Starting phenix.real_space_refine on Sat Mar 16 01:54:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drw_30828/03_2024/7drw_30828.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drw_30828/03_2024/7drw_30828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drw_30828/03_2024/7drw_30828.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drw_30828/03_2024/7drw_30828.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drw_30828/03_2024/7drw_30828.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drw_30828/03_2024/7drw_30828.pdb" } resolution = 4.2 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 ------------------------------------------------------------------------------- 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= 0.006 sd= 0.070 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 383 5.16 5 C 45514 2.51 5 N 12239 2.21 5 O 13514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 93": "NH1" <-> "NH2" Residue "E PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 123": "NH1" <-> "NH2" Residue "X TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 123": "NH1" <-> "NH2" Residue "1 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 71650 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1841 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "B" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1763 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain: "C" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1927 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 5, 'TRANS': 239} Chain: "D" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1824 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 7, 'TRANS': 224} Chain: "E" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1790 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Chain: "F" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1846 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain: "G" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1879 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "H" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1684 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1721 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 200} Chain breaks: 1 Chain: "J" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1663 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain breaks: 1 Chain: "K" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1678 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 8, 'TRANS': 198} Chain breaks: 1 Chain: "L" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1672 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 1 Chain: "M" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1689 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 9, 'TRANS': 199} Chain breaks: 1 Chain: "N" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1654 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 1 Chain: "O" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1684 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1721 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 200} Chain breaks: 1 Chain: "a" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1663 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain breaks: 1 Chain: "c" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1658 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 8, 'TRANS': 196} Chain breaks: 1 Chain: "e" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1672 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 1 Chain: "g" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1689 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 9, 'TRANS': 199} Chain breaks: 1 Chain: "i" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1654 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 1 Chain: "P" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1824 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 7, 'TRANS': 224} Chain: "R" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1790 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Chain: "b" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1846 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain: "d" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1879 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "f" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1861 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain: "h" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1777 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain: "j" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1936 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 5, 'TRANS': 240} Chain: "k" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1594 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "l" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1593 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "m" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1645 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "n" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1685 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "S" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1594 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "T" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1584 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "U" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1644 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "V" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1682 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "W" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1500 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "X" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1611 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "Y" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1561 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain: "Z" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1500 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "1" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1611 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "2" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1561 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Time building chain proxies: 27.01, per 1000 atoms: 0.38 Number of scatterers: 71650 At special positions: 0 Unit cell: (260.964, 146.298, 238.558, 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 383 16.00 O 13514 8.00 N 12239 7.00 C 45514 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.37 Conformation dependent library (CDL) restraints added in 9.6 seconds 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17010 Finding SS restraints... Secondary structure from input PDB file: 253 helices and 74 sheets defined 51.6% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.04 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 32 through 36 removed outlier: 3.508A pdb=" N GLY A 36 " --> pdb=" O ASN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 106 removed outlier: 3.502A pdb=" N LYS A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 128 Processing helix chain 'A' and resid 172 through 185 removed outlier: 3.670A pdb=" N LYS A 182 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 207 removed outlier: 3.624A pdb=" N VAL A 205 " --> pdb=" O CYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 231 through 241 removed outlier: 3.802A pdb=" N ALA A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 removed outlier: 3.549A pdb=" N TYR B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 102 removed outlier: 3.622A pdb=" N TYR B 83 " --> pdb=" O MET B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.566A pdb=" N VAL B 117 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 178 removed outlier: 3.682A pdb=" N GLY B 170 " --> pdb=" O ASN B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 removed outlier: 3.686A pdb=" N SER B 198 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'C' and resid 18 through 30 Processing helix chain 'C' and resid 79 through 101 removed outlier: 3.771A pdb=" N VAL C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN C 100 " --> pdb=" O ARG C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 124 removed outlier: 3.772A pdb=" N VAL C 111 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 176 Processing helix chain 'C' and resid 185 through 201 removed outlier: 3.612A pdb=" N ALA C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 245 removed outlier: 3.654A pdb=" N GLU C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 28 Processing helix chain 'D' and resid 76 through 98 removed outlier: 3.722A pdb=" N ARG D 81 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 121 removed outlier: 3.730A pdb=" N TYR D 110 " --> pdb=" O TYR D 106 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 140 No H-bonds generated for 'chain 'D' and resid 138 through 140' Processing helix chain 'D' and resid 164 through 176 Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'E' and resid 21 through 30 Processing helix chain 'E' and resid 31 through 34 Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 81 through 103 removed outlier: 3.751A pdb=" N ALA E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP E 90 " --> pdb=" O LYS E 86 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS E 91 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 removed outlier: 4.299A pdb=" N LEU E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 185 removed outlier: 4.036A pdb=" N SER E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN E 182 " --> pdb=" O GLN E 178 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 206 Processing helix chain 'E' and resid 230 through 239 Processing helix chain 'F' and resid 19 through 30 removed outlier: 3.669A pdb=" N VAL F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS F 30 " --> pdb=" O MET F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 99 Processing helix chain 'F' and resid 104 through 121 Proline residue: F 119 - end of helix Processing helix chain 'F' and resid 165 through 175 Processing helix chain 'F' and resid 175 through 182 removed outlier: 4.091A pdb=" N MET F 180 " --> pdb=" O MET F 176 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU F 181 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 197 removed outlier: 4.063A pdb=" N GLU F 197 " --> pdb=" O ARG F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 234 removed outlier: 3.881A pdb=" N PHE F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.501A pdb=" N GLU G 25 " --> pdb=" O VAL G 21 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 126 removed outlier: 4.048A pdb=" N TYR G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR G 124 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU G 125 " --> pdb=" O HIS G 121 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR G 126 " --> pdb=" O ALA G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 179 removed outlier: 3.573A pdb=" N GLU G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 202 removed outlier: 3.880A pdb=" N LYS G 192 " --> pdb=" O ARG G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 242 Processing helix chain 'H' and resid 10 through 34 Processing helix chain 'H' and resid 34 through 49 removed outlier: 3.683A pdb=" N ILE H 41 " --> pdb=" O PRO H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 61 removed outlier: 3.728A pdb=" N ARG H 61 " --> pdb=" O THR H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 127 Proline residue: H 109 - end of helix Processing helix chain 'H' and resid 137 through 181 removed outlier: 4.102A pdb=" N PHE H 168 " --> pdb=" O ILE H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 229 removed outlier: 3.957A pdb=" N ALA H 189 " --> pdb=" O MET H 185 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLU H 225 " --> pdb=" O SER H 221 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS H 226 " --> pdb=" O SER H 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 31 removed outlier: 4.131A pdb=" N VAL I 14 " --> pdb=" O ALA I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 46 Processing helix chain 'I' and resid 53 through 58 Processing helix chain 'I' and resid 107 through 139 Proline residue: I 119 - end of helix Processing helix chain 'I' and resid 146 through 191 removed outlier: 3.812A pdb=" N VAL I 150 " --> pdb=" O ASN I 146 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS I 171 " --> pdb=" O LEU I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 239 removed outlier: 3.874A pdb=" N ALA I 224 " --> pdb=" O ARG I 220 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN I 233 " --> pdb=" O ILE I 229 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLU I 235 " --> pdb=" O LEU I 231 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LYS I 236 " --> pdb=" O LYS I 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 31 removed outlier: 3.533A pdb=" N VAL J 14 " --> pdb=" O ALA J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 46 Processing helix chain 'J' and resid 54 through 58 Processing helix chain 'J' and resid 107 through 139 removed outlier: 3.903A pdb=" N ARG J 116 " --> pdb=" O VAL J 112 " (cutoff:3.500A) Proline residue: J 119 - end of helix removed outlier: 3.508A pdb=" N LEU J 137 " --> pdb=" O THR J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 191 removed outlier: 3.936A pdb=" N PHE J 157 " --> pdb=" O GLN J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 239 removed outlier: 4.023A pdb=" N GLN J 199 " --> pdb=" O GLY J 195 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG J 213 " --> pdb=" O TYR J 209 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU J 235 " --> pdb=" O LEU J 231 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LYS J 236 " --> pdb=" O LYS J 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 15 No H-bonds generated for 'chain 'K' and resid 13 through 15' Processing helix chain 'K' and resid 16 through 22 removed outlier: 4.434A pdb=" N PHE K 20 " --> pdb=" O GLN K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 34 removed outlier: 3.833A pdb=" N TYR K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 47 Processing helix chain 'K' and resid 49 through 54 removed outlier: 3.595A pdb=" N ASN K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 61 Processing helix chain 'K' and resid 98 through 127 Proline residue: K 109 - end of helix Processing helix chain 'K' and resid 137 through 181 removed outlier: 3.925A pdb=" N PHE K 168 " --> pdb=" O ILE K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 190 Processing helix chain 'K' and resid 190 through 223 removed outlier: 4.084A pdb=" N ARG K 194 " --> pdb=" O LEU K 190 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP K 195 " --> pdb=" O VAL K 191 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR K 199 " --> pdb=" O ASP K 195 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR K 217 " --> pdb=" O TYR K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 229 Processing helix chain 'L' and resid 9 through 31 Processing helix chain 'L' and resid 31 through 45 Processing helix chain 'L' and resid 107 through 138 Proline residue: L 119 - end of helix removed outlier: 3.509A pdb=" N GLU L 126 " --> pdb=" O LYS L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 191 removed outlier: 3.500A pdb=" N MET L 160 " --> pdb=" O VAL L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 233 Processing helix chain 'M' and resid 10 through 34 removed outlier: 3.666A pdb=" N PHE M 31 " --> pdb=" O GLU M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 48 removed outlier: 3.788A pdb=" N ILE M 41 " --> pdb=" O PRO M 37 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN M 48 " --> pdb=" O ASN M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 128 removed outlier: 3.825A pdb=" N LEU M 106 " --> pdb=" O SER M 102 " (cutoff:3.500A) Proline residue: M 109 - end of helix removed outlier: 3.604A pdb=" N ILE M 119 " --> pdb=" O LYS M 115 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU M 128 " --> pdb=" O TRP M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 181 removed outlier: 3.768A pdb=" N PHE M 168 " --> pdb=" O ILE M 164 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA M 176 " --> pdb=" O GLY M 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 191 Processing helix chain 'M' and resid 192 through 229 removed outlier: 3.582A pdb=" N GLU M 196 " --> pdb=" O HIS M 192 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR M 213 " --> pdb=" O LEU M 209 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLU M 225 " --> pdb=" O SER M 221 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LYS M 226 " --> pdb=" O SER M 222 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN M 229 " --> pdb=" O GLU M 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 31 removed outlier: 3.672A pdb=" N GLY N 30 " --> pdb=" O GLU N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 46 Processing helix chain 'N' and resid 107 through 139 Proline residue: N 119 - end of helix Processing helix chain 'N' and resid 147 through 191 removed outlier: 3.531A pdb=" N ARG N 181 " --> pdb=" O TYR N 177 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 233 Processing helix chain 'O' and resid 10 through 34 removed outlier: 3.644A pdb=" N ARG O 14 " --> pdb=" O SER O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 49 removed outlier: 3.792A pdb=" N ILE O 40 " --> pdb=" O LEU O 36 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE O 41 " --> pdb=" O PRO O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 128 removed outlier: 4.296A pdb=" N ALA O 105 " --> pdb=" O LEU O 101 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU O 106 " --> pdb=" O SER O 102 " (cutoff:3.500A) Proline residue: O 109 - end of helix Processing helix chain 'O' and resid 137 through 181 removed outlier: 4.044A pdb=" N PHE O 168 " --> pdb=" O ILE O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 229 removed outlier: 4.768A pdb=" N GLU O 225 " --> pdb=" O SER O 221 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LYS O 226 " --> pdb=" O SER O 222 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 31 Processing helix chain 'Q' and resid 31 through 46 Processing helix chain 'Q' and resid 53 through 57 Processing helix chain 'Q' and resid 107 through 139 Proline residue: Q 119 - end of helix Processing helix chain 'Q' and resid 147 through 191 removed outlier: 3.513A pdb=" N GLN Q 153 " --> pdb=" O GLY Q 149 " (cutoff:3.500A) Processing helix chain 'Q' and resid 195 through 239 removed outlier: 3.712A pdb=" N ALA Q 224 " --> pdb=" O ARG Q 220 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLU Q 235 " --> pdb=" O LEU Q 231 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LYS Q 236 " --> pdb=" O LYS Q 232 " (cutoff:3.500A) Processing helix chain 'a' and resid 7 through 31 removed outlier: 3.668A pdb=" N LYS a 13 " --> pdb=" O GLU a 9 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL a 14 " --> pdb=" O ALA a 10 " (cutoff:3.500A) Processing helix chain 'a' and resid 31 through 46 Processing helix chain 'a' and resid 54 through 58 Processing helix chain 'a' and resid 107 through 139 removed outlier: 3.897A pdb=" N ARG a 116 " --> pdb=" O VAL a 112 " (cutoff:3.500A) Proline residue: a 119 - end of helix removed outlier: 3.508A pdb=" N LEU a 137 " --> pdb=" O THR a 133 " (cutoff:3.500A) Processing helix chain 'a' and resid 150 through 191 removed outlier: 3.935A pdb=" N PHE a 157 " --> pdb=" O GLN a 153 " (cutoff:3.500A) Processing helix chain 'a' and resid 195 through 239 removed outlier: 4.022A pdb=" N GLN a 199 " --> pdb=" O GLY a 195 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLU a 235 " --> pdb=" O LEU a 231 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LYS a 236 " --> pdb=" O LYS a 232 " (cutoff:3.500A) Processing helix chain 'c' and resid 13 through 16 Processing helix chain 'c' and resid 17 through 22 Processing helix chain 'c' and resid 22 through 34 Processing helix chain 'c' and resid 34 through 48 removed outlier: 3.855A pdb=" N ILE c 41 " --> pdb=" O PRO c 37 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR c 42 " --> pdb=" O GLN c 38 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN c 48 " --> pdb=" O ASN c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 54 Processing helix chain 'c' and resid 56 through 61 Processing helix chain 'c' and resid 99 through 127 removed outlier: 4.353A pdb=" N LEU c 103 " --> pdb=" O LYS c 99 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU c 106 " --> pdb=" O SER c 102 " (cutoff:3.500A) Proline residue: c 109 - end of helix removed outlier: 3.782A pdb=" N LEU c 114 " --> pdb=" O GLU c 110 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE c 119 " --> pdb=" O LYS c 115 " (cutoff:3.500A) Processing helix chain 'c' and resid 137 through 179 removed outlier: 4.045A pdb=" N PHE c 168 " --> pdb=" O ILE c 164 " (cutoff:3.500A) Processing helix chain 'c' and resid 184 through 223 removed outlier: 4.419A pdb=" N ARG c 188 " --> pdb=" O VAL c 184 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS c 192 " --> pdb=" O ARG c 188 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU c 193 " --> pdb=" O ALA c 189 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG c 194 " --> pdb=" O LEU c 190 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP c 195 " --> pdb=" O VAL c 191 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR c 199 " --> pdb=" O ASP c 195 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU c 202 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'c' and resid 223 through 229 Processing helix chain 'e' and resid 7 through 31 removed outlier: 3.617A pdb=" N ALA e 12 " --> pdb=" O PRO e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 31 through 45 Processing helix chain 'e' and resid 107 through 138 Proline residue: e 119 - end of helix removed outlier: 3.502A pdb=" N GLU e 126 " --> pdb=" O LYS e 122 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL e 131 " --> pdb=" O GLN e 127 " (cutoff:3.500A) Processing helix chain 'e' and resid 147 through 191 Processing helix chain 'e' and resid 195 through 233 removed outlier: 4.276A pdb=" N LEU e 226 " --> pdb=" O ALA e 222 " (cutoff:3.500A) Processing helix chain 'e' and resid 244 through 248 removed outlier: 4.521A pdb=" N ILE e 248 " --> pdb=" O LYS e 245 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 34 removed outlier: 3.668A pdb=" N PHE g 31 " --> pdb=" O GLU g 27 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 48 removed outlier: 3.789A pdb=" N ILE g 41 " --> pdb=" O PRO g 37 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN g 48 " --> pdb=" O ASN g 44 " (cutoff:3.500A) Processing helix chain 'g' and resid 97 through 128 removed outlier: 3.826A pdb=" N LEU g 106 " --> pdb=" O SER g 102 " (cutoff:3.500A) Proline residue: g 109 - end of helix removed outlier: 3.603A pdb=" N ILE g 119 " --> pdb=" O LYS g 115 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU g 128 " --> pdb=" O TRP g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 181 removed outlier: 3.768A pdb=" N PHE g 168 " --> pdb=" O ILE g 164 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA g 176 " --> pdb=" O GLY g 172 " (cutoff:3.500A) Processing helix chain 'g' and resid 186 through 191 Processing helix chain 'g' and resid 192 through 229 removed outlier: 3.582A pdb=" N GLU g 196 " --> pdb=" O HIS g 192 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR g 213 " --> pdb=" O LEU g 209 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLU g 225 " --> pdb=" O SER g 221 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LYS g 226 " --> pdb=" O SER g 222 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN g 229 " --> pdb=" O GLU g 225 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 31 Processing helix chain 'i' and resid 31 through 46 removed outlier: 3.704A pdb=" N SER i 38 " --> pdb=" O PRO i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 107 through 139 Proline residue: i 119 - end of helix Processing helix chain 'i' and resid 147 through 191 removed outlier: 3.791A pdb=" N SER i 162 " --> pdb=" O GLU i 158 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU i 163 " --> pdb=" O LEU i 159 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER i 175 " --> pdb=" O HIS i 171 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE i 178 " --> pdb=" O ILE i 174 " (cutoff:3.500A) Processing helix chain 'i' and resid 194 through 233 removed outlier: 4.354A pdb=" N ARG i 198 " --> pdb=" O VAL i 194 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN i 233 " --> pdb=" O ILE i 229 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 28 Processing helix chain 'P' and resid 76 through 98 removed outlier: 3.710A pdb=" N ARG P 81 " --> pdb=" O THR P 77 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE P 82 " --> pdb=" O ALA P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 121 removed outlier: 4.682A pdb=" N LEU P 114 " --> pdb=" O TYR P 110 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR P 119 " --> pdb=" O LYS P 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 138 through 140 No H-bonds generated for 'chain 'P' and resid 138 through 140' Processing helix chain 'P' and resid 164 through 176 Processing helix chain 'P' and resid 183 through 197 removed outlier: 4.065A pdb=" N GLU P 197 " --> pdb=" O LYS P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 230 Processing helix chain 'R' and resid 21 through 30 Processing helix chain 'R' and resid 31 through 34 Processing helix chain 'R' and resid 60 through 64 Processing helix chain 'R' and resid 81 through 103 removed outlier: 3.751A pdb=" N ALA R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP R 90 " --> pdb=" O LYS R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 119 removed outlier: 4.299A pdb=" N LEU R 119 " --> pdb=" O ALA R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 185 removed outlier: 4.036A pdb=" N SER R 179 " --> pdb=" O GLU R 175 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN R 182 " --> pdb=" O GLN R 178 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU R 183 " --> pdb=" O SER R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 206 Processing helix chain 'R' and resid 230 through 239 Processing helix chain 'b' and resid 19 through 30 removed outlier: 3.670A pdb=" N VAL b 29 " --> pdb=" O ALA b 25 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS b 30 " --> pdb=" O MET b 26 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 99 Processing helix chain 'b' and resid 104 through 121 Proline residue: b 119 - end of helix Processing helix chain 'b' and resid 165 through 175 Processing helix chain 'b' and resid 175 through 182 removed outlier: 4.077A pdb=" N MET b 180 " --> pdb=" O MET b 176 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU b 181 " --> pdb=" O SER b 177 " (cutoff:3.500A) Processing helix chain 'b' and resid 183 through 197 removed outlier: 4.062A pdb=" N GLU b 197 " --> pdb=" O ARG b 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 228 through 234 removed outlier: 3.881A pdb=" N PHE b 232 " --> pdb=" O ASP b 228 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 32 removed outlier: 3.513A pdb=" N GLU d 25 " --> pdb=" O VAL d 21 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL d 31 " --> pdb=" O ALA d 27 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 104 Processing helix chain 'd' and resid 108 through 126 removed outlier: 4.145A pdb=" N TYR d 123 " --> pdb=" O TYR d 119 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR d 124 " --> pdb=" O VAL d 120 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU d 125 " --> pdb=" O HIS d 121 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR d 126 " --> pdb=" O ALA d 122 " (cutoff:3.500A) Processing helix chain 'd' and resid 170 through 179 removed outlier: 3.571A pdb=" N GLU d 176 " --> pdb=" O ALA d 172 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 202 removed outlier: 3.905A pdb=" N LYS d 192 " --> pdb=" O ARG d 188 " (cutoff:3.500A) Processing helix chain 'd' and resid 229 through 242 Processing helix chain 'f' and resid 22 through 31 Processing helix chain 'f' and resid 32 through 36 removed outlier: 3.509A pdb=" N GLY f 36 " --> pdb=" O ASN f 33 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 106 removed outlier: 3.502A pdb=" N LYS f 102 " --> pdb=" O ALA f 98 " (cutoff:3.500A) Processing helix chain 'f' and resid 110 through 128 Processing helix chain 'f' and resid 172 through 185 removed outlier: 3.670A pdb=" N LYS f 182 " --> pdb=" O PHE f 178 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS f 185 " --> pdb=" O LYS f 181 " (cutoff:3.500A) Processing helix chain 'f' and resid 190 through 207 removed outlier: 3.624A pdb=" N VAL f 205 " --> pdb=" O CYS f 201 " (cutoff:3.500A) Processing helix chain 'f' and resid 211 through 213 No H-bonds generated for 'chain 'f' and resid 211 through 213' Processing helix chain 'f' and resid 231 through 245 removed outlier: 3.803A pdb=" N ALA f 241 " --> pdb=" O ALA f 237 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU f 242 " --> pdb=" O HIS f 238 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG f 245 " --> pdb=" O ALA f 241 " (cutoff:3.500A) Processing helix chain 'h' and resid 19 through 30 removed outlier: 3.549A pdb=" N TYR h 24 " --> pdb=" O VAL h 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 102 removed outlier: 3.621A pdb=" N TYR h 83 " --> pdb=" O MET h 79 " (cutoff:3.500A) Processing helix chain 'h' and resid 106 through 121 removed outlier: 3.566A pdb=" N VAL h 117 " --> pdb=" O ARG h 113 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET h 118 " --> pdb=" O VAL h 114 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR h 121 " --> pdb=" O VAL h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 166 through 177 removed outlier: 3.681A pdb=" N GLY h 170 " --> pdb=" O ASN h 166 " (cutoff:3.500A) Processing helix chain 'h' and resid 183 through 199 removed outlier: 3.686A pdb=" N SER h 198 " --> pdb=" O THR h 194 " (cutoff:3.500A) Processing helix chain 'h' and resid 222 through 230 Processing helix chain 'j' and resid 2 through 6 Processing helix chain 'j' and resid 18 through 30 Processing helix chain 'j' and resid 79 through 101 removed outlier: 3.770A pdb=" N VAL j 85 " --> pdb=" O SER j 81 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN j 100 " --> pdb=" O ARG j 96 " (cutoff:3.500A) Processing helix chain 'j' and resid 106 through 124 removed outlier: 3.772A pdb=" N VAL j 111 " --> pdb=" O CYS j 107 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE j 117 " --> pdb=" O ALA j 113 " (cutoff:3.500A) Processing helix chain 'j' and resid 167 through 176 Processing helix chain 'j' and resid 185 through 201 removed outlier: 3.611A pdb=" N ALA j 191 " --> pdb=" O LYS j 187 " (cutoff:3.500A) Processing helix chain 'j' and resid 229 through 246 removed outlier: 3.651A pdb=" N GLU j 242 " --> pdb=" O LYS j 238 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA j 245 " --> pdb=" O GLU j 241 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 78 removed outlier: 3.583A pdb=" N LEU k 73 " --> pdb=" O PHE k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 83 through 97 removed outlier: 3.826A pdb=" N SER k 89 " --> pdb=" O TYR k 85 " (cutoff:3.500A) Processing helix chain 'k' and resid 142 through 154 removed outlier: 4.325A pdb=" N GLY k 148 " --> pdb=" O GLU k 144 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET k 149 " --> pdb=" O GLN k 145 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS k 150 " --> pdb=" O MET k 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER k 152 " --> pdb=" O GLY k 148 " (cutoff:3.500A) Processing helix chain 'k' and resid 159 through 176 removed outlier: 3.540A pdb=" N GLU k 165 " --> pdb=" O GLU k 161 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP k 176 " --> pdb=" O LEU k 172 " (cutoff:3.500A) Processing helix chain 'l' and resid 49 through 72 removed outlier: 4.220A pdb=" N VAL l 54 " --> pdb=" O ALA l 50 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN l 55 " --> pdb=" O GLY l 51 " (cutoff:3.500A) Processing helix chain 'l' and resid 76 through 91 removed outlier: 3.574A pdb=" N ARG l 86 " --> pdb=" O ASN l 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR l 91 " --> pdb=" O ASN l 87 " (cutoff:3.500A) Processing helix chain 'l' and resid 135 through 147 removed outlier: 4.652A pdb=" N SER l 141 " --> pdb=" O PHE l 137 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ILE l 142 " --> pdb=" O LEU l 138 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG l 145 " --> pdb=" O SER l 141 " (cutoff:3.500A) Processing helix chain 'l' and resid 152 through 165 removed outlier: 3.622A pdb=" N GLU l 158 " --> pdb=" O GLU l 154 " (cutoff:3.500A) Processing helix chain 'l' and resid 166 through 168 No H-bonds generated for 'chain 'l' and resid 166 through 168' Processing helix chain 'm' and resid 85 through 108 Processing helix chain 'm' and resid 112 through 126 removed outlier: 3.747A pdb=" N THR m 122 " --> pdb=" O ALA m 118 " (cutoff:3.500A) Processing helix chain 'm' and resid 169 through 181 Proline residue: m 175 - end of helix Processing helix chain 'm' and resid 195 through 214 removed outlier: 3.567A pdb=" N ARG m 201 " --> pdb=" O ASP m 197 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE m 207 " --> pdb=" O VAL m 203 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG m 213 " --> pdb=" O SER m 209 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 123 Processing helix chain 'n' and resid 129 through 147 removed outlier: 3.774A pdb=" N ARG n 144 " --> pdb=" O ALA n 140 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG n 145 " --> pdb=" O MET n 141 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER n 146 " --> pdb=" O TYR n 142 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS n 147 " --> pdb=" O SER n 143 " (cutoff:3.500A) Processing helix chain 'n' and resid 190 through 202 removed outlier: 3.931A pdb=" N LEU n 194 " --> pdb=" O LEU n 190 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL n 198 " --> pdb=" O LEU n 194 " (cutoff:3.500A) Processing helix chain 'n' and resid 206 through 225 Processing helix chain 'n' and resid 255 through 261 Processing helix chain 'S' and resid 56 through 78 removed outlier: 3.582A pdb=" N LEU S 73 " --> pdb=" O PHE S 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 97 removed outlier: 3.826A pdb=" N SER S 89 " --> pdb=" O TYR S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 142 through 154 removed outlier: 4.326A pdb=" N GLY S 148 " --> pdb=" O GLU S 144 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET S 149 " --> pdb=" O GLN S 145 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS S 150 " --> pdb=" O MET S 146 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER S 152 " --> pdb=" O GLY S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 159 through 176 removed outlier: 3.539A pdb=" N GLU S 165 " --> pdb=" O GLU S 161 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP S 176 " --> pdb=" O LEU S 172 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 72 removed outlier: 4.220A pdb=" N VAL T 54 " --> pdb=" O ALA T 50 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN T 55 " --> pdb=" O GLY T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 91 removed outlier: 3.595A pdb=" N ARG T 86 " --> pdb=" O ASN T 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR T 91 " --> pdb=" O ASN T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 147 removed outlier: 4.652A pdb=" N SER T 141 " --> pdb=" O PHE T 137 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ILE T 142 " --> pdb=" O LEU T 138 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG T 145 " --> pdb=" O SER T 141 " (cutoff:3.500A) Processing helix chain 'T' and resid 152 through 165 removed outlier: 3.621A pdb=" N GLU T 158 " --> pdb=" O GLU T 154 " (cutoff:3.500A) Processing helix chain 'T' and resid 166 through 168 No H-bonds generated for 'chain 'T' and resid 166 through 168' Processing helix chain 'U' and resid 85 through 108 Processing helix chain 'U' and resid 112 through 126 removed outlier: 3.746A pdb=" N THR U 122 " --> pdb=" O ALA U 118 " (cutoff:3.500A) Processing helix chain 'U' and resid 169 through 181 Proline residue: U 175 - end of helix Processing helix chain 'U' and resid 195 through 214 removed outlier: 3.567A pdb=" N ARG U 201 " --> pdb=" O ASP U 197 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE U 207 " --> pdb=" O VAL U 203 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG U 213 " --> pdb=" O SER U 209 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 123 Processing helix chain 'V' and resid 129 through 147 removed outlier: 3.775A pdb=" N ARG V 144 " --> pdb=" O ALA V 140 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG V 145 " --> pdb=" O MET V 141 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER V 146 " --> pdb=" O TYR V 142 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS V 147 " --> pdb=" O SER V 143 " (cutoff:3.500A) Processing helix chain 'V' and resid 190 through 202 removed outlier: 3.931A pdb=" N LEU V 194 " --> pdb=" O LEU V 190 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL V 198 " --> pdb=" O LEU V 194 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 225 Processing helix chain 'V' and resid 255 through 262 Processing helix chain 'W' and resid 68 through 91 removed outlier: 3.613A pdb=" N LEU W 85 " --> pdb=" O TYR W 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 111 removed outlier: 3.517A pdb=" N VAL W 103 " --> pdb=" O ALA W 99 " (cutoff:3.500A) Processing helix chain 'W' and resid 135 through 138 removed outlier: 3.503A pdb=" N MET W 138 " --> pdb=" O MET W 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 135 through 138' Processing helix chain 'W' and resid 154 through 161 Processing helix chain 'W' and resid 167 through 186 Processing helix chain 'W' and resid 209 through 213 removed outlier: 3.661A pdb=" N LEU W 213 " --> pdb=" O GLY W 210 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 110 removed outlier: 3.527A pdb=" N LEU X 104 " --> pdb=" O SER X 100 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 129 removed outlier: 3.675A pdb=" N VAL X 118 " --> pdb=" O ARG X 114 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR X 119 " --> pdb=" O VAL X 115 " (cutoff:3.500A) Processing helix chain 'X' and resid 169 through 181 removed outlier: 3.536A pdb=" N ALA X 173 " --> pdb=" O GLY X 169 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL X 176 " --> pdb=" O ALA X 172 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG X 180 " --> pdb=" O VAL X 176 " (cutoff:3.500A) Processing helix chain 'X' and resid 186 through 204 Processing helix chain 'Y' and resid 120 through 142 removed outlier: 3.756A pdb=" N ARG Y 129 " --> pdb=" O LEU Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 162 removed outlier: 3.639A pdb=" N MET Y 159 " --> pdb=" O LEU Y 155 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN Y 161 " --> pdb=" O ASN Y 157 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR Y 162 " --> pdb=" O MET Y 158 " (cutoff:3.500A) Processing helix chain 'Y' and resid 203 through 213 removed outlier: 3.811A pdb=" N GLY Y 209 " --> pdb=" O SER Y 205 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL Y 210 " --> pdb=" O HIS Y 206 " (cutoff:3.500A) Processing helix chain 'Y' and resid 220 through 238 removed outlier: 3.512A pdb=" N ASP Y 226 " --> pdb=" O GLU Y 222 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE Y 232 " --> pdb=" O GLY Y 228 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG Y 238 " --> pdb=" O HIS Y 234 " (cutoff:3.500A) Processing helix chain 'Y' and resid 264 through 272 removed outlier: 3.839A pdb=" N GLN Y 270 " --> pdb=" O ASP Y 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 91 removed outlier: 3.614A pdb=" N LEU Z 85 " --> pdb=" O TYR Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 95 through 111 removed outlier: 3.516A pdb=" N VAL Z 103 " --> pdb=" O ALA Z 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 135 through 138 removed outlier: 3.503A pdb=" N MET Z 138 " --> pdb=" O MET Z 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 135 through 138' Processing helix chain 'Z' and resid 154 through 161 Processing helix chain 'Z' and resid 167 through 186 Processing helix chain 'Z' and resid 209 through 213 removed outlier: 3.660A pdb=" N LEU Z 213 " --> pdb=" O GLY Z 210 " (cutoff:3.500A) Processing helix chain '1' and resid 87 through 110 removed outlier: 3.525A pdb=" N LEU 1 104 " --> pdb=" O SER 1 100 " (cutoff:3.500A) Processing helix chain '1' and resid 114 through 129 removed outlier: 3.676A pdb=" N VAL 1 118 " --> pdb=" O ARG 1 114 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR 1 119 " --> pdb=" O VAL 1 115 " (cutoff:3.500A) Processing helix chain '1' and resid 169 through 181 removed outlier: 3.535A pdb=" N ALA 1 173 " --> pdb=" O GLY 1 169 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL 1 176 " --> pdb=" O ALA 1 172 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG 1 180 " --> pdb=" O VAL 1 176 " (cutoff:3.500A) Processing helix chain '1' and resid 186 through 204 Processing helix chain '2' and resid 120 through 142 removed outlier: 3.755A pdb=" N ARG 2 129 " --> pdb=" O LEU 2 125 " (cutoff:3.500A) Processing helix chain '2' and resid 147 through 162 removed outlier: 3.639A pdb=" N MET 2 159 " --> pdb=" O LEU 2 155 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN 2 161 " --> pdb=" O ASN 2 157 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR 2 162 " --> pdb=" O MET 2 158 " (cutoff:3.500A) Processing helix chain '2' and resid 203 through 213 removed outlier: 3.811A pdb=" N GLY 2 209 " --> pdb=" O SER 2 205 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL 2 210 " --> pdb=" O HIS 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 220 through 238 removed outlier: 3.514A pdb=" N ASP 2 226 " --> pdb=" O GLU 2 222 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE 2 232 " --> pdb=" O GLY 2 228 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG 2 238 " --> pdb=" O HIS 2 234 " (cutoff:3.500A) Processing helix chain '2' and resid 264 through 272 removed outlier: 3.839A pdb=" N GLN 2 270 " --> pdb=" O ASP 2 266 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 169 removed outlier: 6.319A pdb=" N THR A 38 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN A 53 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 71 removed outlier: 4.127A pdb=" N LYS A 153 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS A 161 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY A 162 " --> pdb=" O ASP B 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 144 Processing sheet with id=AA4, first strand: chain 'B' and resid 160 through 163 Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.611A pdb=" N SER B 77 " --> pdb=" O SER B 133 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 133 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN B 140 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AA7, first strand: chain 'C' and resid 65 through 66 removed outlier: 3.767A pdb=" N LEU C 135 " --> pdb=" O SER C 75 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 134 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.851A pdb=" N LEU D 208 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 62 through 64 Processing sheet with id=AB1, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AB2, first strand: chain 'E' and resid 77 through 78 removed outlier: 3.662A pdb=" N LEU E 142 " --> pdb=" O ALA E 77 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU E 141 " --> pdb=" O MET E 156 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS E 155 " --> pdb=" O VAL E 163 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 67 removed outlier: 3.556A pdb=" N ILE F 72 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL F 66 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE F 70 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU F 132 " --> pdb=" O THR F 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 163 through 166 removed outlier: 4.840A pdb=" N ALA G 209 " --> pdb=" O VAL G 54 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 67 through 71 removed outlier: 6.607A pdb=" N VAL G 74 " --> pdb=" O VAL G 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 158 through 161 removed outlier: 4.851A pdb=" N LEU P 208 " --> pdb=" O LEU P 220 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 62 through 64 Processing sheet with id=AB9, first strand: chain 'R' and resid 167 through 170 Processing sheet with id=AC1, first strand: chain 'R' and resid 77 through 78 removed outlier: 3.661A pdb=" N LEU R 142 " --> pdb=" O ALA R 77 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU R 141 " --> pdb=" O MET R 156 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS R 155 " --> pdb=" O VAL R 163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 158 through 161 Processing sheet with id=AC3, first strand: chain 'b' and resid 63 through 67 removed outlier: 3.556A pdb=" N ILE b 72 " --> pdb=" O LEU b 64 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL b 66 " --> pdb=" O ILE b 70 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE b 70 " --> pdb=" O VAL b 66 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU b 132 " --> pdb=" O THR b 147 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'd' and resid 163 through 166 removed outlier: 4.839A pdb=" N ALA d 209 " --> pdb=" O VAL d 54 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'd' and resid 67 through 71 removed outlier: 6.606A pdb=" N VAL d 74 " --> pdb=" O VAL d 70 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'f' and resid 165 through 169 removed outlier: 6.319A pdb=" N THR f 38 " --> pdb=" O GLN f 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN f 53 " --> pdb=" O THR f 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'f' and resid 69 through 71 removed outlier: 4.128A pdb=" N LYS f 153 " --> pdb=" O CYS f 161 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N CYS f 161 " --> pdb=" O LYS f 153 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'f' and resid 143 through 144 Processing sheet with id=AC9, first strand: chain 'h' and resid 160 through 163 Processing sheet with id=AD1, first strand: chain 'h' and resid 66 through 67 removed outlier: 3.610A pdb=" N SER h 77 " --> pdb=" O SER h 133 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER h 133 " --> pdb=" O SER h 77 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN h 140 " --> pdb=" O ARG h 143 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'j' and resid 161 through 164 Processing sheet with id=AD3, first strand: chain 'j' and resid 65 through 66 removed outlier: 3.767A pdb=" N LEU j 135 " --> pdb=" O SER j 75 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU j 134 " --> pdb=" O SER j 150 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'k' and resid 136 through 140 removed outlier: 6.260A pdb=" N ALA k 10 " --> pdb=" O ASP k 25 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP k 25 " --> pdb=" O ALA k 10 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL k 185 " --> pdb=" O LEU k 200 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'k' and resid 28 through 30 removed outlier: 7.073A pdb=" N PHE k 28 " --> pdb=" O VAL k 35 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'k' and resid 42 through 44 Processing sheet with id=AD7, first strand: chain 'l' and resid 129 through 132 removed outlier: 4.065A pdb=" N LEU l 4 " --> pdb=" O HIS l 132 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP l 184 " --> pdb=" O GLY l 187 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'l' and resid 21 through 23 removed outlier: 6.414A pdb=" N SER l 23 " --> pdb=" O GLN l 27 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLN l 27 " --> pdb=" O SER l 23 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'l' and resid 35 through 37 removed outlier: 3.578A pdb=" N ALA l 105 " --> pdb=" O LEU l 43 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'm' and resid 163 through 167 removed outlier: 6.411A pdb=" N THR m 39 " --> pdb=" O ASP m 54 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP m 54 " --> pdb=" O THR m 39 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'm' and resid 57 through 59 removed outlier: 6.695A pdb=" N GLU m 59 " --> pdb=" O ILE m 63 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ILE m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'm' and resid 72 through 75 removed outlier: 6.753A pdb=" N THR m 78 " --> pdb=" O LEU m 74 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL m 149 " --> pdb=" O ASP m 161 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER m 151 " --> pdb=" O GLN m 159 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN m 159 " --> pdb=" O SER m 151 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'n' and resid 181 through 183 removed outlier: 3.629A pdb=" N GLY n 64 " --> pdb=" O PHE n 61 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'n' and resid 74 through 75 Processing sheet with id=AE6, first strand: chain 'n' and resid 87 through 90 Processing sheet with id=AE7, first strand: chain 'S' and resid 136 through 140 removed outlier: 6.260A pdb=" N ALA S 10 " --> pdb=" O ASP S 25 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP S 25 " --> pdb=" O ALA S 10 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL S 185 " --> pdb=" O LEU S 200 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE S 195 " --> pdb=" O VAL 1 255 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL 1 255 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N THR S 197 " --> pdb=" O GLN 1 253 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLN 1 253 " --> pdb=" O THR S 197 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR S 199 " --> pdb=" O LEU 1 251 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 28 through 30 removed outlier: 7.072A pdb=" N PHE S 28 " --> pdb=" O VAL S 35 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 42 through 44 Processing sheet with id=AF1, first strand: chain 'T' and resid 129 through 132 removed outlier: 4.065A pdb=" N LEU T 4 " --> pdb=" O HIS T 132 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP T 184 " --> pdb=" O GLY T 187 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 21 through 23 removed outlier: 6.415A pdb=" N SER T 23 " --> pdb=" O GLN T 27 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLN T 27 " --> pdb=" O SER T 23 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 35 through 37 removed outlier: 3.577A pdb=" N ALA T 105 " --> pdb=" O LEU T 43 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 163 through 167 removed outlier: 6.410A pdb=" N THR U 39 " --> pdb=" O ASP U 54 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP U 54 " --> pdb=" O THR U 39 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 57 through 59 removed outlier: 6.693A pdb=" N GLU U 59 " --> pdb=" O ILE U 63 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE U 63 " --> pdb=" O GLU U 59 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 72 through 75 removed outlier: 6.752A pdb=" N THR U 78 " --> pdb=" O LEU U 74 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL U 149 " --> pdb=" O ASP U 161 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 181 through 183 removed outlier: 3.630A pdb=" N GLY V 64 " --> pdb=" O PHE V 61 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 74 through 75 Processing sheet with id=AF9, first strand: chain 'V' and resid 87 through 90 Processing sheet with id=AG1, first strand: chain 'W' and resid 144 through 147 Processing sheet with id=AG2, first strand: chain 'W' and resid 40 through 42 removed outlier: 6.282A pdb=" N ALA W 42 " --> pdb=" O VAL W 46 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL W 46 " --> pdb=" O ALA W 42 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 54 through 56 removed outlier: 3.782A pdb=" N HIS W 117 " --> pdb=" O SER W 66 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY W 133 " --> pdb=" O ILE W 140 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE W 140 " --> pdb=" O GLY W 133 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 163 through 167 removed outlier: 3.552A pdb=" N THR X 164 " --> pdb=" O GLY X 44 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR X 41 " --> pdb=" O ASP X 56 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP X 56 " --> pdb=" O THR X 41 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL X 212 " --> pdb=" O ALA X 227 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA X 227 " --> pdb=" O VAL X 212 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 59 through 61 removed outlier: 5.641A pdb=" N ASN X 61 " --> pdb=" O VAL X 65 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N VAL X 65 " --> pdb=" O ASN X 61 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 74 through 75 removed outlier: 3.913A pdb=" N CYS X 82 " --> pdb=" O HIS X 74 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL X 139 " --> pdb=" O TYR X 150 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 197 through 201 removed outlier: 3.858A pdb=" N GLU Y 260 " --> pdb=" O MET Y 248 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N HIS Y 250 " --> pdb=" O LYS Y 258 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LYS Y 258 " --> pdb=" O HIS Y 250 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 92 through 94 removed outlier: 7.501A pdb=" N ALA Y 92 " --> pdb=" O ALA Y 99 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Y' and resid 107 through 108 Processing sheet with id=AH1, first strand: chain 'Y' and resid 107 through 108 removed outlier: 3.531A pdb=" N GLY Y 175 " --> pdb=" O GLY Y 182 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 144 through 147 Processing sheet with id=AH3, first strand: chain 'Z' and resid 40 through 42 removed outlier: 6.282A pdb=" N ALA Z 42 " --> pdb=" O VAL Z 46 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Z' and resid 54 through 56 removed outlier: 3.780A pdb=" N HIS Z 117 " --> pdb=" O SER Z 66 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY Z 133 " --> pdb=" O ILE Z 140 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE Z 140 " --> pdb=" O GLY Z 133 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '1' and resid 163 through 167 removed outlier: 3.551A pdb=" N THR 1 164 " --> pdb=" O GLY 1 44 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR 1 41 " --> pdb=" O ASP 1 56 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP 1 56 " --> pdb=" O THR 1 41 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL 1 212 " --> pdb=" O ALA 1 227 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA 1 227 " --> pdb=" O VAL 1 212 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '1' and resid 59 through 61 removed outlier: 5.641A pdb=" N ASN 1 61 " --> pdb=" O VAL 1 65 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL 1 65 " --> pdb=" O ASN 1 61 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain '1' and resid 74 through 75 removed outlier: 3.912A pdb=" N CYS 1 82 " --> pdb=" O HIS 1 74 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL 1 139 " --> pdb=" O TYR 1 150 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain '2' and resid 197 through 201 removed outlier: 3.860A pdb=" N GLU 2 260 " --> pdb=" O MET 2 248 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS 2 250 " --> pdb=" O LYS 2 258 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LYS 2 258 " --> pdb=" O HIS 2 250 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain '2' and resid 92 through 94 removed outlier: 7.500A pdb=" N ALA 2 92 " --> pdb=" O ALA 2 99 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain '2' and resid 107 through 108 Processing sheet with id=AI2, first strand: chain '2' and resid 107 through 108 removed outlier: 3.531A pdb=" N GLY 2 175 " --> pdb=" O GLY 2 182 " (cutoff:3.500A) 4319 hydrogen bonds defined for protein. 12540 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 28.80 Time building geometry restraints manager: 22.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23625 1.34 - 1.46: 9854 1.46 - 1.58: 38830 1.58 - 1.69: 0 1.69 - 1.81: 628 Bond restraints: 72937 Sorted by residual: bond pdb=" CA PHE C 61 " pdb=" C PHE C 61 " ideal model delta sigma weight residual 1.519 1.558 -0.039 5.30e-03 3.56e+04 5.50e+01 bond pdb=" C ALA i 59 " pdb=" N PRO i 60 " ideal model delta sigma weight residual 1.334 1.449 -0.115 2.34e-02 1.83e+03 2.43e+01 bond pdb=" C GLN L 191 " pdb=" N PRO L 192 " ideal model delta sigma weight residual 1.334 1.435 -0.101 2.34e-02 1.83e+03 1.86e+01 bond pdb=" C GLY e 102 " pdb=" N PRO e 103 " ideal model delta sigma weight residual 1.334 1.423 -0.089 2.34e-02 1.83e+03 1.44e+01 bond pdb=" C GLN Q 191 " pdb=" N PRO Q 192 " ideal model delta sigma weight residual 1.334 1.413 -0.079 2.34e-02 1.83e+03 1.15e+01 ... (remaining 72932 not shown) Histogram of bond angle deviations from ideal: 98.99 - 106.00: 1530 106.00 - 113.02: 39637 113.02 - 120.03: 24321 120.03 - 127.04: 32443 127.04 - 134.05: 611 Bond angle restraints: 98542 Sorted by residual: angle pdb=" CA ALA h 232 " pdb=" C ALA h 232 " pdb=" O ALA h 232 " ideal model delta sigma weight residual 120.12 127.72 -7.60 1.15e+00 7.56e-01 4.37e+01 angle pdb=" N VAL D 50 " pdb=" CA VAL D 50 " pdb=" C VAL D 50 " ideal model delta sigma weight residual 108.12 116.25 -8.13 1.44e+00 4.82e-01 3.18e+01 angle pdb=" C ARG P 213 " pdb=" CA ARG P 213 " pdb=" CB ARG P 213 " ideal model delta sigma weight residual 116.54 110.55 5.99 1.15e+00 7.56e-01 2.72e+01 angle pdb=" C ARG D 213 " pdb=" CA ARG D 213 " pdb=" CB ARG D 213 " ideal model delta sigma weight residual 116.54 110.57 5.97 1.15e+00 7.56e-01 2.70e+01 angle pdb=" N ALA D 51 " pdb=" CA ALA D 51 " pdb=" C ALA D 51 " ideal model delta sigma weight residual 111.74 118.71 -6.97 1.35e+00 5.49e-01 2.67e+01 ... (remaining 98537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.32: 43370 16.32 - 32.65: 656 32.65 - 48.97: 285 48.97 - 65.29: 35 65.29 - 81.61: 13 Dihedral angle restraints: 44359 sinusoidal: 17914 harmonic: 26445 Sorted by residual: dihedral pdb=" CA MET n 50 " pdb=" C MET n 50 " pdb=" N VAL n 51 " pdb=" CA VAL n 51 " ideal model delta harmonic sigma weight residual 180.00 150.80 29.20 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA GLY S 101 " pdb=" C GLY S 101 " pdb=" N PRO S 102 " pdb=" CA PRO S 102 " ideal model delta harmonic sigma weight residual 180.00 -152.76 -27.24 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA GLY k 101 " pdb=" C GLY k 101 " pdb=" N PRO k 102 " pdb=" CA PRO k 102 " ideal model delta harmonic sigma weight residual -180.00 -152.85 -27.15 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 44356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 9065 0.049 - 0.099: 1655 0.099 - 0.148: 397 0.148 - 0.198: 8 0.198 - 0.247: 2 Chirality restraints: 11127 Sorted by residual: chirality pdb=" CA ALA D 51 " pdb=" N ALA D 51 " pdb=" C ALA D 51 " pdb=" CB ALA D 51 " both_signs ideal model delta sigma weight residual False 2.48 2.24 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA SER P 201 " pdb=" N SER P 201 " pdb=" C SER P 201 " pdb=" CB SER P 201 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CG LEU E 121 " pdb=" CB LEU E 121 " pdb=" CD1 LEU E 121 " pdb=" CD2 LEU E 121 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.94e-01 ... (remaining 11124 not shown) Planarity restraints: 12692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 232 " -0.024 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" C ILE D 232 " 0.084 2.00e-02 2.50e+03 pdb=" O ILE D 232 " -0.032 2.00e-02 2.50e+03 pdb=" N GLU D 233 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 60 " -0.022 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C PHE C 60 " 0.073 2.00e-02 2.50e+03 pdb=" O PHE C 60 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE C 61 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER d 243 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C SER d 243 " 0.067 2.00e-02 2.50e+03 pdb=" O SER d 243 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU d 244 " -0.023 2.00e-02 2.50e+03 ... (remaining 12689 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4756 2.74 - 3.28: 72681 3.28 - 3.82: 114661 3.82 - 4.36: 142227 4.36 - 4.90: 241023 Nonbonded interactions: 575348 Sorted by model distance: nonbonded pdb=" O LEU a 61 " pdb=" NE ARG a 198 " model vdw 2.196 2.520 nonbonded pdb=" OH TYR H 187 " pdb=" OG1 THR J 186 " model vdw 2.213 2.440 nonbonded pdb=" NH1 ARG P 36 " pdb=" OE2 GLU R 60 " model vdw 2.222 2.520 nonbonded pdb=" OE1 GLN D 146 " pdb=" ND2 ASN D 159 " model vdw 2.223 2.520 nonbonded pdb=" NH1 ARG P 88 " pdb=" O MET l 69 " model vdw 2.224 2.520 ... (remaining 575343 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 '1' selection = chain 'X' } ncs_group { reference = chain '2' selection = chain 'Y' } ncs_group { reference = chain 'A' selection = (chain 'f' and resid 9 through 243) } ncs_group { reference = chain 'B' selection = (chain 'h' and resid 7 through 232) } ncs_group { reference = chain 'C' selection = (chain 'j' and resid 1 through 245) } ncs_group { reference = chain 'D' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'b' } ncs_group { reference = chain 'G' selection = chain 'd' } ncs_group { reference = (chain 'H' and (resid 7 through 67 or resid 94 through 236)) selection = (chain 'K' and (resid 7 through 200 or (resid 201 and (name N or name CA or name \ C or name O or name CB )) or resid 202 through 236)) selection = (chain 'M' and (resid 7 through 67 or resid 94 through 200 or (resid 201 and (na \ me N or name CA or name C or name O or name CB )) or resid 202 through 236)) selection = (chain 'O' and (resid 7 through 67 or resid 94 through 236)) selection = (chain 'c' and (resid 7 through 200 or (resid 201 and (name N or name CA or name \ C or name O or name CB )) or resid 202 through 236)) selection = (chain 'g' and (resid 7 through 67 or resid 94 through 200 or (resid 201 and (na \ me N or name CA or name C or name O or name CB )) or resid 202 through 236)) } ncs_group { reference = (chain 'I' and (resid 4 through 63 or resid 102 through 242)) selection = (chain 'J' and (resid 4 through 63 or resid 102 through 242)) selection = (chain 'L' and resid 4 through 242) selection = (chain 'N' and (resid 4 through 63 or resid 102 through 242)) selection = (chain 'Q' and (resid 4 through 63 or resid 102 through 242)) selection = (chain 'a' and (resid 4 through 63 or resid 102 through 242)) selection = (chain 'e' and resid 4 through 242) selection = (chain 'i' and (resid 4 through 63 or resid 102 through 242)) } ncs_group { reference = chain 'S' selection = chain 'k' } ncs_group { reference = chain 'T' selection = (chain 'l' and resid 1 through 197) } ncs_group { reference = chain 'U' selection = (chain 'm' and (resid 29 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 241)) } ncs_group { reference = (chain 'V' and resid 47 through 261) selection = (chain 'n' and resid 47 through 261) } ncs_group { reference = chain 'W' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 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: 0.040 Extract box with map and model: 11.780 Check model and map are aligned: 0.790 Set scattering table: 0.490 Process input model: 142.710 Find NCS groups from input model: 6.800 Set up NCS constraints: 0.600 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4963 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 : 0.002 0.115 72937 Z= 0.140 Angle : 0.533 8.125 98542 Z= 0.329 Chirality : 0.040 0.247 11127 Planarity : 0.003 0.060 12692 Dihedral : 7.880 81.613 27349 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.98 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.07), residues: 8996 helix: -2.28 (0.06), residues: 4314 sheet: -0.48 (0.12), residues: 1458 loop : -0.84 (0.10), residues: 3224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 101 HIS 0.005 0.001 HIS E 155 PHE 0.020 0.001 PHE E 123 TYR 0.023 0.001 TYR S 6 ARG 0.011 0.000 ARG V 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3540 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3540 time to evaluate : 5.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.6599 (p90) cc_final: 0.6386 (p90) REVERT: A 113 MET cc_start: 0.7410 (mmm) cc_final: 0.6155 (mmt) REVERT: A 134 LEU cc_start: 0.8696 (mt) cc_final: 0.7649 (mt) REVERT: A 154 CYS cc_start: 0.7810 (t) cc_final: 0.7422 (m) REVERT: A 159 TYR cc_start: 0.4977 (t80) cc_final: 0.4322 (t80) REVERT: A 201 CYS cc_start: 0.6550 (t) cc_final: 0.6289 (t) REVERT: B 96 GLN cc_start: 0.7025 (mt0) cc_final: 0.6594 (mt0) REVERT: B 130 PHE cc_start: 0.7455 (m-10) cc_final: 0.6836 (m-10) REVERT: C 20 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8048 (mp10) REVERT: C 140 ASP cc_start: 0.6904 (p0) cc_final: 0.6521 (m-30) REVERT: C 159 TRP cc_start: 0.7289 (m100) cc_final: 0.6746 (m100) REVERT: D 13 ASP cc_start: 0.6943 (p0) cc_final: 0.6462 (t70) REVERT: D 106 TYR cc_start: 0.6788 (t80) cc_final: 0.6380 (t80) REVERT: F 67 ASP cc_start: 0.7368 (t0) cc_final: 0.7023 (t70) REVERT: G 153 ASP cc_start: 0.7536 (p0) cc_final: 0.6860 (m-30) REVERT: I 25 THR cc_start: 0.6770 (m) cc_final: 0.6198 (m) REVERT: J 28 LEU cc_start: 0.5177 (tp) cc_final: 0.4401 (tp) REVERT: J 172 THR cc_start: 0.4861 (m) cc_final: 0.4166 (m) REVERT: L 128 LEU cc_start: 0.7433 (tp) cc_final: 0.7133 (tp) REVERT: L 135 LEU cc_start: 0.6237 (mt) cc_final: 0.5847 (tp) REVERT: M 40 ILE cc_start: 0.5973 (mt) cc_final: 0.5684 (tp) REVERT: M 54 VAL cc_start: 0.7211 (t) cc_final: 0.6996 (t) REVERT: N 3 MET cc_start: 0.0733 (mtm) cc_final: -0.0637 (ttt) REVERT: Q 38 SER cc_start: 0.5138 (p) cc_final: 0.4933 (t) REVERT: Q 238 LYS cc_start: 0.3049 (tttt) cc_final: 0.2569 (tttp) REVERT: a 123 ASP cc_start: 0.2120 (m-30) cc_final: 0.1812 (t0) REVERT: P 156 TRP cc_start: 0.6974 (m100) cc_final: 0.6758 (m100) REVERT: R 204 GLN cc_start: 0.6063 (mt0) cc_final: 0.5286 (tp-100) REVERT: b 72 ILE cc_start: 0.7367 (tt) cc_final: 0.7062 (tt) REVERT: b 93 LEU cc_start: 0.7776 (mt) cc_final: 0.6774 (mt) REVERT: b 118 ILE cc_start: 0.8236 (mt) cc_final: 0.8005 (mm) REVERT: d 47 VAL cc_start: 0.7489 (t) cc_final: 0.6951 (t) REVERT: d 152 ILE cc_start: 0.8733 (mt) cc_final: 0.8162 (mt) REVERT: d 154 PRO cc_start: 0.7341 (Cg_exo) cc_final: 0.6954 (Cg_endo) REVERT: f 154 CYS cc_start: 0.7079 (t) cc_final: 0.6862 (p) REVERT: f 202 LEU cc_start: 0.6880 (mt) cc_final: 0.6320 (mt) REVERT: f 226 LYS cc_start: 0.6740 (tttt) cc_final: 0.6517 (mppt) REVERT: h 127 VAL cc_start: 0.8333 (m) cc_final: 0.8111 (t) REVERT: j 20 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7412 (mp10) REVERT: j 93 ILE cc_start: 0.8635 (mt) cc_final: 0.8319 (tp) REVERT: k 53 LEU cc_start: 0.8136 (mt) cc_final: 0.7498 (tt) REVERT: k 164 PHE cc_start: 0.5468 (t80) cc_final: 0.5180 (t80) REVERT: k 175 VAL cc_start: 0.7749 (t) cc_final: 0.7460 (t) REVERT: k 181 SER cc_start: 0.7541 (m) cc_final: 0.7195 (t) REVERT: m 39 THR cc_start: 0.8066 (m) cc_final: 0.7830 (p) REVERT: m 116 ILE cc_start: 0.7664 (mt) cc_final: 0.7091 (mt) REVERT: m 194 LEU cc_start: 0.5846 (tp) cc_final: 0.5123 (tp) REVERT: n 143 SER cc_start: 0.8097 (p) cc_final: 0.7714 (t) REVERT: n 184 THR cc_start: 0.7223 (p) cc_final: 0.6982 (p) REVERT: n 242 VAL cc_start: 0.5630 (t) cc_final: 0.4712 (t) REVERT: n 252 THR cc_start: 0.2660 (p) cc_final: 0.2355 (p) REVERT: S 106 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8156 (mp0) REVERT: S 113 ASP cc_start: 0.5654 (t0) cc_final: 0.5231 (m-30) REVERT: T 63 ASN cc_start: 0.8654 (m-40) cc_final: 0.7971 (t0) REVERT: T 68 LYS cc_start: 0.8780 (tttt) cc_final: 0.8519 (tttt) REVERT: U 83 SER cc_start: 0.7633 (t) cc_final: 0.7096 (t) REVERT: U 178 ASP cc_start: 0.7076 (m-30) cc_final: 0.6802 (m-30) REVERT: V 106 GLN cc_start: 0.8373 (mt0) cc_final: 0.8128 (mm-40) REVERT: V 118 ASP cc_start: 0.7501 (m-30) cc_final: 0.7272 (m-30) REVERT: V 225 ASP cc_start: 0.7182 (t0) cc_final: 0.6838 (t0) REVERT: V 252 THR cc_start: 0.3437 (p) cc_final: 0.2906 (p) REVERT: W 23 ILE cc_start: 0.9232 (pt) cc_final: 0.8596 (pt) REVERT: W 89 GLU cc_start: 0.6236 (mt-10) cc_final: 0.6022 (tm-30) REVERT: W 113 ASP cc_start: 0.7855 (m-30) cc_final: 0.7362 (t0) REVERT: X 95 THR cc_start: 0.8925 (p) cc_final: 0.8685 (t) REVERT: X 102 MET cc_start: 0.7801 (mmm) cc_final: 0.7512 (tpp) REVERT: X 202 ILE cc_start: 0.8955 (mt) cc_final: 0.8705 (mm) REVERT: Y 86 VAL cc_start: 0.7742 (t) cc_final: 0.7495 (m) REVERT: Y 130 LEU cc_start: 0.7993 (mt) cc_final: 0.7645 (tt) REVERT: Y 135 CYS cc_start: 0.8416 (m) cc_final: 0.8032 (m) REVERT: Y 159 MET cc_start: 0.6486 (mmm) cc_final: 0.6162 (mmt) REVERT: Y 232 ILE cc_start: 0.8325 (mm) cc_final: 0.7931 (mm) REVERT: Y 236 THR cc_start: 0.8580 (p) cc_final: 0.8256 (t) REVERT: Y 246 VAL cc_start: 0.8134 (t) cc_final: 0.7881 (p) REVERT: Y 259 VAL cc_start: 0.8257 (t) cc_final: 0.7770 (t) REVERT: Z 52 ASP cc_start: 0.8320 (t0) cc_final: 0.6951 (p0) REVERT: Z 58 HIS cc_start: 0.5440 (t-90) cc_final: 0.4741 (t70) REVERT: Z 85 LEU cc_start: 0.8784 (mt) cc_final: 0.8485 (mt) REVERT: Z 198 ILE cc_start: 0.4009 (mp) cc_final: 0.3381 (mp) REVERT: 1 138 ILE cc_start: 0.6822 (tt) cc_final: 0.6521 (tt) REVERT: 1 184 ASN cc_start: 0.6653 (m-40) cc_final: 0.6294 (m110) REVERT: 1 203 LEU cc_start: 0.7525 (mt) cc_final: 0.7227 (mt) REVERT: 1 224 MET cc_start: 0.8006 (tpt) cc_final: 0.7449 (tpp) REVERT: 2 117 MET cc_start: 0.5764 (mtp) cc_final: 0.5190 (ttp) outliers start: 0 outliers final: 0 residues processed: 3540 average time/residue: 0.7121 time to fit residues: 4147.6544 Evaluate side-chains 1892 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1892 time to evaluate : 6.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 749 optimal weight: 5.9990 chunk 673 optimal weight: 0.9980 chunk 373 optimal weight: 3.9990 chunk 229 optimal weight: 0.0870 chunk 454 optimal weight: 5.9990 chunk 359 optimal weight: 9.9990 chunk 696 optimal weight: 1.9990 chunk 269 optimal weight: 0.9990 chunk 423 optimal weight: 1.9990 chunk 518 optimal weight: 3.9990 chunk 806 optimal weight: 2.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN C 146 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS ** F 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN F 175 HIS G 148 GLN G 171 GLN G 225 HIS I 173 GLN I 199 GLN I 233 ASN K 136 ASN L 136 GLN L 138 GLN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 127 HIS N 202 HIS O 126 GLN ** Q 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 193 HIS ** a 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 97 ASN c 192 HIS i 7 GLN i 129 ASN i 171 HIS P 15 HIS ** P 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 120 GLN ** R 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN R 224 GLN b 5 GLN b 31 GLN b 175 HIS b 190 HIS d 23 GLN ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 181 GLN d 225 HIS ** f 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 52 GLN h 88 HIS ** h 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 146 GLN k 61 GLN ** k 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 ASN k 188 HIS l 63 ASN l 110 HIS m 174 GLN n 106 GLN n 114 GLN S 7 ASN S 33 GLN ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 93 ASN S 173 ASN S 188 HIS T 27 GLN ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 189 HIS U 107 ASN V 91 ASN ** V 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 192 GLN ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 HIS ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 148 GLN Y 82 HIS Y 237 HIS Y 269 HIS Y 270 GLN 1 105 HIS 2 104 ASN 2 161 GLN 2 234 HIS 2 269 HIS Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5652 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 72937 Z= 0.260 Angle : 0.698 10.096 98542 Z= 0.368 Chirality : 0.046 0.309 11127 Planarity : 0.005 0.089 12692 Dihedral : 4.571 37.424 9923 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.00 % Favored : 97.98 % Rotamer: Outliers : 0.14 % Allowed : 2.85 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.08), residues: 8996 helix: 0.09 (0.07), residues: 4342 sheet: 0.02 (0.13), residues: 1425 loop : -0.64 (0.10), residues: 3229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP V 136 HIS 0.014 0.001 HIS R 99 PHE 0.042 0.002 PHE e 178 TYR 0.031 0.002 TYR G 26 ARG 0.009 0.001 ARG W 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2461 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 2450 time to evaluate : 6.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6765 (tm-30) cc_final: 0.6450 (tm-30) REVERT: A 91 VAL cc_start: 0.8781 (m) cc_final: 0.8554 (t) REVERT: A 134 LEU cc_start: 0.9000 (mt) cc_final: 0.8526 (mt) REVERT: B 38 ILE cc_start: 0.6033 (mm) cc_final: 0.5802 (mm) REVERT: B 96 GLN cc_start: 0.7426 (mt0) cc_final: 0.7112 (mt0) REVERT: B 130 PHE cc_start: 0.7536 (m-10) cc_final: 0.7213 (m-10) REVERT: B 203 MET cc_start: 0.5656 (ppp) cc_final: 0.5368 (mpp) REVERT: C 49 ARG cc_start: 0.7953 (mmm-85) cc_final: 0.7291 (mmm-85) REVERT: C 75 SER cc_start: 0.8079 (p) cc_final: 0.7720 (t) REVERT: C 86 LEU cc_start: 0.8972 (mp) cc_final: 0.8653 (mt) REVERT: C 88 ASN cc_start: 0.8057 (m110) cc_final: 0.7715 (t0) REVERT: C 115 CYS cc_start: 0.7021 (p) cc_final: 0.6454 (p) REVERT: D 76 LEU cc_start: 0.7761 (mt) cc_final: 0.7049 (mt) REVERT: D 79 ASP cc_start: 0.7126 (t0) cc_final: 0.6824 (t0) REVERT: D 106 TYR cc_start: 0.7081 (t80) cc_final: 0.6629 (t80) REVERT: D 120 GLN cc_start: 0.8222 (tt0) cc_final: 0.7500 (tt0) REVERT: D 134 VAL cc_start: 0.8172 (p) cc_final: 0.7906 (p) REVERT: F 67 ASP cc_start: 0.7146 (t0) cc_final: 0.6870 (t0) REVERT: F 87 PHE cc_start: 0.6986 (t80) cc_final: 0.6687 (t80) REVERT: F 93 LEU cc_start: 0.7942 (mt) cc_final: 0.7556 (mt) REVERT: F 115 LYS cc_start: 0.9092 (tppt) cc_final: 0.8650 (tttt) REVERT: F 120 THR cc_start: 0.8089 (p) cc_final: 0.7795 (t) REVERT: G 153 ASP cc_start: 0.7781 (p0) cc_final: 0.7282 (m-30) REVERT: G 227 ILE cc_start: 0.8309 (tt) cc_final: 0.7725 (tt) REVERT: H 107 VAL cc_start: 0.7821 (t) cc_final: 0.7529 (t) REVERT: H 125 ILE cc_start: 0.5741 (mm) cc_final: 0.5211 (mm) REVERT: H 148 GLU cc_start: 0.7420 (pt0) cc_final: 0.7208 (pt0) REVERT: J 135 LEU cc_start: 0.7502 (mt) cc_final: 0.7151 (mt) REVERT: J 241 ARG cc_start: 0.4384 (mpt180) cc_final: 0.4111 (mmt-90) REVERT: K 61 ARG cc_start: 0.3083 (ptt180) cc_final: 0.2809 (ptt180) REVERT: K 149 ARG cc_start: 0.7629 (mtp-110) cc_final: 0.6909 (ttm-80) REVERT: L 211 ASP cc_start: 0.7259 (m-30) cc_final: 0.7039 (m-30) REVERT: L 215 MET cc_start: 0.5197 (mmp) cc_final: 0.4909 (mmm) REVERT: M 19 VAL cc_start: 0.6343 (p) cc_final: 0.6008 (p) REVERT: M 40 ILE cc_start: 0.6436 (mt) cc_final: 0.5434 (tp) REVERT: M 44 ASN cc_start: 0.4886 (m-40) cc_final: 0.4528 (m-40) REVERT: O 153 VAL cc_start: 0.3565 (t) cc_final: 0.3264 (t) REVERT: O 155 THR cc_start: 0.6885 (m) cc_final: 0.6216 (m) REVERT: O 227 ILE cc_start: 0.6827 (mt) cc_final: 0.6173 (mt) REVERT: a 122 LYS cc_start: 0.5922 (mmmt) cc_final: 0.5204 (mmmt) REVERT: c 224 LEU cc_start: 0.6860 (tp) cc_final: 0.6647 (tp) REVERT: e 121 ILE cc_start: 0.4396 (mt) cc_final: 0.3889 (mt) REVERT: i 160 MET cc_start: 0.6646 (ttm) cc_final: 0.6398 (ttp) REVERT: i 210 ARG cc_start: 0.4055 (tpp80) cc_final: 0.3578 (tmt170) REVERT: P 208 LEU cc_start: 0.7799 (mm) cc_final: 0.7530 (mm) REVERT: R 25 GLU cc_start: 0.7491 (pt0) cc_final: 0.7241 (pt0) REVERT: R 52 LYS cc_start: 0.6720 (mttt) cc_final: 0.5615 (mtpp) REVERT: R 175 GLU cc_start: 0.6748 (pp20) cc_final: 0.6382 (pp20) REVERT: R 219 THR cc_start: 0.3255 (p) cc_final: 0.2683 (p) REVERT: b 19 ILE cc_start: 0.8467 (mt) cc_final: 0.8033 (mm) REVERT: b 84 LEU cc_start: 0.8798 (tt) cc_final: 0.8324 (tt) REVERT: b 103 LEU cc_start: 0.8709 (tp) cc_final: 0.8345 (tp) REVERT: d 47 VAL cc_start: 0.7408 (t) cc_final: 0.7192 (t) REVERT: d 222 ASN cc_start: 0.7201 (t0) cc_final: 0.6733 (t0) REVERT: f 79 VAL cc_start: 0.8252 (m) cc_final: 0.7695 (m) REVERT: f 126 THR cc_start: 0.8417 (m) cc_final: 0.8213 (p) REVERT: f 226 LYS cc_start: 0.7133 (tttt) cc_final: 0.6834 (mppt) REVERT: h 87 VAL cc_start: 0.8143 (t) cc_final: 0.7838 (t) REVERT: j 20 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7500 (mt0) REVERT: j 69 ASN cc_start: 0.8566 (p0) cc_final: 0.7968 (p0) REVERT: j 82 ASP cc_start: 0.7253 (p0) cc_final: 0.6543 (p0) REVERT: k 14 MET cc_start: 0.5989 (mtm) cc_final: 0.5123 (mtm) REVERT: k 103 TYR cc_start: 0.6705 (m-10) cc_final: 0.6435 (m-10) REVERT: k 138 VAL cc_start: 0.8878 (m) cc_final: 0.8649 (m) REVERT: l 5 ILE cc_start: 0.8699 (tt) cc_final: 0.7960 (tt) REVERT: l 36 PHE cc_start: 0.7563 (m-80) cc_final: 0.7343 (m-80) REVERT: l 85 ARG cc_start: 0.8429 (tmm160) cc_final: 0.8141 (tmm-80) REVERT: l 170 ARG cc_start: 0.7114 (mmp80) cc_final: 0.6903 (mmp80) REVERT: m 120 LEU cc_start: 0.8694 (tp) cc_final: 0.8071 (tp) REVERT: m 180 GLN cc_start: 0.8545 (pt0) cc_final: 0.8247 (pt0) REVERT: n 80 ARG cc_start: 0.7255 (ttm-80) cc_final: 0.7032 (ttm-80) REVERT: n 143 SER cc_start: 0.8513 (p) cc_final: 0.7955 (t) REVERT: n 155 MET cc_start: 0.5636 (mtm) cc_final: 0.5105 (mtm) REVERT: n 233 GLN cc_start: 0.7617 (mp10) cc_final: 0.7248 (tm-30) REVERT: S 12 MET cc_start: 0.5727 (ttm) cc_final: 0.4613 (ttm) REVERT: S 17 LYS cc_start: 0.6377 (tptp) cc_final: 0.6059 (tmtt) REVERT: S 95 LEU cc_start: 0.9150 (mm) cc_final: 0.8867 (mm) REVERT: S 96 TYR cc_start: 0.8566 (t80) cc_final: 0.8228 (t80) REVERT: S 138 VAL cc_start: 0.9497 (m) cc_final: 0.9290 (p) REVERT: S 168 SER cc_start: 0.7871 (p) cc_final: 0.5456 (p) REVERT: S 171 MET cc_start: 0.7909 (tpp) cc_final: 0.7409 (tpp) REVERT: S 204 MET cc_start: 0.6158 (mpp) cc_final: 0.5739 (mpp) REVERT: S 205 ASP cc_start: 0.2875 (t0) cc_final: 0.1648 (m-30) REVERT: T 63 ASN cc_start: 0.8933 (m-40) cc_final: 0.8622 (m-40) REVERT: T 65 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8646 (tp-100) REVERT: T 68 LYS cc_start: 0.8807 (tttt) cc_final: 0.8510 (tttt) REVERT: T 145 ARG cc_start: 0.7518 (tpp-160) cc_final: 0.6936 (tpp-160) REVERT: T 181 ARG cc_start: 0.8284 (mmt90) cc_final: 0.7789 (mmm-85) REVERT: U 64 HIS cc_start: 0.7719 (m-70) cc_final: 0.7357 (m90) REVERT: U 83 SER cc_start: 0.7955 (t) cc_final: 0.7465 (t) REVERT: U 89 CYS cc_start: 0.8294 (m) cc_final: 0.8024 (t) REVERT: V 106 GLN cc_start: 0.8817 (mt0) cc_final: 0.8521 (mt0) REVERT: V 139 ARG cc_start: 0.7943 (tpt170) cc_final: 0.7534 (tpp-160) REVERT: V 177 TYR cc_start: 0.7729 (p90) cc_final: 0.7375 (p90) REVERT: V 180 PRO cc_start: 0.8816 (Cg_endo) cc_final: 0.8593 (Cg_exo) REVERT: V 225 ASP cc_start: 0.7655 (t0) cc_final: 0.7147 (t0) REVERT: V 252 THR cc_start: 0.3813 (p) cc_final: 0.3450 (p) REVERT: W 104 ARG cc_start: 0.9110 (tmm-80) cc_final: 0.8906 (tmm-80) REVERT: W 123 TRP cc_start: 0.7263 (t60) cc_final: 0.6918 (t60) REVERT: W 124 ASP cc_start: 0.5999 (p0) cc_final: 0.5762 (p0) REVERT: W 174 PHE cc_start: 0.7611 (t80) cc_final: 0.7382 (t80) REVERT: X 123 ARG cc_start: 0.5176 (ptt-90) cc_final: 0.4973 (ptm-80) REVERT: X 202 ILE cc_start: 0.9123 (mt) cc_final: 0.8899 (mm) REVERT: X 224 MET cc_start: 0.7767 (mmp) cc_final: 0.7461 (mmp) REVERT: Y 160 CYS cc_start: 0.7678 (m) cc_final: 0.6629 (m) REVERT: Y 236 THR cc_start: 0.8649 (p) cc_final: 0.8425 (t) REVERT: Y 237 HIS cc_start: 0.7900 (t-90) cc_final: 0.7609 (t70) REVERT: Y 246 VAL cc_start: 0.8869 (t) cc_final: 0.8521 (p) REVERT: Z 48 ASN cc_start: 0.8309 (p0) cc_final: 0.8086 (t0) REVERT: Z 52 ASP cc_start: 0.8522 (t0) cc_final: 0.7290 (p0) REVERT: Z 58 HIS cc_start: 0.5420 (t-90) cc_final: 0.5174 (t70) REVERT: Z 109 LYS cc_start: 0.8883 (ttmm) cc_final: 0.8573 (tppp) REVERT: Z 135 MET cc_start: 0.7856 (pmm) cc_final: 0.7652 (pmm) REVERT: Z 139 LEU cc_start: 0.8712 (pp) cc_final: 0.8418 (pp) REVERT: Z 146 ILE cc_start: 0.7945 (pt) cc_final: 0.7666 (pt) REVERT: 1 73 ILE cc_start: 0.8758 (mt) cc_final: 0.8337 (mt) REVERT: 1 105 HIS cc_start: 0.5955 (t-170) cc_final: 0.5734 (t70) REVERT: 1 163 PHE cc_start: 0.6974 (p90) cc_final: 0.6770 (p90) REVERT: 2 127 TRP cc_start: 0.6812 (m100) cc_final: 0.6608 (m100) REVERT: 2 222 GLU cc_start: 0.6816 (tp30) cc_final: 0.6485 (tp30) REVERT: 2 260 GLU cc_start: 0.8158 (pp20) cc_final: 0.7940 (pp20) outliers start: 11 outliers final: 3 residues processed: 2457 average time/residue: 0.6815 time to fit residues: 2798.6111 Evaluate side-chains 1775 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1772 time to evaluate : 6.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 448 optimal weight: 3.9990 chunk 250 optimal weight: 0.9980 chunk 671 optimal weight: 0.9990 chunk 549 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 807 optimal weight: 0.8980 chunk 872 optimal weight: 0.9980 chunk 719 optimal weight: 4.9990 chunk 801 optimal weight: 0.0050 chunk 275 optimal weight: 0.8980 chunk 648 optimal weight: 4.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN F 53 GLN ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 HIS I 202 HIS J 191 GLN J 233 ASN K 126 GLN L 7 GLN N 129 ASN c 97 ASN c 161 GLN ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 27 ASN P 54 GLN ** P 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 120 GLN ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 146 GLN b 190 HIS d 111 HIS d 148 GLN d 181 GLN ** f 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 HIS ** f 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 109 GLN j 109 GLN k 61 GLN ** k 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 169 GLN ** l 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 63 ASN ** m 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 114 GLN n 126 HIS n 192 GLN S 93 ASN S 169 GLN ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 189 HIS U 86 HIS ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 91 ASN ** V 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 HIS ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 148 GLN Z 117 HIS 1 124 GLN 1 184 ASN 1 240 GLN 2 110 ASN 2 161 GLN 2 196 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5751 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 72937 Z= 0.202 Angle : 0.622 10.489 98542 Z= 0.325 Chirality : 0.044 0.287 11127 Planarity : 0.005 0.110 12692 Dihedral : 4.517 37.233 9923 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.17 % Favored : 97.82 % Rotamer: Outliers : 0.13 % Allowed : 2.65 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.08), residues: 8996 helix: 0.63 (0.07), residues: 4351 sheet: 0.12 (0.13), residues: 1454 loop : -0.53 (0.10), residues: 3191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP 2 127 HIS 0.016 0.001 HIS F 190 PHE 0.055 0.002 PHE a 170 TYR 0.028 0.002 TYR G 26 ARG 0.019 0.001 ARG H 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2283 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 2273 time to evaluate : 5.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TRP cc_start: 0.7437 (t-100) cc_final: 0.7064 (t-100) REVERT: C 49 ARG cc_start: 0.8060 (mmm-85) cc_final: 0.7519 (mmm-85) REVERT: C 67 LYS cc_start: 0.8364 (mmtm) cc_final: 0.8102 (mmtm) REVERT: C 75 SER cc_start: 0.8241 (p) cc_final: 0.7589 (t) REVERT: C 86 LEU cc_start: 0.8951 (mp) cc_final: 0.8596 (tp) REVERT: C 96 ARG cc_start: 0.7688 (mtm110) cc_final: 0.7215 (ttp80) REVERT: C 97 TYR cc_start: 0.8864 (t80) cc_final: 0.8586 (t80) REVERT: C 101 TYR cc_start: 0.8231 (m-80) cc_final: 0.7633 (m-10) REVERT: C 155 ASN cc_start: 0.8337 (t0) cc_final: 0.8061 (t0) REVERT: D 21 TYR cc_start: 0.8679 (m-80) cc_final: 0.8358 (m-80) REVERT: D 73 PHE cc_start: 0.8405 (p90) cc_final: 0.8203 (p90) REVERT: D 115 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8839 (mtpt) REVERT: D 129 ILE cc_start: 0.8328 (pt) cc_final: 0.8107 (pt) REVERT: D 130 SER cc_start: 0.8623 (m) cc_final: 0.8310 (m) REVERT: E 112 VAL cc_start: 0.7822 (t) cc_final: 0.7486 (p) REVERT: E 133 MET cc_start: 0.4607 (ptm) cc_final: 0.4305 (ptp) REVERT: E 159 SER cc_start: 0.7397 (p) cc_final: 0.7041 (p) REVERT: E 206 MET cc_start: 0.5097 (ptp) cc_final: 0.4610 (mtp) REVERT: F 53 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7670 (pp30) REVERT: F 67 ASP cc_start: 0.7504 (t0) cc_final: 0.7091 (t0) REVERT: F 90 GLN cc_start: 0.7892 (pp30) cc_final: 0.7406 (pp30) REVERT: F 91 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7384 (mm-30) REVERT: F 115 LYS cc_start: 0.8978 (tppt) cc_final: 0.8573 (tttt) REVERT: G 14 THR cc_start: 0.7552 (t) cc_final: 0.7275 (t) REVERT: G 59 TYR cc_start: 0.5443 (m-80) cc_final: 0.5210 (m-80) REVERT: G 67 LEU cc_start: 0.7134 (mt) cc_final: 0.6879 (pp) REVERT: G 114 ASP cc_start: 0.7755 (m-30) cc_final: 0.7455 (m-30) REVERT: G 149 LEU cc_start: 0.6462 (tt) cc_final: 0.6037 (tt) REVERT: H 107 VAL cc_start: 0.7939 (t) cc_final: 0.7535 (t) REVERT: H 125 ILE cc_start: 0.5774 (mm) cc_final: 0.5388 (mm) REVERT: H 148 GLU cc_start: 0.7376 (pt0) cc_final: 0.7087 (pt0) REVERT: I 53 ASN cc_start: 0.2834 (m-40) cc_final: 0.2438 (m-40) REVERT: J 165 THR cc_start: 0.7157 (p) cc_final: 0.6928 (p) REVERT: M 44 ASN cc_start: 0.4553 (m-40) cc_final: 0.4281 (m110) REVERT: N 212 ILE cc_start: 0.5205 (mm) cc_final: 0.4566 (mm) REVERT: N 216 VAL cc_start: 0.8032 (t) cc_final: 0.7808 (t) REVERT: O 153 VAL cc_start: 0.3464 (t) cc_final: 0.3098 (t) REVERT: O 223 ASN cc_start: 0.7333 (p0) cc_final: 0.7126 (p0) REVERT: O 227 ILE cc_start: 0.6877 (mt) cc_final: 0.6215 (mt) REVERT: Q 160 MET cc_start: 0.4547 (mmp) cc_final: 0.4269 (mmp) REVERT: Q 238 LYS cc_start: 0.3221 (tttt) cc_final: 0.2981 (tttt) REVERT: Q 247 MET cc_start: 0.2065 (mpp) cc_final: 0.1468 (mmt) REVERT: a 122 LYS cc_start: 0.5633 (mmmt) cc_final: 0.5362 (mmmt) REVERT: a 215 MET cc_start: 0.6248 (mmp) cc_final: 0.5900 (mmp) REVERT: c 224 LEU cc_start: 0.6947 (tp) cc_final: 0.6742 (tp) REVERT: i 160 MET cc_start: 0.6346 (ttm) cc_final: 0.6145 (ttp) REVERT: P 20 GLU cc_start: 0.7077 (tp30) cc_final: 0.6843 (tp30) REVERT: P 156 TRP cc_start: 0.6744 (m100) cc_final: 0.6529 (m100) REVERT: P 208 LEU cc_start: 0.7809 (mm) cc_final: 0.7572 (mm) REVERT: R 21 LEU cc_start: 0.8047 (mt) cc_final: 0.7841 (mt) REVERT: R 32 LYS cc_start: 0.9009 (mmmm) cc_final: 0.7673 (tmtt) REVERT: R 67 ILE cc_start: 0.8732 (mt) cc_final: 0.8404 (mm) REVERT: R 175 GLU cc_start: 0.6778 (pp20) cc_final: 0.6299 (pp20) REVERT: R 219 THR cc_start: 0.3200 (p) cc_final: 0.2921 (p) REVERT: b 26 MET cc_start: 0.8192 (mmm) cc_final: 0.7722 (mmm) REVERT: b 86 ASN cc_start: 0.8145 (m-40) cc_final: 0.7927 (m-40) REVERT: b 88 MET cc_start: 0.8066 (mtp) cc_final: 0.7838 (mtp) REVERT: b 90 GLN cc_start: 0.8488 (tt0) cc_final: 0.8219 (tt0) REVERT: d 40 ILE cc_start: 0.7188 (mm) cc_final: 0.6846 (mt) REVERT: d 91 ILE cc_start: 0.9147 (tp) cc_final: 0.8846 (mm) REVERT: d 222 ASN cc_start: 0.7387 (t0) cc_final: 0.6918 (t0) REVERT: f 84 THR cc_start: 0.7585 (p) cc_final: 0.7358 (p) REVERT: f 226 LYS cc_start: 0.7156 (tttt) cc_final: 0.6815 (mppt) REVERT: j 82 ASP cc_start: 0.7183 (p0) cc_final: 0.6934 (p0) REVERT: j 115 CYS cc_start: 0.7149 (m) cc_final: 0.6735 (m) REVERT: j 128 ARG cc_start: 0.8952 (ptt90) cc_final: 0.8730 (ttp-170) REVERT: k 136 PHE cc_start: 0.8133 (p90) cc_final: 0.7806 (p90) REVERT: k 137 VAL cc_start: 0.8538 (t) cc_final: 0.8263 (t) REVERT: k 198 ARG cc_start: 0.6624 (mtm180) cc_final: 0.6389 (mtm180) REVERT: l 30 ASP cc_start: 0.8467 (p0) cc_final: 0.8124 (p0) REVERT: l 75 LEU cc_start: 0.8877 (mt) cc_final: 0.8536 (mt) REVERT: l 85 ARG cc_start: 0.8281 (tmm160) cc_final: 0.8078 (tmm-80) REVERT: m 50 ILE cc_start: 0.8318 (tt) cc_final: 0.8085 (mp) REVERT: m 83 SER cc_start: 0.8686 (t) cc_final: 0.8382 (t) REVERT: m 151 SER cc_start: 0.8888 (m) cc_final: 0.8227 (m) REVERT: m 155 VAL cc_start: 0.8636 (m) cc_final: 0.8344 (m) REVERT: m 186 MET cc_start: 0.5410 (ptp) cc_final: 0.5171 (ptp) REVERT: n 80 ARG cc_start: 0.7145 (ttm-80) cc_final: 0.6714 (ttm-80) REVERT: n 114 GLN cc_start: 0.6825 (tp-100) cc_final: 0.6542 (tp-100) REVERT: n 155 MET cc_start: 0.5418 (mtm) cc_final: 0.5166 (mtm) REVERT: n 232 PHE cc_start: 0.6680 (p90) cc_final: 0.6419 (p90) REVERT: n 259 MET cc_start: 0.5723 (ttt) cc_final: 0.5429 (ttp) REVERT: S 95 LEU cc_start: 0.9186 (mm) cc_final: 0.8861 (mt) REVERT: S 96 TYR cc_start: 0.8683 (t80) cc_final: 0.8253 (t80) REVERT: S 155 GLU cc_start: 0.5525 (mp0) cc_final: 0.4948 (mp0) REVERT: S 167 ILE cc_start: 0.8339 (tt) cc_final: 0.7766 (tt) REVERT: S 175 VAL cc_start: 0.8296 (t) cc_final: 0.8000 (t) REVERT: S 204 MET cc_start: 0.6367 (mpp) cc_final: 0.5968 (mpp) REVERT: S 205 ASP cc_start: 0.3249 (t0) cc_final: 0.1805 (m-30) REVERT: T 4 LEU cc_start: 0.8450 (mt) cc_final: 0.8229 (mt) REVERT: T 8 GLN cc_start: 0.8340 (tm-30) cc_final: 0.8111 (tm-30) REVERT: T 40 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7783 (mm-30) REVERT: T 63 ASN cc_start: 0.8842 (m-40) cc_final: 0.8443 (m110) REVERT: T 65 GLN cc_start: 0.8908 (tp-100) cc_final: 0.8606 (tp-100) REVERT: T 68 LYS cc_start: 0.8836 (tttt) cc_final: 0.8585 (tttt) REVERT: T 168 GLN cc_start: 0.7042 (tm-30) cc_final: 0.6814 (tm-30) REVERT: T 181 ARG cc_start: 0.8367 (mmt90) cc_final: 0.7914 (mmm-85) REVERT: U 56 ARG cc_start: 0.7935 (ttm170) cc_final: 0.6960 (ttm-80) REVERT: U 64 HIS cc_start: 0.7948 (m-70) cc_final: 0.7581 (m90) REVERT: U 83 SER cc_start: 0.7984 (t) cc_final: 0.7542 (t) REVERT: U 152 PHE cc_start: 0.6589 (m-10) cc_final: 0.6354 (m-10) REVERT: U 225 ILE cc_start: 0.8007 (mp) cc_final: 0.7583 (mt) REVERT: V 106 GLN cc_start: 0.8901 (mt0) cc_final: 0.8572 (mt0) REVERT: V 177 TYR cc_start: 0.7845 (p90) cc_final: 0.7553 (p90) REVERT: V 228 SER cc_start: 0.8298 (p) cc_final: 0.8064 (t) REVERT: V 252 THR cc_start: 0.4649 (p) cc_final: 0.4326 (p) REVERT: W 85 LEU cc_start: 0.9121 (tp) cc_final: 0.8915 (tp) REVERT: Y 146 ILE cc_start: 0.8648 (tp) cc_final: 0.8432 (tp) REVERT: Y 160 CYS cc_start: 0.6738 (m) cc_final: 0.6476 (m) REVERT: Y 246 VAL cc_start: 0.8820 (t) cc_final: 0.8458 (p) REVERT: Z 52 ASP cc_start: 0.8408 (t0) cc_final: 0.7412 (p0) REVERT: Z 58 HIS cc_start: 0.5429 (t-90) cc_final: 0.5155 (t70) REVERT: Z 109 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8656 (tppp) REVERT: Z 138 MET cc_start: 0.8089 (ppp) cc_final: 0.7636 (ppp) REVERT: 1 90 ASP cc_start: 0.7753 (m-30) cc_final: 0.7263 (m-30) REVERT: 2 124 CYS cc_start: 0.7907 (m) cc_final: 0.6402 (m) outliers start: 10 outliers final: 2 residues processed: 2277 average time/residue: 0.6697 time to fit residues: 2572.6873 Evaluate side-chains 1699 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1696 time to evaluate : 6.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 798 optimal weight: 4.9990 chunk 607 optimal weight: 0.9990 chunk 419 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 385 optimal weight: 0.9990 chunk 542 optimal weight: 9.9990 chunk 810 optimal weight: 0.0470 chunk 858 optimal weight: 3.9990 chunk 423 optimal weight: 6.9990 chunk 768 optimal weight: 0.7980 chunk 231 optimal weight: 0.9980 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS D 92 GLN ** I 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 143 GLN i 27 ASN ** P 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 154 HIS P 159 ASN ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 HIS ** b 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 111 HIS ** f 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 95 GLN l 55 GLN l 87 ASN l 99 HIS ** m 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 207 GLN S 33 GLN S 93 ASN S 169 GLN S 173 ASN T 24 ASN ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 189 HIS ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 74 HIS ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 148 GLN Z 101 ASN Z 117 HIS Z 205 HIS 1 61 ASN 2 196 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5843 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 72937 Z= 0.193 Angle : 0.608 9.280 98542 Z= 0.317 Chirality : 0.043 0.223 11127 Planarity : 0.004 0.080 12692 Dihedral : 4.482 39.367 9923 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.15 % Favored : 97.83 % Rotamer: Outliers : 0.14 % Allowed : 2.03 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.08), residues: 8996 helix: 0.87 (0.07), residues: 4361 sheet: 0.19 (0.13), residues: 1437 loop : -0.48 (0.10), residues: 3198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Y 176 HIS 0.018 0.001 HIS J 164 PHE 0.042 0.002 PHE O 212 TYR 0.027 0.002 TYR S 96 ARG 0.011 0.001 ARG X 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2217 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 2206 time to evaluate : 6.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TRP cc_start: 0.7442 (t-100) cc_final: 0.7220 (t-100) REVERT: B 66 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7357 (mt-10) REVERT: C 75 SER cc_start: 0.8249 (p) cc_final: 0.7700 (t) REVERT: C 96 ARG cc_start: 0.7437 (mtm110) cc_final: 0.7157 (ttp80) REVERT: C 97 TYR cc_start: 0.8952 (t80) cc_final: 0.8695 (t80) REVERT: C 101 TYR cc_start: 0.8332 (m-80) cc_final: 0.7820 (m-10) REVERT: C 155 ASN cc_start: 0.8352 (t0) cc_final: 0.8131 (t0) REVERT: D 115 LYS cc_start: 0.9025 (mtpt) cc_final: 0.8818 (mtpt) REVERT: D 129 ILE cc_start: 0.8328 (pt) cc_final: 0.8045 (pt) REVERT: D 130 SER cc_start: 0.8591 (m) cc_final: 0.8298 (m) REVERT: E 112 VAL cc_start: 0.8148 (t) cc_final: 0.7795 (p) REVERT: E 133 MET cc_start: 0.4866 (ptm) cc_final: 0.4325 (ptp) REVERT: E 156 MET cc_start: 0.7424 (ttp) cc_final: 0.7128 (ttm) REVERT: E 157 ASP cc_start: 0.7232 (p0) cc_final: 0.6640 (p0) REVERT: F 62 LYS cc_start: 0.7288 (tptt) cc_final: 0.6837 (mppt) REVERT: F 65 HIS cc_start: 0.5619 (t-170) cc_final: 0.5409 (t-170) REVERT: F 82 ARG cc_start: 0.7074 (mtp180) cc_final: 0.6864 (mmm-85) REVERT: F 90 GLN cc_start: 0.7924 (pp30) cc_final: 0.7689 (pp30) REVERT: F 115 LYS cc_start: 0.8979 (tppt) cc_final: 0.8596 (tttt) REVERT: G 14 THR cc_start: 0.7498 (t) cc_final: 0.7279 (t) REVERT: G 67 LEU cc_start: 0.7316 (mt) cc_final: 0.6947 (pt) REVERT: G 114 ASP cc_start: 0.7975 (m-30) cc_final: 0.7547 (m-30) REVERT: G 153 ASP cc_start: 0.7663 (p0) cc_final: 0.7350 (m-30) REVERT: G 227 ILE cc_start: 0.8238 (tt) cc_final: 0.7712 (tt) REVERT: H 125 ILE cc_start: 0.5785 (mm) cc_final: 0.5565 (mm) REVERT: H 148 GLU cc_start: 0.7355 (pt0) cc_final: 0.7090 (pt0) REVERT: I 206 GLU cc_start: 0.7386 (pt0) cc_final: 0.7039 (pt0) REVERT: I 238 LYS cc_start: 0.5784 (tttt) cc_final: 0.5014 (pttt) REVERT: K 149 ARG cc_start: 0.7527 (mtp-110) cc_final: 0.7060 (mtp85) REVERT: M 44 ASN cc_start: 0.4471 (m-40) cc_final: 0.4207 (m110) REVERT: N 3 MET cc_start: 0.1162 (mtm) cc_final: 0.0190 (ptm) REVERT: N 212 ILE cc_start: 0.5994 (mm) cc_final: 0.5794 (mm) REVERT: O 227 ILE cc_start: 0.6975 (mt) cc_final: 0.6218 (mt) REVERT: Q 36 LYS cc_start: 0.5725 (mptt) cc_final: 0.5506 (mptt) REVERT: Q 160 MET cc_start: 0.4479 (mmt) cc_final: 0.4015 (mmp) REVERT: Q 247 MET cc_start: 0.2090 (mpp) cc_final: 0.1270 (mmt) REVERT: a 122 LYS cc_start: 0.5739 (mmmt) cc_final: 0.5370 (mmmt) REVERT: a 215 MET cc_start: 0.6598 (mmp) cc_final: 0.5643 (mmp) REVERT: c 224 LEU cc_start: 0.6793 (tp) cc_final: 0.6553 (tp) REVERT: P 20 GLU cc_start: 0.6981 (tp30) cc_final: 0.6774 (tp30) REVERT: P 26 VAL cc_start: 0.8301 (t) cc_final: 0.8007 (t) REVERT: P 130 SER cc_start: 0.8858 (p) cc_final: 0.8600 (m) REVERT: P 159 ASN cc_start: 0.6909 (m110) cc_final: 0.6700 (m110) REVERT: P 208 LEU cc_start: 0.7705 (mm) cc_final: 0.7488 (mm) REVERT: R 21 LEU cc_start: 0.8422 (mt) cc_final: 0.7830 (mt) REVERT: R 175 GLU cc_start: 0.6786 (pp20) cc_final: 0.6159 (pp20) REVERT: b 26 MET cc_start: 0.8165 (mmm) cc_final: 0.7927 (mmm) REVERT: b 88 MET cc_start: 0.8032 (mtp) cc_final: 0.7734 (mtp) REVERT: b 90 GLN cc_start: 0.8521 (tt0) cc_final: 0.8278 (tt0) REVERT: d 69 ASN cc_start: 0.7404 (t0) cc_final: 0.6699 (p0) REVERT: d 222 ASN cc_start: 0.7440 (t0) cc_final: 0.6890 (t0) REVERT: f 84 THR cc_start: 0.7543 (p) cc_final: 0.7270 (p) REVERT: f 226 LYS cc_start: 0.7136 (tttt) cc_final: 0.6792 (mppt) REVERT: h 92 LYS cc_start: 0.8545 (mttt) cc_final: 0.7889 (mttt) REVERT: j 69 ASN cc_start: 0.8479 (p0) cc_final: 0.8197 (p0) REVERT: j 82 ASP cc_start: 0.7339 (p0) cc_final: 0.6747 (p0) REVERT: j 115 CYS cc_start: 0.7280 (m) cc_final: 0.6945 (m) REVERT: j 128 ARG cc_start: 0.8971 (ptt90) cc_final: 0.8676 (ttp-170) REVERT: k 103 TYR cc_start: 0.6629 (m-10) cc_final: 0.6355 (m-10) REVERT: k 137 VAL cc_start: 0.8504 (t) cc_final: 0.7928 (t) REVERT: k 138 VAL cc_start: 0.8952 (m) cc_final: 0.8473 (m) REVERT: l 61 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8277 (tm-30) REVERT: l 75 LEU cc_start: 0.8843 (mt) cc_final: 0.8606 (mt) REVERT: l 85 ARG cc_start: 0.8111 (tmm160) cc_final: 0.7798 (tmt170) REVERT: l 109 GLU cc_start: 0.8142 (pm20) cc_final: 0.7903 (pm20) REVERT: l 170 ARG cc_start: 0.7455 (mmp80) cc_final: 0.7158 (mmp80) REVERT: n 155 MET cc_start: 0.6096 (mtm) cc_final: 0.5429 (mtm) REVERT: S 27 ARG cc_start: 0.8263 (tmt170) cc_final: 0.7839 (tmt170) REVERT: S 30 ILE cc_start: 0.8604 (tt) cc_final: 0.8342 (mp) REVERT: S 42 ILE cc_start: 0.9102 (mp) cc_final: 0.8887 (mm) REVERT: S 76 LEU cc_start: 0.8576 (mm) cc_final: 0.8308 (mm) REVERT: S 91 VAL cc_start: 0.9060 (t) cc_final: 0.8783 (m) REVERT: S 93 ASN cc_start: 0.8734 (t160) cc_final: 0.8508 (t0) REVERT: S 95 LEU cc_start: 0.9241 (mm) cc_final: 0.8963 (mt) REVERT: S 204 MET cc_start: 0.6618 (mpp) cc_final: 0.6035 (mpp) REVERT: S 205 ASP cc_start: 0.2739 (t0) cc_final: 0.1541 (m-30) REVERT: T 1 MET cc_start: 0.7273 (ppp) cc_final: 0.6585 (ppp) REVERT: T 4 LEU cc_start: 0.8564 (mt) cc_final: 0.8275 (mt) REVERT: T 27 GLN cc_start: 0.7422 (tm-30) cc_final: 0.6800 (tm-30) REVERT: T 53 THR cc_start: 0.8756 (p) cc_final: 0.8144 (t) REVERT: T 62 LYS cc_start: 0.9178 (ptmt) cc_final: 0.8927 (tttt) REVERT: T 63 ASN cc_start: 0.8939 (m-40) cc_final: 0.8498 (m110) REVERT: T 65 GLN cc_start: 0.9025 (tp-100) cc_final: 0.8137 (tp-100) REVERT: T 68 LYS cc_start: 0.8894 (tttt) cc_final: 0.8669 (tttt) REVERT: T 145 ARG cc_start: 0.7846 (tpm170) cc_final: 0.7167 (tpp-160) REVERT: T 168 GLN cc_start: 0.6999 (tm-30) cc_final: 0.6740 (tm-30) REVERT: T 181 ARG cc_start: 0.8322 (mmt90) cc_final: 0.8016 (mmm-85) REVERT: U 64 HIS cc_start: 0.7791 (m-70) cc_final: 0.7470 (m90) REVERT: U 194 LEU cc_start: 0.5871 (tp) cc_final: 0.5562 (tp) REVERT: V 177 TYR cc_start: 0.8040 (p90) cc_final: 0.7699 (p90) REVERT: V 225 ASP cc_start: 0.7698 (t0) cc_final: 0.7292 (t0) REVERT: V 252 THR cc_start: 0.4855 (p) cc_final: 0.4393 (p) REVERT: X 120 ARG cc_start: 0.7093 (mmt180) cc_final: 0.6517 (mmt180) REVERT: X 206 LEU cc_start: 0.8447 (mm) cc_final: 0.7989 (mm) REVERT: Y 129 ARG cc_start: 0.8074 (mtp180) cc_final: 0.7701 (mtm180) REVERT: Y 146 ILE cc_start: 0.8653 (tp) cc_final: 0.8334 (tp) REVERT: Y 230 ARG cc_start: 0.7305 (mtt90) cc_final: 0.7069 (mtt90) REVERT: Y 237 HIS cc_start: 0.8379 (t70) cc_final: 0.7980 (t70) REVERT: Y 262 THR cc_start: 0.8048 (m) cc_final: 0.7709 (m) REVERT: Z 52 ASP cc_start: 0.8346 (t0) cc_final: 0.7428 (p0) REVERT: Z 58 HIS cc_start: 0.5677 (t-90) cc_final: 0.5424 (t70) REVERT: Z 91 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7362 (mt-10) REVERT: Z 105 ASN cc_start: 0.8598 (t0) cc_final: 0.8369 (t0) REVERT: Z 109 LYS cc_start: 0.8885 (ttmm) cc_final: 0.8675 (tppp) REVERT: Z 138 MET cc_start: 0.8155 (ppp) cc_final: 0.7785 (ppp) REVERT: Z 183 MET cc_start: 0.7947 (mtt) cc_final: 0.7304 (mtt) REVERT: Z 184 LYS cc_start: 0.8551 (ptmt) cc_final: 0.8273 (ptmm) REVERT: 1 75 PHE cc_start: 0.6921 (t80) cc_final: 0.6356 (t80) REVERT: 1 92 GLU cc_start: 0.7359 (pp20) cc_final: 0.7117 (pp20) REVERT: 2 135 CYS cc_start: 0.6040 (p) cc_final: 0.5618 (p) outliers start: 11 outliers final: 2 residues processed: 2214 average time/residue: 0.6666 time to fit residues: 2491.1682 Evaluate side-chains 1709 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1707 time to evaluate : 6.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 714 optimal weight: 5.9990 chunk 487 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 639 optimal weight: 8.9990 chunk 354 optimal weight: 0.9980 chunk 732 optimal weight: 0.8980 chunk 593 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 438 optimal weight: 0.9990 chunk 770 optimal weight: 0.6980 chunk 216 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN E 227 HIS ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 ASN ** I 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 115 GLN ** Q 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 53 ASN e 193 HIS ** P 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 154 HIS ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 HIS ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 HIS ** b 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 111 HIS ** f 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN ** j 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 61 GLN ** k 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 169 GLN ** l 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 63 ASN l 87 ASN l 99 HIS ** l 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 126 HIS ** n 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 33 GLN S 93 ASN ** S 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 91 ASN ** V 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 HIS ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 148 GLN Z 59 GLN Z 86 HIS Z 117 HIS ** Z 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 72937 Z= 0.189 Angle : 0.600 10.484 98542 Z= 0.314 Chirality : 0.043 0.266 11127 Planarity : 0.004 0.097 12692 Dihedral : 4.436 38.437 9923 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.29 % Favored : 97.69 % Rotamer: Outliers : 0.09 % Allowed : 2.11 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.09), residues: 8996 helix: 1.01 (0.08), residues: 4381 sheet: 0.17 (0.13), residues: 1468 loop : -0.45 (0.11), residues: 3147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Y 176 HIS 0.012 0.001 HIS F 190 PHE 0.050 0.002 PHE l 56 TYR 0.030 0.002 TYR Q 223 ARG 0.013 0.001 ARG 2 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2141 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2134 time to evaluate : 6.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6261 (tm-30) cc_final: 0.5661 (tm-30) REVERT: A 109 ILE cc_start: 0.8819 (tt) cc_final: 0.8171 (tt) REVERT: A 205 VAL cc_start: 0.6757 (m) cc_final: 0.6533 (m) REVERT: B 60 ARG cc_start: 0.6457 (ptm-80) cc_final: 0.5876 (ptm-80) REVERT: C 67 LYS cc_start: 0.8438 (mmtm) cc_final: 0.8201 (mmtm) REVERT: C 75 SER cc_start: 0.8350 (p) cc_final: 0.7784 (t) REVERT: C 92 LEU cc_start: 0.9022 (mt) cc_final: 0.8614 (tt) REVERT: C 101 TYR cc_start: 0.8500 (m-80) cc_final: 0.8216 (m-10) REVERT: C 146 GLN cc_start: 0.7849 (mm-40) cc_final: 0.6965 (mp10) REVERT: C 155 ASN cc_start: 0.8632 (t0) cc_final: 0.8075 (t0) REVERT: D 115 LYS cc_start: 0.9063 (mtpt) cc_final: 0.8807 (mtpt) REVERT: D 129 ILE cc_start: 0.8386 (pt) cc_final: 0.8184 (pt) REVERT: D 130 SER cc_start: 0.8748 (m) cc_final: 0.8405 (m) REVERT: E 112 VAL cc_start: 0.8444 (t) cc_final: 0.8208 (p) REVERT: E 133 MET cc_start: 0.5011 (ptm) cc_final: 0.4772 (ptp) REVERT: E 157 ASP cc_start: 0.7510 (p0) cc_final: 0.7109 (p0) REVERT: E 206 MET cc_start: 0.5348 (ptp) cc_final: 0.4734 (mtp) REVERT: F 62 LYS cc_start: 0.7321 (tptt) cc_final: 0.6968 (mppt) REVERT: F 93 LEU cc_start: 0.8072 (mt) cc_final: 0.7754 (mt) REVERT: F 115 LYS cc_start: 0.8944 (tppt) cc_final: 0.8640 (tttt) REVERT: G 67 LEU cc_start: 0.7273 (mt) cc_final: 0.7001 (pt) REVERT: G 114 ASP cc_start: 0.7820 (m-30) cc_final: 0.7525 (m-30) REVERT: G 151 MET cc_start: 0.7398 (tmm) cc_final: 0.6756 (tmm) REVERT: G 227 ILE cc_start: 0.8316 (tt) cc_final: 0.7797 (tt) REVERT: H 125 ILE cc_start: 0.5958 (mm) cc_final: 0.5716 (mm) REVERT: I 206 GLU cc_start: 0.7556 (pt0) cc_final: 0.7115 (pt0) REVERT: I 238 LYS cc_start: 0.5550 (tttt) cc_final: 0.4884 (pttt) REVERT: K 57 LEU cc_start: 0.4277 (tt) cc_final: 0.3987 (mp) REVERT: K 97 ASN cc_start: 0.2040 (t0) cc_final: 0.1225 (p0) REVERT: K 149 ARG cc_start: 0.7334 (mtp-110) cc_final: 0.6801 (mtp85) REVERT: M 44 ASN cc_start: 0.4449 (m-40) cc_final: 0.4201 (m110) REVERT: N 3 MET cc_start: 0.1222 (mtm) cc_final: 0.0044 (ptm) REVERT: N 212 ILE cc_start: 0.6141 (mm) cc_final: 0.5863 (mm) REVERT: O 185 MET cc_start: 0.2705 (tmm) cc_final: 0.2429 (tpp) REVERT: Q 154 GLU cc_start: 0.6725 (mp0) cc_final: 0.6386 (mm-30) REVERT: Q 160 MET cc_start: 0.4535 (mmt) cc_final: 0.4033 (mmp) REVERT: Q 190 LYS cc_start: 0.4523 (tttt) cc_final: 0.4123 (tptt) REVERT: Q 247 MET cc_start: 0.2117 (mpp) cc_final: 0.1052 (mmt) REVERT: a 122 LYS cc_start: 0.5537 (mmmt) cc_final: 0.5151 (mmmt) REVERT: a 215 MET cc_start: 0.6876 (mmp) cc_final: 0.6437 (mmp) REVERT: c 224 LEU cc_start: 0.6788 (tp) cc_final: 0.6562 (tp) REVERT: i 1 MET cc_start: 0.3532 (ptt) cc_final: 0.1975 (mtm) REVERT: P 159 ASN cc_start: 0.6944 (m110) cc_final: 0.6619 (m110) REVERT: P 208 LEU cc_start: 0.7772 (mm) cc_final: 0.7502 (mm) REVERT: R 21 LEU cc_start: 0.8260 (mt) cc_final: 0.7189 (mt) REVERT: R 32 LYS cc_start: 0.9134 (mmmm) cc_final: 0.7973 (tmtt) REVERT: R 175 GLU cc_start: 0.6796 (pp20) cc_final: 0.6278 (pp20) REVERT: b 26 MET cc_start: 0.8229 (mmm) cc_final: 0.7706 (tpp) REVERT: d 69 ASN cc_start: 0.7660 (t0) cc_final: 0.6977 (p0) REVERT: d 222 ASN cc_start: 0.7579 (t0) cc_final: 0.7015 (t0) REVERT: f 90 GLN cc_start: 0.8516 (tp-100) cc_final: 0.8200 (tp-100) REVERT: f 104 LYS cc_start: 0.9178 (ttmt) cc_final: 0.8768 (ttpp) REVERT: f 117 ARG cc_start: 0.8224 (mmm160) cc_final: 0.7900 (mmm-85) REVERT: f 123 GLN cc_start: 0.9189 (tp40) cc_final: 0.8354 (tm-30) REVERT: f 140 LEU cc_start: 0.8911 (mt) cc_final: 0.8707 (mt) REVERT: f 226 LYS cc_start: 0.7174 (tttt) cc_final: 0.6875 (mppt) REVERT: j 69 ASN cc_start: 0.8524 (p0) cc_final: 0.8177 (p0) REVERT: j 82 ASP cc_start: 0.7378 (p0) cc_final: 0.6700 (p0) REVERT: j 93 ILE cc_start: 0.8599 (tp) cc_final: 0.8357 (tp) REVERT: j 115 CYS cc_start: 0.7265 (m) cc_final: 0.6989 (m) REVERT: j 128 ARG cc_start: 0.8948 (ptt90) cc_final: 0.8678 (ttp-170) REVERT: k 27 ARG cc_start: 0.8043 (ttm-80) cc_final: 0.7710 (ttm-80) REVERT: k 137 VAL cc_start: 0.8520 (t) cc_final: 0.8127 (t) REVERT: k 138 VAL cc_start: 0.9020 (m) cc_final: 0.8526 (m) REVERT: l 27 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7602 (pp30) REVERT: l 30 ASP cc_start: 0.8601 (p0) cc_final: 0.8169 (p0) REVERT: m 50 ILE cc_start: 0.8766 (tt) cc_final: 0.8478 (mp) REVERT: n 155 MET cc_start: 0.6128 (mtm) cc_final: 0.5482 (mtm) REVERT: S 42 ILE cc_start: 0.9110 (mp) cc_final: 0.8804 (mm) REVERT: S 49 LEU cc_start: 0.6956 (mt) cc_final: 0.6522 (mt) REVERT: S 76 LEU cc_start: 0.8625 (mm) cc_final: 0.8307 (mm) REVERT: S 91 VAL cc_start: 0.9010 (t) cc_final: 0.8743 (m) REVERT: S 95 LEU cc_start: 0.9266 (mm) cc_final: 0.8995 (mt) REVERT: S 142 CYS cc_start: 0.7491 (p) cc_final: 0.7112 (p) REVERT: S 155 GLU cc_start: 0.5829 (mp0) cc_final: 0.5361 (mp0) REVERT: S 167 ILE cc_start: 0.8941 (tt) cc_final: 0.8495 (tt) REVERT: S 175 VAL cc_start: 0.8484 (t) cc_final: 0.8199 (t) REVERT: T 4 LEU cc_start: 0.8631 (mt) cc_final: 0.8285 (mt) REVERT: T 27 GLN cc_start: 0.7748 (tm-30) cc_final: 0.7213 (tm-30) REVERT: T 53 THR cc_start: 0.9023 (p) cc_final: 0.8577 (t) REVERT: T 63 ASN cc_start: 0.8888 (m-40) cc_final: 0.8555 (m110) REVERT: T 65 GLN cc_start: 0.8897 (tp-100) cc_final: 0.8286 (tp-100) REVERT: T 68 LYS cc_start: 0.8915 (tttt) cc_final: 0.8524 (tttt) REVERT: T 87 ASN cc_start: 0.8367 (m-40) cc_final: 0.8127 (m-40) REVERT: T 145 ARG cc_start: 0.7664 (tpm170) cc_final: 0.6753 (tpp-160) REVERT: T 147 TYR cc_start: 0.8236 (t80) cc_final: 0.7969 (t80) REVERT: T 168 GLN cc_start: 0.7179 (tm-30) cc_final: 0.6888 (tm-30) REVERT: T 181 ARG cc_start: 0.8246 (mmt90) cc_final: 0.8036 (mmm-85) REVERT: U 56 ARG cc_start: 0.7968 (ttm170) cc_final: 0.7745 (ttm-80) REVERT: U 217 THR cc_start: 0.6974 (m) cc_final: 0.6703 (m) REVERT: U 225 ILE cc_start: 0.8159 (mp) cc_final: 0.7719 (mt) REVERT: V 114 GLN cc_start: 0.7858 (tp40) cc_final: 0.7137 (tp40) REVERT: V 118 ASP cc_start: 0.7080 (m-30) cc_final: 0.6693 (m-30) REVERT: V 177 TYR cc_start: 0.7992 (p90) cc_final: 0.7611 (p90) REVERT: V 225 ASP cc_start: 0.7800 (t0) cc_final: 0.7369 (t0) REVERT: V 252 THR cc_start: 0.4568 (p) cc_final: 0.4278 (p) REVERT: W 63 CYS cc_start: 0.8310 (t) cc_final: 0.7970 (t) REVERT: W 113 ASP cc_start: 0.7072 (t0) cc_final: 0.6610 (t0) REVERT: W 216 PHE cc_start: 0.6549 (m-10) cc_final: 0.6300 (m-10) REVERT: X 120 ARG cc_start: 0.6992 (mmm160) cc_final: 0.6317 (mmt180) REVERT: X 160 ARG cc_start: 0.7850 (ttp80) cc_final: 0.7575 (tpt-90) REVERT: X 161 LEU cc_start: 0.8043 (pp) cc_final: 0.7510 (pp) REVERT: X 206 LEU cc_start: 0.8425 (mm) cc_final: 0.7879 (mm) REVERT: Y 129 ARG cc_start: 0.8197 (mtp180) cc_final: 0.7776 (mtm180) REVERT: Y 146 ILE cc_start: 0.8760 (tp) cc_final: 0.8372 (tp) REVERT: Y 230 ARG cc_start: 0.7147 (mtt90) cc_final: 0.6763 (mtt180) REVERT: Z 52 ASP cc_start: 0.8399 (t0) cc_final: 0.7829 (p0) REVERT: Z 58 HIS cc_start: 0.5937 (t-90) cc_final: 0.5596 (t70) REVERT: Z 59 GLN cc_start: 0.7739 (mt0) cc_final: 0.7451 (mt0) REVERT: Z 91 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7257 (mt-10) REVERT: Z 183 MET cc_start: 0.8137 (mtt) cc_final: 0.7583 (mtt) REVERT: Z 184 LYS cc_start: 0.8648 (ptmt) cc_final: 0.8188 (ptmm) REVERT: 1 75 PHE cc_start: 0.6895 (t80) cc_final: 0.6339 (t80) REVERT: 1 92 GLU cc_start: 0.7685 (pp20) cc_final: 0.7261 (pp20) REVERT: 1 93 MET cc_start: 0.7655 (tpp) cc_final: 0.7329 (tpp) REVERT: 1 103 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7156 (tm-30) REVERT: 1 163 PHE cc_start: 0.7656 (p90) cc_final: 0.6909 (p90) REVERT: 2 135 CYS cc_start: 0.6230 (p) cc_final: 0.5945 (p) REVERT: 2 159 MET cc_start: 0.7423 (tpp) cc_final: 0.7062 (tpp) REVERT: 2 187 ASP cc_start: 0.6419 (t0) cc_final: 0.5890 (t70) outliers start: 7 outliers final: 1 residues processed: 2136 average time/residue: 0.6571 time to fit residues: 2384.4920 Evaluate side-chains 1668 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1667 time to evaluate : 6.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 288 optimal weight: 4.9990 chunk 772 optimal weight: 0.3980 chunk 169 optimal weight: 1.9990 chunk 503 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 859 optimal weight: 0.0040 chunk 713 optimal weight: 0.7980 chunk 397 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 284 optimal weight: 2.9990 chunk 451 optimal weight: 0.6980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN G 102 ASN ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 GLN ** J 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN ** Q 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 173 GLN ** P 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 154 HIS R 99 HIS ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 HIS ** b 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 111 HIS ** f 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 169 GLN l 27 GLN l 55 GLN l 87 ASN l 99 HIS l 101 ASN ** m 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 33 GLN ** S 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 188 HIS ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 205 HIS X 61 ASN ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 105 ASN Z 117 HIS Z 130 GLN ** Z 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 124 GLN 2 96 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5936 moved from start: 0.7002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 72937 Z= 0.179 Angle : 0.606 10.130 98542 Z= 0.315 Chirality : 0.043 0.303 11127 Planarity : 0.004 0.108 12692 Dihedral : 4.408 36.582 9923 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.26 % Favored : 97.72 % Rotamer: Outliers : 0.05 % Allowed : 1.62 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.09), residues: 8996 helix: 1.16 (0.08), residues: 4372 sheet: 0.20 (0.13), residues: 1455 loop : -0.48 (0.11), residues: 3169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP 2 127 HIS 0.010 0.001 HIS F 175 PHE 0.040 0.002 PHE l 56 TYR 0.045 0.001 TYR D 110 ARG 0.012 0.001 ARG X 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2108 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2104 time to evaluate : 5.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6490 (tm-30) cc_final: 0.6010 (tm-30) REVERT: A 109 ILE cc_start: 0.8910 (tt) cc_final: 0.8073 (tt) REVERT: A 205 VAL cc_start: 0.6397 (m) cc_final: 0.6180 (m) REVERT: B 50 LYS cc_start: 0.4996 (tmtt) cc_final: 0.4000 (tptt) REVERT: B 60 ARG cc_start: 0.6604 (ptm-80) cc_final: 0.6016 (ptm-80) REVERT: B 66 GLU cc_start: 0.7289 (mt-10) cc_final: 0.7014 (mt-10) REVERT: C 67 LYS cc_start: 0.8475 (mmtm) cc_final: 0.8189 (mmtm) REVERT: C 75 SER cc_start: 0.8392 (p) cc_final: 0.7850 (t) REVERT: C 101 TYR cc_start: 0.8613 (m-80) cc_final: 0.8356 (m-10) REVERT: C 146 GLN cc_start: 0.7733 (mm-40) cc_final: 0.6868 (mp10) REVERT: C 155 ASN cc_start: 0.8425 (t0) cc_final: 0.8017 (t0) REVERT: C 201 MET cc_start: 0.6442 (mmm) cc_final: 0.6038 (mmt) REVERT: D 115 LYS cc_start: 0.9085 (mtpt) cc_final: 0.8818 (mtpt) REVERT: D 130 SER cc_start: 0.8725 (m) cc_final: 0.8427 (m) REVERT: E 100 TRP cc_start: 0.8043 (t60) cc_final: 0.7809 (t60) REVERT: E 206 MET cc_start: 0.5407 (ptp) cc_final: 0.4669 (mtp) REVERT: F 87 PHE cc_start: 0.6975 (t80) cc_final: 0.6103 (t80) REVERT: F 93 LEU cc_start: 0.8002 (mt) cc_final: 0.7647 (mt) REVERT: F 115 LYS cc_start: 0.8964 (tppt) cc_final: 0.8584 (tttt) REVERT: G 9 ASP cc_start: 0.7946 (p0) cc_final: 0.7698 (p0) REVERT: G 67 LEU cc_start: 0.7553 (mt) cc_final: 0.7209 (pt) REVERT: G 94 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7416 (tm-30) REVERT: H 125 ILE cc_start: 0.5860 (mm) cc_final: 0.5643 (mm) REVERT: I 206 GLU cc_start: 0.7523 (pt0) cc_final: 0.7104 (pt0) REVERT: I 238 LYS cc_start: 0.5334 (tttt) cc_final: 0.4836 (pttt) REVERT: J 241 ARG cc_start: 0.4801 (mpt180) cc_final: 0.4497 (mpt180) REVERT: K 97 ASN cc_start: 0.2122 (t0) cc_final: 0.1440 (p0) REVERT: M 44 ASN cc_start: 0.4493 (m-40) cc_final: 0.4251 (m110) REVERT: N 3 MET cc_start: 0.1464 (mtm) cc_final: 0.0430 (ptm) REVERT: O 185 MET cc_start: 0.2654 (tmm) cc_final: 0.2367 (tpp) REVERT: Q 154 GLU cc_start: 0.6646 (mp0) cc_final: 0.6245 (mm-30) REVERT: Q 160 MET cc_start: 0.4644 (mmt) cc_final: 0.4321 (mmp) REVERT: Q 190 LYS cc_start: 0.4437 (tttt) cc_final: 0.3990 (tptt) REVERT: Q 247 MET cc_start: 0.2119 (mpp) cc_final: 0.1083 (mmt) REVERT: a 122 LYS cc_start: 0.5789 (mmmt) cc_final: 0.5508 (mmmt) REVERT: a 133 THR cc_start: 0.5144 (p) cc_final: 0.4902 (p) REVERT: a 212 ILE cc_start: 0.2890 (mt) cc_final: 0.2407 (tt) REVERT: c 106 LEU cc_start: 0.5897 (tp) cc_final: 0.5696 (tp) REVERT: c 224 LEU cc_start: 0.6828 (tp) cc_final: 0.6591 (tp) REVERT: i 1 MET cc_start: 0.3865 (ptt) cc_final: 0.2096 (mtm) REVERT: i 210 ARG cc_start: 0.4741 (mmt-90) cc_final: 0.4453 (mmt-90) REVERT: P 108 THR cc_start: 0.8740 (m) cc_final: 0.8432 (t) REVERT: P 116 GLN cc_start: 0.8251 (tm-30) cc_final: 0.8024 (tm-30) REVERT: P 208 LEU cc_start: 0.7752 (mm) cc_final: 0.7508 (mm) REVERT: R 21 LEU cc_start: 0.8397 (mt) cc_final: 0.7378 (mt) REVERT: R 25 GLU cc_start: 0.7682 (pm20) cc_final: 0.7381 (pm20) REVERT: R 32 LYS cc_start: 0.9159 (mmmm) cc_final: 0.8018 (tmtt) REVERT: R 175 GLU cc_start: 0.6928 (pp20) cc_final: 0.6271 (pp20) REVERT: b 26 MET cc_start: 0.8146 (mmm) cc_final: 0.7707 (tpp) REVERT: b 88 MET cc_start: 0.8109 (mtp) cc_final: 0.7883 (mtp) REVERT: b 92 CYS cc_start: 0.8368 (p) cc_final: 0.8037 (p) REVERT: b 128 TYR cc_start: 0.7895 (m-80) cc_final: 0.7388 (m-80) REVERT: d 40 ILE cc_start: 0.7275 (mm) cc_final: 0.6920 (mt) REVERT: d 69 ASN cc_start: 0.7543 (t0) cc_final: 0.7042 (p0) REVERT: d 151 MET cc_start: 0.8942 (tmm) cc_final: 0.8613 (tmm) REVERT: d 222 ASN cc_start: 0.7566 (t0) cc_final: 0.6965 (t0) REVERT: f 80 MET cc_start: 0.8094 (mpp) cc_final: 0.7418 (mtm) REVERT: f 90 GLN cc_start: 0.8459 (tp-100) cc_final: 0.8194 (tp-100) REVERT: f 123 GLN cc_start: 0.9297 (tp40) cc_final: 0.8611 (tm-30) REVERT: f 127 GLN cc_start: 0.7288 (tm-30) cc_final: 0.7082 (tm-30) REVERT: h 102 GLN cc_start: 0.7208 (mm-40) cc_final: 0.6510 (mm-40) REVERT: j 82 ASP cc_start: 0.7410 (p0) cc_final: 0.6845 (p0) REVERT: j 115 CYS cc_start: 0.7214 (m) cc_final: 0.6822 (m) REVERT: j 128 ARG cc_start: 0.8904 (ptt90) cc_final: 0.8651 (ttp-170) REVERT: k 103 TYR cc_start: 0.6594 (m-10) cc_final: 0.6364 (m-10) REVERT: k 137 VAL cc_start: 0.8476 (t) cc_final: 0.7953 (m) REVERT: k 145 GLN cc_start: 0.8050 (mt0) cc_final: 0.7791 (mt0) REVERT: l 27 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7580 (pp30) REVERT: l 30 ASP cc_start: 0.8621 (p0) cc_final: 0.8207 (p0) REVERT: l 75 LEU cc_start: 0.8786 (mt) cc_final: 0.8368 (mt) REVERT: l 88 LEU cc_start: 0.9121 (tp) cc_final: 0.8870 (tp) REVERT: n 154 THR cc_start: 0.9042 (m) cc_final: 0.8477 (p) REVERT: n 155 MET cc_start: 0.6187 (mtm) cc_final: 0.5715 (mtm) REVERT: n 225 ASP cc_start: 0.7594 (t0) cc_final: 0.7369 (t0) REVERT: S 27 ARG cc_start: 0.8133 (tmt170) cc_final: 0.7641 (ttm-80) REVERT: S 34 MET cc_start: 0.6846 (mmp) cc_final: 0.6610 (mmt) REVERT: S 42 ILE cc_start: 0.9112 (mp) cc_final: 0.8908 (mm) REVERT: S 49 LEU cc_start: 0.6916 (mt) cc_final: 0.6673 (mt) REVERT: S 76 LEU cc_start: 0.8610 (mm) cc_final: 0.8344 (mm) REVERT: S 91 VAL cc_start: 0.8998 (t) cc_final: 0.8705 (m) REVERT: S 95 LEU cc_start: 0.9250 (mm) cc_final: 0.9015 (mt) REVERT: S 142 CYS cc_start: 0.7599 (p) cc_final: 0.6986 (p) REVERT: S 155 GLU cc_start: 0.5790 (mp0) cc_final: 0.5381 (mp0) REVERT: S 173 ASN cc_start: 0.8224 (m-40) cc_final: 0.8014 (t0) REVERT: S 175 VAL cc_start: 0.8359 (t) cc_final: 0.8095 (t) REVERT: S 204 MET cc_start: 0.6405 (mpp) cc_final: 0.6195 (mpp) REVERT: T 1 MET cc_start: 0.6686 (ppp) cc_final: 0.5826 (ptm) REVERT: T 8 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7851 (tm-30) REVERT: T 27 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7389 (tm-30) REVERT: T 45 LEU cc_start: 0.8327 (mt) cc_final: 0.7943 (mt) REVERT: T 53 THR cc_start: 0.9002 (p) cc_final: 0.8606 (t) REVERT: T 63 ASN cc_start: 0.8918 (m-40) cc_final: 0.8453 (m110) REVERT: T 65 GLN cc_start: 0.8893 (tp-100) cc_final: 0.8210 (tp-100) REVERT: T 87 ASN cc_start: 0.8592 (m-40) cc_final: 0.8307 (m-40) REVERT: T 168 GLN cc_start: 0.7286 (tm-30) cc_final: 0.6989 (tm-30) REVERT: T 179 SER cc_start: 0.8531 (t) cc_final: 0.8272 (t) REVERT: U 41 LEU cc_start: 0.8321 (mt) cc_final: 0.7957 (tt) REVERT: U 217 THR cc_start: 0.6872 (m) cc_final: 0.6518 (m) REVERT: U 225 ILE cc_start: 0.8187 (mp) cc_final: 0.7722 (mt) REVERT: V 81 PHE cc_start: 0.8104 (m-10) cc_final: 0.7751 (m-10) REVERT: V 114 GLN cc_start: 0.7796 (tp40) cc_final: 0.7082 (tp40) REVERT: V 118 ASP cc_start: 0.7066 (m-30) cc_final: 0.6780 (m-30) REVERT: V 177 TYR cc_start: 0.8054 (p90) cc_final: 0.7638 (p90) REVERT: W 52 ASP cc_start: 0.8179 (t0) cc_final: 0.7050 (p0) REVERT: W 113 ASP cc_start: 0.7124 (t0) cc_final: 0.6665 (t0) REVERT: X 208 SER cc_start: 0.7322 (m) cc_final: 0.6957 (m) REVERT: Y 91 ARG cc_start: 0.7853 (ttp-170) cc_final: 0.7192 (ttp-170) REVERT: Y 129 ARG cc_start: 0.8294 (mtp180) cc_final: 0.7909 (mtm180) REVERT: Y 146 ILE cc_start: 0.8730 (tp) cc_final: 0.8391 (tp) REVERT: Y 153 LYS cc_start: 0.8611 (mmpt) cc_final: 0.7877 (mmmt) REVERT: Y 230 ARG cc_start: 0.7409 (mtt90) cc_final: 0.7092 (mtt90) REVERT: Y 232 ILE cc_start: 0.8921 (mm) cc_final: 0.8713 (mm) REVERT: Y 262 THR cc_start: 0.8055 (m) cc_final: 0.7735 (m) REVERT: Z 52 ASP cc_start: 0.8391 (t0) cc_final: 0.7918 (p0) REVERT: Z 91 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7297 (mt-10) REVERT: Z 183 MET cc_start: 0.8124 (mtt) cc_final: 0.7803 (mtt) REVERT: 1 75 PHE cc_start: 0.6918 (t80) cc_final: 0.6494 (t80) REVERT: 1 90 ASP cc_start: 0.8223 (m-30) cc_final: 0.7348 (m-30) REVERT: 1 92 GLU cc_start: 0.7691 (pp20) cc_final: 0.7319 (pp20) REVERT: 1 93 MET cc_start: 0.7780 (tpp) cc_final: 0.7271 (tpp) REVERT: 1 103 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7136 (tm-30) REVERT: 1 120 ARG cc_start: 0.6321 (mtp-110) cc_final: 0.5953 (ttm170) REVERT: 1 123 ARG cc_start: 0.7226 (ptp90) cc_final: 0.6868 (ptt90) REVERT: 1 124 GLN cc_start: 0.7844 (mt0) cc_final: 0.7576 (mt0) REVERT: 1 163 PHE cc_start: 0.7669 (p90) cc_final: 0.7318 (p90) REVERT: 1 188 GLU cc_start: 0.6322 (tm-30) cc_final: 0.6039 (tp30) REVERT: 1 196 GLU cc_start: 0.8298 (tt0) cc_final: 0.8063 (tt0) REVERT: 2 135 CYS cc_start: 0.6341 (p) cc_final: 0.6037 (p) REVERT: 2 234 HIS cc_start: 0.7970 (m-70) cc_final: 0.7746 (m-70) outliers start: 4 outliers final: 0 residues processed: 2104 average time/residue: 0.6549 time to fit residues: 2350.7708 Evaluate side-chains 1680 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1679 time to evaluate : 6.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 828 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 489 optimal weight: 5.9990 chunk 627 optimal weight: 4.9990 chunk 486 optimal weight: 0.7980 chunk 723 optimal weight: 3.9990 chunk 479 optimal weight: 3.9990 chunk 855 optimal weight: 0.7980 chunk 535 optimal weight: 3.9990 chunk 521 optimal weight: 1.9990 chunk 395 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN ** I 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 HIS ** J 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 ASN L 193 HIS ** M 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 154 HIS ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 HIS ** b 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 111 HIS ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 193 GLN ** j 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 169 GLN k 173 ASN l 55 GLN l 63 ASN l 99 HIS ** l 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 126 HIS ** n 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 188 HIS ** T 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 91 ASN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 148 GLN Y 234 HIS ** Z 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 117 HIS 2 104 ASN 2 196 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6051 moved from start: 0.7450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 72937 Z= 0.210 Angle : 0.632 10.651 98542 Z= 0.330 Chirality : 0.044 0.233 11127 Planarity : 0.004 0.113 12692 Dihedral : 4.477 40.102 9923 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % Rotamer: Outliers : 0.03 % Allowed : 1.33 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.09), residues: 8996 helix: 1.19 (0.08), residues: 4373 sheet: 0.18 (0.13), residues: 1456 loop : -0.51 (0.11), residues: 3167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP 2 127 HIS 0.016 0.001 HIS F 175 PHE 0.033 0.002 PHE F 179 TYR 0.043 0.002 TYR D 110 ARG 0.029 0.001 ARG J 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2039 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2037 time to evaluate : 6.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.8942 (tt) cc_final: 0.8136 (tt) REVERT: B 50 LYS cc_start: 0.5335 (tmtt) cc_final: 0.4693 (tptt) REVERT: B 60 ARG cc_start: 0.6677 (ptm-80) cc_final: 0.6033 (ptm-80) REVERT: B 83 TYR cc_start: 0.6685 (t80) cc_final: 0.6074 (t80) REVERT: C 20 GLN cc_start: 0.8890 (mp10) cc_final: 0.8415 (mp10) REVERT: C 67 LYS cc_start: 0.8566 (mmtm) cc_final: 0.8190 (mmtm) REVERT: C 75 SER cc_start: 0.8697 (p) cc_final: 0.7891 (t) REVERT: C 155 ASN cc_start: 0.8554 (t0) cc_final: 0.8138 (t0) REVERT: C 201 MET cc_start: 0.6295 (mmm) cc_final: 0.5859 (mmt) REVERT: D 115 LYS cc_start: 0.9141 (mtpt) cc_final: 0.8840 (mtpt) REVERT: D 130 SER cc_start: 0.8899 (m) cc_final: 0.8633 (m) REVERT: D 220 LEU cc_start: 0.7567 (tt) cc_final: 0.7335 (tt) REVERT: F 87 PHE cc_start: 0.6957 (t80) cc_final: 0.6157 (t80) REVERT: F 93 LEU cc_start: 0.8052 (mt) cc_final: 0.7714 (mt) REVERT: F 114 SER cc_start: 0.8960 (m) cc_final: 0.8635 (p) REVERT: F 115 LYS cc_start: 0.9022 (tppt) cc_final: 0.8543 (tttt) REVERT: G 67 LEU cc_start: 0.7754 (mt) cc_final: 0.7501 (pt) REVERT: G 94 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7435 (tm-30) REVERT: H 125 ILE cc_start: 0.5806 (mm) cc_final: 0.5423 (mm) REVERT: I 206 GLU cc_start: 0.7611 (pt0) cc_final: 0.7133 (pt0) REVERT: I 238 LYS cc_start: 0.5464 (tttt) cc_final: 0.4968 (pttt) REVERT: K 97 ASN cc_start: 0.1986 (t0) cc_final: 0.1377 (p0) REVERT: N 3 MET cc_start: 0.1764 (mtm) cc_final: 0.0665 (ptm) REVERT: N 212 ILE cc_start: 0.5674 (mm) cc_final: 0.5265 (mm) REVERT: N 214 LEU cc_start: 0.4384 (pp) cc_final: 0.4181 (pp) REVERT: O 185 MET cc_start: 0.2491 (tmm) cc_final: 0.2288 (tpp) REVERT: O 210 ARG cc_start: 0.3058 (ppt170) cc_final: 0.2725 (ttt180) REVERT: Q 154 GLU cc_start: 0.6846 (mp0) cc_final: 0.6190 (mm-30) REVERT: Q 160 MET cc_start: 0.4649 (mmt) cc_final: 0.4404 (mmp) REVERT: Q 218 GLU cc_start: 0.5064 (tm-30) cc_final: 0.4618 (mm-30) REVERT: Q 247 MET cc_start: 0.1703 (mpp) cc_final: 0.0703 (mmt) REVERT: a 122 LYS cc_start: 0.5539 (mmmt) cc_final: 0.5258 (mmmt) REVERT: a 215 MET cc_start: 0.6310 (mmp) cc_final: 0.5972 (mmp) REVERT: c 106 LEU cc_start: 0.5992 (tp) cc_final: 0.5739 (tp) REVERT: c 203 ARG cc_start: 0.3677 (tpt90) cc_final: 0.0798 (mmt-90) REVERT: c 205 MET cc_start: 0.4188 (ptm) cc_final: 0.3970 (ptm) REVERT: c 224 LEU cc_start: 0.6901 (tp) cc_final: 0.6677 (tp) REVERT: i 1 MET cc_start: 0.3914 (ptt) cc_final: 0.2004 (mtm) REVERT: i 210 ARG cc_start: 0.4873 (mmt-90) cc_final: 0.3596 (mmt-90) REVERT: i 213 ARG cc_start: 0.4780 (pmt-80) cc_final: 0.3967 (ttm170) REVERT: P 108 THR cc_start: 0.8688 (m) cc_final: 0.8415 (t) REVERT: P 208 LEU cc_start: 0.7523 (mm) cc_final: 0.7304 (mm) REVERT: R 175 GLU cc_start: 0.7037 (pp20) cc_final: 0.6548 (pp20) REVERT: b 19 ILE cc_start: 0.8572 (mm) cc_final: 0.7974 (mm) REVERT: b 26 MET cc_start: 0.8289 (mmm) cc_final: 0.7738 (tpp) REVERT: b 92 CYS cc_start: 0.8581 (p) cc_final: 0.8266 (p) REVERT: b 103 LEU cc_start: 0.8946 (tp) cc_final: 0.8715 (tp) REVERT: d 21 VAL cc_start: 0.7562 (t) cc_final: 0.7124 (m) REVERT: d 69 ASN cc_start: 0.7840 (t0) cc_final: 0.7262 (p0) REVERT: d 82 LEU cc_start: 0.8821 (mm) cc_final: 0.8317 (pt) REVERT: d 151 MET cc_start: 0.8862 (tmm) cc_final: 0.8619 (tmm) REVERT: d 222 ASN cc_start: 0.7723 (t0) cc_final: 0.7093 (t0) REVERT: f 90 GLN cc_start: 0.8484 (tp-100) cc_final: 0.8235 (tp-100) REVERT: f 123 GLN cc_start: 0.9390 (tp40) cc_final: 0.8621 (tm-30) REVERT: f 152 TYR cc_start: 0.5875 (m-10) cc_final: 0.5672 (m-10) REVERT: h 139 TRP cc_start: 0.3852 (t-100) cc_final: 0.2752 (t60) REVERT: j 69 ASN cc_start: 0.8742 (p0) cc_final: 0.8499 (p0) REVERT: j 82 ASP cc_start: 0.7419 (p0) cc_final: 0.6769 (p0) REVERT: j 115 CYS cc_start: 0.7321 (m) cc_final: 0.6977 (m) REVERT: k 7 ASN cc_start: 0.7505 (m110) cc_final: 0.6540 (t0) REVERT: k 137 VAL cc_start: 0.8640 (t) cc_final: 0.8413 (m) REVERT: k 138 VAL cc_start: 0.9074 (m) cc_final: 0.8666 (p) REVERT: k 169 GLN cc_start: 0.6652 (tt0) cc_final: 0.6373 (tp40) REVERT: l 75 LEU cc_start: 0.8888 (mt) cc_final: 0.8543 (mt) REVERT: n 141 MET cc_start: 0.7832 (tpt) cc_final: 0.7625 (mmm) REVERT: n 142 TYR cc_start: 0.7703 (t80) cc_final: 0.7387 (t80) REVERT: n 155 MET cc_start: 0.6253 (mtm) cc_final: 0.5890 (mtm) REVERT: n 173 LEU cc_start: 0.8780 (mt) cc_final: 0.7549 (mt) REVERT: n 225 ASP cc_start: 0.7747 (t0) cc_final: 0.7505 (t0) REVERT: S 42 ILE cc_start: 0.9172 (mp) cc_final: 0.8920 (mm) REVERT: S 76 LEU cc_start: 0.8669 (mm) cc_final: 0.8388 (mm) REVERT: S 91 VAL cc_start: 0.9091 (t) cc_final: 0.8767 (m) REVERT: S 95 LEU cc_start: 0.9265 (mm) cc_final: 0.9018 (mt) REVERT: S 142 CYS cc_start: 0.7256 (p) cc_final: 0.6548 (p) REVERT: S 155 GLU cc_start: 0.5548 (mp0) cc_final: 0.5097 (mp0) REVERT: S 204 MET cc_start: 0.6634 (mpp) cc_final: 0.6417 (mpp) REVERT: T 8 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7883 (tm-30) REVERT: T 53 THR cc_start: 0.9030 (p) cc_final: 0.8601 (t) REVERT: T 63 ASN cc_start: 0.8803 (m-40) cc_final: 0.8380 (m110) REVERT: T 65 GLN cc_start: 0.8927 (tp-100) cc_final: 0.8216 (tp-100) REVERT: T 87 ASN cc_start: 0.8528 (m-40) cc_final: 0.8306 (m-40) REVERT: T 134 TYR cc_start: 0.6856 (m-80) cc_final: 0.6534 (m-80) REVERT: T 145 ARG cc_start: 0.7938 (tpm170) cc_final: 0.5566 (tpp-160) REVERT: T 153 ARG cc_start: 0.7306 (ptp90) cc_final: 0.7048 (ptp90) REVERT: U 41 LEU cc_start: 0.8440 (mt) cc_final: 0.8104 (tt) REVERT: U 56 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.7565 (ttm110) REVERT: V 81 PHE cc_start: 0.8219 (m-10) cc_final: 0.7847 (m-10) REVERT: V 114 GLN cc_start: 0.7863 (tp40) cc_final: 0.7143 (tp40) REVERT: V 118 ASP cc_start: 0.7118 (m-30) cc_final: 0.6715 (m-30) REVERT: V 121 LEU cc_start: 0.8337 (mt) cc_final: 0.7837 (mt) REVERT: V 177 TYR cc_start: 0.8020 (p90) cc_final: 0.7648 (p90) REVERT: V 225 ASP cc_start: 0.8206 (t0) cc_final: 0.7891 (t0) REVERT: V 252 THR cc_start: 0.4474 (p) cc_final: 0.4206 (p) REVERT: W 52 ASP cc_start: 0.8356 (t0) cc_final: 0.7273 (p0) REVERT: W 63 CYS cc_start: 0.8416 (t) cc_final: 0.8178 (t) REVERT: W 113 ASP cc_start: 0.7321 (t0) cc_final: 0.7119 (t0) REVERT: W 123 TRP cc_start: 0.7047 (t60) cc_final: 0.6763 (t60) REVERT: X 96 ARG cc_start: 0.7439 (tpp-160) cc_final: 0.7199 (tpp-160) REVERT: X 138 ILE cc_start: 0.8950 (tt) cc_final: 0.8739 (tt) REVERT: X 163 PHE cc_start: 0.7920 (p90) cc_final: 0.7596 (p90) REVERT: X 226 ARG cc_start: 0.7879 (tpt170) cc_final: 0.7596 (tpt170) REVERT: Y 91 ARG cc_start: 0.7962 (ttp-170) cc_final: 0.7363 (ttp-170) REVERT: Y 146 ILE cc_start: 0.8409 (tp) cc_final: 0.8143 (tp) REVERT: Y 226 ASP cc_start: 0.8178 (m-30) cc_final: 0.7943 (m-30) REVERT: Y 230 ARG cc_start: 0.7467 (mtt90) cc_final: 0.6850 (mtt180) REVERT: Y 262 THR cc_start: 0.8166 (m) cc_final: 0.7623 (m) REVERT: Z 52 ASP cc_start: 0.8510 (t0) cc_final: 0.8186 (p0) REVERT: Z 91 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7389 (mt-10) REVERT: Z 101 ASN cc_start: 0.7953 (m110) cc_final: 0.7580 (m-40) REVERT: Z 183 MET cc_start: 0.8201 (mtt) cc_final: 0.7671 (mtt) REVERT: 1 75 PHE cc_start: 0.7095 (t80) cc_final: 0.6870 (t80) REVERT: 1 90 ASP cc_start: 0.7855 (m-30) cc_final: 0.7574 (m-30) REVERT: 1 103 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7274 (tm-30) REVERT: 1 123 ARG cc_start: 0.7338 (ptp90) cc_final: 0.6486 (ptp90) REVERT: 1 163 PHE cc_start: 0.8102 (p90) cc_final: 0.7315 (p90) REVERT: 2 118 SER cc_start: 0.8579 (t) cc_final: 0.8358 (t) REVERT: 2 135 CYS cc_start: 0.6370 (p) cc_final: 0.5946 (p) REVERT: 2 234 HIS cc_start: 0.7947 (m-70) cc_final: 0.7719 (m-70) outliers start: 2 outliers final: 1 residues processed: 2038 average time/residue: 0.6612 time to fit residues: 2289.0812 Evaluate side-chains 1640 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1639 time to evaluate : 6.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 529 optimal weight: 4.9990 chunk 341 optimal weight: 2.9990 chunk 511 optimal weight: 6.9990 chunk 257 optimal weight: 0.7980 chunk 168 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 544 optimal weight: 3.9990 chunk 583 optimal weight: 5.9990 chunk 423 optimal weight: 0.1980 chunk 79 optimal weight: 0.9990 chunk 672 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN I 50 ASN J 171 HIS ** J 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 HIS ** M 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN N 138 GLN Q 27 ASN ** Q 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 233 ASN a 153 GLN ** a 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 129 ASN ** P 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 154 HIS ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 HIS ** b 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 111 HIS ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 171 GLN f 24 GLN ** f 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 84 ASN ** j 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 169 GLN ** l 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 55 GLN l 63 ASN l 99 HIS m 107 ASN ** m 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 91 ASN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 117 HIS 1 124 GLN 2 104 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 moved from start: 0.8100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 72937 Z= 0.260 Angle : 0.682 11.795 98542 Z= 0.358 Chirality : 0.045 0.212 11127 Planarity : 0.005 0.063 12692 Dihedral : 4.708 36.604 9923 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.13 % Rotamer: Outliers : 0.03 % Allowed : 1.09 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.09), residues: 8996 helix: 1.04 (0.08), residues: 4378 sheet: 0.15 (0.13), residues: 1438 loop : -0.59 (0.11), residues: 3180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP 2 127 HIS 0.018 0.001 HIS l 132 PHE 0.048 0.002 PHE N 170 TYR 0.032 0.002 TYR D 110 ARG 0.013 0.001 ARG W 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2015 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2013 time to evaluate : 6.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.9071 (tt) cc_final: 0.8561 (tt) REVERT: A 192 GLU cc_start: 0.7162 (pp20) cc_final: 0.6556 (tt0) REVERT: B 60 ARG cc_start: 0.6631 (ptm-80) cc_final: 0.5958 (ptm-80) REVERT: B 83 TYR cc_start: 0.7069 (t80) cc_final: 0.6544 (t80) REVERT: B 203 MET cc_start: 0.6344 (ppp) cc_final: 0.5938 (ppp) REVERT: C 155 ASN cc_start: 0.8722 (t0) cc_final: 0.8300 (t0) REVERT: C 201 MET cc_start: 0.6311 (mmm) cc_final: 0.5776 (mmm) REVERT: D 84 ILE cc_start: 0.8856 (mt) cc_final: 0.8497 (mt) REVERT: D 115 LYS cc_start: 0.9125 (mtpt) cc_final: 0.8800 (mtpt) REVERT: D 129 ILE cc_start: 0.8628 (pt) cc_final: 0.8397 (pt) REVERT: D 130 SER cc_start: 0.8970 (m) cc_final: 0.8691 (m) REVERT: E 113 THR cc_start: 0.8243 (p) cc_final: 0.7992 (p) REVERT: F 87 PHE cc_start: 0.6919 (t80) cc_final: 0.6218 (t80) REVERT: F 114 SER cc_start: 0.8919 (m) cc_final: 0.8618 (p) REVERT: F 115 LYS cc_start: 0.9080 (tppt) cc_final: 0.8611 (tttt) REVERT: G 94 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7512 (tm-30) REVERT: H 107 VAL cc_start: 0.8213 (t) cc_final: 0.7955 (t) REVERT: H 125 ILE cc_start: 0.5975 (mm) cc_final: 0.5544 (mm) REVERT: I 206 GLU cc_start: 0.7664 (pt0) cc_final: 0.7121 (pt0) REVERT: I 238 LYS cc_start: 0.5361 (tttt) cc_final: 0.4892 (pttt) REVERT: K 97 ASN cc_start: 0.2374 (t0) cc_final: 0.1816 (p0) REVERT: K 228 VAL cc_start: 0.7606 (m) cc_final: 0.7190 (t) REVERT: L 134 TRP cc_start: 0.6428 (t60) cc_final: 0.6073 (t60) REVERT: N 3 MET cc_start: 0.2320 (mtm) cc_final: 0.1402 (ptm) REVERT: N 212 ILE cc_start: 0.5489 (mm) cc_final: 0.4944 (mm) REVERT: O 210 ARG cc_start: 0.3233 (ppt170) cc_final: 0.2614 (ttt180) REVERT: Q 154 GLU cc_start: 0.7039 (mp0) cc_final: 0.6266 (mm-30) REVERT: Q 160 MET cc_start: 0.4417 (mmt) cc_final: 0.3998 (mmp) REVERT: Q 247 MET cc_start: 0.1133 (mpp) cc_final: 0.0469 (mtt) REVERT: a 191 GLN cc_start: 0.4734 (mp10) cc_final: 0.4429 (mp10) REVERT: c 203 ARG cc_start: 0.3879 (tpt90) cc_final: 0.0743 (mmp80) REVERT: c 224 LEU cc_start: 0.6879 (tp) cc_final: 0.6679 (tp) REVERT: i 1 MET cc_start: 0.3599 (ptt) cc_final: 0.2004 (mtm) REVERT: i 210 ARG cc_start: 0.4573 (mmt-90) cc_final: 0.3429 (mmt-90) REVERT: i 213 ARG cc_start: 0.4766 (pmt-80) cc_final: 0.3966 (ttm170) REVERT: P 208 LEU cc_start: 0.7590 (mm) cc_final: 0.7343 (mm) REVERT: R 21 LEU cc_start: 0.8517 (mm) cc_final: 0.7989 (mm) REVERT: R 107 MET cc_start: 0.7892 (pmm) cc_final: 0.7686 (pmm) REVERT: R 175 GLU cc_start: 0.7050 (pp20) cc_final: 0.6543 (pp20) REVERT: b 26 MET cc_start: 0.8294 (mmm) cc_final: 0.7734 (tpp) REVERT: b 87 PHE cc_start: 0.7451 (t80) cc_final: 0.6658 (t80) REVERT: b 88 MET cc_start: 0.8125 (mtp) cc_final: 0.7846 (mtp) REVERT: b 91 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7552 (mm-30) REVERT: b 92 CYS cc_start: 0.8746 (p) cc_final: 0.8314 (p) REVERT: b 232 PHE cc_start: 0.5426 (m-10) cc_final: 0.4931 (m-80) REVERT: d 69 ASN cc_start: 0.8208 (t0) cc_final: 0.7554 (p0) REVERT: d 82 LEU cc_start: 0.8851 (mm) cc_final: 0.8358 (pt) REVERT: d 164 CYS cc_start: 0.6930 (t) cc_final: 0.6405 (t) REVERT: d 222 ASN cc_start: 0.7791 (t0) cc_final: 0.7147 (t0) REVERT: f 123 GLN cc_start: 0.9345 (tp40) cc_final: 0.8666 (tm-30) REVERT: j 69 ASN cc_start: 0.8730 (p0) cc_final: 0.8420 (p0) REVERT: j 72 MET cc_start: 0.7783 (tmm) cc_final: 0.7473 (ttp) REVERT: j 82 ASP cc_start: 0.7288 (p0) cc_final: 0.6936 (p0) REVERT: k 27 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.7801 (ttm-80) REVERT: k 145 GLN cc_start: 0.8146 (mt0) cc_final: 0.7922 (mt0) REVERT: k 150 CYS cc_start: 0.6849 (t) cc_final: 0.6532 (t) REVERT: l 115 LEU cc_start: 0.9160 (mt) cc_final: 0.8954 (mm) REVERT: l 172 ILE cc_start: 0.5389 (mt) cc_final: 0.5082 (mm) REVERT: n 67 ILE cc_start: 0.7981 (mt) cc_final: 0.7766 (mt) REVERT: n 102 TYR cc_start: 0.7727 (t80) cc_final: 0.7482 (t80) REVERT: n 142 TYR cc_start: 0.7762 (t80) cc_final: 0.7443 (t80) REVERT: n 155 MET cc_start: 0.6341 (mtm) cc_final: 0.5889 (mtm) REVERT: n 173 LEU cc_start: 0.8852 (mt) cc_final: 0.7676 (mt) REVERT: S 4 MET cc_start: 0.7654 (mmp) cc_final: 0.7314 (mmp) REVERT: S 27 ARG cc_start: 0.8133 (tmt170) cc_final: 0.7559 (tmt170) REVERT: S 42 ILE cc_start: 0.9338 (mp) cc_final: 0.9070 (mm) REVERT: S 65 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8019 (tm-30) REVERT: S 76 LEU cc_start: 0.8757 (mm) cc_final: 0.8530 (mm) REVERT: S 97 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8055 (tm-30) REVERT: S 142 CYS cc_start: 0.7441 (p) cc_final: 0.7027 (p) REVERT: S 164 PHE cc_start: 0.8020 (t80) cc_final: 0.7301 (t80) REVERT: T 8 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7806 (tm-30) REVERT: T 27 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8147 (tm-30) REVERT: T 63 ASN cc_start: 0.8882 (m-40) cc_final: 0.8506 (m110) REVERT: T 65 GLN cc_start: 0.8932 (tp-100) cc_final: 0.8364 (tp-100) REVERT: T 87 ASN cc_start: 0.8491 (m-40) cc_final: 0.8090 (m-40) REVERT: T 145 ARG cc_start: 0.7726 (tpm170) cc_final: 0.7037 (tpm170) REVERT: T 153 ARG cc_start: 0.7509 (ptp90) cc_final: 0.7213 (ptp90) REVERT: U 41 LEU cc_start: 0.8676 (mt) cc_final: 0.8316 (tt) REVERT: U 225 ILE cc_start: 0.8480 (mp) cc_final: 0.7975 (mt) REVERT: V 81 PHE cc_start: 0.8139 (m-10) cc_final: 0.7819 (m-10) REVERT: V 114 GLN cc_start: 0.7875 (tp40) cc_final: 0.7511 (tp-100) REVERT: V 139 ARG cc_start: 0.7927 (tpt170) cc_final: 0.7457 (tpp-160) REVERT: V 177 TYR cc_start: 0.8070 (p90) cc_final: 0.7646 (p90) REVERT: V 225 ASP cc_start: 0.8152 (t0) cc_final: 0.7909 (t0) REVERT: V 252 THR cc_start: 0.4949 (p) cc_final: 0.4686 (p) REVERT: W 52 ASP cc_start: 0.8480 (t0) cc_final: 0.7423 (p0) REVERT: W 63 CYS cc_start: 0.8402 (t) cc_final: 0.8140 (t) REVERT: W 119 MET cc_start: 0.8064 (ttm) cc_final: 0.7848 (tpp) REVERT: W 123 TRP cc_start: 0.7017 (t60) cc_final: 0.6673 (t60) REVERT: W 216 PHE cc_start: 0.6693 (m-10) cc_final: 0.6432 (m-10) REVERT: X 96 ARG cc_start: 0.7524 (tpp-160) cc_final: 0.7129 (tpp-160) REVERT: X 138 ILE cc_start: 0.9061 (tt) cc_final: 0.8825 (tt) REVERT: X 205 ASP cc_start: 0.8742 (t70) cc_final: 0.8254 (t0) REVERT: Y 127 TRP cc_start: 0.7383 (m100) cc_final: 0.7117 (m100) REVERT: Y 131 LEU cc_start: 0.9162 (mt) cc_final: 0.8721 (mt) REVERT: Y 232 ILE cc_start: 0.9048 (mm) cc_final: 0.8815 (mm) REVERT: Y 234 HIS cc_start: 0.7963 (m170) cc_final: 0.7542 (m-70) REVERT: Y 239 ASP cc_start: 0.8081 (t70) cc_final: 0.7800 (t70) REVERT: Y 262 THR cc_start: 0.8225 (m) cc_final: 0.7561 (m) REVERT: Z 52 ASP cc_start: 0.8543 (t0) cc_final: 0.8199 (p0) REVERT: Z 58 HIS cc_start: 0.6018 (t70) cc_final: 0.5639 (t70) REVERT: Z 183 MET cc_start: 0.8151 (mtt) cc_final: 0.7811 (mtt) REVERT: 1 75 PHE cc_start: 0.7271 (t80) cc_final: 0.6978 (t80) REVERT: 1 90 ASP cc_start: 0.8042 (m-30) cc_final: 0.7754 (m-30) REVERT: 1 92 GLU cc_start: 0.7810 (pp20) cc_final: 0.7120 (pp20) REVERT: 1 103 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7308 (tm-30) REVERT: 1 123 ARG cc_start: 0.7959 (ptp90) cc_final: 0.7390 (ptp90) REVERT: 1 163 PHE cc_start: 0.8445 (p90) cc_final: 0.7183 (p90) REVERT: 1 196 GLU cc_start: 0.8239 (tt0) cc_final: 0.7932 (tt0) REVERT: 1 213 ASP cc_start: 0.8143 (t70) cc_final: 0.7885 (t0) REVERT: 2 159 MET cc_start: 0.7984 (tpp) cc_final: 0.7034 (tpp) outliers start: 2 outliers final: 0 residues processed: 2014 average time/residue: 0.6903 time to fit residues: 2367.9118 Evaluate side-chains 1565 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1565 time to evaluate : 6.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 778 optimal weight: 0.9990 chunk 819 optimal weight: 1.9990 chunk 748 optimal weight: 1.9990 chunk 797 optimal weight: 0.4980 chunk 480 optimal weight: 2.9990 chunk 347 optimal weight: 0.6980 chunk 626 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 chunk 720 optimal weight: 1.9990 chunk 754 optimal weight: 0.9990 chunk 794 optimal weight: 0.0050 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 HIS ** J 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 127 HIS L 193 HIS ** M 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 138 GLN ** Q 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 153 GLN a 191 GLN ** e 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 129 ASN ** P 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 155 HIS b 16 GLN ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 55 GLN l 61 GLN l 63 ASN l 87 ASN l 99 HIS m 107 ASN ** m 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 91 ASN ** n 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 188 HIS ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 ASN ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 91 ASN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 117 HIS ** Z 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 96 ASN 2 104 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.8330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 72937 Z= 0.195 Angle : 0.655 11.821 98542 Z= 0.340 Chirality : 0.045 0.297 11127 Planarity : 0.004 0.114 12692 Dihedral : 4.618 36.794 9923 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.45 % Favored : 97.52 % Rotamer: Outliers : 0.01 % Allowed : 0.65 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.09), residues: 8996 helix: 1.15 (0.08), residues: 4365 sheet: 0.13 (0.13), residues: 1422 loop : -0.54 (0.11), residues: 3209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 139 HIS 0.032 0.001 HIS F 175 PHE 0.061 0.002 PHE L 170 TYR 0.046 0.002 TYR 2 126 ARG 0.013 0.001 ARG W 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2027 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2026 time to evaluate : 6.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.9034 (tt) cc_final: 0.8309 (tt) REVERT: A 192 GLU cc_start: 0.7137 (pp20) cc_final: 0.6654 (tt0) REVERT: B 60 ARG cc_start: 0.6481 (ptm-80) cc_final: 0.5788 (ptm-80) REVERT: B 83 TYR cc_start: 0.7002 (t80) cc_final: 0.6603 (t80) REVERT: B 203 MET cc_start: 0.6072 (ppp) cc_final: 0.5168 (mpp) REVERT: C 20 GLN cc_start: 0.9030 (mp10) cc_final: 0.8648 (mp10) REVERT: C 49 ARG cc_start: 0.8144 (mmm-85) cc_final: 0.7389 (mmm-85) REVERT: C 96 ARG cc_start: 0.7648 (mtm110) cc_final: 0.7191 (ttp80) REVERT: C 155 ASN cc_start: 0.8568 (t0) cc_final: 0.8306 (t0) REVERT: C 201 MET cc_start: 0.6230 (mmm) cc_final: 0.5722 (mmm) REVERT: D 115 LYS cc_start: 0.9086 (mtpt) cc_final: 0.8801 (mtpt) REVERT: D 130 SER cc_start: 0.8921 (m) cc_final: 0.8598 (m) REVERT: E 181 LEU cc_start: 0.8001 (pp) cc_final: 0.6986 (tt) REVERT: F 26 MET cc_start: 0.7666 (mmm) cc_final: 0.7451 (mmp) REVERT: F 87 PHE cc_start: 0.7003 (t80) cc_final: 0.6055 (t80) REVERT: F 93 LEU cc_start: 0.8076 (tt) cc_final: 0.7848 (tt) REVERT: F 114 SER cc_start: 0.8870 (m) cc_final: 0.8605 (p) REVERT: F 115 LYS cc_start: 0.9118 (tppt) cc_final: 0.8593 (tttt) REVERT: G 67 LEU cc_start: 0.7999 (mm) cc_final: 0.7310 (pt) REVERT: G 94 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7490 (tm-30) REVERT: H 107 VAL cc_start: 0.8193 (t) cc_final: 0.7981 (t) REVERT: H 125 ILE cc_start: 0.5753 (mm) cc_final: 0.5543 (mm) REVERT: I 206 GLU cc_start: 0.7572 (pt0) cc_final: 0.7087 (pt0) REVERT: I 238 LYS cc_start: 0.5541 (tttt) cc_final: 0.5007 (pttt) REVERT: J 209 TYR cc_start: 0.3696 (t80) cc_final: 0.3465 (t80) REVERT: K 57 LEU cc_start: 0.4886 (tt) cc_final: 0.4410 (tt) REVERT: K 97 ASN cc_start: 0.2154 (t0) cc_final: 0.1789 (p0) REVERT: K 228 VAL cc_start: 0.7630 (m) cc_final: 0.7295 (t) REVERT: L 134 TRP cc_start: 0.6344 (t60) cc_final: 0.5990 (t60) REVERT: M 131 LYS cc_start: 0.7114 (tmtt) cc_final: 0.5417 (mmtp) REVERT: N 3 MET cc_start: 0.2121 (mtm) cc_final: 0.1336 (ptm) REVERT: O 210 ARG cc_start: 0.3407 (ppt170) cc_final: 0.2846 (ttt180) REVERT: Q 154 GLU cc_start: 0.6544 (mp0) cc_final: 0.6116 (mm-30) REVERT: Q 160 MET cc_start: 0.4425 (mmt) cc_final: 0.4061 (mmp) REVERT: Q 203 GLU cc_start: 0.5822 (mm-30) cc_final: 0.5231 (mm-30) REVERT: Q 218 GLU cc_start: 0.5335 (tm-30) cc_final: 0.4721 (mm-30) REVERT: Q 247 MET cc_start: 0.1388 (mpp) cc_final: 0.0699 (mtt) REVERT: a 122 LYS cc_start: 0.6570 (mmmt) cc_final: 0.6268 (mmmm) REVERT: a 191 GLN cc_start: 0.4685 (mp-120) cc_final: 0.4482 (mp10) REVERT: a 213 ARG cc_start: 0.4070 (ttt90) cc_final: 0.3205 (ttp80) REVERT: c 203 ARG cc_start: 0.3712 (tpt90) cc_final: 0.0525 (mmp80) REVERT: c 224 LEU cc_start: 0.6721 (tp) cc_final: 0.6489 (tp) REVERT: g 39 LYS cc_start: 0.1187 (mmpt) cc_final: 0.0485 (mmpt) REVERT: i 1 MET cc_start: 0.3871 (ptt) cc_final: 0.2246 (mtm) REVERT: i 210 ARG cc_start: 0.4700 (mmt-90) cc_final: 0.3663 (mmt-90) REVERT: i 213 ARG cc_start: 0.4687 (pmt-80) cc_final: 0.3952 (ttm170) REVERT: P 116 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7934 (tm-30) REVERT: P 208 LEU cc_start: 0.7440 (mm) cc_final: 0.7231 (mm) REVERT: R 21 LEU cc_start: 0.8299 (mm) cc_final: 0.8084 (mm) REVERT: R 175 GLU cc_start: 0.6929 (pp20) cc_final: 0.6437 (pp20) REVERT: b 26 MET cc_start: 0.8208 (mmm) cc_final: 0.7536 (tpp) REVERT: b 87 PHE cc_start: 0.7568 (t80) cc_final: 0.6855 (t80) REVERT: b 88 MET cc_start: 0.8093 (mtp) cc_final: 0.7665 (mtp) REVERT: b 91 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7342 (mm-30) REVERT: b 92 CYS cc_start: 0.8746 (p) cc_final: 0.8334 (p) REVERT: b 160 SER cc_start: 0.7914 (t) cc_final: 0.7611 (t) REVERT: b 232 PHE cc_start: 0.5403 (m-10) cc_final: 0.4876 (m-80) REVERT: d 69 ASN cc_start: 0.8171 (t0) cc_final: 0.7664 (p0) REVERT: d 82 LEU cc_start: 0.8840 (mm) cc_final: 0.8168 (pt) REVERT: d 151 MET cc_start: 0.8906 (tmm) cc_final: 0.8651 (tmm) REVERT: d 164 CYS cc_start: 0.6722 (t) cc_final: 0.6190 (t) REVERT: d 222 ASN cc_start: 0.7949 (t0) cc_final: 0.7485 (t0) REVERT: f 123 GLN cc_start: 0.9255 (tp40) cc_final: 0.8639 (tm-30) REVERT: h 196 LYS cc_start: 0.7600 (pttm) cc_final: 0.7346 (tptt) REVERT: j 82 ASP cc_start: 0.7348 (p0) cc_final: 0.6740 (p0) REVERT: j 115 CYS cc_start: 0.7357 (m) cc_final: 0.7148 (m) REVERT: k 7 ASN cc_start: 0.7667 (m110) cc_final: 0.6771 (t0) REVERT: k 12 MET cc_start: 0.7275 (mmt) cc_final: 0.6517 (tpp) REVERT: k 27 ARG cc_start: 0.8424 (ttm-80) cc_final: 0.7656 (ttm-80) REVERT: k 88 MET cc_start: 0.6413 (mtt) cc_final: 0.6189 (tmm) REVERT: k 103 TYR cc_start: 0.7400 (m-80) cc_final: 0.6957 (m-10) REVERT: k 173 ASN cc_start: 0.7548 (m110) cc_final: 0.7258 (m110) REVERT: l 12 TYR cc_start: 0.8012 (p90) cc_final: 0.7554 (p90) REVERT: n 152 TRP cc_start: 0.7093 (m100) cc_final: 0.6842 (m100) REVERT: n 155 MET cc_start: 0.6148 (mtm) cc_final: 0.5671 (mtm) REVERT: n 173 LEU cc_start: 0.8789 (mt) cc_final: 0.7508 (mt) REVERT: n 225 ASP cc_start: 0.7997 (t0) cc_final: 0.7706 (t0) REVERT: S 27 ARG cc_start: 0.8200 (tmt170) cc_final: 0.7637 (ttm-80) REVERT: S 91 VAL cc_start: 0.9078 (t) cc_final: 0.8632 (p) REVERT: S 97 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8007 (tm-30) REVERT: S 142 CYS cc_start: 0.7127 (p) cc_final: 0.6379 (p) REVERT: S 173 ASN cc_start: 0.8420 (m-40) cc_final: 0.7863 (m-40) REVERT: S 175 VAL cc_start: 0.8587 (t) cc_final: 0.8328 (t) REVERT: S 178 ASP cc_start: 0.8866 (t70) cc_final: 0.8626 (t0) REVERT: S 181 SER cc_start: 0.9015 (t) cc_final: 0.8551 (t) REVERT: T 63 ASN cc_start: 0.8836 (m-40) cc_final: 0.8452 (m110) REVERT: T 65 GLN cc_start: 0.8855 (tp-100) cc_final: 0.8121 (tp-100) REVERT: T 87 ASN cc_start: 0.8496 (m-40) cc_final: 0.8144 (m-40) REVERT: T 153 ARG cc_start: 0.7364 (ptp90) cc_final: 0.7109 (ptp90) REVERT: U 41 LEU cc_start: 0.8690 (mt) cc_final: 0.8377 (tt) REVERT: U 56 ARG cc_start: 0.8122 (ttm-80) cc_final: 0.7496 (ttm110) REVERT: U 225 ILE cc_start: 0.8509 (mp) cc_final: 0.8045 (mt) REVERT: V 81 PHE cc_start: 0.7959 (m-10) cc_final: 0.7658 (m-10) REVERT: V 114 GLN cc_start: 0.7768 (tp40) cc_final: 0.7263 (tp40) REVERT: V 139 ARG cc_start: 0.7878 (tpt170) cc_final: 0.7439 (tpp-160) REVERT: V 177 TYR cc_start: 0.7912 (p90) cc_final: 0.7491 (p90) REVERT: V 211 ARG cc_start: 0.7953 (mtm-85) cc_final: 0.7734 (ttp-110) REVERT: V 225 ASP cc_start: 0.8111 (t0) cc_final: 0.7833 (t0) REVERT: W 52 ASP cc_start: 0.8509 (t0) cc_final: 0.7356 (p0) REVERT: W 63 CYS cc_start: 0.8437 (t) cc_final: 0.8197 (t) REVERT: X 95 THR cc_start: 0.9157 (p) cc_final: 0.8902 (t) REVERT: X 96 ARG cc_start: 0.7496 (tpp-160) cc_final: 0.6988 (tpp-160) REVERT: X 138 ILE cc_start: 0.9029 (tt) cc_final: 0.8802 (tt) REVERT: X 160 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7610 (tpt-90) REVERT: X 193 LEU cc_start: 0.8602 (tp) cc_final: 0.8398 (tp) REVERT: X 205 ASP cc_start: 0.8703 (t70) cc_final: 0.8177 (t0) REVERT: Y 91 ARG cc_start: 0.7933 (ttp-170) cc_final: 0.7454 (ttp-170) REVERT: Y 146 ILE cc_start: 0.8638 (tp) cc_final: 0.8399 (tp) REVERT: Y 153 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8522 (mttt) REVERT: Z 52 ASP cc_start: 0.8514 (t0) cc_final: 0.8005 (p0) REVERT: Z 58 HIS cc_start: 0.5837 (t70) cc_final: 0.5556 (t70) REVERT: Z 183 MET cc_start: 0.8127 (mtt) cc_final: 0.7762 (mmm) REVERT: 1 92 GLU cc_start: 0.7670 (pp20) cc_final: 0.7032 (pp20) REVERT: 1 120 ARG cc_start: 0.6831 (mtp-110) cc_final: 0.6302 (ttp80) REVERT: 1 123 ARG cc_start: 0.7651 (ptt-90) cc_final: 0.6985 (ptt-90) REVERT: 1 163 PHE cc_start: 0.8350 (p90) cc_final: 0.7196 (p90) REVERT: 1 196 GLU cc_start: 0.8157 (tt0) cc_final: 0.7870 (tt0) REVERT: 1 213 ASP cc_start: 0.8203 (t70) cc_final: 0.7866 (t0) REVERT: 2 144 GLU cc_start: 0.8149 (pp20) cc_final: 0.6891 (tt0) REVERT: 2 153 LYS cc_start: 0.9065 (mmmt) cc_final: 0.7656 (mmmt) REVERT: 2 234 HIS cc_start: 0.8113 (m-70) cc_final: 0.7885 (m-70) outliers start: 1 outliers final: 0 residues processed: 2027 average time/residue: 0.6561 time to fit residues: 2258.9612 Evaluate side-chains 1594 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1594 time to evaluate : 6.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 523 optimal weight: 0.5980 chunk 843 optimal weight: 2.9990 chunk 514 optimal weight: 0.0770 chunk 400 optimal weight: 4.9990 chunk 586 optimal weight: 3.9990 chunk 884 optimal weight: 2.9990 chunk 814 optimal weight: 5.9990 chunk 704 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 544 optimal weight: 1.9990 chunk 431 optimal weight: 0.7980 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN F 53 GLN ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 153 GLN I 193 HIS J 171 HIS ** J 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 127 HIS ** M 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 153 GLN a 193 HIS ** e 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 129 ASN ** P 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 HIS ** b 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 111 HIS ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 55 GLN l 61 GLN l 63 ASN l 99 HIS ** l 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 107 ASN m 180 GLN ** n 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 91 ASN ** n 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 ASN ** S 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 188 HIS ** T 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 91 ASN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 117 HIS ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 184 ASN ** Z 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 101 ASN 2 104 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.8709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 72937 Z= 0.241 Angle : 0.687 11.838 98542 Z= 0.358 Chirality : 0.045 0.256 11127 Planarity : 0.005 0.064 12692 Dihedral : 4.705 38.401 9923 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.02 % Rotamer: Outliers : 0.04 % Allowed : 0.26 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.09), residues: 8996 helix: 1.00 (0.08), residues: 4374 sheet: 0.07 (0.13), residues: 1418 loop : -0.61 (0.11), residues: 3204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 139 HIS 0.015 0.001 HIS F 175 PHE 0.067 0.002 PHE N 170 TYR 0.038 0.002 TYR 2 126 ARG 0.016 0.001 ARG X 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17992 Ramachandran restraints generated. 8996 Oldfield, 0 Emsley, 8996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1931 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1928 time to evaluate : 6.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TRP cc_start: 0.8242 (t-100) cc_final: 0.7888 (t-100) REVERT: A 109 ILE cc_start: 0.8746 (tt) cc_final: 0.8492 (tt) REVERT: A 192 GLU cc_start: 0.7223 (pp20) cc_final: 0.6697 (tt0) REVERT: B 60 ARG cc_start: 0.6432 (ptm-80) cc_final: 0.5849 (ptm-80) REVERT: B 109 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7828 (mt0) REVERT: B 112 GLN cc_start: 0.7980 (mt0) cc_final: 0.7771 (mt0) REVERT: C 1 MET cc_start: 0.4424 (ttm) cc_final: 0.3270 (mtm) REVERT: C 68 LEU cc_start: 0.7975 (mt) cc_final: 0.7218 (mt) REVERT: C 82 ASP cc_start: 0.5443 (t0) cc_final: 0.5227 (t0) REVERT: C 92 LEU cc_start: 0.9216 (mt) cc_final: 0.8863 (mt) REVERT: C 95 GLN cc_start: 0.8564 (tp40) cc_final: 0.8070 (mm-40) REVERT: C 155 ASN cc_start: 0.8718 (t0) cc_final: 0.8145 (m-40) REVERT: C 201 MET cc_start: 0.6333 (mmm) cc_final: 0.5859 (mmm) REVERT: D 77 THR cc_start: 0.8354 (p) cc_final: 0.8093 (p) REVERT: D 115 LYS cc_start: 0.9081 (mtpt) cc_final: 0.8810 (mtpt) REVERT: E 157 ASP cc_start: 0.7657 (p0) cc_final: 0.7438 (p0) REVERT: E 189 MET cc_start: 0.4631 (mmm) cc_final: 0.4260 (mmm) REVERT: F 26 MET cc_start: 0.7673 (mmm) cc_final: 0.7451 (mmp) REVERT: F 87 PHE cc_start: 0.7077 (t80) cc_final: 0.6254 (t80) REVERT: F 114 SER cc_start: 0.8811 (m) cc_final: 0.8596 (p) REVERT: F 115 LYS cc_start: 0.9168 (tppt) cc_final: 0.8663 (tttt) REVERT: F 137 TYR cc_start: 0.7797 (t80) cc_final: 0.7168 (t80) REVERT: F 180 MET cc_start: 0.6842 (pmm) cc_final: 0.5717 (pmm) REVERT: G 67 LEU cc_start: 0.7882 (mm) cc_final: 0.7553 (pt) REVERT: H 107 VAL cc_start: 0.8184 (t) cc_final: 0.7949 (t) REVERT: H 125 ILE cc_start: 0.5984 (mm) cc_final: 0.5738 (mm) REVERT: I 206 GLU cc_start: 0.7636 (pt0) cc_final: 0.7083 (pt0) REVERT: I 238 LYS cc_start: 0.5674 (tttt) cc_final: 0.5230 (pttt) REVERT: K 57 LEU cc_start: 0.4909 (tt) cc_final: 0.4486 (tt) REVERT: K 97 ASN cc_start: 0.2488 (t0) cc_final: 0.2079 (p0) REVERT: K 228 VAL cc_start: 0.7765 (m) cc_final: 0.7353 (t) REVERT: N 3 MET cc_start: 0.2316 (mtm) cc_final: 0.1773 (ptm) REVERT: O 210 ARG cc_start: 0.3677 (ppt170) cc_final: 0.2955 (ttt-90) REVERT: Q 154 GLU cc_start: 0.6213 (mp0) cc_final: 0.5975 (mm-30) REVERT: Q 160 MET cc_start: 0.4435 (mmt) cc_final: 0.4119 (mmp) REVERT: Q 247 MET cc_start: 0.1269 (mpp) cc_final: 0.0790 (mtt) REVERT: a 122 LYS cc_start: 0.6789 (mmmt) cc_final: 0.6345 (mmmm) REVERT: i 210 ARG cc_start: 0.4510 (mmt-90) cc_final: 0.4281 (mmt-90) REVERT: P 116 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7789 (tm-30) REVERT: R 21 LEU cc_start: 0.8288 (mm) cc_final: 0.8060 (mm) REVERT: R 175 GLU cc_start: 0.6936 (pp20) cc_final: 0.6489 (pp20) REVERT: b 19 ILE cc_start: 0.8826 (mm) cc_final: 0.8426 (mm) REVERT: b 26 MET cc_start: 0.8215 (mmm) cc_final: 0.7536 (tpp) REVERT: b 87 PHE cc_start: 0.7647 (t80) cc_final: 0.6883 (t80) REVERT: b 88 MET cc_start: 0.8042 (mtp) cc_final: 0.7729 (mtp) REVERT: b 91 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7475 (mm-30) REVERT: b 92 CYS cc_start: 0.8732 (p) cc_final: 0.8346 (p) REVERT: b 117 GLN cc_start: 0.8363 (tp40) cc_final: 0.7811 (tp40) REVERT: b 232 PHE cc_start: 0.5698 (m-10) cc_final: 0.5491 (m-80) REVERT: d 69 ASN cc_start: 0.8364 (t0) cc_final: 0.7830 (p0) REVERT: d 82 LEU cc_start: 0.8762 (mm) cc_final: 0.8241 (pt) REVERT: d 164 CYS cc_start: 0.6815 (t) cc_final: 0.6543 (t) REVERT: d 222 ASN cc_start: 0.7813 (t0) cc_final: 0.7390 (t0) REVERT: f 88 ARG cc_start: 0.7916 (mtt180) cc_final: 0.7442 (mtt90) REVERT: f 123 GLN cc_start: 0.9122 (tp40) cc_final: 0.8720 (tm-30) REVERT: j 82 ASP cc_start: 0.7295 (p0) cc_final: 0.6928 (p0) REVERT: j 115 CYS cc_start: 0.7408 (m) cc_final: 0.7195 (m) REVERT: k 103 TYR cc_start: 0.7551 (m-80) cc_final: 0.6918 (m-10) REVERT: l 12 TYR cc_start: 0.8030 (p90) cc_final: 0.7574 (p90) REVERT: l 68 LYS cc_start: 0.8227 (pttm) cc_final: 0.7865 (tttm) REVERT: m 200 MET cc_start: 0.7951 (tpp) cc_final: 0.7704 (tpt) REVERT: n 67 ILE cc_start: 0.7901 (mt) cc_final: 0.7644 (mt) REVERT: n 102 TYR cc_start: 0.7328 (t80) cc_final: 0.6916 (t80) REVERT: n 152 TRP cc_start: 0.7190 (m100) cc_final: 0.6930 (m100) REVERT: n 155 MET cc_start: 0.6200 (mtm) cc_final: 0.5865 (mtm) REVERT: n 173 LEU cc_start: 0.8774 (mt) cc_final: 0.7468 (mt) REVERT: n 225 ASP cc_start: 0.7839 (t0) cc_final: 0.7383 (t0) REVERT: S 27 ARG cc_start: 0.8133 (tmt170) cc_final: 0.7825 (tmt170) REVERT: S 75 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7456 (tp30) REVERT: S 91 VAL cc_start: 0.9065 (t) cc_final: 0.8695 (p) REVERT: S 142 CYS cc_start: 0.7033 (p) cc_final: 0.6479 (p) REVERT: T 62 LYS cc_start: 0.9115 (ttmm) cc_final: 0.8865 (tptp) REVERT: T 63 ASN cc_start: 0.8967 (m-40) cc_final: 0.8548 (m110) REVERT: T 65 GLN cc_start: 0.8853 (tp-100) cc_final: 0.8112 (tp-100) REVERT: T 87 ASN cc_start: 0.8573 (m-40) cc_final: 0.8122 (m-40) REVERT: T 153 ARG cc_start: 0.7353 (ptp90) cc_final: 0.7079 (ptp90) REVERT: U 41 LEU cc_start: 0.8727 (mt) cc_final: 0.8441 (tt) REVERT: U 56 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.7545 (ttm110) REVERT: U 225 ILE cc_start: 0.8600 (mp) cc_final: 0.8105 (mt) REVERT: V 88 MET cc_start: 0.6264 (tmm) cc_final: 0.5714 (tmm) REVERT: V 114 GLN cc_start: 0.7820 (tp40) cc_final: 0.7488 (tp-100) REVERT: V 139 ARG cc_start: 0.7883 (tpt170) cc_final: 0.7613 (tpp-160) REVERT: V 177 TYR cc_start: 0.7948 (p90) cc_final: 0.7503 (p90) REVERT: V 252 THR cc_start: 0.5270 (p) cc_final: 0.4924 (p) REVERT: W 52 ASP cc_start: 0.8489 (t0) cc_final: 0.7435 (p0) REVERT: W 63 CYS cc_start: 0.8451 (t) cc_final: 0.8163 (t) REVERT: W 169 GLU cc_start: 0.6881 (tp30) cc_final: 0.6315 (tp30) REVERT: X 95 THR cc_start: 0.9202 (p) cc_final: 0.8904 (t) REVERT: X 96 ARG cc_start: 0.7594 (tpp-160) cc_final: 0.7104 (tpp-160) REVERT: X 138 ILE cc_start: 0.9034 (tt) cc_final: 0.8737 (tt) REVERT: X 160 ARG cc_start: 0.8200 (ttp80) cc_final: 0.7423 (tpt-90) REVERT: X 166 LEU cc_start: 0.8412 (mm) cc_final: 0.8159 (mm) REVERT: X 174 ILE cc_start: 0.8616 (tt) cc_final: 0.8079 (tt) REVERT: X 205 ASP cc_start: 0.8682 (t70) cc_final: 0.8248 (t0) REVERT: Y 91 ARG cc_start: 0.7988 (ttp-170) cc_final: 0.7579 (ttp-170) REVERT: Y 146 ILE cc_start: 0.8851 (tp) cc_final: 0.8590 (tp) REVERT: Y 153 LYS cc_start: 0.9007 (mmmt) cc_final: 0.8704 (mttt) REVERT: Y 189 ASN cc_start: 0.8451 (p0) cc_final: 0.8235 (p0) REVERT: Y 232 ILE cc_start: 0.9045 (mm) cc_final: 0.8741 (mm) REVERT: Z 52 ASP cc_start: 0.8611 (t0) cc_final: 0.7942 (p0) REVERT: Z 58 HIS cc_start: 0.5567 (t70) cc_final: 0.5283 (t70) REVERT: Z 183 MET cc_start: 0.8344 (mtt) cc_final: 0.7608 (mmm) REVERT: 1 90 ASP cc_start: 0.7920 (m-30) cc_final: 0.7572 (m-30) REVERT: 1 92 GLU cc_start: 0.7745 (pp20) cc_final: 0.7149 (pp20) REVERT: 1 120 ARG cc_start: 0.6879 (mtp-110) cc_final: 0.6018 (ttm-80) REVERT: 1 123 ARG cc_start: 0.7878 (ptt-90) cc_final: 0.6849 (ptp90) REVERT: 1 163 PHE cc_start: 0.8269 (p90) cc_final: 0.7646 (p90) REVERT: 2 96 ASN cc_start: 0.8936 (m-40) cc_final: 0.8671 (m-40) REVERT: 2 118 SER cc_start: 0.8543 (t) cc_final: 0.8258 (t) REVERT: 2 139 TYR cc_start: 0.7261 (t80) cc_final: 0.7049 (t80) REVERT: 2 144 GLU cc_start: 0.8159 (pp20) cc_final: 0.7082 (tt0) REVERT: 2 153 LYS cc_start: 0.9131 (mmmt) cc_final: 0.8268 (mmmt) REVERT: 2 160 CYS cc_start: 0.8262 (p) cc_final: 0.8062 (p) REVERT: 2 198 PHE cc_start: 0.7053 (m-80) cc_final: 0.6686 (m-10) outliers start: 3 outliers final: 0 residues processed: 1931 average time/residue: 0.6944 time to fit residues: 2294.2653 Evaluate side-chains 1532 residues out of total 7734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1532 time to evaluate : 6.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 559 optimal weight: 3.9990 chunk 750 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 649 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 195 optimal weight: 0.9990 chunk 705 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 chunk 724 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 HIS ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 ASN ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN I 27 ASN I 50 ASN I 153 GLN ** I 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 127 HIS L 191 GLN ** M 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 171 HIS Q 173 GLN a 193 HIS ** e 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 45 GLN i 129 ASN ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 20 HIS ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 HIS ** b 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 84 ASN ** j 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 63 ASN l 99 HIS m 107 ASN ** n 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 ASN S 162 HIS ** S 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 188 HIS ** T 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 91 ASN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 233 GLN W 117 HIS ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 234 HIS ** Z 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 142 GLN 1 124 GLN 2 104 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.162259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.138162 restraints weight = 187641.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.140191 restraints weight = 121395.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.141711 restraints weight = 90161.483| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.9380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 72937 Z= 0.302 Angle : 0.758 12.097 98542 Z= 0.398 Chirality : 0.047 0.326 11127 Planarity : 0.005 0.100 12692 Dihedral : 5.074 48.610 9923 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.45 % Favored : 96.51 % Rotamer: Outliers : 0.04 % Allowed : 0.48 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.08), residues: 8996 helix: 0.68 (0.07), residues: 4397 sheet: -0.05 (0.13), residues: 1414 loop : -0.77 (0.11), residues: 3185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP C 139 HIS 0.019 0.002 HIS F 175 PHE 0.058 0.002 PHE N 170 TYR 0.036 0.002 TYR 1 158 ARG 0.016 0.001 ARG l 70 =============================================================================== Job complete usr+sys time: 31140.55 seconds wall clock time: 539 minutes 6.84 seconds (32346.84 seconds total)