Starting phenix.real_space_refine on Sun Feb 25 02:40:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr7_30825/02_2024/7dr7_30825.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr7_30825/02_2024/7dr7_30825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr7_30825/02_2024/7dr7_30825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr7_30825/02_2024/7dr7_30825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr7_30825/02_2024/7dr7_30825.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr7_30825/02_2024/7dr7_30825.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 308 5.16 5 C 30531 2.51 5 N 8276 2.21 5 O 9189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 99": "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 "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 3": "NH1" <-> "NH2" Residue "L TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 3": "NH1" <-> "NH2" Residue "N TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 185": "NH1" <-> "NH2" Residue "U TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 185": "NH1" <-> "NH2" Residue "X PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 123": "NH1" <-> "NH2" Residue "Y TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 185": "NH1" <-> "NH2" Residue "1 TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 123": "NH1" <-> "NH2" Residue "1 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 48304 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" 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: "B" 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: "C" 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: "E" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1903 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 8, 'TRANS': 235} Chain: "F" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1804 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1892 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "M" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1790 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "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: 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: "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: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1499 Classifications: {'peptide': 199} 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: 24.52, per 1000 atoms: 0.51 Number of scatterers: 48304 At special positions: 0 Unit cell: (193.746, 175.294, 139.708, 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 308 16.00 O 9189 8.00 N 8276 7.00 C 30531 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.54 Conformation dependent library (CDL) restraints added in 8.9 seconds 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11450 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 73 sheets defined 38.6% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.58 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 removed outlier: 3.575A pdb=" N VAL A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 98 removed outlier: 3.698A pdb=" N ALA A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 121 removed outlier: 3.760A pdb=" N THR A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 176 removed outlier: 3.992A pdb=" N LYS A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 221 through 230 removed outlier: 3.619A pdb=" N TYR A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 32 removed outlier: 3.759A pdb=" N GLU B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.519A pdb=" N SER B 63 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 103 removed outlier: 3.788A pdb=" N ALA B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 118 removed outlier: 3.556A pdb=" N ASN B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 185 removed outlier: 3.687A pdb=" N SER B 180 " --> pdb=" O GLY B 176 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 206 removed outlier: 3.719A pdb=" N GLN B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 238 removed outlier: 3.963A pdb=" N GLU B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'C' and resid 19 through 31 removed outlier: 3.550A pdb=" N ALA C 28 " --> pdb=" O TYR C 24 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 30 " --> pdb=" O MET C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 99 removed outlier: 3.910A pdb=" N LEU C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.603A pdb=" N SER C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 122 removed outlier: 4.100A pdb=" N THR C 120 " --> pdb=" O THR C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 175 removed outlier: 4.350A pdb=" N ALA C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS C 175 " --> pdb=" O TYR C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'C' and resid 183 through 199 removed outlier: 3.551A pdb=" N VAL C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU C 197 " --> pdb=" O ARG C 193 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 234 Processing helix chain 'D' and resid 21 through 33 removed outlier: 3.755A pdb=" N VAL D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 103 removed outlier: 3.677A pdb=" N SER D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 126 removed outlier: 3.702A pdb=" N ASP D 114 " --> pdb=" O LYS D 110 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR D 123 " --> pdb=" O TYR D 119 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU D 125 " --> pdb=" O HIS D 121 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 180 removed outlier: 3.528A pdb=" N GLU D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS D 179 " --> pdb=" O THR D 175 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 202 removed outlier: 4.237A pdb=" N LYS D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU D 193 " --> pdb=" O ASP D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 removed outlier: 3.644A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 34 removed outlier: 3.670A pdb=" N LYS E 30 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN E 33 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 105 removed outlier: 3.520A pdb=" N LYS E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 120 Processing helix chain 'E' and resid 120 through 128 removed outlier: 3.670A pdb=" N VAL E 124 " --> pdb=" O ASP E 120 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR E 125 " --> pdb=" O ILE E 121 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR E 126 " --> pdb=" O SER E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 186 removed outlier: 3.693A pdb=" N LYS E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 184 " --> pdb=" O GLU E 180 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 185 " --> pdb=" O LYS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 207 removed outlier: 3.509A pdb=" N VAL E 195 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E 202 " --> pdb=" O ALA E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 213 No H-bonds generated for 'chain 'E' and resid 211 through 213' Processing helix chain 'E' and resid 231 through 240 removed outlier: 3.691A pdb=" N HIS E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 244 Processing helix chain 'F' and resid 19 through 29 removed outlier: 3.584A pdb=" N ALA F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 79 through 102 removed outlier: 3.569A pdb=" N TYR F 83 " --> pdb=" O MET F 79 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG F 84 " --> pdb=" O GLY F 80 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL F 85 " --> pdb=" O PRO F 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU F 86 " --> pdb=" O ASP F 82 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS F 92 " --> pdb=" O HIS F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 121 removed outlier: 3.563A pdb=" N TYR F 121 " --> pdb=" O VAL F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 178 removed outlier: 3.564A pdb=" N LYS F 176 " --> pdb=" O THR F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 199 removed outlier: 3.501A pdb=" N GLU F 197 " --> pdb=" O LEU F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 230 Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 18 through 30 removed outlier: 3.529A pdb=" N HIS G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 102 removed outlier: 3.526A pdb=" N ALA G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN G 84 " --> pdb=" O THR G 80 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL G 85 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU G 92 " --> pdb=" O ASN G 88 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN G 95 " --> pdb=" O ARG G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 124 removed outlier: 3.660A pdb=" N ASP G 116 " --> pdb=" O THR G 112 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR G 121 " --> pdb=" O ILE G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 179 removed outlier: 3.661A pdb=" N MET G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN G 177 " --> pdb=" O SER G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 201 removed outlier: 3.675A pdb=" N ALA G 191 " --> pdb=" O LYS G 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS G 195 " --> pdb=" O ALA G 191 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS G 199 " --> pdb=" O LYS G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 246 removed outlier: 3.581A pdb=" N GLU G 243 " --> pdb=" O LYS G 239 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA G 245 " --> pdb=" O GLU G 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 78 removed outlier: 3.630A pdb=" N GLN H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 97 removed outlier: 3.592A pdb=" N SER H 89 " --> pdb=" O TYR H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 154 removed outlier: 3.922A pdb=" N GLY H 148 " --> pdb=" O GLU H 144 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER H 152 " --> pdb=" O GLY H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 177 removed outlier: 3.961A pdb=" N ARG H 177 " --> pdb=" O ASN H 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 72 removed outlier: 4.411A pdb=" N VAL I 54 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR I 59 " --> pdb=" O GLN I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 94 removed outlier: 3.557A pdb=" N ARG I 86 " --> pdb=" O ASN I 82 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU I 92 " --> pdb=" O LEU I 88 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG I 93 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER I 94 " --> pdb=" O ASP I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 147 removed outlier: 4.183A pdb=" N LEU I 138 " --> pdb=" O TYR I 134 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER I 141 " --> pdb=" O PHE I 137 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE I 142 " --> pdb=" O LEU I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 165 removed outlier: 3.571A pdb=" N GLU I 158 " --> pdb=" O GLU I 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 108 removed outlier: 3.716A pdb=" N LYS J 101 " --> pdb=" O GLU J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 126 Processing helix chain 'J' and resid 169 through 181 Proline residue: J 175 - end of helix Processing helix chain 'J' and resid 195 through 214 removed outlier: 3.975A pdb=" N ARG J 201 " --> pdb=" O ASP J 197 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE J 207 " --> pdb=" O VAL J 203 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU J 212 " --> pdb=" O ILE J 208 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG J 213 " --> pdb=" O SER J 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 123 removed outlier: 3.847A pdb=" N LEU K 122 " --> pdb=" O ASP K 118 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY K 123 " --> pdb=" O GLU K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 147 Processing helix chain 'K' and resid 191 through 202 removed outlier: 3.570A pdb=" N VAL K 198 " --> pdb=" O LEU K 194 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS K 201 " --> pdb=" O GLU K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 225 Processing helix chain 'K' and resid 255 through 261 removed outlier: 4.114A pdb=" N MET K 259 " --> pdb=" O ASP K 255 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER K 261 " --> pdb=" O ALA K 257 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 34 removed outlier: 3.669A pdb=" N LYS L 30 " --> pdb=" O GLU L 26 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN L 33 " --> pdb=" O PHE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 105 removed outlier: 3.520A pdb=" N LYS L 102 " --> pdb=" O ALA L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 120 Processing helix chain 'L' and resid 120 through 128 removed outlier: 3.670A pdb=" N VAL L 124 " --> pdb=" O ASP L 120 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR L 125 " --> pdb=" O ILE L 121 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 186 removed outlier: 3.693A pdb=" N LYS L 181 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS L 184 " --> pdb=" O GLU L 180 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS L 185 " --> pdb=" O LYS L 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 190 through 207 removed outlier: 3.509A pdb=" N VAL L 195 " --> pdb=" O PHE L 191 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU L 202 " --> pdb=" O ALA L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 213 No H-bonds generated for 'chain 'L' and resid 211 through 213' Processing helix chain 'L' and resid 231 through 240 removed outlier: 3.691A pdb=" N HIS L 238 " --> pdb=" O GLU L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 244 Processing helix chain 'M' and resid 19 through 29 removed outlier: 3.583A pdb=" N ALA M 27 " --> pdb=" O GLU M 23 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL M 29 " --> pdb=" O ALA M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 32 No H-bonds generated for 'chain 'M' and resid 30 through 32' Processing helix chain 'M' and resid 79 through 102 removed outlier: 3.569A pdb=" N TYR M 83 " --> pdb=" O MET M 79 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG M 84 " --> pdb=" O GLY M 80 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL M 85 " --> pdb=" O PRO M 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU M 86 " --> pdb=" O ASP M 82 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS M 92 " --> pdb=" O HIS M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 121 removed outlier: 3.562A pdb=" N TYR M 121 " --> pdb=" O VAL M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 178 removed outlier: 3.504A pdb=" N PHE M 173 " --> pdb=" O ASN M 169 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS M 176 " --> pdb=" O THR M 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 199 removed outlier: 3.534A pdb=" N GLU M 197 " --> pdb=" O LEU M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 230 Processing helix chain 'N' and resid 2 through 6 Processing helix chain 'N' and resid 18 through 30 removed outlier: 3.529A pdb=" N HIS N 30 " --> pdb=" O GLU N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 102 removed outlier: 3.525A pdb=" N ALA N 83 " --> pdb=" O ILE N 79 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN N 84 " --> pdb=" O THR N 80 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL N 85 " --> pdb=" O SER N 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU N 92 " --> pdb=" O ASN N 88 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN N 95 " --> pdb=" O ARG N 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 124 removed outlier: 3.660A pdb=" N ASP N 116 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE N 117 " --> pdb=" O ALA N 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR N 121 " --> pdb=" O ILE N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 179 removed outlier: 3.662A pdb=" N MET N 174 " --> pdb=" O ALA N 170 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN N 177 " --> pdb=" O SER N 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 201 removed outlier: 3.676A pdb=" N ALA N 191 " --> pdb=" O LYS N 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS N 195 " --> pdb=" O ALA N 191 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS N 199 " --> pdb=" O LYS N 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 246 removed outlier: 3.623A pdb=" N GLU N 243 " --> pdb=" O LYS N 239 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA N 245 " --> pdb=" O GLU N 241 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 28 removed outlier: 3.575A pdb=" N VAL O 26 " --> pdb=" O ALA O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 98 removed outlier: 3.697A pdb=" N ALA O 80 " --> pdb=" O LEU O 76 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG O 81 " --> pdb=" O THR O 77 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE O 82 " --> pdb=" O ALA O 78 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL O 89 " --> pdb=" O ASN O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 121 removed outlier: 3.761A pdb=" N THR O 119 " --> pdb=" O LYS O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 176 removed outlier: 3.992A pdb=" N LYS O 174 " --> pdb=" O GLU O 170 " (cutoff:3.500A) Processing helix chain 'O' and resid 183 through 195 Processing helix chain 'O' and resid 196 through 198 No H-bonds generated for 'chain 'O' and resid 196 through 198' Processing helix chain 'O' and resid 221 through 230 removed outlier: 3.619A pdb=" N TYR O 228 " --> pdb=" O GLU O 224 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 32 removed outlier: 3.759A pdb=" N GLU P 29 " --> pdb=" O GLU P 25 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS P 32 " --> pdb=" O ILE P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 64 removed outlier: 3.519A pdb=" N SER P 63 " --> pdb=" O GLU P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 103 removed outlier: 3.788A pdb=" N ALA P 85 " --> pdb=" O LEU P 81 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS P 86 " --> pdb=" O ILE P 82 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR P 87 " --> pdb=" O ALA P 83 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU P 88 " --> pdb=" O ASP P 84 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL P 94 " --> pdb=" O ASP P 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 118 removed outlier: 3.555A pdb=" N ASN P 118 " --> pdb=" O GLN P 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 185 removed outlier: 3.687A pdb=" N SER P 180 " --> pdb=" O GLY P 176 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU P 183 " --> pdb=" O SER P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 190 through 206 removed outlier: 3.721A pdb=" N GLN P 204 " --> pdb=" O ILE P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 230 through 238 removed outlier: 3.963A pdb=" N GLU P 236 " --> pdb=" O GLU P 232 " (cutoff:3.500A) Processing helix chain 'P' and resid 239 through 241 No H-bonds generated for 'chain 'P' and resid 239 through 241' Processing helix chain 'Q' and resid 19 through 31 removed outlier: 3.550A pdb=" N ALA Q 28 " --> pdb=" O TYR Q 24 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL Q 29 " --> pdb=" O ALA Q 25 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS Q 30 " --> pdb=" O MET Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 99 removed outlier: 3.910A pdb=" N LEU Q 83 " --> pdb=" O ALA Q 79 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU Q 84 " --> pdb=" O ASP Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 116 removed outlier: 3.603A pdb=" N SER Q 110 " --> pdb=" O SER Q 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 116 through 122 removed outlier: 4.100A pdb=" N THR Q 120 " --> pdb=" O THR Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 175 removed outlier: 4.349A pdb=" N ALA Q 168 " --> pdb=" O ARG Q 164 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG Q 174 " --> pdb=" O THR Q 170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS Q 175 " --> pdb=" O TYR Q 171 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 179 Processing helix chain 'Q' and resid 183 through 199 removed outlier: 3.551A pdb=" N VAL Q 188 " --> pdb=" O LEU Q 184 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG Q 196 " --> pdb=" O LEU Q 192 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU Q 197 " --> pdb=" O ARG Q 193 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR Q 198 " --> pdb=" O ALA Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 229 through 234 Processing helix chain 'R' and resid 21 through 33 removed outlier: 3.754A pdb=" N VAL R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 103 removed outlier: 3.677A pdb=" N SER R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 126 removed outlier: 3.704A pdb=" N ASP R 114 " --> pdb=" O LYS R 110 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL R 116 " --> pdb=" O LEU R 112 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA R 117 " --> pdb=" O ALA R 113 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR R 123 " --> pdb=" O TYR R 119 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR R 124 " --> pdb=" O VAL R 120 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU R 125 " --> pdb=" O HIS R 121 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR R 126 " --> pdb=" O ALA R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 180 removed outlier: 3.528A pdb=" N GLU R 176 " --> pdb=" O ALA R 172 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU R 178 " --> pdb=" O LYS R 174 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS R 179 " --> pdb=" O THR R 175 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU R 180 " --> pdb=" O GLU R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 202 removed outlier: 4.237A pdb=" N LYS R 192 " --> pdb=" O ARG R 188 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU R 193 " --> pdb=" O ASP R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 243 removed outlier: 3.643A pdb=" N TYR R 239 " --> pdb=" O GLU R 235 " (cutoff:3.500A) Processing helix chain 'S' and resid 56 through 78 removed outlier: 3.629A pdb=" N GLN S 61 " --> pdb=" O ALA S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 97 removed outlier: 3.592A pdb=" N SER S 89 " --> pdb=" O TYR S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 142 through 154 removed outlier: 4.114A pdb=" N GLY S 148 " --> pdb=" O GLU S 144 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER S 152 " --> pdb=" O GLY S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 159 through 177 removed outlier: 3.961A pdb=" N ARG S 177 " --> pdb=" O ASN S 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 72 removed outlier: 4.412A pdb=" N VAL T 54 " --> pdb=" O ALA T 50 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR T 59 " --> pdb=" O GLN T 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 94 removed outlier: 3.557A pdb=" N ARG T 86 " --> pdb=" O ASN T 82 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU T 92 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG T 93 " --> pdb=" O ALA T 89 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER T 94 " --> pdb=" O ASP T 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 147 removed outlier: 4.184A pdb=" N LEU T 138 " --> pdb=" O TYR T 134 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER T 141 " --> pdb=" O PHE T 137 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE T 142 " --> pdb=" O LEU T 138 " (cutoff:3.500A) Processing helix chain 'T' and resid 152 through 165 removed outlier: 3.571A pdb=" N GLU T 158 " --> pdb=" O GLU T 154 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 108 removed outlier: 3.716A pdb=" N LYS U 101 " --> pdb=" O GLU U 97 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 126 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: 3.979A pdb=" N ARG U 201 " --> pdb=" O ASP U 197 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE U 207 " --> pdb=" O VAL U 203 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU U 212 " --> pdb=" O ILE U 208 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG U 213 " --> pdb=" O SER U 209 " (cutoff:3.500A) Processing helix chain 'V' and resid 102 through 123 removed outlier: 3.848A pdb=" N LEU V 122 " --> pdb=" O ASP V 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY V 123 " --> pdb=" O GLU V 119 " (cutoff:3.500A) Processing helix chain 'V' and resid 129 through 147 Processing helix chain 'V' and resid 191 through 202 removed outlier: 3.570A pdb=" N VAL V 198 " --> pdb=" O LEU V 194 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS V 201 " --> pdb=" O GLU V 197 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 225 Processing helix chain 'V' and resid 255 through 262 removed outlier: 4.114A pdb=" N MET V 259 " --> pdb=" O ASP V 255 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER V 261 " --> pdb=" O ALA V 257 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 91 Processing helix chain 'W' and resid 95 through 110 Processing helix chain 'W' and resid 135 through 138 Processing helix chain 'W' and resid 151 through 155 Processing helix chain 'W' and resid 156 through 161 Processing helix chain 'W' and resid 167 through 186 removed outlier: 3.788A pdb=" N LYS W 184 " --> pdb=" O ALA W 180 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG W 185 " --> pdb=" O LEU W 181 " (cutoff:3.500A) Processing helix chain 'X' and resid 89 through 110 removed outlier: 3.642A pdb=" N THR X 94 " --> pdb=" O ASP X 90 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR X 95 " --> pdb=" O ALA X 91 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 129 removed outlier: 3.681A pdb=" N VAL X 118 " --> pdb=" O ARG X 114 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG X 120 " --> pdb=" O ALA X 116 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR X 129 " --> pdb=" O THR X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 169 through 181 removed outlier: 3.650A pdb=" N ALA X 175 " --> pdb=" O ASP X 171 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP X 179 " --> pdb=" O ALA X 175 " (cutoff:3.500A) Processing helix chain 'X' and resid 186 through 203 removed outlier: 4.708A pdb=" N GLU X 192 " --> pdb=" O GLU X 188 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU X 193 " --> pdb=" O ALA X 189 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU X 194 " --> pdb=" O ALA X 190 " (cutoff:3.500A) Processing helix chain 'Y' and resid 120 through 142 removed outlier: 3.528A pdb=" N ARG Y 129 " --> pdb=" O LEU Y 125 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG Y 136 " --> pdb=" O ALA Y 132 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 161 removed outlier: 3.518A pdb=" N LEU Y 155 " --> pdb=" O ALA Y 151 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN Y 161 " --> pdb=" O ASN Y 157 " (cutoff:3.500A) Processing helix chain 'Y' and resid 203 through 212 removed outlier: 3.690A pdb=" N GLY Y 209 " --> pdb=" O SER Y 205 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL Y 210 " --> pdb=" O HIS Y 206 " (cutoff:3.500A) Processing helix chain 'Y' and resid 220 through 239 removed outlier: 3.620A pdb=" N LEU Y 227 " --> pdb=" O GLU Y 223 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG Y 238 " --> pdb=" O HIS Y 234 " (cutoff:3.500A) Processing helix chain 'Y' and resid 264 through 272 removed outlier: 3.575A pdb=" N HIS Y 269 " --> pdb=" O SER Y 265 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN Y 270 " --> pdb=" O ASP Y 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 91 Processing helix chain 'Z' and resid 95 through 110 Processing helix chain 'Z' and resid 135 through 138 Processing helix chain 'Z' and resid 150 through 154 removed outlier: 3.549A pdb=" N TYR Z 153 " --> pdb=" O GLY Z 150 " (cutoff:3.500A) Processing helix chain 'Z' and resid 155 through 161 Processing helix chain 'Z' and resid 167 through 186 removed outlier: 3.788A pdb=" N LYS Z 184 " --> pdb=" O ALA Z 180 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG Z 185 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) Processing helix chain '1' and resid 92 through 110 Processing helix chain '1' and resid 114 through 129 removed outlier: 3.681A pdb=" N VAL 1 118 " --> pdb=" O ARG 1 114 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG 1 120 " --> pdb=" O ALA 1 116 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN 1 124 " --> pdb=" O ARG 1 120 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR 1 129 " --> pdb=" O THR 1 125 " (cutoff:3.500A) Processing helix chain '1' and resid 169 through 181 removed outlier: 3.649A pdb=" N ALA 1 175 " --> pdb=" O ASP 1 171 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP 1 179 " --> pdb=" O ALA 1 175 " (cutoff:3.500A) Processing helix chain '1' and resid 186 through 203 removed outlier: 4.697A pdb=" N GLU 1 192 " --> pdb=" O GLU 1 188 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU 1 193 " --> pdb=" O ALA 1 189 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU 1 194 " --> pdb=" O ALA 1 190 " (cutoff:3.500A) Processing helix chain '2' and resid 120 through 142 removed outlier: 3.528A pdb=" N ARG 2 129 " --> pdb=" O LEU 2 125 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG 2 136 " --> pdb=" O ALA 2 132 " (cutoff:3.500A) Processing helix chain '2' and resid 147 through 162 removed outlier: 3.516A pdb=" N LEU 2 155 " --> pdb=" O ALA 2 151 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN 2 161 " --> pdb=" O ASN 2 157 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR 2 162 " --> pdb=" O MET 2 158 " (cutoff:3.500A) Processing helix chain '2' and resid 203 through 212 removed outlier: 3.690A pdb=" N GLY 2 209 " --> pdb=" O SER 2 205 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL 2 210 " --> pdb=" O HIS 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 220 through 239 removed outlier: 3.620A pdb=" N LEU 2 227 " --> pdb=" O GLU 2 223 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG 2 238 " --> pdb=" O HIS 2 234 " (cutoff:3.500A) Processing helix chain '2' and resid 264 through 272 removed outlier: 3.574A pdb=" N HIS 2 269 " --> pdb=" O SER 2 265 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN 2 270 " --> pdb=" O ASP 2 266 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 3.721A pdb=" N THR A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 167 through 170 removed outlier: 4.887A pdb=" N GLN B 221 " --> pdb=" O ASN B 225 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ASN B 225 " --> pdb=" O GLN B 221 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 80 removed outlier: 3.500A pdb=" N ALA B 140 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 153 " --> pdb=" O CYS B 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 removed outlier: 3.723A pdb=" N ILE C 212 " --> pdb=" O TYR C 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 63 through 67 removed outlier: 5.766A pdb=" N ILE C 63 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE C 74 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N HIS C 65 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE C 72 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 163 through 166 removed outlier: 3.567A pdb=" N PHE D 48 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER D 215 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU D 213 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS D 52 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ALA D 209 " --> pdb=" O VAL D 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 71 removed outlier: 6.424A pdb=" N LEU D 67 " --> pdb=" O VAL D 78 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL D 78 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN D 69 " --> pdb=" O MET D 76 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N MET D 76 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY D 139 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 168 through 169 removed outlier: 5.352A pdb=" N THR E 38 " --> pdb=" O GLN E 53 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU E 216 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL E 217 " --> pdb=" O LEU E 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 69 through 73 removed outlier: 6.435A pdb=" N LEU E 69 " --> pdb=" O MET E 80 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N MET E 80 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LYS E 71 " --> pdb=" O CYS E 78 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N CYS E 78 " --> pdb=" O LYS E 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 160 through 162 removed outlier: 3.735A pdb=" N ASN F 214 " --> pdb=" O GLY F 217 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 66 through 67 removed outlier: 3.670A pdb=" N LEU F 135 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER F 77 " --> pdb=" O SER F 133 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN F 148 " --> pdb=" O PHE F 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 161 through 164 Processing sheet with id=AB5, first strand: chain 'G' and resid 65 through 66 removed outlier: 3.664A pdb=" N LEU G 135 " --> pdb=" O SER G 75 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY G 144 " --> pdb=" O ASP G 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 136 through 140 removed outlier: 6.057A pdb=" N ALA H 10 " --> pdb=" O ASP H 25 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL H 185 " --> pdb=" O LEU H 200 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 28 through 30 removed outlier: 7.119A pdb=" N PHE H 28 " --> pdb=" O VAL H 35 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 42 through 44 Processing sheet with id=AB9, first strand: chain 'I' and resid 129 through 132 removed outlier: 3.569A pdb=" N LEU I 4 " --> pdb=" O HIS I 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 129 through 132 removed outlier: 3.569A pdb=" N LEU I 4 " --> pdb=" O HIS I 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 21 through 23 removed outlier: 6.753A pdb=" N ALA I 21 " --> pdb=" O MET I 28 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 35 through 37 Processing sheet with id=AC4, first strand: chain 'J' and resid 163 through 167 removed outlier: 5.691A pdb=" N THR J 39 " --> pdb=" O ASP J 54 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP J 54 " --> pdb=" O THR J 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.814A pdb=" N GLU J 59 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ILE J 63 " --> pdb=" O GLU J 59 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 72 through 75 removed outlier: 6.653A pdb=" N THR J 78 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASN J 136 " --> pdb=" O PHE J 152 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL J 149 " --> pdb=" O ASP J 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER J 151 " --> pdb=" O GLN J 159 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN J 159 " --> pdb=" O SER J 151 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 181 through 182 removed outlier: 3.528A pdb=" N VAL K 66 " --> pdb=" O LEU K 59 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR K 238 " --> pdb=" O GLY K 241 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 73 through 75 removed outlier: 6.639A pdb=" N TYR K 75 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA K 79 " --> pdb=" O TYR K 75 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 87 through 90 removed outlier: 3.618A pdb=" N THR K 154 " --> pdb=" O SER K 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 168 through 169 removed outlier: 5.350A pdb=" N THR L 38 " --> pdb=" O GLN L 53 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU L 216 " --> pdb=" O THR L 52 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL L 217 " --> pdb=" O LEU L 230 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 69 through 73 removed outlier: 6.435A pdb=" N LEU L 69 " --> pdb=" O MET L 80 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N MET L 80 " --> pdb=" O LEU L 69 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LYS L 71 " --> pdb=" O CYS L 78 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS L 78 " --> pdb=" O LYS L 71 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 160 through 162 removed outlier: 3.735A pdb=" N ASN M 214 " --> pdb=" O GLY M 217 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 66 through 67 removed outlier: 3.670A pdb=" N LEU M 135 " --> pdb=" O VAL M 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER M 77 " --> pdb=" O SER M 133 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN M 148 " --> pdb=" O PHE M 156 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 161 through 164 Processing sheet with id=AD6, first strand: chain 'N' and resid 65 through 66 removed outlier: 3.664A pdb=" N LEU N 135 " --> pdb=" O SER N 75 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY N 144 " --> pdb=" O ASP N 140 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 158 through 161 Processing sheet with id=AD8, first strand: chain 'O' and resid 63 through 64 removed outlier: 3.722A pdb=" N THR O 141 " --> pdb=" O ASP O 137 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 167 through 170 removed outlier: 4.888A pdb=" N GLN P 221 " --> pdb=" O ASN P 225 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASN P 225 " --> pdb=" O GLN P 221 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 78 through 80 removed outlier: 3.500A pdb=" N ALA P 140 " --> pdb=" O SER P 79 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU P 153 " --> pdb=" O CYS P 165 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 158 through 161 removed outlier: 3.723A pdb=" N ILE Q 212 " --> pdb=" O TYR Q 224 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 63 through 67 removed outlier: 5.765A pdb=" N ILE Q 63 " --> pdb=" O ILE Q 74 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE Q 74 " --> pdb=" O ILE Q 63 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N HIS Q 65 " --> pdb=" O ILE Q 72 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE Q 72 " --> pdb=" O HIS Q 65 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 163 through 166 removed outlier: 3.566A pdb=" N PHE R 48 " --> pdb=" O SER R 215 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER R 215 " --> pdb=" O PHE R 48 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU R 213 " --> pdb=" O VAL R 50 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS R 52 " --> pdb=" O GLU R 211 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA R 209 " --> pdb=" O VAL R 54 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 67 through 71 removed outlier: 6.424A pdb=" N LEU R 67 " --> pdb=" O VAL R 78 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL R 78 " --> pdb=" O LEU R 67 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN R 69 " --> pdb=" O MET R 76 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N MET R 76 " --> pdb=" O ASN R 69 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY R 139 " --> pdb=" O GLY R 75 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 136 through 140 removed outlier: 6.057A pdb=" N ALA S 10 " --> pdb=" O ASP S 25 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL S 185 " --> pdb=" O LEU S 200 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 28 through 30 removed outlier: 7.118A pdb=" N PHE S 28 " --> pdb=" O VAL S 35 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 42 through 44 Processing sheet with id=AE9, first strand: chain 'T' and resid 129 through 132 removed outlier: 3.570A pdb=" N LEU T 4 " --> pdb=" O HIS T 132 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 129 through 132 removed outlier: 3.570A pdb=" N LEU T 4 " --> pdb=" O HIS T 132 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 21 through 23 removed outlier: 6.753A pdb=" N ALA T 21 " --> pdb=" O MET T 28 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 35 through 37 Processing sheet with id=AF4, first strand: chain 'U' and resid 163 through 167 removed outlier: 5.692A pdb=" N THR U 39 " --> pdb=" O ASP U 54 " (cutoff:3.500A) removed outlier: 3.618A 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: 6.815A pdb=" N GLU U 59 " --> pdb=" O ILE U 63 " (cutoff:3.500A) removed outlier: 5.338A 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: 6.653A pdb=" N THR U 78 " --> pdb=" O LEU U 74 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASN U 136 " --> pdb=" O PHE U 152 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL U 149 " --> pdb=" O ASP U 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER U 151 " --> pdb=" O GLN U 159 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN U 159 " --> pdb=" O SER U 151 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 181 through 182 removed outlier: 3.511A pdb=" N VAL V 66 " --> pdb=" O LEU V 59 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR V 238 " --> pdb=" O GLY V 241 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 87 through 90 removed outlier: 3.618A pdb=" N THR V 154 " --> pdb=" O SER V 99 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 144 through 147 Processing sheet with id=AG1, first strand: chain 'W' and resid 40 through 42 removed outlier: 6.241A pdb=" N ALA W 42 " --> pdb=" O VAL W 46 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL W 46 " --> pdb=" O ALA W 42 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 54 through 58 removed outlier: 6.579A pdb=" N ILE W 61 " --> pdb=" O LEU W 57 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 163 through 167 removed outlier: 5.877A pdb=" N THR X 41 " --> pdb=" O ASP X 56 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL X 212 " --> pdb=" O ALA X 227 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA X 227 " --> pdb=" O VAL X 212 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 59 through 60 removed outlier: 3.634A pdb=" N ASP X 67 " --> pdb=" O ALA X 59 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 73 through 77 removed outlier: 3.674A pdb=" N CYS X 82 " --> pdb=" O HIS X 74 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE X 80 " --> pdb=" O ILE X 76 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP X 143 " --> pdb=" O GLY X 146 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 197 through 201 removed outlier: 5.794A pdb=" N THR Y 74 " --> pdb=" O ASP Y 89 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU Y 260 " --> pdb=" O MET Y 248 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS Y 250 " --> pdb=" O LYS Y 258 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LYS Y 258 " --> pdb=" O HIS Y 250 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 92 through 94 removed outlier: 3.852A pdb=" N ALA Y 92 " --> pdb=" O THR Y 100 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ALA Y 94 " --> pdb=" O ILE Y 98 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE Y 98 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 107 through 108 Processing sheet with id=AG9, first strand: chain 'Y' and resid 118 through 119 Processing sheet with id=AH1, first strand: chain 'Z' and resid 144 through 147 Processing sheet with id=AH2, first strand: chain 'Z' and resid 40 through 42 removed outlier: 6.242A pdb=" N ALA Z 42 " --> pdb=" O VAL Z 46 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 54 through 56 Processing sheet with id=AH4, first strand: chain '1' and resid 163 through 167 removed outlier: 5.877A pdb=" N THR 1 41 " --> pdb=" O ASP 1 56 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL 1 212 " --> pdb=" O ALA 1 227 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA 1 227 " --> pdb=" O VAL 1 212 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '1' and resid 59 through 60 removed outlier: 3.633A pdb=" N ASP 1 67 " --> pdb=" O ALA 1 59 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '1' and resid 73 through 77 removed outlier: 3.673A pdb=" N CYS 1 82 " --> pdb=" O HIS 1 74 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE 1 80 " --> pdb=" O ILE 1 76 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP 1 143 " --> pdb=" O GLY 1 146 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain '2' and resid 197 through 201 removed outlier: 5.794A pdb=" N THR 2 74 " --> pdb=" O ASP 2 89 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU 2 260 " --> pdb=" O MET 2 248 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS 2 250 " --> pdb=" O LYS 2 258 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LYS 2 258 " --> pdb=" O HIS 2 250 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain '2' and resid 92 through 94 removed outlier: 3.853A pdb=" N ALA 2 92 " --> pdb=" O THR 2 100 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ALA 2 94 " --> pdb=" O ILE 2 98 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE 2 98 " --> pdb=" O ALA 2 94 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain '2' and resid 107 through 108 Processing sheet with id=AI1, first strand: chain '2' and resid 118 through 119 2405 hydrogen bonds defined for protein. 6780 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.52 Time building geometry restraints manager: 18.83 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: 15943 1.34 - 1.46: 6999 1.46 - 1.57: 25734 1.57 - 1.69: 0 1.69 - 1.81: 508 Bond restraints: 49184 Sorted by residual: bond pdb=" C PHE G 61 " pdb=" N SER G 62 " ideal model delta sigma weight residual 1.335 1.302 0.033 1.33e-02 5.65e+03 6.12e+00 bond pdb=" C PHE G 60 " pdb=" N PHE G 61 " ideal model delta sigma weight residual 1.327 1.305 0.022 9.40e-03 1.13e+04 5.57e+00 bond pdb=" C PHE N 60 " pdb=" N PHE N 61 " ideal model delta sigma weight residual 1.332 1.361 -0.028 1.40e-02 5.10e+03 4.11e+00 bond pdb=" N ARG N 4 " pdb=" CA ARG N 4 " ideal model delta sigma weight residual 1.459 1.438 0.021 1.21e-02 6.83e+03 3.13e+00 bond pdb=" N PHE G 61 " pdb=" CA PHE G 61 " ideal model delta sigma weight residual 1.458 1.430 0.028 1.61e-02 3.86e+03 3.07e+00 ... (remaining 49179 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.15: 1083 106.15 - 113.12: 26621 113.12 - 120.10: 16985 120.10 - 127.07: 21373 127.07 - 134.05: 400 Bond angle restraints: 66462 Sorted by residual: angle pdb=" N ARG I 145 " pdb=" CA ARG I 145 " pdb=" C ARG I 145 " ideal model delta sigma weight residual 112.23 120.27 -8.04 1.26e+00 6.30e-01 4.07e+01 angle pdb=" N ARG X 123 " pdb=" CA ARG X 123 " pdb=" C ARG X 123 " ideal model delta sigma weight residual 111.36 117.47 -6.11 1.09e+00 8.42e-01 3.14e+01 angle pdb=" N ARG G 3 " pdb=" CA ARG G 3 " pdb=" C ARG G 3 " ideal model delta sigma weight residual 111.28 105.22 6.06 1.09e+00 8.42e-01 3.09e+01 angle pdb=" N GLU X 236 " pdb=" CA GLU X 236 " pdb=" C GLU X 236 " ideal model delta sigma weight residual 110.42 118.52 -8.10 1.46e+00 4.69e-01 3.07e+01 angle pdb=" N ARG G 8 " pdb=" CA ARG G 8 " pdb=" C ARG G 8 " ideal model delta sigma weight residual 111.28 118.75 -7.47 1.35e+00 5.49e-01 3.07e+01 ... (remaining 66457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 28862 16.20 - 32.40: 565 32.40 - 48.60: 199 48.60 - 64.80: 28 64.80 - 81.00: 10 Dihedral angle restraints: 29664 sinusoidal: 11730 harmonic: 17934 Sorted by residual: dihedral pdb=" CA ILE Z 154 " pdb=" C ILE Z 154 " pdb=" N TYR Z 155 " pdb=" CA TYR Z 155 " ideal model delta harmonic sigma weight residual 180.00 150.66 29.34 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA GLN O 200 " pdb=" C GLN O 200 " pdb=" N SER O 201 " pdb=" CA SER O 201 " ideal model delta harmonic sigma weight residual -180.00 -152.51 -27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA GLN A 200 " pdb=" C GLN A 200 " pdb=" N SER A 201 " pdb=" CA SER A 201 " ideal model delta harmonic sigma weight residual -180.00 -152.57 -27.43 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 29661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 6513 0.066 - 0.132: 915 0.132 - 0.198: 21 0.198 - 0.264: 2 0.264 - 0.330: 4 Chirality restraints: 7455 Sorted by residual: chirality pdb=" CA ARG I 145 " pdb=" N ARG I 145 " pdb=" C ARG I 145 " pdb=" CB ARG I 145 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA ARG G 8 " pdb=" N ARG G 8 " pdb=" C ARG G 8 " pdb=" CB ARG G 8 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA ARG N 3 " pdb=" N ARG N 3 " pdb=" C ARG N 3 " pdb=" CB ARG N 3 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 7452 not shown) Planarity restraints: 8575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 101 " -0.047 5.00e-02 4.00e+02 7.19e-02 8.27e+00 pdb=" N PRO H 102 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO H 102 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 102 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS X 233 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO X 234 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO X 234 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO X 234 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER N 2 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C SER N 2 " -0.045 2.00e-02 2.50e+03 pdb=" O SER N 2 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG N 3 " 0.015 2.00e-02 2.50e+03 ... (remaining 8572 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1311 2.70 - 3.25: 47577 3.25 - 3.80: 73632 3.80 - 4.35: 99276 4.35 - 4.90: 168382 Nonbonded interactions: 390178 Sorted by model distance: nonbonded pdb=" O ARG B 10 " pdb=" O GLY B 11 " model vdw 2.151 3.040 nonbonded pdb=" NH2 ARG A 81 " pdb=" O GLY G 154 " model vdw 2.198 2.520 nonbonded pdb=" OG1 THR O 31 " pdb=" O ARG O 163 " model vdw 2.211 2.440 nonbonded pdb=" OG1 THR A 31 " pdb=" O ARG A 163 " model vdw 2.211 2.440 nonbonded pdb=" O LYS 2 79 " pdb=" OH TYR 2 215 " model vdw 2.211 2.440 ... (remaining 390173 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 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = (chain 'E' and resid 2 through 244) selection = chain 'L' } ncs_group { reference = (chain 'F' and resid 4 through 232) selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = (chain 'I' and resid 1 through 197) selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'U' } ncs_group { reference = (chain 'K' and resid 47 through 261) selection = (chain 'V' and resid 47 through 261) } ncs_group { reference = chain 'W' selection = (chain 'Z' and (resid 21 through 218 or (resid 219 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.530 Check model and map are aligned: 0.780 Set scattering table: 0.520 Process input model: 121.010 Find NCS groups from input model: 5.270 Set up NCS constraints: 0.440 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: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 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 : 0.004 0.036 49184 Z= 0.244 Angle : 0.612 8.238 66462 Z= 0.373 Chirality : 0.044 0.330 7455 Planarity : 0.004 0.072 8575 Dihedral : 8.328 81.000 18214 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.84 % Favored : 96.03 % Rotamer: Outliers : 0.29 % Allowed : 0.33 % Favored : 99.38 % 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: -3.04 (0.09), residues: 6164 helix: -3.18 (0.07), residues: 2162 sheet: -1.35 (0.11), residues: 1458 loop : -1.04 (0.11), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 101 HIS 0.014 0.001 HIS W 117 PHE 0.030 0.002 PHE S 43 TYR 0.022 0.002 TYR Y 249 ARG 0.007 0.001 ARG N 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2281 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 2266 time to evaluate : 5.337 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: A 65 LEU cc_start: 0.8806 (mt) cc_final: 0.8545 (mp) REVERT: A 170 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7608 (mt-10) REVERT: A 193 LYS cc_start: 0.8036 (mttt) cc_final: 0.7768 (mtmt) REVERT: A 207 GLU cc_start: 0.7509 (tt0) cc_final: 0.7269 (tp30) REVERT: B 91 LYS cc_start: 0.7967 (tptt) cc_final: 0.7728 (mmmm) REVERT: B 104 ASN cc_start: 0.8763 (t0) cc_final: 0.8353 (t0) REVERT: B 134 SER cc_start: 0.8255 (p) cc_final: 0.8015 (t) REVERT: B 172 SER cc_start: 0.8031 (p) cc_final: 0.7559 (t) REVERT: B 203 LYS cc_start: 0.8045 (tttt) cc_final: 0.7384 (mtpp) REVERT: C 67 ASP cc_start: 0.7623 (t0) cc_final: 0.7406 (t70) REVERT: C 100 ASP cc_start: 0.7647 (t0) cc_final: 0.7415 (t0) REVERT: D 130 ARG cc_start: 0.8076 (ptt90) cc_final: 0.7705 (ptt90) REVERT: D 168 LYS cc_start: 0.7450 (tttt) cc_final: 0.6549 (mtmt) REVERT: E 86 ASP cc_start: 0.8411 (m-30) cc_final: 0.7929 (m-30) REVERT: F 7 SER cc_start: 0.8499 (m) cc_final: 0.8298 (t) REVERT: F 39 LYS cc_start: 0.7822 (tttt) cc_final: 0.7122 (ttpp) REVERT: F 83 TYR cc_start: 0.8240 (t80) cc_final: 0.7679 (t80) REVERT: F 179 ASN cc_start: 0.5957 (p0) cc_final: 0.5483 (t0) REVERT: F 192 ILE cc_start: 0.8394 (mt) cc_final: 0.7916 (pt) REVERT: F 193 LEU cc_start: 0.7999 (mt) cc_final: 0.7526 (tp) REVERT: F 199 PHE cc_start: 0.6706 (t80) cc_final: 0.6419 (t80) REVERT: G 3 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6691 (mtt-85) REVERT: G 108 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7180 (pt0) REVERT: G 137 ILE cc_start: 0.8513 (pt) cc_final: 0.8297 (pt) REVERT: H 99 ARG cc_start: 0.8964 (tpt90) cc_final: 0.8623 (tmt170) REVERT: H 158 MET cc_start: 0.7814 (mtm) cc_final: 0.7495 (mtp) REVERT: H 168 SER cc_start: 0.8984 (m) cc_final: 0.8760 (m) REVERT: I 12 TYR cc_start: 0.7639 (p90) cc_final: 0.7285 (p90) REVERT: I 41 LYS cc_start: 0.8570 (mttt) cc_final: 0.8328 (mtmm) REVERT: I 155 LYS cc_start: 0.7999 (mttt) cc_final: 0.7694 (tptp) REVERT: J 104 LYS cc_start: 0.8195 (tttt) cc_final: 0.7904 (tmmt) REVERT: J 151 SER cc_start: 0.8255 (t) cc_final: 0.7818 (m) REVERT: J 160 ARG cc_start: 0.7753 (ttt180) cc_final: 0.7529 (ttt180) REVERT: K 218 MET cc_start: 0.8566 (mmm) cc_final: 0.8190 (mmp) REVERT: K 233 GLN cc_start: 0.8059 (mt0) cc_final: 0.7734 (mt0) REVERT: L 86 ASP cc_start: 0.8509 (m-30) cc_final: 0.8117 (m-30) REVERT: L 90 GLN cc_start: 0.8091 (mt0) cc_final: 0.7585 (mt0) REVERT: L 230 LEU cc_start: 0.6465 (mt) cc_final: 0.5972 (mt) REVERT: M 7 SER cc_start: 0.8811 (m) cc_final: 0.8582 (t) REVERT: M 39 LYS cc_start: 0.7775 (tttt) cc_final: 0.7534 (ttpp) REVERT: M 83 TYR cc_start: 0.8146 (t80) cc_final: 0.7652 (t80) REVERT: M 102 GLN cc_start: 0.8473 (mm-40) cc_final: 0.7709 (mm110) REVERT: M 179 ASN cc_start: 0.6064 (p0) cc_final: 0.5811 (t0) REVERT: M 192 ILE cc_start: 0.8340 (mt) cc_final: 0.7979 (pt) REVERT: M 203 MET cc_start: 0.6588 (ttm) cc_final: 0.6075 (ttm) REVERT: O 170 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7549 (mt-10) REVERT: O 184 ASP cc_start: 0.7415 (m-30) cc_final: 0.7118 (m-30) REVERT: O 193 LYS cc_start: 0.7894 (mttt) cc_final: 0.7399 (mtmt) REVERT: P 104 ASN cc_start: 0.8712 (t0) cc_final: 0.7988 (t0) REVERT: P 193 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6325 (mp0) REVERT: P 203 LYS cc_start: 0.7670 (tttt) cc_final: 0.7061 (mtpp) REVERT: P 210 LEU cc_start: 0.7460 (tp) cc_final: 0.7255 (tp) REVERT: Q 88 MET cc_start: 0.8427 (mtp) cc_final: 0.8140 (mtp) REVERT: Q 100 ASP cc_start: 0.7700 (t0) cc_final: 0.7456 (t0) REVERT: R 82 LEU cc_start: 0.8489 (mt) cc_final: 0.7824 (tt) REVERT: R 168 LYS cc_start: 0.7698 (tttt) cc_final: 0.6858 (mtmt) REVERT: S 158 MET cc_start: 0.7875 (mtm) cc_final: 0.7285 (mtp) REVERT: T 12 TYR cc_start: 0.7995 (p90) cc_final: 0.7594 (p90) REVERT: T 41 LYS cc_start: 0.8779 (mttt) cc_final: 0.8425 (mtmm) REVERT: T 155 LYS cc_start: 0.8119 (mttt) cc_final: 0.7735 (tptp) REVERT: U 47 ASP cc_start: 0.8177 (m-30) cc_final: 0.7896 (m-30) REVERT: U 77 LYS cc_start: 0.7613 (mttt) cc_final: 0.7208 (mtmt) REVERT: U 104 LYS cc_start: 0.8360 (tttt) cc_final: 0.8120 (tmmt) REVERT: U 151 SER cc_start: 0.8200 (t) cc_final: 0.7838 (m) REVERT: U 160 ARG cc_start: 0.7597 (ttt180) cc_final: 0.7284 (ttt180) REVERT: U 205 ASP cc_start: 0.7835 (m-30) cc_final: 0.7610 (m-30) REVERT: V 59 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8833 (pt) REVERT: V 218 MET cc_start: 0.8503 (mmm) cc_final: 0.8115 (mmp) REVERT: V 233 GLN cc_start: 0.8072 (mt0) cc_final: 0.7814 (mt0) REVERT: W 68 SER cc_start: 0.8944 (t) cc_final: 0.8580 (p) REVERT: W 115 SER cc_start: 0.8913 (p) cc_final: 0.8602 (t) REVERT: Y 123 ASP cc_start: 0.8766 (m-30) cc_final: 0.8470 (m-30) REVERT: Y 187 ASP cc_start: 0.8049 (t0) cc_final: 0.7847 (t0) REVERT: Y 191 THR cc_start: 0.9033 (m) cc_final: 0.8670 (p) REVERT: Y 242 SER cc_start: 0.8885 (m) cc_final: 0.8544 (m) REVERT: Z 114 LEU cc_start: 0.8770 (mt) cc_final: 0.8522 (mt) REVERT: 1 208 SER cc_start: 0.7561 (m) cc_final: 0.7344 (m) REVERT: 2 194 SER cc_start: 0.8389 (p) cc_final: 0.8187 (t) REVERT: 2 239 ASP cc_start: 0.8235 (t0) cc_final: 0.7962 (t0) REVERT: 2 256 TRP cc_start: 0.8460 (p-90) cc_final: 0.8165 (p-90) outliers start: 15 outliers final: 7 residues processed: 2274 average time/residue: 0.7111 time to fit residues: 2529.5586 Evaluate side-chains 1396 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1387 time to evaluate : 5.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain K residue 59 LEU Chi-restraints excluded: chain O residue 38 LYS Chi-restraints excluded: chain T residue 185 ARG Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain X residue 237 ARG Chi-restraints excluded: chain Y residue 112 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 514 optimal weight: 6.9990 chunk 461 optimal weight: 0.9990 chunk 256 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 311 optimal weight: 6.9990 chunk 246 optimal weight: 6.9990 chunk 477 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 290 optimal weight: 8.9990 chunk 355 optimal weight: 8.9990 chunk 553 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS C 43 HIS ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 ASN D 171 GLN D 181 GLN ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN F 52 GLN F 88 HIS ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN G 40 ASN G 100 GLN G 102 GLN G 142 HIS G 230 GLN G 235 GLN H 33 GLN I 8 GLN I 168 GLN J 159 GLN J 180 GLN ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 GLN K 202 GLN L 75 ASN ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN M 109 GLN M 207 ASN N 100 GLN N 142 HIS N 240 HIS O 94 HIS ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 182 GLN P 227 HIS Q 43 HIS R 144 ASN R 171 GLN R 181 GLN S 162 HIS T 8 GLN T 27 GLN T 110 HIS T 168 GLN T 193 ASN U 159 GLN U 174 GLN V 83 ASN V 114 GLN V 126 HIS V 149 ASN V 192 GLN W 58 HIS W 105 ASN W 117 HIS X 74 HIS X 105 HIS Y 247 ASN Z 58 HIS ** Z 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 205 HIS 1 105 HIS 2 104 ASN 2 196 ASN 2 234 HIS 2 247 ASN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 49184 Z= 0.387 Angle : 0.701 12.690 66462 Z= 0.370 Chirality : 0.048 0.214 7455 Planarity : 0.005 0.067 8575 Dihedral : 5.412 52.740 6855 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.68 % Favored : 97.31 % Rotamer: Outliers : 3.51 % Allowed : 11.10 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.09), residues: 6164 helix: -0.98 (0.10), residues: 2235 sheet: -0.91 (0.12), residues: 1464 loop : -0.98 (0.12), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 101 HIS 0.011 0.002 HIS I 110 PHE 0.033 0.002 PHE M 199 TYR 0.030 0.002 TYR Y 208 ARG 0.010 0.001 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1609 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1428 time to evaluate : 5.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 SER cc_start: 0.8134 (m) cc_final: 0.7725 (p) REVERT: A 40 ILE cc_start: 0.7245 (tp) cc_final: 0.6846 (tt) REVERT: A 65 LEU cc_start: 0.8780 (mt) cc_final: 0.8515 (mp) REVERT: A 157 LYS cc_start: 0.7543 (mttt) cc_final: 0.7335 (ptpp) REVERT: A 193 LYS cc_start: 0.7213 (mttt) cc_final: 0.6867 (mtmt) REVERT: A 207 GLU cc_start: 0.7585 (tt0) cc_final: 0.7330 (tp30) REVERT: A 228 TYR cc_start: 0.6527 (m-80) cc_final: 0.6004 (m-80) REVERT: B 20 ARG cc_start: 0.7363 (mtm110) cc_final: 0.6743 (mtp85) REVERT: B 104 ASN cc_start: 0.8862 (t0) cc_final: 0.8223 (t0) REVERT: B 134 SER cc_start: 0.8431 (p) cc_final: 0.8197 (t) REVERT: B 157 ASP cc_start: 0.7745 (p0) cc_final: 0.7435 (p0) REVERT: B 172 SER cc_start: 0.8051 (p) cc_final: 0.7695 (t) REVERT: C 67 ASP cc_start: 0.7524 (t0) cc_final: 0.7285 (t70) REVERT: C 94 ASP cc_start: 0.7963 (m-30) cc_final: 0.7527 (m-30) REVERT: C 176 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7408 (ttp) REVERT: C 207 THR cc_start: 0.8389 (p) cc_final: 0.8019 (t) REVERT: D 130 ARG cc_start: 0.8037 (ptt90) cc_final: 0.7747 (ptt90) REVERT: D 145 ASP cc_start: 0.6475 (m-30) cc_final: 0.6240 (m-30) REVERT: D 168 LYS cc_start: 0.7494 (tttt) cc_final: 0.6737 (mtmt) REVERT: E 43 ARG cc_start: 0.8000 (ttp-110) cc_final: 0.7414 (ttp-110) REVERT: E 224 ASN cc_start: 0.6651 (t0) cc_final: 0.6360 (t0) REVERT: F 83 TYR cc_start: 0.8307 (t80) cc_final: 0.7795 (t80) REVERT: F 179 ASN cc_start: 0.5972 (p0) cc_final: 0.5521 (t0) REVERT: G 3 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6788 (ptp-170) REVERT: G 89 GLU cc_start: 0.7816 (tp30) cc_final: 0.7588 (mm-30) REVERT: G 244 GLU cc_start: 0.4790 (mm-30) cc_final: 0.4480 (mt-10) REVERT: H 158 MET cc_start: 0.7853 (mtm) cc_final: 0.7465 (mtp) REVERT: I 12 TYR cc_start: 0.7871 (p90) cc_final: 0.7565 (p90) REVERT: I 35 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7555 (mmm) REVERT: J 104 LYS cc_start: 0.8259 (tttt) cc_final: 0.8020 (tmmt) REVERT: K 218 MET cc_start: 0.8568 (mmm) cc_final: 0.8176 (mmp) REVERT: L 89 SER cc_start: 0.8556 (t) cc_final: 0.8323 (p) REVERT: L 97 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6832 (mm-30) REVERT: M 7 SER cc_start: 0.8772 (m) cc_final: 0.8527 (t) REVERT: M 83 TYR cc_start: 0.8151 (t80) cc_final: 0.7637 (t80) REVERT: M 179 ASN cc_start: 0.6084 (p0) cc_final: 0.5760 (t0) REVERT: N 217 THR cc_start: 0.8332 (m) cc_final: 0.7992 (p) REVERT: O 46 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6744 (mm-30) REVERT: O 65 LEU cc_start: 0.9004 (mt) cc_final: 0.8537 (mp) REVERT: O 157 LYS cc_start: 0.7139 (mttt) cc_final: 0.6446 (ptpp) REVERT: O 190 LEU cc_start: 0.8184 (tp) cc_final: 0.7675 (tp) REVERT: P 20 ARG cc_start: 0.7190 (mtm110) cc_final: 0.6605 (mtp85) REVERT: Q 15 PRO cc_start: 0.8560 (Cg_exo) cc_final: 0.8263 (Cg_endo) REVERT: Q 100 ASP cc_start: 0.7673 (t0) cc_final: 0.7360 (t0) REVERT: R 82 LEU cc_start: 0.8618 (mt) cc_final: 0.7562 (tt) REVERT: R 162 TRP cc_start: 0.7196 (m100) cc_final: 0.6859 (m100) REVERT: R 168 LYS cc_start: 0.7620 (tttt) cc_final: 0.7015 (ptpt) REVERT: S 158 MET cc_start: 0.7957 (mtm) cc_final: 0.7227 (mtp) REVERT: T 12 TYR cc_start: 0.8172 (p90) cc_final: 0.7946 (p90) REVERT: T 35 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7397 (mmm) REVERT: T 155 LYS cc_start: 0.8064 (mttt) cc_final: 0.7699 (tptt) REVERT: U 77 LYS cc_start: 0.7529 (mttt) cc_final: 0.7239 (mtmt) REVERT: U 205 ASP cc_start: 0.8115 (m-30) cc_final: 0.7860 (m-30) REVERT: V 148 MET cc_start: 0.8100 (mmt) cc_final: 0.7882 (mmt) REVERT: V 218 MET cc_start: 0.8537 (mmm) cc_final: 0.8171 (mmp) REVERT: X 75 PHE cc_start: 0.8046 (t80) cc_final: 0.7707 (t80) REVERT: Y 187 ASP cc_start: 0.8210 (t0) cc_final: 0.7945 (t0) REVERT: Z 55 SER cc_start: 0.8277 (t) cc_final: 0.7995 (p) REVERT: Z 114 LEU cc_start: 0.8723 (mt) cc_final: 0.8469 (mt) REVERT: 1 75 PHE cc_start: 0.8151 (t80) cc_final: 0.7776 (t80) REVERT: 2 251 MET cc_start: 0.7685 (tpp) cc_final: 0.7483 (tpp) REVERT: 2 256 TRP cc_start: 0.8561 (p-90) cc_final: 0.8199 (p-90) outliers start: 181 outliers final: 112 residues processed: 1526 average time/residue: 0.6157 time to fit residues: 1522.7455 Evaluate side-chains 1309 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1192 time to evaluate : 5.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain G residue 19 TYR Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 5 SER Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 61 PHE Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 137 CYS Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 213 SER Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain N residue 194 ILE Chi-restraints excluded: chain O residue 38 LYS Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 207 THR Chi-restraints excluded: chain R residue 9 ASP Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain S residue 5 SER Chi-restraints excluded: chain S residue 159 ASP Chi-restraints excluded: chain S residue 196 THR Chi-restraints excluded: chain T residue 35 MET Chi-restraints excluded: chain T residue 194 ILE Chi-restraints excluded: chain U residue 71 CYS Chi-restraints excluded: chain U residue 238 LEU Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 249 SER Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 204 ASP Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 143 ASP Chi-restraints excluded: chain X residue 157 SER Chi-restraints excluded: chain X residue 186 THR Chi-restraints excluded: chain Y residue 112 TYR Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 165 MET Chi-restraints excluded: chain Y residue 202 SER Chi-restraints excluded: chain Z residue 29 ASP Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 197 THR Chi-restraints excluded: chain 1 residue 159 SER Chi-restraints excluded: chain 2 residue 191 THR Chi-restraints excluded: chain 2 residue 202 SER Chi-restraints excluded: chain 2 residue 232 ILE Chi-restraints excluded: chain 2 residue 242 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 307 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 460 optimal weight: 2.9990 chunk 376 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 554 optimal weight: 0.8980 chunk 598 optimal weight: 3.9990 chunk 493 optimal weight: 2.9990 chunk 549 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 444 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 GLN B 186 HIS C 117 GLN D 69 ASN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN J 159 GLN J 180 GLN K 114 GLN L 90 GLN ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 ASN P 178 GLN ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 GLN T 87 ASN U 180 GLN X 130 GLN Y 96 ASN Y 247 ASN Z 117 HIS Z 130 GLN 1 74 HIS 1 130 GLN 2 82 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 49184 Z= 0.276 Angle : 0.597 9.623 66462 Z= 0.316 Chirality : 0.045 0.230 7455 Planarity : 0.004 0.048 8575 Dihedral : 5.051 46.710 6841 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.08 % Favored : 96.90 % Rotamer: Outliers : 3.76 % Allowed : 13.97 % Favored : 82.27 % 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: -0.87 (0.10), residues: 6164 helix: -0.04 (0.10), residues: 2244 sheet: -0.60 (0.12), residues: 1474 loop : -0.90 (0.12), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 216 HIS 0.008 0.001 HIS D 73 PHE 0.026 0.002 PHE F 199 TYR 0.026 0.002 TYR C 153 ARG 0.013 0.001 ARG S 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1475 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1281 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: A 30 SER cc_start: 0.8158 (m) cc_final: 0.7724 (p) REVERT: A 40 ILE cc_start: 0.7194 (tp) cc_final: 0.6716 (tt) REVERT: A 157 LYS cc_start: 0.7648 (mttt) cc_final: 0.7306 (ptpp) REVERT: A 193 LYS cc_start: 0.6886 (mttt) cc_final: 0.6463 (mtmt) REVERT: A 207 GLU cc_start: 0.7621 (tt0) cc_final: 0.7308 (tp30) REVERT: B 106 THR cc_start: 0.8858 (m) cc_final: 0.8648 (p) REVERT: B 134 SER cc_start: 0.8469 (p) cc_final: 0.8233 (t) REVERT: B 172 SER cc_start: 0.8058 (p) cc_final: 0.7738 (t) REVERT: B 210 LEU cc_start: 0.7725 (tp) cc_final: 0.7513 (tp) REVERT: C 67 ASP cc_start: 0.7596 (t0) cc_final: 0.7337 (t70) REVERT: C 159 MET cc_start: 0.7168 (tpt) cc_final: 0.6918 (tpp) REVERT: C 207 THR cc_start: 0.8422 (p) cc_final: 0.8055 (t) REVERT: D 130 ARG cc_start: 0.8021 (ptt90) cc_final: 0.7786 (ptt90) REVERT: D 168 LYS cc_start: 0.7635 (tttt) cc_final: 0.6842 (mtmt) REVERT: D 222 ASN cc_start: 0.8363 (m110) cc_final: 0.8035 (p0) REVERT: E 43 ARG cc_start: 0.7921 (ttp-110) cc_final: 0.7395 (ttp-110) REVERT: E 45 LYS cc_start: 0.7619 (tmmt) cc_final: 0.7283 (tmmt) REVERT: E 93 ARG cc_start: 0.7817 (tpp80) cc_final: 0.7549 (tpt-90) REVERT: F 145 TYR cc_start: 0.8191 (m-80) cc_final: 0.7983 (m-80) REVERT: F 192 ILE cc_start: 0.8253 (mt) cc_final: 0.7988 (pt) REVERT: G 89 GLU cc_start: 0.7802 (tp30) cc_final: 0.7579 (mm-30) REVERT: G 244 GLU cc_start: 0.5165 (mm-30) cc_final: 0.4583 (mt-10) REVERT: H 78 GLU cc_start: 0.7291 (mp0) cc_final: 0.7078 (mp0) REVERT: H 158 MET cc_start: 0.7905 (mtm) cc_final: 0.7494 (mtp) REVERT: H 169 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7629 (mp10) REVERT: H 171 MET cc_start: 0.8757 (tpt) cc_final: 0.8483 (tpt) REVERT: H 172 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8500 (mp) REVERT: I 12 TYR cc_start: 0.7820 (p90) cc_final: 0.7587 (p90) REVERT: I 140 LEU cc_start: 0.8684 (mt) cc_final: 0.8414 (mt) REVERT: K 218 MET cc_start: 0.8571 (mmm) cc_final: 0.8153 (mmp) REVERT: L 89 SER cc_start: 0.8665 (t) cc_final: 0.8437 (p) REVERT: L 97 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7067 (mm-30) REVERT: M 7 SER cc_start: 0.8754 (m) cc_final: 0.8467 (t) REVERT: M 179 ASN cc_start: 0.6015 (p0) cc_final: 0.5792 (t0) REVERT: N 217 THR cc_start: 0.8380 (m) cc_final: 0.8063 (p) REVERT: O 40 ILE cc_start: 0.7201 (tp) cc_final: 0.6673 (tt) REVERT: O 71 MET cc_start: 0.7798 (ptm) cc_final: 0.7566 (ptm) REVERT: O 157 LYS cc_start: 0.7185 (mttt) cc_final: 0.6506 (ptpp) REVERT: P 20 ARG cc_start: 0.7357 (mtm110) cc_final: 0.6656 (mtp85) REVERT: P 172 SER cc_start: 0.8053 (p) cc_final: 0.7706 (t) REVERT: Q 100 ASP cc_start: 0.7655 (t0) cc_final: 0.7402 (t0) REVERT: R 44 ASP cc_start: 0.6908 (m-30) cc_final: 0.6155 (m-30) REVERT: R 168 LYS cc_start: 0.7656 (tttt) cc_final: 0.6798 (ptpt) REVERT: S 158 MET cc_start: 0.7805 (mtm) cc_final: 0.7274 (mtp) REVERT: S 172 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8497 (mp) REVERT: T 92 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8157 (mp) REVERT: U 77 LYS cc_start: 0.7542 (mttt) cc_final: 0.7191 (mtmt) REVERT: U 125 TYR cc_start: 0.9051 (t80) cc_final: 0.8572 (t80) REVERT: V 94 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8272 (t) REVERT: V 148 MET cc_start: 0.8056 (mmt) cc_final: 0.7817 (mmt) REVERT: V 218 MET cc_start: 0.8521 (mmm) cc_final: 0.8141 (mmp) REVERT: X 178 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8189 (mm-30) REVERT: Y 187 ASP cc_start: 0.8232 (t0) cc_final: 0.7909 (t0) REVERT: Y 251 MET cc_start: 0.7962 (tpp) cc_final: 0.7014 (tpp) REVERT: Z 153 TYR cc_start: 0.8377 (m-80) cc_final: 0.7993 (m-80) REVERT: 1 185 MET cc_start: 0.8503 (mtp) cc_final: 0.8285 (mtp) REVERT: 2 159 MET cc_start: 0.7513 (mmm) cc_final: 0.7216 (mmm) outliers start: 194 outliers final: 126 residues processed: 1383 average time/residue: 0.6143 time to fit residues: 1401.4762 Evaluate side-chains 1315 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1185 time to evaluate : 5.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 130 GLU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain G residue 19 TYR Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain H residue 5 SER Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain I residue 118 MET Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 61 PHE Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain J residue 228 LYS Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 137 CYS Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain M residue 199 PHE Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 11 SER Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 ASP Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 35 THR Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 206 THR Chi-restraints excluded: chain Q residue 207 THR Chi-restraints excluded: chain Q residue 228 ASP Chi-restraints excluded: chain R residue 9 ASP Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 159 ASP Chi-restraints excluded: chain S residue 172 LEU Chi-restraints excluded: chain S residue 193 ASP Chi-restraints excluded: chain T residue 33 ASP Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 118 MET Chi-restraints excluded: chain T residue 194 ILE Chi-restraints excluded: chain U residue 71 CYS Chi-restraints excluded: chain U residue 151 SER Chi-restraints excluded: chain U residue 223 VAL Chi-restraints excluded: chain U residue 228 LYS Chi-restraints excluded: chain U residue 238 LEU Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 71 MET Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 249 SER Chi-restraints excluded: chain W residue 113 ASP Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 143 ASP Chi-restraints excluded: chain X residue 157 SER Chi-restraints excluded: chain X residue 186 THR Chi-restraints excluded: chain X residue 254 THR Chi-restraints excluded: chain Y residue 96 ASN Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 112 TYR Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 165 MET Chi-restraints excluded: chain Y residue 191 THR Chi-restraints excluded: chain Y residue 202 SER Chi-restraints excluded: chain Y residue 254 ASP Chi-restraints excluded: chain Z residue 29 ASP Chi-restraints excluded: chain Z residue 117 HIS Chi-restraints excluded: chain 1 residue 143 ASP Chi-restraints excluded: chain 1 residue 159 SER Chi-restraints excluded: chain 2 residue 100 THR Chi-restraints excluded: chain 2 residue 103 VAL Chi-restraints excluded: chain 2 residue 191 THR Chi-restraints excluded: chain 2 residue 202 SER Chi-restraints excluded: chain 2 residue 232 ILE Chi-restraints excluded: chain 2 residue 242 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 547 optimal weight: 9.9990 chunk 416 optimal weight: 0.9990 chunk 287 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 chunk 372 optimal weight: 3.9990 chunk 556 optimal weight: 7.9990 chunk 588 optimal weight: 5.9990 chunk 290 optimal weight: 7.9990 chunk 526 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 175 HIS D 69 ASN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN J 105 HIS J 159 GLN K 126 HIS ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 ASN P 178 GLN Q 175 HIS ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 GLN ** R 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 8 GLN Y 247 ASN ** Y 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 125 GLN Z 130 GLN 1 130 GLN 2 82 HIS 2 196 ASN 2 247 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 49184 Z= 0.551 Angle : 0.728 10.217 66462 Z= 0.382 Chirality : 0.050 0.196 7455 Planarity : 0.005 0.054 8575 Dihedral : 5.376 54.670 6833 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 5.43 % Allowed : 15.19 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.10), residues: 6164 helix: -0.05 (0.10), residues: 2245 sheet: -0.78 (0.12), residues: 1472 loop : -1.10 (0.12), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP D 216 HIS 0.012 0.002 HIS Z 117 PHE 0.029 0.003 PHE T 178 TYR 0.032 0.003 TYR Z 153 ARG 0.009 0.001 ARG L 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1485 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1205 time to evaluate : 5.378 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: A 30 SER cc_start: 0.7895 (m) cc_final: 0.7564 (p) REVERT: A 40 ILE cc_start: 0.7167 (tp) cc_final: 0.6724 (tt) REVERT: A 65 LEU cc_start: 0.8895 (mt) cc_final: 0.8497 (mp) REVERT: A 193 LYS cc_start: 0.7188 (mttt) cc_final: 0.6740 (mtmt) REVERT: B 10 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7826 (mtp85) REVERT: B 91 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8166 (ttpt) REVERT: B 134 SER cc_start: 0.8347 (p) cc_final: 0.8111 (t) REVERT: B 172 SER cc_start: 0.8125 (p) cc_final: 0.7896 (t) REVERT: B 210 LEU cc_start: 0.7799 (tp) cc_final: 0.7587 (tp) REVERT: C 9 ASP cc_start: 0.7331 (t0) cc_final: 0.6929 (t0) REVERT: C 207 THR cc_start: 0.8656 (p) cc_final: 0.8345 (t) REVERT: D 130 ARG cc_start: 0.8124 (ptt90) cc_final: 0.7890 (ptt90) REVERT: D 168 LYS cc_start: 0.7849 (tttt) cc_final: 0.7085 (mtmt) REVERT: E 43 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.6900 (ttp-170) REVERT: E 45 LYS cc_start: 0.7687 (tmmt) cc_final: 0.7261 (tmmt) REVERT: E 93 ARG cc_start: 0.7956 (tpp80) cc_final: 0.7719 (tpt-90) REVERT: G 117 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8102 (mm) REVERT: G 212 GLU cc_start: 0.7779 (pp20) cc_final: 0.6806 (mp0) REVERT: H 78 GLU cc_start: 0.7526 (mp0) cc_final: 0.7246 (mp0) REVERT: H 158 MET cc_start: 0.8074 (mtm) cc_final: 0.7777 (mtp) REVERT: H 159 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7324 (t70) REVERT: H 169 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7730 (mm-40) REVERT: H 172 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8546 (mp) REVERT: I 109 GLU cc_start: 0.5987 (pm20) cc_final: 0.5650 (pm20) REVERT: J 101 LYS cc_start: 0.8451 (mttm) cc_final: 0.8244 (mttp) REVERT: K 218 MET cc_start: 0.8588 (mmm) cc_final: 0.8227 (mmp) REVERT: L 89 SER cc_start: 0.8605 (t) cc_final: 0.8331 (p) REVERT: M 182 LEU cc_start: 0.7427 (tt) cc_final: 0.7157 (mp) REVERT: O 40 ILE cc_start: 0.7254 (tp) cc_final: 0.6766 (tt) REVERT: O 71 MET cc_start: 0.7805 (ptm) cc_final: 0.7561 (ptm) REVERT: P 44 GLU cc_start: 0.6252 (tt0) cc_final: 0.6015 (tt0) REVERT: P 91 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8287 (ttpt) REVERT: P 172 SER cc_start: 0.8124 (p) cc_final: 0.7845 (t) REVERT: Q 100 ASP cc_start: 0.7692 (t0) cc_final: 0.7409 (t0) REVERT: Q 164 ARG cc_start: 0.7841 (mtt90) cc_final: 0.7499 (mtm110) REVERT: R 44 ASP cc_start: 0.7078 (m-30) cc_final: 0.6342 (m-30) REVERT: R 168 LYS cc_start: 0.7960 (tttt) cc_final: 0.7271 (mtmt) REVERT: S 158 MET cc_start: 0.7827 (mtm) cc_final: 0.7473 (mtp) REVERT: S 169 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7698 (mm-40) REVERT: S 172 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8480 (mp) REVERT: S 198 ARG cc_start: 0.7792 (mtt90) cc_final: 0.7506 (mtt-85) REVERT: U 160 ARG cc_start: 0.7735 (ttt180) cc_final: 0.7529 (ttt180) REVERT: V 94 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8313 (t) REVERT: V 106 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8415 (mt0) REVERT: V 145 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8544 (ttt90) REVERT: V 148 MET cc_start: 0.8012 (mmt) cc_final: 0.7742 (mmt) REVERT: V 218 MET cc_start: 0.8567 (mmm) cc_final: 0.8205 (mmp) REVERT: V 233 GLN cc_start: 0.7747 (mt0) cc_final: 0.7396 (mt0) REVERT: Y 82 HIS cc_start: 0.8197 (m-70) cc_final: 0.7889 (m-70) REVERT: Y 187 ASP cc_start: 0.8322 (t0) cc_final: 0.8100 (t0) REVERT: Y 251 MET cc_start: 0.7888 (tpp) cc_final: 0.7455 (tpp) REVERT: 1 161 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8731 (pp) REVERT: 2 117 MET cc_start: 0.7623 (ttm) cc_final: 0.7408 (mtp) REVERT: 2 251 MET cc_start: 0.7816 (tpp) cc_final: 0.7570 (tpp) outliers start: 280 outliers final: 199 residues processed: 1362 average time/residue: 0.6159 time to fit residues: 1385.7891 Evaluate side-chains 1341 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1131 time to evaluate : 5.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 130 GLU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 92 LYS Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 199 PHE Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain G residue 19 TYR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 5 SER Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 61 PHE Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 260 ILE Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 137 CYS Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain L residue 213 SER Chi-restraints excluded: chain L residue 240 VAL Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 212 ILE Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 19 TYR Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain O residue 4 ASP Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 ASP Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 163 ARG Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 170 ILE Chi-restraints excluded: chain P residue 211 ASN Chi-restraints excluded: chain Q residue 9 ASP Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 35 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 139 ASP Chi-restraints excluded: chain Q residue 186 GLU Chi-restraints excluded: chain Q residue 206 THR Chi-restraints excluded: chain Q residue 207 THR Chi-restraints excluded: chain Q residue 228 ASP Chi-restraints excluded: chain R residue 9 ASP Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 131 MET Chi-restraints excluded: chain S residue 150 CYS Chi-restraints excluded: chain S residue 159 ASP Chi-restraints excluded: chain S residue 171 MET Chi-restraints excluded: chain S residue 172 LEU Chi-restraints excluded: chain S residue 193 ASP Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 31 ASP Chi-restraints excluded: chain T residue 33 ASP Chi-restraints excluded: chain T residue 163 CYS Chi-restraints excluded: chain T residue 194 ILE Chi-restraints excluded: chain U residue 71 CYS Chi-restraints excluded: chain U residue 151 SER Chi-restraints excluded: chain U residue 223 VAL Chi-restraints excluded: chain U residue 238 LEU Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 71 MET Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 106 GLN Chi-restraints excluded: chain V residue 145 ARG Chi-restraints excluded: chain V residue 170 VAL Chi-restraints excluded: chain V residue 249 SER Chi-restraints excluded: chain W residue 113 ASP Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 143 ASP Chi-restraints excluded: chain X residue 157 SER Chi-restraints excluded: chain X residue 186 THR Chi-restraints excluded: chain X residue 254 THR Chi-restraints excluded: chain Y residue 112 TYR Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 149 SER Chi-restraints excluded: chain Y residue 165 MET Chi-restraints excluded: chain Y residue 191 THR Chi-restraints excluded: chain Y residue 202 SER Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 254 ASP Chi-restraints excluded: chain Z residue 29 ASP Chi-restraints excluded: chain Z residue 113 ASP Chi-restraints excluded: chain Z residue 197 THR Chi-restraints excluded: chain 1 residue 52 ILE Chi-restraints excluded: chain 1 residue 143 ASP Chi-restraints excluded: chain 1 residue 159 SER Chi-restraints excluded: chain 1 residue 161 LEU Chi-restraints excluded: chain 1 residue 254 THR Chi-restraints excluded: chain 2 residue 100 THR Chi-restraints excluded: chain 2 residue 149 SER Chi-restraints excluded: chain 2 residue 191 THR Chi-restraints excluded: chain 2 residue 202 SER Chi-restraints excluded: chain 2 residue 232 ILE Chi-restraints excluded: chain 2 residue 242 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 490 optimal weight: 0.9980 chunk 334 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 438 optimal weight: 2.9990 chunk 242 optimal weight: 0.0050 chunk 502 optimal weight: 0.8980 chunk 406 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 300 optimal weight: 0.9980 chunk 528 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 HIS B 186 HIS D 69 ASN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 ASN J 159 GLN ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 ASN ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 178 GLN R 181 GLN T 193 ASN U 107 ASN W 125 GLN Y 96 ASN Y 247 ASN Z 117 HIS Z 125 GLN 1 130 GLN 2 161 GLN 2 237 HIS 2 247 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 49184 Z= 0.175 Angle : 0.551 8.415 66462 Z= 0.292 Chirality : 0.043 0.170 7455 Planarity : 0.004 0.055 8575 Dihedral : 4.803 46.096 6831 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.81 % Favored : 97.14 % Rotamer: Outliers : 3.80 % Allowed : 17.54 % Favored : 78.66 % 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: -0.47 (0.10), residues: 6164 helix: 0.58 (0.11), residues: 2240 sheet: -0.51 (0.13), residues: 1459 loop : -0.90 (0.12), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 216 HIS 0.022 0.001 HIS B 186 PHE 0.029 0.001 PHE O 73 TYR 0.027 0.001 TYR C 153 ARG 0.012 0.001 ARG D 170 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1458 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1262 time to evaluate : 5.400 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: A 40 ILE cc_start: 0.7058 (tp) cc_final: 0.6627 (tt) REVERT: A 193 LYS cc_start: 0.7014 (mttt) cc_final: 0.6472 (mtmt) REVERT: A 207 GLU cc_start: 0.7648 (tt0) cc_final: 0.7377 (tp30) REVERT: B 104 ASN cc_start: 0.8918 (t0) cc_final: 0.8502 (t0) REVERT: B 134 SER cc_start: 0.8293 (p) cc_final: 0.8072 (t) REVERT: C 38 LEU cc_start: 0.8345 (pt) cc_final: 0.8105 (pt) REVERT: C 164 ARG cc_start: 0.7641 (mtt90) cc_final: 0.7185 (mtm110) REVERT: C 207 THR cc_start: 0.8598 (p) cc_final: 0.8282 (t) REVERT: D 168 LYS cc_start: 0.7748 (tttt) cc_final: 0.6866 (ptpt) REVERT: E 43 ARG cc_start: 0.7692 (ttp-110) cc_final: 0.6847 (ttp-170) REVERT: E 45 LYS cc_start: 0.7985 (tmmt) cc_final: 0.7670 (tmmt) REVERT: E 76 ILE cc_start: 0.8143 (mt) cc_final: 0.7828 (mt) REVERT: E 118 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8502 (mm) REVERT: F 192 ILE cc_start: 0.8112 (mt) cc_final: 0.7808 (pt) REVERT: G 1 MET cc_start: 0.5388 (OUTLIER) cc_final: 0.4706 (ttm) REVERT: G 89 GLU cc_start: 0.7797 (tp30) cc_final: 0.7596 (mm-30) REVERT: G 108 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6918 (mt-10) REVERT: H 78 GLU cc_start: 0.7344 (mp0) cc_final: 0.6948 (mp0) REVERT: H 158 MET cc_start: 0.7977 (mtm) cc_final: 0.7621 (mtp) REVERT: H 159 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7090 (t70) REVERT: H 169 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7543 (mm-40) REVERT: H 171 MET cc_start: 0.8830 (tpt) cc_final: 0.8584 (tpt) REVERT: H 172 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8528 (mp) REVERT: I 166 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6334 (mm-30) REVERT: J 101 LYS cc_start: 0.8480 (mttm) cc_final: 0.8278 (mttp) REVERT: K 52 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8479 (p) REVERT: K 94 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8255 (t) REVERT: K 218 MET cc_start: 0.8542 (mmm) cc_final: 0.8105 (mmp) REVERT: M 192 ILE cc_start: 0.8036 (mt) cc_final: 0.7772 (pt) REVERT: O 65 LEU cc_start: 0.8883 (mt) cc_final: 0.8528 (mp) REVERT: O 71 MET cc_start: 0.7385 (ptm) cc_final: 0.7173 (ptm) REVERT: O 215 GLN cc_start: 0.7169 (mp10) cc_final: 0.6605 (mp10) REVERT: P 135 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8429 (ptt-90) REVERT: P 172 SER cc_start: 0.8157 (p) cc_final: 0.7861 (t) REVERT: R 44 ASP cc_start: 0.6958 (m-30) cc_final: 0.6270 (m-30) REVERT: R 61 GLU cc_start: 0.6022 (mp0) cc_final: 0.5767 (mp0) REVERT: R 91 ILE cc_start: 0.8017 (tt) cc_final: 0.7738 (mt) REVERT: R 168 LYS cc_start: 0.7797 (tttt) cc_final: 0.6956 (ptpt) REVERT: S 158 MET cc_start: 0.7794 (mtm) cc_final: 0.7302 (mtp) REVERT: S 165 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7348 (mm-30) REVERT: S 172 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8437 (mp) REVERT: S 198 ARG cc_start: 0.7639 (mtt90) cc_final: 0.7308 (mtt-85) REVERT: V 94 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8207 (t) REVERT: V 145 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8050 (ttt90) REVERT: V 148 MET cc_start: 0.7948 (mmt) cc_final: 0.7695 (mmt) REVERT: V 218 MET cc_start: 0.8495 (mmm) cc_final: 0.8127 (mmp) REVERT: X 58 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7918 (ttt180) REVERT: X 75 PHE cc_start: 0.7930 (t80) cc_final: 0.7558 (t80) REVERT: Y 187 ASP cc_start: 0.8234 (t0) cc_final: 0.7973 (t0) REVERT: Y 251 MET cc_start: 0.7779 (tpp) cc_final: 0.7037 (tpp) REVERT: 1 75 PHE cc_start: 0.7980 (t80) cc_final: 0.7581 (t80) REVERT: 2 82 HIS cc_start: 0.7976 (m-70) cc_final: 0.7547 (m90) REVERT: 2 117 MET cc_start: 0.7592 (ttm) cc_final: 0.7337 (mtp) REVERT: 2 251 MET cc_start: 0.7620 (tpp) cc_final: 0.7226 (tpp) outliers start: 196 outliers final: 118 residues processed: 1360 average time/residue: 0.5879 time to fit residues: 1316.4091 Evaluate side-chains 1293 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1163 time to evaluate : 5.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 130 GLU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 199 PHE Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain H residue 5 SER Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 118 MET Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 61 PHE Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 137 CYS Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 ASP Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 163 ARG Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 135 ARG Chi-restraints excluded: chain P residue 170 ILE Chi-restraints excluded: chain P residue 178 GLN Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 139 ASP Chi-restraints excluded: chain Q residue 207 THR Chi-restraints excluded: chain Q residue 228 ASP Chi-restraints excluded: chain R residue 9 ASP Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 172 LEU Chi-restraints excluded: chain S residue 193 ASP Chi-restraints excluded: chain T residue 31 ASP Chi-restraints excluded: chain T residue 33 ASP Chi-restraints excluded: chain T residue 118 MET Chi-restraints excluded: chain T residue 194 ILE Chi-restraints excluded: chain U residue 71 CYS Chi-restraints excluded: chain U residue 151 SER Chi-restraints excluded: chain U residue 223 VAL Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain V residue 145 ARG Chi-restraints excluded: chain W residue 113 ASP Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 58 ARG Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 143 ASP Chi-restraints excluded: chain X residue 158 TYR Chi-restraints excluded: chain X residue 186 THR Chi-restraints excluded: chain X residue 254 THR Chi-restraints excluded: chain Y residue 96 ASN Chi-restraints excluded: chain Y residue 112 TYR Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 189 ASN Chi-restraints excluded: chain Y residue 254 ASP Chi-restraints excluded: chain Z residue 29 ASP Chi-restraints excluded: chain Z residue 113 ASP Chi-restraints excluded: chain Z residue 125 GLN Chi-restraints excluded: chain 1 residue 52 ILE Chi-restraints excluded: chain 1 residue 143 ASP Chi-restraints excluded: chain 1 residue 159 SER Chi-restraints excluded: chain 1 residue 254 THR Chi-restraints excluded: chain 2 residue 100 THR Chi-restraints excluded: chain 2 residue 124 CYS Chi-restraints excluded: chain 2 residue 189 ASN Chi-restraints excluded: chain 2 residue 232 ILE Chi-restraints excluded: chain 2 residue 242 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 198 optimal weight: 4.9990 chunk 530 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 345 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 589 optimal weight: 5.9990 chunk 489 optimal weight: 8.9990 chunk 272 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 309 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 HIS F 96 GLN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 ASN I 8 GLN J 105 HIS J 159 GLN ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 GLN S 18 ASN T 8 GLN W 125 GLN Y 234 HIS Y 247 ASN Y 250 HIS Z 117 HIS 2 96 ASN 2 247 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.095 49184 Z= 0.577 Angle : 0.746 8.213 66462 Z= 0.390 Chirality : 0.050 0.249 7455 Planarity : 0.005 0.062 8575 Dihedral : 5.315 45.519 6831 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.62 % Favored : 95.34 % Rotamer: Outliers : 5.31 % Allowed : 17.71 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -0.93 (0.10), residues: 6164 helix: 0.23 (0.11), residues: 2243 sheet: -0.76 (0.13), residues: 1460 loop : -1.19 (0.12), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP R 216 HIS 0.010 0.002 HIS Z 117 PHE 0.028 0.003 PHE O 73 TYR 0.031 0.003 TYR C 153 ARG 0.009 0.001 ARG L 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1458 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 1184 time to evaluate : 5.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ILE cc_start: 0.7165 (tp) cc_final: 0.6705 (tt) REVERT: A 65 LEU cc_start: 0.8866 (mt) cc_final: 0.8581 (mp) REVERT: A 193 LYS cc_start: 0.6645 (mttt) cc_final: 0.6118 (mtmt) REVERT: A 228 TYR cc_start: 0.6453 (m-80) cc_final: 0.6214 (m-80) REVERT: B 10 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8021 (mtp85) REVERT: B 104 ASN cc_start: 0.8997 (t0) cc_final: 0.8538 (t0) REVERT: C 38 LEU cc_start: 0.8504 (pt) cc_final: 0.8239 (pt) REVERT: C 207 THR cc_start: 0.8487 (p) cc_final: 0.8189 (t) REVERT: D 137 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7680 (ptt) REVERT: D 168 LYS cc_start: 0.8008 (tttt) cc_final: 0.7170 (mtmt) REVERT: E 29 PHE cc_start: 0.7715 (m-10) cc_final: 0.7486 (m-80) REVERT: E 43 ARG cc_start: 0.7997 (ttp-110) cc_final: 0.6844 (ttp-170) REVERT: E 45 LYS cc_start: 0.7914 (tmmt) cc_final: 0.7549 (tmmt) REVERT: E 118 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8597 (mm) REVERT: E 217 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8299 (p) REVERT: G 108 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6969 (mt-10) REVERT: G 117 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8085 (mm) REVERT: H 78 GLU cc_start: 0.7414 (mp0) cc_final: 0.7067 (mp0) REVERT: H 172 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8547 (mp) REVERT: I 155 LYS cc_start: 0.7915 (mttt) cc_final: 0.7519 (tptt) REVERT: I 166 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6643 (mm-30) REVERT: J 194 LEU cc_start: 0.7340 (tp) cc_final: 0.7132 (pt) REVERT: K 94 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8443 (t) REVERT: K 143 SER cc_start: 0.9207 (OUTLIER) cc_final: 0.8822 (t) REVERT: K 218 MET cc_start: 0.8623 (mmm) cc_final: 0.8272 (mmp) REVERT: L 21 ARG cc_start: 0.8754 (mtm180) cc_final: 0.8521 (mtm180) REVERT: N 119 GLN cc_start: 0.8358 (tm-30) cc_final: 0.8141 (tm-30) REVERT: O 24 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7028 (tm-30) REVERT: O 65 LEU cc_start: 0.8991 (mt) cc_final: 0.8522 (mp) REVERT: O 71 MET cc_start: 0.7750 (ptm) cc_final: 0.7541 (ptm) REVERT: P 104 ASN cc_start: 0.9008 (t0) cc_final: 0.8154 (t0) REVERT: P 135 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8364 (ptt-90) REVERT: P 172 SER cc_start: 0.8204 (p) cc_final: 0.7871 (t) REVERT: R 44 ASP cc_start: 0.7214 (m-30) cc_final: 0.6556 (m-30) REVERT: R 61 GLU cc_start: 0.6146 (mp0) cc_final: 0.5824 (mp0) REVERT: R 168 LYS cc_start: 0.8065 (tttt) cc_final: 0.7222 (ptpt) REVERT: S 158 MET cc_start: 0.7917 (mtm) cc_final: 0.7471 (mtp) REVERT: S 172 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8570 (mp) REVERT: U 104 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7618 (ttpt) REVERT: U 160 ARG cc_start: 0.7823 (ttt180) cc_final: 0.7613 (ttt180) REVERT: U 194 LEU cc_start: 0.7449 (tp) cc_final: 0.7224 (pt) REVERT: V 94 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8339 (t) REVERT: V 145 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8461 (ttt90) REVERT: V 148 MET cc_start: 0.7950 (mmt) cc_final: 0.7678 (mmt) REVERT: V 218 MET cc_start: 0.8596 (mmm) cc_final: 0.8260 (mmp) REVERT: V 227 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8577 (mtt-85) REVERT: X 75 PHE cc_start: 0.8124 (t80) cc_final: 0.7744 (t80) REVERT: Y 82 HIS cc_start: 0.8217 (m-70) cc_final: 0.7925 (m-70) REVERT: 2 82 HIS cc_start: 0.8149 (m-70) cc_final: 0.7660 (m90) REVERT: 2 251 MET cc_start: 0.7886 (tpp) cc_final: 0.7486 (tpp) outliers start: 274 outliers final: 202 residues processed: 1343 average time/residue: 0.6262 time to fit residues: 1387.0813 Evaluate side-chains 1341 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1123 time to evaluate : 6.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 130 GLU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 199 PHE Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain G residue 19 TYR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 17 LYS Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 61 PHE Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 260 ILE Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 137 CYS Chi-restraints excluded: chain L residue 163 PHE Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 201 CYS Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain M residue 199 PHE Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain N residue 19 TYR Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain O residue 4 ASP Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 24 GLU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 ASP Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 121 SER Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 148 ASP Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 135 ARG Chi-restraints excluded: chain P residue 147 ASP Chi-restraints excluded: chain P residue 170 ILE Chi-restraints excluded: chain P residue 211 ASN Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 139 ASP Chi-restraints excluded: chain Q residue 183 ASN Chi-restraints excluded: chain Q residue 206 THR Chi-restraints excluded: chain Q residue 207 THR Chi-restraints excluded: chain Q residue 222 THR Chi-restraints excluded: chain Q residue 228 ASP Chi-restraints excluded: chain R residue 9 ASP Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 131 MET Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 172 LEU Chi-restraints excluded: chain S residue 193 ASP Chi-restraints excluded: chain T residue 31 ASP Chi-restraints excluded: chain T residue 33 ASP Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 118 MET Chi-restraints excluded: chain T residue 163 CYS Chi-restraints excluded: chain T residue 194 ILE Chi-restraints excluded: chain U residue 71 CYS Chi-restraints excluded: chain U residue 104 LYS Chi-restraints excluded: chain U residue 151 SER Chi-restraints excluded: chain U residue 238 LEU Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain V residue 145 ARG Chi-restraints excluded: chain V residue 164 GLU Chi-restraints excluded: chain V residue 227 ARG Chi-restraints excluded: chain W residue 113 ASP Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 68 LYS Chi-restraints excluded: chain X residue 143 ASP Chi-restraints excluded: chain X residue 157 SER Chi-restraints excluded: chain X residue 186 THR Chi-restraints excluded: chain X residue 254 THR Chi-restraints excluded: chain Y residue 112 TYR Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 165 MET Chi-restraints excluded: chain Y residue 191 THR Chi-restraints excluded: chain Y residue 193 LEU Chi-restraints excluded: chain Y residue 211 MET Chi-restraints excluded: chain Y residue 232 ILE Chi-restraints excluded: chain Y residue 254 ASP Chi-restraints excluded: chain Z residue 29 ASP Chi-restraints excluded: chain Z residue 109 LYS Chi-restraints excluded: chain Z residue 113 ASP Chi-restraints excluded: chain Z residue 117 HIS Chi-restraints excluded: chain Z residue 197 THR Chi-restraints excluded: chain 1 residue 49 ASP Chi-restraints excluded: chain 1 residue 51 VAL Chi-restraints excluded: chain 1 residue 52 ILE Chi-restraints excluded: chain 1 residue 82 CYS Chi-restraints excluded: chain 1 residue 143 ASP Chi-restraints excluded: chain 1 residue 159 SER Chi-restraints excluded: chain 1 residue 254 THR Chi-restraints excluded: chain 2 residue 96 ASN Chi-restraints excluded: chain 2 residue 100 THR Chi-restraints excluded: chain 2 residue 191 THR Chi-restraints excluded: chain 2 residue 202 SER Chi-restraints excluded: chain 2 residue 232 ILE Chi-restraints excluded: chain 2 residue 242 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 568 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 335 optimal weight: 4.9990 chunk 430 optimal weight: 1.9990 chunk 333 optimal weight: 1.9990 chunk 496 optimal weight: 1.9990 chunk 329 optimal weight: 0.9990 chunk 586 optimal weight: 0.9990 chunk 367 optimal weight: 0.9990 chunk 357 optimal weight: 7.9990 chunk 270 optimal weight: 0.5980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN I 110 HIS J 105 HIS J 159 GLN L 75 ASN ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 GLN V 106 GLN W 101 ASN W 125 GLN Y 247 ASN ** Z 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 117 HIS Z 125 GLN 2 96 ASN 2 247 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 49184 Z= 0.210 Angle : 0.573 8.095 66462 Z= 0.302 Chirality : 0.044 0.183 7455 Planarity : 0.004 0.058 8575 Dihedral : 4.887 46.889 6831 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.39 % Favored : 96.56 % Rotamer: Outliers : 3.95 % Allowed : 19.30 % Favored : 76.74 % 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 (0.10), residues: 6164 helix: 0.72 (0.11), residues: 2240 sheet: -0.58 (0.13), residues: 1448 loop : -1.03 (0.12), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 216 HIS 0.011 0.001 HIS Z 117 PHE 0.029 0.001 PHE O 73 TYR 0.027 0.001 TYR 2 97 ARG 0.008 0.000 ARG S 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1407 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1203 time to evaluate : 5.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ILE cc_start: 0.7048 (tp) cc_final: 0.6605 (tt) REVERT: A 193 LYS cc_start: 0.6426 (mttt) cc_final: 0.5879 (mtmt) REVERT: B 10 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8049 (mtp85) REVERT: B 104 ASN cc_start: 0.8884 (t0) cc_final: 0.8478 (t0) REVERT: C 38 LEU cc_start: 0.8367 (pt) cc_final: 0.8069 (pt) REVERT: C 207 THR cc_start: 0.8444 (p) cc_final: 0.8133 (t) REVERT: D 94 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7281 (mm-30) REVERT: D 168 LYS cc_start: 0.7976 (tttt) cc_final: 0.7128 (mtmt) REVERT: E 43 ARG cc_start: 0.7770 (ttp-110) cc_final: 0.6819 (ttp-170) REVERT: E 76 ILE cc_start: 0.8149 (mt) cc_final: 0.7905 (mt) REVERT: E 118 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8542 (mm) REVERT: E 217 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8237 (p) REVERT: E 232 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6514 (pt0) REVERT: F 192 ILE cc_start: 0.8003 (mt) cc_final: 0.7663 (pt) REVERT: G 1 MET cc_start: 0.5503 (ttm) cc_final: 0.4301 (ttp) REVERT: G 108 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6866 (mt-10) REVERT: H 78 GLU cc_start: 0.7337 (mp0) cc_final: 0.6915 (mp0) REVERT: H 158 MET cc_start: 0.7993 (mtm) cc_final: 0.7668 (mtp) REVERT: H 172 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8598 (mp) REVERT: I 155 LYS cc_start: 0.7832 (mttt) cc_final: 0.7408 (tptt) REVERT: I 166 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6456 (mm-30) REVERT: J 201 ARG cc_start: 0.6834 (ttm-80) cc_final: 0.6548 (ttm-80) REVERT: K 94 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8317 (t) REVERT: K 143 SER cc_start: 0.9166 (OUTLIER) cc_final: 0.8807 (t) REVERT: K 155 MET cc_start: 0.7679 (mmm) cc_final: 0.7446 (mmt) REVERT: K 218 MET cc_start: 0.8557 (mmm) cc_final: 0.8169 (mmp) REVERT: L 141 ILE cc_start: 0.9014 (pt) cc_final: 0.8764 (pt) REVERT: M 135 LEU cc_start: 0.8454 (mt) cc_final: 0.8248 (mt) REVERT: M 145 TYR cc_start: 0.8161 (m-80) cc_final: 0.7739 (m-80) REVERT: O 40 ILE cc_start: 0.7294 (tp) cc_final: 0.6867 (tt) REVERT: O 65 LEU cc_start: 0.8916 (mt) cc_final: 0.8481 (mp) REVERT: O 217 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7491 (mp) REVERT: P 104 ASN cc_start: 0.8909 (t0) cc_final: 0.8479 (t0) REVERT: P 135 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8441 (ptt-90) REVERT: P 172 SER cc_start: 0.8177 (p) cc_final: 0.7837 (t) REVERT: Q 38 LEU cc_start: 0.8478 (pt) cc_final: 0.8224 (pt) REVERT: R 44 ASP cc_start: 0.7195 (m-30) cc_final: 0.6558 (m-30) REVERT: R 61 GLU cc_start: 0.6066 (mp0) cc_final: 0.5821 (mp0) REVERT: R 168 LYS cc_start: 0.7949 (tttt) cc_final: 0.7018 (ptpt) REVERT: S 149 MET cc_start: 0.8268 (mmm) cc_final: 0.8015 (mmm) REVERT: S 158 MET cc_start: 0.7897 (mtm) cc_final: 0.7355 (mtp) REVERT: S 172 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8475 (mp) REVERT: S 198 ARG cc_start: 0.7687 (mtt90) cc_final: 0.7467 (mtt-85) REVERT: T 184 ASP cc_start: 0.8473 (p0) cc_final: 0.8052 (p0) REVERT: U 104 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7685 (ttpt) REVERT: U 194 LEU cc_start: 0.7486 (tp) cc_final: 0.7237 (pt) REVERT: V 94 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8174 (t) REVERT: V 145 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8143 (ttt90) REVERT: V 148 MET cc_start: 0.7919 (mmt) cc_final: 0.7673 (mmt) REVERT: V 218 MET cc_start: 0.8482 (mmm) cc_final: 0.8082 (mmp) REVERT: X 75 PHE cc_start: 0.7994 (t80) cc_final: 0.7657 (t80) REVERT: Y 82 HIS cc_start: 0.8144 (m-70) cc_final: 0.7625 (m90) REVERT: 1 75 PHE cc_start: 0.8040 (t80) cc_final: 0.7601 (t80) REVERT: 2 82 HIS cc_start: 0.8056 (m-70) cc_final: 0.7586 (m90) REVERT: 2 191 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8649 (p) REVERT: 2 251 MET cc_start: 0.7791 (tpp) cc_final: 0.7007 (tpp) outliers start: 204 outliers final: 149 residues processed: 1317 average time/residue: 0.6438 time to fit residues: 1400.7530 Evaluate side-chains 1332 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1168 time to evaluate : 5.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 130 GLU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 199 PHE Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain G residue 19 TYR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 118 MET Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 61 PHE Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 137 CYS Chi-restraints excluded: chain L residue 201 CYS Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain O residue 4 ASP Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 17 PHE Chi-restraints excluded: chain O residue 38 LYS Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 ASP Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 121 SER Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 217 LEU Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 135 ARG Chi-restraints excluded: chain P residue 147 ASP Chi-restraints excluded: chain P residue 170 ILE Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 139 ASP Chi-restraints excluded: chain Q residue 183 ASN Chi-restraints excluded: chain Q residue 207 THR Chi-restraints excluded: chain Q residue 228 ASP Chi-restraints excluded: chain R residue 9 ASP Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 172 LEU Chi-restraints excluded: chain S residue 193 ASP Chi-restraints excluded: chain T residue 31 ASP Chi-restraints excluded: chain T residue 33 ASP Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 163 CYS Chi-restraints excluded: chain T residue 194 ILE Chi-restraints excluded: chain U residue 61 PHE Chi-restraints excluded: chain U residue 71 CYS Chi-restraints excluded: chain U residue 104 LYS Chi-restraints excluded: chain U residue 151 SER Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain V residue 145 ARG Chi-restraints excluded: chain V residue 164 GLU Chi-restraints excluded: chain V residue 249 SER Chi-restraints excluded: chain W residue 113 ASP Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 68 LYS Chi-restraints excluded: chain X residue 143 ASP Chi-restraints excluded: chain X residue 157 SER Chi-restraints excluded: chain X residue 186 THR Chi-restraints excluded: chain X residue 254 THR Chi-restraints excluded: chain Y residue 112 TYR Chi-restraints excluded: chain Y residue 191 THR Chi-restraints excluded: chain Y residue 193 LEU Chi-restraints excluded: chain Y residue 254 ASP Chi-restraints excluded: chain Z residue 29 ASP Chi-restraints excluded: chain Z residue 109 LYS Chi-restraints excluded: chain Z residue 113 ASP Chi-restraints excluded: chain Z residue 117 HIS Chi-restraints excluded: chain 1 residue 52 ILE Chi-restraints excluded: chain 1 residue 82 CYS Chi-restraints excluded: chain 1 residue 143 ASP Chi-restraints excluded: chain 1 residue 159 SER Chi-restraints excluded: chain 1 residue 254 THR Chi-restraints excluded: chain 2 residue 96 ASN Chi-restraints excluded: chain 2 residue 100 THR Chi-restraints excluded: chain 2 residue 189 ASN Chi-restraints excluded: chain 2 residue 191 THR Chi-restraints excluded: chain 2 residue 202 SER Chi-restraints excluded: chain 2 residue 232 ILE Chi-restraints excluded: chain 2 residue 242 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 363 optimal weight: 5.9990 chunk 234 optimal weight: 0.7980 chunk 350 optimal weight: 0.0030 chunk 176 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 373 optimal weight: 0.9990 chunk 399 optimal weight: 5.9990 chunk 290 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 461 optimal weight: 4.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 159 GLN L 75 ASN ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 120 GLN ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 GLN W 125 GLN X 191 GLN Y 142 ASN Y 247 ASN ** Z 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 125 GLN 2 247 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 49184 Z= 0.196 Angle : 0.564 9.007 66462 Z= 0.296 Chirality : 0.043 0.233 7455 Planarity : 0.004 0.062 8575 Dihedral : 4.740 47.995 6831 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 3.76 % Allowed : 19.59 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.10), residues: 6164 helix: 0.91 (0.11), residues: 2245 sheet: -0.45 (0.13), residues: 1438 loop : -0.97 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 216 HIS 0.015 0.001 HIS Z 117 PHE 0.030 0.001 PHE O 73 TYR 0.028 0.001 TYR C 153 ARG 0.008 0.000 ARG D 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1383 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1189 time to evaluate : 5.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ILE cc_start: 0.7059 (tp) cc_final: 0.6594 (tt) REVERT: A 193 LYS cc_start: 0.6393 (mttt) cc_final: 0.5826 (mtmt) REVERT: A 207 GLU cc_start: 0.7634 (tt0) cc_final: 0.7384 (tp30) REVERT: B 10 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8035 (mtp85) REVERT: B 104 ASN cc_start: 0.8877 (t0) cc_final: 0.8480 (t0) REVERT: B 134 SER cc_start: 0.8823 (t) cc_final: 0.8512 (t) REVERT: C 38 LEU cc_start: 0.8342 (pt) cc_final: 0.8055 (pt) REVERT: C 207 THR cc_start: 0.8478 (p) cc_final: 0.8176 (t) REVERT: D 94 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7140 (mm-30) REVERT: D 168 LYS cc_start: 0.8022 (tttt) cc_final: 0.7110 (mtmt) REVERT: E 43 ARG cc_start: 0.7642 (ttp-110) cc_final: 0.7015 (ttp-110) REVERT: E 76 ILE cc_start: 0.8163 (mt) cc_final: 0.7888 (mt) REVERT: E 118 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8348 (mm) REVERT: E 232 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6537 (pt0) REVERT: F 192 ILE cc_start: 0.8093 (mt) cc_final: 0.7822 (pt) REVERT: G 1 MET cc_start: 0.5540 (OUTLIER) cc_final: 0.4255 (ttp) REVERT: G 108 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6834 (mt-10) REVERT: G 200 THR cc_start: 0.8231 (t) cc_final: 0.8030 (m) REVERT: H 158 MET cc_start: 0.7948 (mtm) cc_final: 0.7632 (mtp) REVERT: I 155 LYS cc_start: 0.7826 (mttt) cc_final: 0.7412 (tptt) REVERT: I 166 GLU cc_start: 0.6700 (mm-30) cc_final: 0.6168 (mm-30) REVERT: I 185 ARG cc_start: 0.7745 (ptm160) cc_final: 0.7505 (ptm160) REVERT: K 94 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8350 (t) REVERT: K 143 SER cc_start: 0.9130 (OUTLIER) cc_final: 0.8774 (t) REVERT: K 218 MET cc_start: 0.8524 (mmm) cc_final: 0.8143 (mmp) REVERT: L 43 ARG cc_start: 0.7575 (ttp-110) cc_final: 0.6766 (ttp-110) REVERT: L 141 ILE cc_start: 0.8999 (pt) cc_final: 0.8742 (pt) REVERT: M 6 TYR cc_start: 0.8594 (m-10) cc_final: 0.8361 (m-10) REVERT: M 145 TYR cc_start: 0.8235 (m-80) cc_final: 0.7909 (m-80) REVERT: M 192 ILE cc_start: 0.7967 (mt) cc_final: 0.7743 (pt) REVERT: O 40 ILE cc_start: 0.7290 (tp) cc_final: 0.6858 (tt) REVERT: O 56 GLU cc_start: 0.6998 (pm20) cc_final: 0.6505 (tt0) REVERT: O 65 LEU cc_start: 0.8825 (mt) cc_final: 0.8549 (mp) REVERT: O 120 GLN cc_start: 0.8135 (tt0) cc_final: 0.7932 (tt0) REVERT: O 217 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7406 (mt) REVERT: P 104 ASN cc_start: 0.8882 (t0) cc_final: 0.8454 (t0) REVERT: P 135 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8236 (ptt-90) REVERT: P 172 SER cc_start: 0.8147 (p) cc_final: 0.7817 (t) REVERT: Q 38 LEU cc_start: 0.8588 (pt) cc_final: 0.8337 (pt) REVERT: Q 159 MET cc_start: 0.7293 (tpt) cc_final: 0.7063 (tpt) REVERT: Q 176 MET cc_start: 0.7237 (ttp) cc_final: 0.6882 (ttp) REVERT: R 61 GLU cc_start: 0.6031 (mp0) cc_final: 0.5688 (mp0) REVERT: R 145 ASP cc_start: 0.6318 (m-30) cc_final: 0.5967 (m-30) REVERT: R 168 LYS cc_start: 0.7937 (tttt) cc_final: 0.6974 (ptpt) REVERT: S 149 MET cc_start: 0.8203 (mmm) cc_final: 0.7989 (mmm) REVERT: S 158 MET cc_start: 0.7884 (mtm) cc_final: 0.7410 (mtp) REVERT: S 169 GLN cc_start: 0.7694 (mm-40) cc_final: 0.7485 (mm-40) REVERT: S 172 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8480 (mp) REVERT: S 198 ARG cc_start: 0.7683 (mtt90) cc_final: 0.7434 (mtt-85) REVERT: U 194 LEU cc_start: 0.7529 (tp) cc_final: 0.7236 (pt) REVERT: V 94 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8206 (t) REVERT: V 145 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8035 (ttt90) REVERT: V 148 MET cc_start: 0.7952 (mmt) cc_final: 0.7730 (mmt) REVERT: V 218 MET cc_start: 0.8535 (mmm) cc_final: 0.8152 (mmp) REVERT: X 58 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7518 (ttt180) REVERT: X 75 PHE cc_start: 0.7968 (t80) cc_final: 0.7630 (t80) REVERT: Y 82 HIS cc_start: 0.8118 (m-70) cc_final: 0.7848 (m-70) REVERT: 1 75 PHE cc_start: 0.7942 (t80) cc_final: 0.7513 (t80) REVERT: 2 82 HIS cc_start: 0.8077 (m-70) cc_final: 0.7584 (m90) REVERT: 2 191 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8566 (p) REVERT: 2 251 MET cc_start: 0.7753 (tpp) cc_final: 0.7380 (tpt) outliers start: 194 outliers final: 149 residues processed: 1294 average time/residue: 0.6000 time to fit residues: 1278.0791 Evaluate side-chains 1328 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1165 time to evaluate : 5.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 130 GLU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 199 PHE Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 19 TYR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 118 MET Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 61 PHE Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 137 CYS Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain L residue 201 CYS Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 219 GLU Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain O residue 4 ASP Chi-restraints excluded: chain O residue 17 PHE Chi-restraints excluded: chain O residue 38 LYS Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 ASP Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 121 SER Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 217 LEU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 135 ARG Chi-restraints excluded: chain P residue 147 ASP Chi-restraints excluded: chain P residue 170 ILE Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 139 ASP Chi-restraints excluded: chain Q residue 207 THR Chi-restraints excluded: chain Q residue 228 ASP Chi-restraints excluded: chain R residue 9 ASP Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 172 LEU Chi-restraints excluded: chain S residue 193 ASP Chi-restraints excluded: chain T residue 31 ASP Chi-restraints excluded: chain T residue 33 ASP Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 163 CYS Chi-restraints excluded: chain T residue 194 ILE Chi-restraints excluded: chain U residue 61 PHE Chi-restraints excluded: chain U residue 228 LYS Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain V residue 145 ARG Chi-restraints excluded: chain V residue 164 GLU Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 58 ARG Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 68 LYS Chi-restraints excluded: chain X residue 143 ASP Chi-restraints excluded: chain X residue 157 SER Chi-restraints excluded: chain X residue 158 TYR Chi-restraints excluded: chain X residue 186 THR Chi-restraints excluded: chain X residue 254 THR Chi-restraints excluded: chain Y residue 112 TYR Chi-restraints excluded: chain Y residue 189 ASN Chi-restraints excluded: chain Y residue 191 THR Chi-restraints excluded: chain Y residue 232 ILE Chi-restraints excluded: chain Y residue 254 ASP Chi-restraints excluded: chain Z residue 29 ASP Chi-restraints excluded: chain Z residue 109 LYS Chi-restraints excluded: chain Z residue 113 ASP Chi-restraints excluded: chain Z residue 125 GLN Chi-restraints excluded: chain 1 residue 52 ILE Chi-restraints excluded: chain 1 residue 82 CYS Chi-restraints excluded: chain 1 residue 143 ASP Chi-restraints excluded: chain 1 residue 159 SER Chi-restraints excluded: chain 1 residue 254 THR Chi-restraints excluded: chain 2 residue 100 THR Chi-restraints excluded: chain 2 residue 191 THR Chi-restraints excluded: chain 2 residue 202 SER Chi-restraints excluded: chain 2 residue 232 ILE Chi-restraints excluded: chain 2 residue 242 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 533 optimal weight: 4.9990 chunk 562 optimal weight: 4.9990 chunk 513 optimal weight: 0.9990 chunk 546 optimal weight: 0.9980 chunk 329 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 429 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 494 optimal weight: 0.9990 chunk 517 optimal weight: 3.9990 chunk 545 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN I 27 GLN J 159 GLN L 75 ASN ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 GLN T 8 GLN U 107 ASN V 110 GLN W 125 GLN Y 247 ASN ** Z 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 117 HIS Z 125 GLN 2 247 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 49184 Z= 0.199 Angle : 0.567 11.147 66462 Z= 0.296 Chirality : 0.044 0.241 7455 Planarity : 0.004 0.056 8575 Dihedral : 4.651 47.589 6829 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.41 % Favored : 96.54 % Rotamer: Outliers : 3.57 % Allowed : 20.23 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.19 (0.11), residues: 6164 helix: 1.01 (0.11), residues: 2249 sheet: -0.38 (0.13), residues: 1430 loop : -0.93 (0.12), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 216 HIS 0.006 0.001 HIS Z 117 PHE 0.028 0.001 PHE O 73 TYR 0.028 0.001 TYR Q 153 ARG 0.012 0.000 ARG D 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1367 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1183 time to evaluate : 5.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ILE cc_start: 0.7042 (tp) cc_final: 0.6582 (tt) REVERT: A 71 MET cc_start: 0.7635 (ptm) cc_final: 0.7416 (ptm) REVERT: A 193 LYS cc_start: 0.6362 (mttt) cc_final: 0.5767 (mtmt) REVERT: A 207 GLU cc_start: 0.7662 (tt0) cc_final: 0.7392 (tp30) REVERT: B 10 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8099 (mtp85) REVERT: B 104 ASN cc_start: 0.8884 (t0) cc_final: 0.8466 (t0) REVERT: B 134 SER cc_start: 0.8739 (t) cc_final: 0.8420 (t) REVERT: C 38 LEU cc_start: 0.8334 (pt) cc_final: 0.8052 (pt) REVERT: C 88 MET cc_start: 0.8266 (mtm) cc_final: 0.7906 (mtm) REVERT: C 207 THR cc_start: 0.8440 (p) cc_final: 0.8130 (t) REVERT: D 94 GLU cc_start: 0.7214 (mm-30) cc_final: 0.7001 (mm-30) REVERT: D 168 LYS cc_start: 0.8009 (tttt) cc_final: 0.6896 (ptpt) REVERT: E 43 ARG cc_start: 0.7697 (ttp-110) cc_final: 0.6989 (ttp-110) REVERT: E 76 ILE cc_start: 0.8143 (mt) cc_final: 0.7848 (mt) REVERT: E 232 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6389 (pt0) REVERT: F 145 TYR cc_start: 0.8311 (m-80) cc_final: 0.7786 (m-80) REVERT: G 1 MET cc_start: 0.5500 (ttm) cc_final: 0.4216 (ttp) REVERT: G 108 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6822 (mt-10) REVERT: H 158 MET cc_start: 0.7999 (mtm) cc_final: 0.7615 (mtp) REVERT: H 171 MET cc_start: 0.8833 (tpt) cc_final: 0.8599 (tpt) REVERT: I 155 LYS cc_start: 0.7829 (mttt) cc_final: 0.7450 (tptt) REVERT: I 185 ARG cc_start: 0.7768 (ptm160) cc_final: 0.7514 (ptm160) REVERT: K 94 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8354 (t) REVERT: K 143 SER cc_start: 0.9145 (OUTLIER) cc_final: 0.8795 (t) REVERT: K 218 MET cc_start: 0.8536 (mmm) cc_final: 0.8121 (mmp) REVERT: L 141 ILE cc_start: 0.8994 (pt) cc_final: 0.8762 (pt) REVERT: M 145 TYR cc_start: 0.8231 (m-80) cc_final: 0.7881 (m-80) REVERT: O 40 ILE cc_start: 0.7282 (tp) cc_final: 0.6865 (tt) REVERT: O 163 ARG cc_start: 0.6609 (ptm160) cc_final: 0.6361 (ptm160) REVERT: O 217 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7351 (mp) REVERT: P 104 ASN cc_start: 0.8868 (t0) cc_final: 0.8462 (t0) REVERT: P 135 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8315 (ptt-90) REVERT: P 172 SER cc_start: 0.8128 (p) cc_final: 0.7809 (t) REVERT: Q 38 LEU cc_start: 0.8492 (pt) cc_final: 0.8244 (pt) REVERT: Q 159 MET cc_start: 0.7234 (tpt) cc_final: 0.7022 (tpt) REVERT: Q 164 ARG cc_start: 0.7784 (mtt90) cc_final: 0.7327 (mtm110) REVERT: Q 176 MET cc_start: 0.7362 (ttp) cc_final: 0.6961 (ttp) REVERT: R 61 GLU cc_start: 0.6026 (mp0) cc_final: 0.5680 (mp0) REVERT: R 145 ASP cc_start: 0.6208 (m-30) cc_final: 0.5880 (m-30) REVERT: R 168 LYS cc_start: 0.7936 (tttt) cc_final: 0.6940 (ptpt) REVERT: S 14 MET cc_start: 0.8404 (mmt) cc_final: 0.8141 (mmt) REVERT: S 158 MET cc_start: 0.7888 (mtm) cc_final: 0.7333 (mtp) REVERT: S 169 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7460 (mm-40) REVERT: S 172 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8452 (mp) REVERT: S 198 ARG cc_start: 0.7679 (mtt90) cc_final: 0.7429 (mtt-85) REVERT: U 160 ARG cc_start: 0.7718 (ttt180) cc_final: 0.7516 (ttt180) REVERT: U 194 LEU cc_start: 0.7524 (tp) cc_final: 0.7226 (pt) REVERT: V 94 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8207 (t) REVERT: V 145 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7970 (ttt90) REVERT: V 148 MET cc_start: 0.8044 (mmt) cc_final: 0.7841 (mmt) REVERT: V 218 MET cc_start: 0.8527 (mmm) cc_final: 0.8154 (mmp) REVERT: X 58 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7641 (ttt180) REVERT: X 75 PHE cc_start: 0.7902 (t80) cc_final: 0.7560 (t80) REVERT: Y 82 HIS cc_start: 0.8098 (m-70) cc_final: 0.7815 (m-70) REVERT: 1 75 PHE cc_start: 0.7926 (t80) cc_final: 0.7509 (t80) REVERT: 2 82 HIS cc_start: 0.8067 (m-70) cc_final: 0.7570 (m90) REVERT: 2 251 MET cc_start: 0.7588 (tpp) cc_final: 0.7164 (tpt) outliers start: 184 outliers final: 155 residues processed: 1288 average time/residue: 0.5946 time to fit residues: 1254.8260 Evaluate side-chains 1313 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1147 time to evaluate : 5.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 130 GLU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 199 PHE Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain G residue 19 TYR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 118 MET Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 61 PHE Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 137 CYS Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain L residue 201 CYS Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 167 TYR Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 219 GLU Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain O residue 4 ASP Chi-restraints excluded: chain O residue 17 PHE Chi-restraints excluded: chain O residue 38 LYS Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 ASP Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 121 SER Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 217 LEU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 135 ARG Chi-restraints excluded: chain P residue 147 ASP Chi-restraints excluded: chain P residue 170 ILE Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 139 ASP Chi-restraints excluded: chain Q residue 207 THR Chi-restraints excluded: chain Q residue 228 ASP Chi-restraints excluded: chain R residue 9 ASP Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 17 LYS Chi-restraints excluded: chain S residue 172 LEU Chi-restraints excluded: chain S residue 193 ASP Chi-restraints excluded: chain T residue 31 ASP Chi-restraints excluded: chain T residue 33 ASP Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 118 MET Chi-restraints excluded: chain T residue 163 CYS Chi-restraints excluded: chain T residue 194 ILE Chi-restraints excluded: chain U residue 61 PHE Chi-restraints excluded: chain U residue 223 VAL Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain V residue 145 ARG Chi-restraints excluded: chain V residue 164 GLU Chi-restraints excluded: chain W residue 113 ASP Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 58 ARG Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 143 ASP Chi-restraints excluded: chain X residue 157 SER Chi-restraints excluded: chain X residue 158 TYR Chi-restraints excluded: chain X residue 186 THR Chi-restraints excluded: chain Y residue 112 TYR Chi-restraints excluded: chain Y residue 189 ASN Chi-restraints excluded: chain Y residue 191 THR Chi-restraints excluded: chain Y residue 202 SER Chi-restraints excluded: chain Y residue 232 ILE Chi-restraints excluded: chain Y residue 254 ASP Chi-restraints excluded: chain Z residue 29 ASP Chi-restraints excluded: chain Z residue 109 LYS Chi-restraints excluded: chain Z residue 113 ASP Chi-restraints excluded: chain 1 residue 82 CYS Chi-restraints excluded: chain 1 residue 143 ASP Chi-restraints excluded: chain 1 residue 159 SER Chi-restraints excluded: chain 1 residue 254 THR Chi-restraints excluded: chain 2 residue 100 THR Chi-restraints excluded: chain 2 residue 189 ASN Chi-restraints excluded: chain 2 residue 191 THR Chi-restraints excluded: chain 2 residue 232 ILE Chi-restraints excluded: chain 2 residue 242 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 359 optimal weight: 2.9990 chunk 578 optimal weight: 3.9990 chunk 353 optimal weight: 2.9990 chunk 274 optimal weight: 0.8980 chunk 402 optimal weight: 3.9990 chunk 606 optimal weight: 4.9990 chunk 558 optimal weight: 6.9990 chunk 483 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 373 optimal weight: 0.9990 chunk 296 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 HIS D 69 ASN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN I 87 ASN J 159 GLN L 75 ASN ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 GLN T 71 ASN V 110 GLN ** V 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 125 GLN Y 247 ASN Z 101 ASN Z 117 HIS Z 125 GLN 2 247 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 49184 Z= 0.276 Angle : 0.599 11.594 66462 Z= 0.312 Chirality : 0.045 0.267 7455 Planarity : 0.004 0.066 8575 Dihedral : 4.735 47.792 6829 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.91 % Favored : 96.03 % Rotamer: Outliers : 3.59 % Allowed : 20.43 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.23 (0.11), residues: 6164 helix: 0.97 (0.11), residues: 2243 sheet: -0.43 (0.13), residues: 1437 loop : -0.95 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 216 HIS 0.009 0.001 HIS Z 117 PHE 0.027 0.002 PHE O 73 TYR 0.030 0.002 TYR C 153 ARG 0.016 0.001 ARG D 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1349 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1164 time to evaluate : 5.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ILE cc_start: 0.7055 (tp) cc_final: 0.6591 (tt) REVERT: A 193 LYS cc_start: 0.6437 (mttt) cc_final: 0.5860 (mtmt) REVERT: A 207 GLU cc_start: 0.7671 (tt0) cc_final: 0.7393 (tp30) REVERT: B 10 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8172 (mtp85) REVERT: B 104 ASN cc_start: 0.8891 (t0) cc_final: 0.8481 (t0) REVERT: C 38 LEU cc_start: 0.8370 (pt) cc_final: 0.8086 (pt) REVERT: C 207 THR cc_start: 0.8449 (p) cc_final: 0.8147 (t) REVERT: E 43 ARG cc_start: 0.7708 (ttp-110) cc_final: 0.6908 (ttp-110) REVERT: E 76 ILE cc_start: 0.8200 (mt) cc_final: 0.7883 (mt) REVERT: E 232 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6314 (pt0) REVERT: F 145 TYR cc_start: 0.8353 (m-80) cc_final: 0.7813 (m-80) REVERT: G 1 MET cc_start: 0.5427 (ttm) cc_final: 0.5169 (mmt) REVERT: G 108 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6846 (mt-10) REVERT: H 17 LYS cc_start: 0.7448 (tppt) cc_final: 0.7234 (tptp) REVERT: I 155 LYS cc_start: 0.7863 (mttt) cc_final: 0.7481 (tptt) REVERT: I 185 ARG cc_start: 0.7748 (ptm160) cc_final: 0.7507 (ptm160) REVERT: K 94 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8325 (t) REVERT: K 143 SER cc_start: 0.9063 (OUTLIER) cc_final: 0.8765 (t) REVERT: K 218 MET cc_start: 0.8484 (mmm) cc_final: 0.8130 (mmp) REVERT: L 21 ARG cc_start: 0.8692 (mtm180) cc_final: 0.8479 (mtm180) REVERT: L 141 ILE cc_start: 0.8978 (pt) cc_final: 0.8752 (pt) REVERT: L 214 GLU cc_start: 0.6242 (mm-30) cc_final: 0.5914 (tp30) REVERT: M 145 TYR cc_start: 0.8227 (m-80) cc_final: 0.7932 (m-80) REVERT: O 24 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6813 (tm-30) REVERT: O 40 ILE cc_start: 0.7305 (tp) cc_final: 0.6894 (tt) REVERT: O 217 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7496 (mp) REVERT: P 104 ASN cc_start: 0.8882 (t0) cc_final: 0.8456 (t0) REVERT: P 172 SER cc_start: 0.8201 (p) cc_final: 0.7900 (t) REVERT: Q 159 MET cc_start: 0.7333 (tpt) cc_final: 0.7068 (tpt) REVERT: Q 164 ARG cc_start: 0.7813 (mtt90) cc_final: 0.7182 (mtm110) REVERT: Q 176 MET cc_start: 0.7404 (ttp) cc_final: 0.7015 (ttp) REVERT: R 44 ASP cc_start: 0.7119 (m-30) cc_final: 0.6593 (m-30) REVERT: R 145 ASP cc_start: 0.6366 (m-30) cc_final: 0.6050 (m-30) REVERT: R 168 LYS cc_start: 0.8038 (tttt) cc_final: 0.6881 (ptpt) REVERT: S 149 MET cc_start: 0.8357 (mmm) cc_final: 0.8126 (mmm) REVERT: S 158 MET cc_start: 0.7914 (mtm) cc_final: 0.7337 (mtp) REVERT: S 169 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7399 (mm-40) REVERT: S 172 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8453 (mp) REVERT: S 198 ARG cc_start: 0.7738 (mtt90) cc_final: 0.7480 (mtt-85) REVERT: U 160 ARG cc_start: 0.7801 (ttt180) cc_final: 0.7573 (ttt180) REVERT: U 194 LEU cc_start: 0.7487 (tp) cc_final: 0.7173 (pt) REVERT: V 94 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8183 (t) REVERT: V 145 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8154 (ttt90) REVERT: V 148 MET cc_start: 0.8109 (mmt) cc_final: 0.7890 (mmt) REVERT: V 218 MET cc_start: 0.8487 (mmm) cc_final: 0.8132 (mmp) REVERT: V 227 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8590 (mtt-85) REVERT: X 58 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7579 (ttt180) REVERT: X 75 PHE cc_start: 0.7978 (t80) cc_final: 0.7637 (t80) REVERT: Y 82 HIS cc_start: 0.8078 (m-70) cc_final: 0.7799 (m-70) REVERT: Y 108 GLU cc_start: 0.7493 (mm-30) cc_final: 0.6952 (mt-10) REVERT: 1 75 PHE cc_start: 0.8008 (t80) cc_final: 0.7601 (t80) REVERT: 2 82 HIS cc_start: 0.8092 (m-70) cc_final: 0.7629 (m90) REVERT: 2 108 GLU cc_start: 0.7291 (mm-30) cc_final: 0.7041 (mm-30) REVERT: 2 159 MET cc_start: 0.7231 (mtm) cc_final: 0.6736 (mtt) REVERT: 2 187 ASP cc_start: 0.8232 (t0) cc_final: 0.7856 (t0) REVERT: 2 191 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8546 (p) REVERT: 2 251 MET cc_start: 0.7591 (tpp) cc_final: 0.7299 (tpt) outliers start: 185 outliers final: 155 residues processed: 1274 average time/residue: 0.5989 time to fit residues: 1256.8281 Evaluate side-chains 1315 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1147 time to evaluate : 6.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 130 GLU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain G residue 19 TYR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 193 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain I residue 118 MET Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 61 PHE Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 137 CYS Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain L residue 201 CYS Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 167 TYR Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 219 GLU Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain O residue 4 ASP Chi-restraints excluded: chain O residue 17 PHE Chi-restraints excluded: chain O residue 24 GLU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 ASP Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 113 SER Chi-restraints excluded: chain O residue 121 SER Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 217 LEU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 147 ASP Chi-restraints excluded: chain P residue 170 ILE Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 139 ASP Chi-restraints excluded: chain Q residue 207 THR Chi-restraints excluded: chain Q residue 228 ASP Chi-restraints excluded: chain R residue 9 ASP Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 172 LEU Chi-restraints excluded: chain S residue 193 ASP Chi-restraints excluded: chain T residue 31 ASP Chi-restraints excluded: chain T residue 33 ASP Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 118 MET Chi-restraints excluded: chain T residue 163 CYS Chi-restraints excluded: chain U residue 61 PHE Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain V residue 145 ARG Chi-restraints excluded: chain V residue 164 GLU Chi-restraints excluded: chain V residue 227 ARG Chi-restraints excluded: chain V residue 249 SER Chi-restraints excluded: chain W residue 113 ASP Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 58 ARG Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 143 ASP Chi-restraints excluded: chain X residue 157 SER Chi-restraints excluded: chain X residue 186 THR Chi-restraints excluded: chain Y residue 112 TYR Chi-restraints excluded: chain Y residue 189 ASN Chi-restraints excluded: chain Y residue 191 THR Chi-restraints excluded: chain Y residue 202 SER Chi-restraints excluded: chain Y residue 254 ASP Chi-restraints excluded: chain Z residue 29 ASP Chi-restraints excluded: chain Z residue 109 LYS Chi-restraints excluded: chain Z residue 113 ASP Chi-restraints excluded: chain Z residue 117 HIS Chi-restraints excluded: chain 1 residue 52 ILE Chi-restraints excluded: chain 1 residue 82 CYS Chi-restraints excluded: chain 1 residue 143 ASP Chi-restraints excluded: chain 1 residue 159 SER Chi-restraints excluded: chain 1 residue 254 THR Chi-restraints excluded: chain 2 residue 100 THR Chi-restraints excluded: chain 2 residue 189 ASN Chi-restraints excluded: chain 2 residue 191 THR Chi-restraints excluded: chain 2 residue 232 ILE Chi-restraints excluded: chain 2 residue 242 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 609 random chunks: chunk 383 optimal weight: 0.3980 chunk 514 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 445 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 483 optimal weight: 0.5980 chunk 202 optimal weight: 0.7980 chunk 496 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN D 181 GLN ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN F 119 GLN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN H 33 GLN J 159 GLN L 75 ASN ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 GLN V 110 GLN ** V 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 247 ASN Z 117 HIS 2 247 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.157217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128752 restraints weight = 62109.071| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.07 r_work: 0.3377 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 49184 Z= 0.174 Angle : 0.569 11.121 66462 Z= 0.297 Chirality : 0.043 0.318 7455 Planarity : 0.004 0.067 8575 Dihedral : 4.606 46.946 6829 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 3.33 % Allowed : 20.89 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.01 (0.11), residues: 6164 helix: 1.21 (0.11), residues: 2225 sheet: -0.31 (0.13), residues: 1440 loop : -0.85 (0.12), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP Y 256 HIS 0.026 0.001 HIS Z 117 PHE 0.028 0.001 PHE O 73 TYR 0.031 0.001 TYR F 24 ARG 0.015 0.000 ARG D 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20187.70 seconds wall clock time: 360 minutes 39.68 seconds (21639.68 seconds total)