded: chain b residue 191 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 491 optimal weight: 2.9990 chunk 334 optimal weight: 0.0070 chunk 8 optimal weight: 3.9990 chunk 439 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 503 optimal weight: 4.9990 chunk 407 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 301 optimal weight: 2.9990 chunk 529 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN B 95 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN C 40 ASN C 198 ASN D 116 GLN E 23 GLN E 186 HIS E 225 ASN F 21 GLN F 65 HIS F 121 GLN G 32 ASN G 180 GLN H 123 GLN J 17 ASN J 39 GLN J 156 ASN K 65 GLN L 29 GLN P 95 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 122 GLN Q 40 ASN Q 198 ASN R 116 GLN S 13 ASN S 23 GLN S 186 HIS S 225 ASN T 21 GLN T 65 HIS T 121 GLN U 32 ASN U 97 ASN U 180 GLN V 123 GLN X 17 ASN X 39 GLN X 156 ASN Y 65 GLN Z 29 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 46182 Z= 0.305 Angle : 0.593 8.791 62708 Z= 0.308 Chirality : 0.045 0.215 7346 Planarity : 0.004 0.078 7974 Dihedral : 5.034 42.582 6798 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.13 % Rotamer: Outliers : 5.06 % Allowed : 22.24 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.11), residues: 6142 helix: 1.09 (0.11), residues: 2280 sheet: -0.51 (0.13), residues: 1526 loop : -0.82 (0.13), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 215 HIS 0.006 0.001 HIS S 227 PHE 0.016 0.001 PHE O 191 TYR 0.017 0.001 TYR K 117 ARG 0.007 0.001 ARG O 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1368 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1152 time to evaluate : 5.041 Fit side-chains REVERT: A 30 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7946 (mmtp) REVERT: D 124 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7462 (mtp180) REVERT: G 80 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8140 (mp) REVERT: J 112 ASP cc_start: 0.7429 (t0) cc_final: 0.7129 (t0) REVERT: K 161 ARG cc_start: 0.7435 (ttm-80) cc_final: 0.7168 (mtt-85) REVERT: O 30 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7948 (mmtp) REVERT: R 124 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7449 (mtp180) REVERT: Y 161 ARG cc_start: 0.7438 (ttm-80) cc_final: 0.7172 (mtt-85) outliers start: 216 outliers final: 130 residues processed: 1268 average time/residue: 1.5015 time to fit residues: 2359.0492 Evaluate side-chains 1257 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1122 time to evaluate : 5.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 29 LYS Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 105 GLU Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 130 TYR Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 30 LYS Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 231 THR Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 124 ARG Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 190 THR Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 189 LYS Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain T residue 230 SER Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 185 THR Chi-restraints excluded: chain U residue 206 ASP Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 29 LYS Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 175 LEU Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain X residue 47 ARG Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 105 GLU Chi-restraints excluded: chain X residue 108 ILE Chi-restraints excluded: chain X residue 151 SER Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 45 LEU Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 29 GLN Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 99 THR Chi-restraints excluded: chain Z residue 155 LEU Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 129 SER Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 183 SER Chi-restraints excluded: chain b residue 189 ILE Chi-restraints excluded: chain b residue 191 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 198 optimal weight: 6.9990 chunk 530 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 346 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 590 optimal weight: 0.9990 chunk 489 optimal weight: 3.9990 chunk 273 optimal weight: 0.0570 chunk 49 optimal weight: 10.0000 chunk 195 optimal weight: 0.7980 chunk 309 optimal weight: 1.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS B 95 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN C 40 ASN C 198 ASN D 154 HIS E 13 ASN E 225 ASN F 21 GLN F 65 HIS F 117 GLN F 121 GLN F 175 HIS H 123 GLN J 17 ASN J 39 GLN J 156 ASN K 65 GLN L 29 GLN O 68 HIS P 95 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 122 GLN Q 40 ASN Q 198 ASN R 154 HIS S 13 ASN S 225 ASN T 21 GLN T 65 HIS T 117 GLN T 121 GLN T 175 HIS V 123 GLN X 17 ASN X 39 GLN X 156 ASN Y 65 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 46182 Z= 0.184 Angle : 0.561 8.438 62708 Z= 0.292 Chirality : 0.044 0.174 7346 Planarity : 0.004 0.067 7974 Dihedral : 4.899 41.824 6798 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.43 % Rotamer: Outliers : 4.80 % Allowed : 22.99 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.11), residues: 6142 helix: 1.35 (0.11), residues: 2282 sheet: -0.41 (0.13), residues: 1504 loop : -0.76 (0.13), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 215 HIS 0.007 0.001 HIS S 227 PHE 0.014 0.001 PHE O 191 TYR 0.015 0.001 TYR Y 117 ARG 0.009 0.000 ARG O 228 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1430 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1225 time to evaluate : 5.064 Fit side-chains REVERT: A 30 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7934 (mmtp) REVERT: D 124 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7415 (mtp180) REVERT: I 146 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8225 (mtp) REVERT: K 38 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.6691 (mtm) REVERT: K 161 ARG cc_start: 0.7380 (ttm-80) cc_final: 0.7124 (mtt-85) REVERT: O 30 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7936 (mmtp) REVERT: O 228 ARG cc_start: 0.7996 (ttp-110) cc_final: 0.7790 (ttp80) REVERT: R 124 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7409 (mtp180) REVERT: W 146 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8221 (mtp) REVERT: Y 38 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.6685 (mtm) REVERT: Y 161 ARG cc_start: 0.7392 (ttm-80) cc_final: 0.7134 (mtt-85) outliers start: 205 outliers final: 108 residues processed: 1314 average time/residue: 1.4764 time to fit residues: 2412.9696 Evaluate side-chains 1271 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1155 time to evaluate : 5.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 29 LYS Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 130 TYR Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 30 LYS Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 231 THR Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain P residue 207 ILE Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 73 PHE Chi-restraints excluded: chain R residue 124 ARG Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 190 THR Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 156 CYS Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain T residue 230 SER Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 185 THR Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 29 LYS Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 175 LEU Chi-restraints excluded: chain X residue 47 ARG Chi-restraints excluded: chain X residue 108 ILE Chi-restraints excluded: chain X residue 122 SER Chi-restraints excluded: chain X residue 151 SER Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 38 MET Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 129 SER Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 183 SER Chi-restraints excluded: chain b residue 189 ILE Chi-restraints excluded: chain b residue 191 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 569 optimal weight: 0.8980 chunk 66 optimal weight: 20.0000 chunk 336 optimal weight: 4.9990 chunk 431 optimal weight: 2.9990 chunk 333 optimal weight: 7.9990 chunk 496 optimal weight: 6.9990 chunk 329 optimal weight: 6.9990 chunk 587 optimal weight: 6.9990 chunk 367 optimal weight: 2.9990 chunk 358 optimal weight: 5.9990 chunk 271 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN C 40 ASN C 146 GLN C 198 ASN D 116 GLN E 13 ASN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN F 21 GLN F 121 GLN G 97 ASN H 123 GLN J 17 ASN J 39 GLN K 65 GLN L 29 GLN M 8 ASN P 95 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 122 GLN Q 40 ASN Q 146 GLN Q 198 ASN R 116 GLN S 13 ASN ** S 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 225 ASN T 21 GLN T 121 GLN V 123 GLN X 17 ASN X 39 GLN Y 65 GLN Z 29 GLN a 8 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 46182 Z= 0.384 Angle : 0.630 9.314 62708 Z= 0.326 Chirality : 0.047 0.224 7346 Planarity : 0.004 0.054 7974 Dihedral : 5.035 41.071 6798 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.01 % Favored : 95.96 % Rotamer: Outliers : 5.37 % Allowed : 22.73 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.11), residues: 6142 helix: 1.35 (0.11), residues: 2290 sheet: -0.42 (0.13), residues: 1510 loop : -0.75 (0.13), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 215 HIS 0.006 0.001 HIS S 227 PHE 0.014 0.002 PHE E 22 TYR 0.018 0.001 TYR Y 117 ARG 0.008 0.001 ARG P 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1380 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1151 time to evaluate : 5.002 Fit side-chains REVERT: A 30 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8010 (mmtp) REVERT: C 226 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7411 (ptm160) REVERT: D 124 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7500 (mtp180) REVERT: F 107 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8132 (mtm-85) REVERT: I 146 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8245 (mtp) REVERT: M 158 MET cc_start: 0.7481 (mtt) cc_final: 0.6951 (mtt) REVERT: O 30 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8008 (mmtp) REVERT: Q 226 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7411 (ptm160) REVERT: R 124 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7503 (mtp180) REVERT: T 107 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8135 (mtm-85) REVERT: U 240 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8382 (mtpt) REVERT: W 146 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8240 (mtp) REVERT: a 158 MET cc_start: 0.7482 (mtt) cc_final: 0.6952 (mtt) outliers start: 229 outliers final: 144 residues processed: 1277 average time/residue: 1.5164 time to fit residues: 2396.8007 Evaluate side-chains 1278 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1123 time to evaluate : 4.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 29 LYS Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 97 LYS Chi-restraints excluded: chain J residue 105 GLU Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 130 TYR Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 70 MET Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 30 LYS Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 231 THR Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain P residue 224 GLU Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 226 ARG Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 124 ARG Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 190 THR Chi-restraints excluded: chain S residue 227 HIS Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 33 SER Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 107 ARG Chi-restraints excluded: chain T residue 156 CYS Chi-restraints excluded: chain T residue 189 LYS Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain T residue 230 SER Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain U residue 185 THR Chi-restraints excluded: chain U residue 240 LYS Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 29 LYS Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 175 LEU Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 97 LYS Chi-restraints excluded: chain X residue 105 GLU Chi-restraints excluded: chain X residue 108 ILE Chi-restraints excluded: chain X residue 122 SER Chi-restraints excluded: chain X residue 151 SER Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain Y residue 150 THR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 29 GLN Chi-restraints excluded: chain Z residue 99 THR Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 129 SER Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 183 SER Chi-restraints excluded: chain b residue 191 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 363 optimal weight: 0.8980 chunk 234 optimal weight: 2.9990 chunk 351 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 373 optimal weight: 9.9990 chunk 400 optimal weight: 6.9990 chunk 290 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 462 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN B 122 GLN C 40 ASN C 198 ASN E 13 ASN E 186 HIS ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN F 21 GLN F 65 HIS F 117 GLN F 121 GLN H 123 GLN J 17 ASN J 39 GLN J 156 ASN K 65 GLN L 29 GLN M 8 ASN P 95 GLN P 101 GLN P 122 GLN Q 40 ASN Q 198 ASN S 13 ASN S 186 HIS ** S 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 225 ASN T 21 GLN T 65 HIS T 121 GLN V 123 GLN ** W 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN X 39 GLN X 156 ASN Y 65 GLN Z 29 GLN a 8 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 46182 Z= 0.181 Angle : 0.581 8.649 62708 Z= 0.301 Chirality : 0.044 0.205 7346 Planarity : 0.004 0.059 7974 Dihedral : 4.878 42.488 6798 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.29 % Rotamer: Outliers : 4.19 % Allowed : 24.02 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.11), residues: 6142 helix: 1.67 (0.11), residues: 2260 sheet: -0.37 (0.13), residues: 1510 loop : -0.64 (0.13), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 156 HIS 0.007 0.001 HIS S 227 PHE 0.039 0.001 PHE R 73 TYR 0.017 0.001 TYR X 5 ARG 0.017 0.000 ARG P 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1395 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1216 time to evaluate : 4.929 Fit side-chains REVERT: A 30 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7949 (mmtp) REVERT: F 107 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8043 (mtm-85) REVERT: F 122 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7399 (mtp-110) REVERT: I 146 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8256 (mtp) REVERT: K 38 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.6671 (mtm) REVERT: M 158 MET cc_start: 0.7477 (mtt) cc_final: 0.6943 (mtt) REVERT: O 30 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7943 (mmtp) REVERT: T 107 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8049 (mtm-85) REVERT: U 240 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8355 (mtpt) REVERT: W 146 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8255 (mtp) REVERT: Y 38 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.6639 (mtm) REVERT: a 158 MET cc_start: 0.7475 (mtt) cc_final: 0.6941 (mtt) outliers start: 179 outliers final: 103 residues processed: 1301 average time/residue: 1.4913 time to fit residues: 2421.9418 Evaluate side-chains 1285 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1172 time to evaluate : 5.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 29 LYS Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 97 LYS Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 130 TYR Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 30 LYS Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 231 THR Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 82 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 190 THR Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 107 ARG Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 156 CYS Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 230 SER Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain U residue 185 THR Chi-restraints excluded: chain U residue 240 LYS Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 29 LYS Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 175 LEU Chi-restraints excluded: chain X residue 47 ARG Chi-restraints excluded: chain X residue 97 LYS Chi-restraints excluded: chain X residue 108 ILE Chi-restraints excluded: chain X residue 151 SER Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 38 MET Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain Y residue 150 THR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 129 SER Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain b residue 27 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 183 SER Chi-restraints excluded: chain b residue 191 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 534 optimal weight: 6.9990 chunk 563 optimal weight: 5.9990 chunk 513 optimal weight: 0.8980 chunk 547 optimal weight: 3.9990 chunk 329 optimal weight: 8.9990 chunk 238 optimal weight: 0.7980 chunk 430 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 495 optimal weight: 2.9990 chunk 518 optimal weight: 1.9990 chunk 545 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN C 40 ASN C 198 ASN D 116 GLN E 13 ASN E 114 GLN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN F 21 GLN F 65 HIS F 90 GLN F 121 GLN H 123 GLN J 39 GLN J 156 ASN K 65 GLN L 29 GLN M 8 ASN P 95 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 122 GLN Q 40 ASN R 116 GLN S 13 ASN S 186 HIS ** S 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 225 ASN T 21 GLN T 65 HIS T 90 GLN T 121 GLN V 123 GLN ** W 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 GLN Y 65 GLN Z 29 GLN a 8 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 46182 Z= 0.238 Angle : 0.613 9.823 62708 Z= 0.316 Chirality : 0.045 0.256 7346 Planarity : 0.004 0.093 7974 Dihedral : 4.865 41.864 6796 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.81 % Favored : 96.16 % Rotamer: Outliers : 3.82 % Allowed : 25.16 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.11), residues: 6142 helix: 1.70 (0.11), residues: 2272 sheet: -0.36 (0.13), residues: 1536 loop : -0.55 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 156 HIS 0.004 0.001 HIS N 89 PHE 0.013 0.001 PHE O 191 TYR 0.018 0.001 TYR J 5 ARG 0.017 0.000 ARG P 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1183 time to evaluate : 5.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7906 (mmtp) REVERT: F 107 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8024 (mtm-85) REVERT: I 146 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8225 (mtp) REVERT: M 158 MET cc_start: 0.7490 (mtt) cc_final: 0.6986 (mtt) REVERT: O 30 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7916 (mmtp) REVERT: T 107 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8026 (mtm-85) REVERT: T 178 GLU cc_start: 0.7699 (pt0) cc_final: 0.7364 (pt0) REVERT: U 240 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8363 (mtpt) REVERT: W 146 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8226 (mtp) REVERT: a 158 MET cc_start: 0.7491 (mtt) cc_final: 0.6988 (mtt) outliers start: 163 outliers final: 119 residues processed: 1268 average time/residue: 1.5160 time to fit residues: 2390.7757 Evaluate side-chains 1276 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1150 time to evaluate : 5.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 29 LYS Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 130 TYR Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 30 LYS Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 231 THR Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 168 SER Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain S residue 82 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 190 THR Chi-restraints excluded: chain S residue 227 HIS Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 107 ARG Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 156 CYS Chi-restraints excluded: chain T residue 176 MET Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 230 SER Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain U residue 185 THR Chi-restraints excluded: chain U residue 240 LYS Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 29 LYS Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 175 LEU Chi-restraints excluded: chain X residue 47 ARG Chi-restraints excluded: chain X residue 108 ILE Chi-restraints excluded: chain X residue 151 SER Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain Y residue 150 THR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 12 ILE Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 129 SER Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 183 SER Chi-restraints excluded: chain b residue 189 ILE Chi-restraints excluded: chain b residue 191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 359 optimal weight: 0.9990 chunk 579 optimal weight: 5.9990 chunk 353 optimal weight: 1.9990 chunk 274 optimal weight: 5.9990 chunk 402 optimal weight: 4.9990 chunk 607 optimal weight: 0.8980 chunk 559 optimal weight: 6.9990 chunk 483 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 373 optimal weight: 6.9990 chunk 296 optimal weight: 0.1980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN C 40 ASN E 13 ASN E 114 GLN E 186 HIS E 225 ASN F 21 GLN F 65 HIS F 90 GLN F 121 GLN H 123 GLN J 17 ASN J 39 GLN K 65 GLN L 29 GLN M 8 ASN P 95 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 122 GLN Q 40 ASN S 13 ASN S 114 GLN S 225 ASN T 21 GLN T 65 HIS T 90 GLN T 121 GLN V 123 GLN X 17 ASN X 39 GLN X 156 ASN Y 65 GLN Y 189 HIS Z 29 GLN a 8 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 46182 Z= 0.270 Angle : 0.632 11.069 62708 Z= 0.324 Chirality : 0.045 0.247 7346 Planarity : 0.004 0.095 7974 Dihedral : 4.893 41.884 6796 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 3.56 % Allowed : 25.98 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.11), residues: 6142 helix: 1.72 (0.11), residues: 2272 sheet: -0.38 (0.13), residues: 1540 loop : -0.52 (0.13), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 156 HIS 0.004 0.001 HIS K 132 PHE 0.041 0.001 PHE D 73 TYR 0.023 0.001 TYR F 171 ARG 0.017 0.001 ARG P 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1333 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1181 time to evaluate : 5.150 Fit side-chains REVERT: A 30 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7953 (mmtp) REVERT: F 107 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8047 (mtm-85) REVERT: F 122 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7386 (mtp-110) REVERT: I 146 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8239 (mtp) REVERT: M 158 MET cc_start: 0.7523 (mtt) cc_final: 0.7009 (mtt) REVERT: O 30 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7952 (mmtp) REVERT: T 107 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.8049 (mtm-85) REVERT: U 240 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8362 (mtpt) REVERT: W 146 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8242 (mtp) REVERT: a 158 MET cc_start: 0.7520 (mtt) cc_final: 0.7011 (mtt) outliers start: 152 outliers final: 117 residues processed: 1256 average time/residue: 1.5618 time to fit residues: 2455.9410 Evaluate side-chains 1276 residues out of total 5146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1151 time to evaluate : 5.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 29 LYS Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 97 LYS Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 130 TYR Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 30 LYS Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 231 THR Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 190 THR Chi-restraints excluded: chain S residue 227 HIS Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 107 ARG Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 156 CYS Chi-restraints excluded: chain T residue 176 MET Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 230 SER Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain U residue 185 THR Chi-restraints excluded: chain U residue 240 LYS Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 29 LYS Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 175 LEU Chi-restraints excluded: chain X residue 47 ARG Chi-restraints excluded: chain X residue 97 LYS Chi-restraints excluded: chain X residue 108 ILE Chi-restraints excluded: chain X residue 151 SER Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain Y residue 150 THR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 29 GLN Chi-restraints excluded: chain Z residue 174 VAL Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 12 ILE Chi-restraints excluded: chain a residue 78 SER Chi-restraints excluded: chain a residue 129 SER Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 183 SER Chi-restraints excluded: chain b residue 191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 384 optimal weight: 3.9990 chunk 515 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 446 optimal weight: 7.9990 chunk 71 optimal weight: 0.0980 chunk 134 optimal weight: 0.6980 chunk 484 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 497 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN C 40 ASN E 13 ASN E 114 GLN E 186 HIS E 225 ASN F 21 GLN F 65 HIS F 90 GLN F 121 GLN H 123 GLN J 17 ASN J 39 GLN J 156 ASN K 65 GLN K 189 HIS L 29 GLN M 8 ASN P 95 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 122 GLN Q 40 ASN Q 240 HIS S 13 ASN ** S 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 225 ASN T 21 GLN T 65 HIS T 90 GLN T 121 GLN V 123 GLN ** W 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 GLN X 156 ASN Y 65 GLN Y 189 HIS Z 29 GLN a 8 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.100259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.080771 restraints weight = 65837.226| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.51 r_work: 0.2836 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 46182 Z= 0.179 Angle : 0.611 13.666 62708 Z= 0.314 Chirality : 0.044 0.243 7346 Planarity : 0.004 0.089 7974 Dihedral : 4.802 42.892 6796 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.66 % Favored : 96.30 % Rotamer: Outliers : 3.37 % Allowed : 26.48 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.11), residues: 6142 helix: 1.87 (0.11), residues: 2262 sheet: -0.36 (0.13), residues: 1530 loop : -0.47 (0.13), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Z 55 HIS 0.004 0.001 HIS b 89 PHE 0.014 0.001 PHE O 191 TYR 0.018 0.001 TYR X 5 ARG 0.017 0.001 ARG P 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30358.03 seconds wall clock time: 532 minutes 5.59 seconds (31925.59 seconds total)