Starting phenix.real_space_refine on Mon Mar 11 03:35:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t08_40938/03_2024/8t08_40938.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t08_40938/03_2024/8t08_40938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t08_40938/03_2024/8t08_40938.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t08_40938/03_2024/8t08_40938.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t08_40938/03_2024/8t08_40938.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t08_40938/03_2024/8t08_40938.pdb" } resolution = 3.0 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= 0.003 sd= 0.105 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 202 5.16 5 C 35064 2.51 5 N 9242 2.21 5 O 10596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 141": "OE1" <-> "OE2" Residue "B TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H GLU 120": "OE1" <-> "OE2" Residue "I PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 97": "OE1" <-> "OE2" Residue "S GLU 141": "OE1" <-> "OE2" Residue "S TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 89": "OE1" <-> "OE2" Residue "Y GLU 120": "OE1" <-> "OE2" Residue "Z PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 97": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 55104 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1823 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1891 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 12, 'TRANS': 234} Chain: "C" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1827 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain breaks: 1 Chain: "D" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1752 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 3 Chain: "E" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1881 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain breaks: 1 Chain: "F" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1803 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain: "G" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1809 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 9, 'TRANS': 224} Chain breaks: 2 Chain: "H" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 977 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain breaks: 1 Chain: "I" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1738 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Chain: "J" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1359 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 6, 'TRANS': 168} Chain breaks: 2 Chain: "K" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain breaks: 3 Chain: "L" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 821 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 3 Chain: "M" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1590 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain breaks: 1 Chain: "N" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1550 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 197} Chain: "O" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1845 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 218} Chain breaks: 2 Chain: "P" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1852 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 213} Chain breaks: 5 Chain: "Q" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1576 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain breaks: 1 Chain: "R" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1823 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "S" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1891 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 12, 'TRANS': 234} Chain: "T" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1827 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain breaks: 1 Chain: "U" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1752 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 3 Chain: "V" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1881 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain breaks: 1 Chain: "W" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1803 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain: "X" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1809 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 9, 'TRANS': 224} Chain breaks: 2 Chain: "Y" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 977 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain breaks: 1 Chain: "Z" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1738 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Chain: "a" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1359 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 6, 'TRANS': 168} Chain breaks: 2 Chain: "b" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain breaks: 3 Chain: "c" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 821 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 3 Chain: "d" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1590 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain breaks: 1 Chain: "e" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1550 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 197} Chain: "f" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1845 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 218} Chain breaks: 2 Chain: "g" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1852 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 213} Chain breaks: 5 Chain: "h" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1576 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain breaks: 1 Time building chain proxies: 21.08, per 1000 atoms: 0.38 Number of scatterers: 55104 At special positions: 0 Unit cell: (210.94, 208.82, 137.8, 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 202 16.00 O 10596 8.00 N 9242 7.00 C 35064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS W 66 " - pdb=" SG CYS W 92 " distance=2.04 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: 15.30 Conformation dependent library (CDL) restraints added in 7.4 seconds 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13032 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 72 sheets defined 40.8% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.66 Creating SS restraints... Processing helix chain 'A' and resid 11 through 16 removed outlier: 4.006A pdb=" N HIS A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.599A pdb=" N PHE A 32 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.523A pdb=" N THR A 68 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 109 removed outlier: 4.153A pdb=" N ALA A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 131 removed outlier: 3.614A pdb=" N TYR A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.641A pdb=" N ASN A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 215 removed outlier: 3.840A pdb=" N VAL A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'B' and resid 18 through 31 Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 78 through 96 removed outlier: 3.504A pdb=" N HIS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.728A pdb=" N ALA B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 178 Processing helix chain 'B' and resid 184 through 200 removed outlier: 3.521A pdb=" N GLU B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 239 through 249 removed outlier: 3.524A pdb=" N ALA B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 30 Processing helix chain 'C' and resid 80 through 103 removed outlier: 3.964A pdb=" N ILE C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.548A pdb=" N THR C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 185 through 201 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 231 through 243 Processing helix chain 'D' and resid 17 through 29 removed outlier: 3.646A pdb=" N LEU D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 26 " --> pdb=" O TYR D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 removed outlier: 3.913A pdb=" N THR D 60 " --> pdb=" O THR D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 100 removed outlier: 3.524A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 168 through 179 Processing helix chain 'D' and resid 187 through 201 removed outlier: 3.627A pdb=" N GLU D 201 " --> pdb=" O ARG D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 Processing helix chain 'E' and resid 21 through 34 removed outlier: 3.632A pdb=" N LEU E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 81 through 104 removed outlier: 4.124A pdb=" N SER E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 122 through 124 No H-bonds generated for 'chain 'E' and resid 122 through 124' Processing helix chain 'E' and resid 175 through 187 Processing helix chain 'E' and resid 192 through 208 removed outlier: 3.569A pdb=" N GLN E 206 " --> pdb=" O LYS E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 247 Processing helix chain 'F' and resid 2 through 7 removed outlier: 3.938A pdb=" N TYR F 6 " --> pdb=" O PHE F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 29 removed outlier: 3.724A pdb=" N ALA F 25 " --> pdb=" O GLN F 21 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE 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 77 through 100 removed outlier: 3.947A pdb=" N SER F 96 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU F 97 " --> pdb=" O ASN F 93 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL F 98 " --> pdb=" O TYR F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 120 removed outlier: 3.654A pdb=" N LEU F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP F 114 " --> pdb=" O HIS F 110 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR F 120 " --> pdb=" O ALA F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 175 removed outlier: 4.456A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 180 removed outlier: 3.639A pdb=" N ILE F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 199 removed outlier: 3.650A pdb=" N GLN F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 231 Processing helix chain 'G' and resid 21 through 33 Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 123 removed outlier: 3.717A pdb=" N HIS G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 183 Processing helix chain 'G' and resid 188 through 204 removed outlier: 3.536A pdb=" N VAL G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 225 Processing helix chain 'G' and resid 232 through 243 removed outlier: 3.613A pdb=" N LEU G 236 " --> pdb=" O LYS G 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 47 Processing helix chain 'H' and resid 51 through 59 removed outlier: 4.283A pdb=" N SER H 55 " --> pdb=" O HIS H 51 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR H 56 " --> pdb=" O PRO H 52 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 77 Processing helix chain 'H' and resid 78 through 95 Processing helix chain 'H' and resid 104 through 112 removed outlier: 3.694A pdb=" N ILE H 109 " --> pdb=" O ILE H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 123 Processing helix chain 'H' and resid 137 through 147 removed outlier: 3.782A pdb=" N LYS H 141 " --> pdb=" O ASP H 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 18 Processing helix chain 'I' and resid 77 through 100 Processing helix chain 'I' and resid 104 through 119 removed outlier: 3.519A pdb=" N ALA I 108 " --> pdb=" O ARG I 104 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR I 119 " --> pdb=" O HIS I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.568A pdb=" N VAL I 166 " --> pdb=" O ALA I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 195 Processing helix chain 'J' and resid 56 through 79 Processing helix chain 'J' and resid 83 through 97 removed outlier: 3.546A pdb=" N GLN J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 154 removed outlier: 3.535A pdb=" N LEU J 146 " --> pdb=" O ALA J 142 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY J 148 " --> pdb=" O ASP J 144 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET J 149 " --> pdb=" O GLN J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 175 Processing helix chain 'K' and resid 51 through 72 removed outlier: 3.922A pdb=" N PHE K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 93 Processing helix chain 'K' and resid 134 through 138 removed outlier: 3.712A pdb=" N PHE K 138 " --> pdb=" O TYR K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 148 removed outlier: 3.857A pdb=" N LEU K 143 " --> pdb=" O TYR K 139 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS K 146 " --> pdb=" O PHE K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 172 Processing helix chain 'L' and resid 127 through 145 Processing helix chain 'L' and resid 150 through 165 Processing helix chain 'M' and resid 76 through 98 Processing helix chain 'M' and resid 104 through 118 Processing helix chain 'M' and resid 161 through 174 Proline residue: M 167 - end of helix removed outlier: 3.578A pdb=" N GLN M 172 " --> pdb=" O PHE M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 198 through 214 Processing helix chain 'N' and resid 68 through 90 removed outlier: 3.691A pdb=" N GLN N 88 " --> pdb=" O LEU N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 108 Processing helix chain 'N' and resid 149 through 152 Processing helix chain 'N' and resid 153 through 161 removed outlier: 3.566A pdb=" N ASP N 158 " --> pdb=" O TYR N 154 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS N 159 " --> pdb=" O GLY N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 185 Processing helix chain 'N' and resid 208 through 213 removed outlier: 3.549A pdb=" N TYR N 212 " --> pdb=" O TYR N 208 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 47 Processing helix chain 'O' and resid 54 through 61 Proline residue: O 59 - end of helix Processing helix chain 'O' and resid 62 through 67 removed outlier: 3.638A pdb=" N GLN O 67 " --> pdb=" O LYS O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 159 removed outlier: 3.988A pdb=" N GLY O 147 " --> pdb=" O SER O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 206 Processing helix chain 'O' and resid 231 through 247 removed outlier: 3.717A pdb=" N LEU O 241 " --> pdb=" O SER O 237 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN O 244 " --> pdb=" O ASP O 240 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP O 245 " --> pdb=" O LEU O 241 " (cutoff:3.500A) Processing helix chain 'O' and resid 249 through 263 removed outlier: 3.662A pdb=" N ARG O 259 " --> pdb=" O GLU O 255 " (cutoff:3.500A) Processing helix chain 'O' and resid 268 through 273 removed outlier: 4.247A pdb=" N SER O 272 " --> pdb=" O GLY O 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 13 through 26 Processing helix chain 'P' and resid 94 through 102 Processing helix chain 'P' and resid 102 through 111 removed outlier: 3.542A pdb=" N PHE P 106 " --> pdb=" O ILE P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 193 removed outlier: 3.760A pdb=" N LYS P 187 " --> pdb=" O GLN P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 217 through 231 Processing helix chain 'P' and resid 246 through 254 removed outlier: 4.224A pdb=" N TYR P 253 " --> pdb=" O GLN P 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 108 removed outlier: 3.556A pdb=" N LEU Q 99 " --> pdb=" O HIS Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 139 Processing helix chain 'Q' and resid 179 through 192 removed outlier: 3.572A pdb=" N MET Q 183 " --> pdb=" O PHE Q 179 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN Q 185 " --> pdb=" O ALA Q 181 " (cutoff:3.500A) Proline residue: Q 186 - end of helix removed outlier: 3.833A pdb=" N VAL Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 198 Processing helix chain 'Q' and resid 202 through 221 Processing helix chain 'R' and resid 12 through 16 Processing helix chain 'R' and resid 25 through 35 removed outlier: 3.599A pdb=" N PHE R 32 " --> pdb=" O VAL R 28 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS R 33 " --> pdb=" O GLU R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 69 removed outlier: 3.522A pdb=" N THR R 68 " --> pdb=" O ASP R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 109 removed outlier: 4.152A pdb=" N ALA R 102 " --> pdb=" O LYS R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 131 removed outlier: 3.614A pdb=" N TYR R 128 " --> pdb=" O LEU R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 186 removed outlier: 3.640A pdb=" N ASN R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 215 removed outlier: 3.840A pdb=" N VAL R 202 " --> pdb=" O SER R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 250 Processing helix chain 'S' and resid 18 through 31 Processing helix chain 'S' and resid 57 through 61 Processing helix chain 'S' and resid 78 through 96 removed outlier: 3.504A pdb=" N HIS S 94 " --> pdb=" O ARG S 90 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 102 Processing helix chain 'S' and resid 106 through 121 removed outlier: 3.729A pdb=" N ALA S 121 " --> pdb=" O ILE S 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 167 through 178 Processing helix chain 'S' and resid 184 through 200 removed outlier: 3.520A pdb=" N GLU S 198 " --> pdb=" O LEU S 194 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER S 199 " --> pdb=" O THR S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 218 through 222 Processing helix chain 'S' and resid 239 through 249 removed outlier: 3.523A pdb=" N ALA S 249 " --> pdb=" O ASP S 245 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 30 Processing helix chain 'T' and resid 80 through 103 removed outlier: 3.963A pdb=" N ILE T 86 " --> pdb=" O ALA T 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 107 through 123 removed outlier: 3.547A pdb=" N THR T 123 " --> pdb=" O LYS T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 180 Processing helix chain 'T' and resid 185 through 201 Processing helix chain 'T' and resid 207 through 209 No H-bonds generated for 'chain 'T' and resid 207 through 209' Processing helix chain 'T' and resid 231 through 243 Processing helix chain 'U' and resid 17 through 29 removed outlier: 3.646A pdb=" N LEU U 24 " --> pdb=" O VAL U 20 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA U 26 " --> pdb=" O TYR U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 60 removed outlier: 3.912A pdb=" N THR U 60 " --> pdb=" O THR U 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 78 through 100 removed outlier: 3.524A pdb=" N ILE U 84 " --> pdb=" O ALA U 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 105 through 120 Processing helix chain 'U' and resid 168 through 179 Processing helix chain 'U' and resid 187 through 201 removed outlier: 3.627A pdb=" N GLU U 201 " --> pdb=" O ARG U 197 " (cutoff:3.500A) Processing helix chain 'U' and resid 227 through 237 Processing helix chain 'V' and resid 21 through 34 removed outlier: 3.632A pdb=" N LEU V 33 " --> pdb=" O GLU V 29 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY V 34 " --> pdb=" O ALA V 30 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 64 Processing helix chain 'V' and resid 81 through 104 removed outlier: 4.125A pdb=" N SER V 87 " --> pdb=" O ALA V 83 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET V 88 " --> pdb=" O ASP V 84 " (cutoff:3.500A) Processing helix chain 'V' and resid 108 through 121 Processing helix chain 'V' and resid 122 through 124 No H-bonds generated for 'chain 'V' and resid 122 through 124' Processing helix chain 'V' and resid 175 through 187 Processing helix chain 'V' and resid 192 through 208 removed outlier: 3.568A pdb=" N GLN V 206 " --> pdb=" O LYS V 202 " (cutoff:3.500A) Processing helix chain 'V' and resid 232 through 247 Processing helix chain 'W' and resid 2 through 7 removed outlier: 3.938A pdb=" N TYR W 6 " --> pdb=" O PHE W 2 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 29 removed outlier: 3.723A pdb=" N ALA W 25 " --> pdb=" O GLN W 21 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE W 29 " --> pdb=" O ALA W 25 " (cutoff:3.500A) Processing helix chain 'W' and resid 30 through 32 No H-bonds generated for 'chain 'W' and resid 30 through 32' Processing helix chain 'W' and resid 77 through 100 removed outlier: 3.946A pdb=" N SER W 96 " --> pdb=" O CYS W 92 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU W 97 " --> pdb=" O ASN W 93 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL W 98 " --> pdb=" O TYR W 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 104 through 120 removed outlier: 3.653A pdb=" N LEU W 112 " --> pdb=" O ALA W 108 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP W 114 " --> pdb=" O HIS W 110 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS W 115 " --> pdb=" O LEU W 111 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN W 119 " --> pdb=" O LYS W 115 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR W 120 " --> pdb=" O ALA W 116 " (cutoff:3.500A) Processing helix chain 'W' and resid 164 through 175 removed outlier: 4.456A pdb=" N ALA W 168 " --> pdb=" O ARG W 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 175 through 180 removed outlier: 3.638A pdb=" N ILE W 180 " --> pdb=" O LEU W 176 " (cutoff:3.500A) Processing helix chain 'W' and resid 185 through 199 removed outlier: 3.651A pdb=" N GLN W 199 " --> pdb=" O GLU W 195 " (cutoff:3.500A) Processing helix chain 'W' and resid 228 through 231 Processing helix chain 'X' and resid 21 through 33 Processing helix chain 'X' and resid 81 through 104 Processing helix chain 'X' and resid 108 through 123 removed outlier: 3.718A pdb=" N HIS X 123 " --> pdb=" O TYR X 119 " (cutoff:3.500A) Processing helix chain 'X' and resid 169 through 183 Processing helix chain 'X' and resid 188 through 204 removed outlier: 3.536A pdb=" N VAL X 193 " --> pdb=" O ALA X 189 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS X 194 " --> pdb=" O ARG X 190 " (cutoff:3.500A) Processing helix chain 'X' and resid 221 through 225 Processing helix chain 'X' and resid 232 through 243 removed outlier: 3.613A pdb=" N LEU X 236 " --> pdb=" O LYS X 232 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 47 Processing helix chain 'Y' and resid 51 through 59 removed outlier: 4.282A pdb=" N SER Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR Y 56 " --> pdb=" O PRO Y 52 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN Y 59 " --> pdb=" O SER Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 59 through 77 Processing helix chain 'Y' and resid 78 through 95 Processing helix chain 'Y' and resid 104 through 112 removed outlier: 3.695A pdb=" N ILE Y 109 " --> pdb=" O ILE Y 105 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 123 Processing helix chain 'Y' and resid 137 through 147 removed outlier: 3.781A pdb=" N LYS Y 141 " --> pdb=" O ASP Y 137 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 18 Processing helix chain 'Z' and resid 77 through 100 Processing helix chain 'Z' and resid 104 through 119 removed outlier: 3.519A pdb=" N ALA Z 108 " --> pdb=" O ARG Z 104 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 159 through 171 removed outlier: 3.568A pdb=" N VAL Z 166 " --> pdb=" O ALA Z 162 " (cutoff:3.500A) Processing helix chain 'Z' and resid 176 through 195 Processing helix chain 'a' and resid 56 through 79 Processing helix chain 'a' and resid 83 through 97 removed outlier: 3.547A pdb=" N GLN a 89 " --> pdb=" O GLU a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 142 through 154 removed outlier: 3.535A pdb=" N LEU a 146 " --> pdb=" O ALA a 142 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY a 148 " --> pdb=" O ASP a 144 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET a 149 " --> pdb=" O GLN a 145 " (cutoff:3.500A) Processing helix chain 'a' and resid 159 through 175 Processing helix chain 'b' and resid 51 through 72 removed outlier: 3.923A pdb=" N PHE b 56 " --> pdb=" O ASP b 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 93 Processing helix chain 'b' and resid 134 through 138 removed outlier: 3.712A pdb=" N PHE b 138 " --> pdb=" O TYR b 135 " (cutoff:3.500A) Processing helix chain 'b' and resid 139 through 148 removed outlier: 3.858A pdb=" N LEU b 143 " --> pdb=" O TYR b 139 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS b 146 " --> pdb=" O PHE b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 153 through 172 Processing helix chain 'c' and resid 127 through 145 Processing helix chain 'c' and resid 150 through 165 Processing helix chain 'd' and resid 76 through 98 Processing helix chain 'd' and resid 104 through 118 Processing helix chain 'd' and resid 161 through 174 Proline residue: d 167 - end of helix removed outlier: 3.578A pdb=" N GLN d 172 " --> pdb=" O PHE d 168 " (cutoff:3.500A) Processing helix chain 'd' and resid 198 through 214 Processing helix chain 'e' and resid 68 through 90 removed outlier: 3.692A pdb=" N GLN e 88 " --> pdb=" O LEU e 84 " (cutoff:3.500A) Processing helix chain 'e' and resid 93 through 108 Processing helix chain 'e' and resid 149 through 152 Processing helix chain 'e' and resid 153 through 161 removed outlier: 3.565A pdb=" N ASP e 158 " --> pdb=" O TYR e 154 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS e 159 " --> pdb=" O GLY e 155 " (cutoff:3.500A) Processing helix chain 'e' and resid 166 through 185 Processing helix chain 'e' and resid 208 through 213 removed outlier: 3.550A pdb=" N TYR e 212 " --> pdb=" O TYR e 208 " (cutoff:3.500A) Processing helix chain 'f' and resid 43 through 47 Processing helix chain 'f' and resid 54 through 61 Proline residue: f 59 - end of helix Processing helix chain 'f' and resid 62 through 67 removed outlier: 3.639A pdb=" N GLN f 67 " --> pdb=" O LYS f 63 " (cutoff:3.500A) Processing helix chain 'f' and resid 143 through 159 removed outlier: 3.987A pdb=" N GLY f 147 " --> pdb=" O SER f 143 " (cutoff:3.500A) Processing helix chain 'f' and resid 195 through 206 Processing helix chain 'f' and resid 231 through 247 removed outlier: 3.716A pdb=" N LEU f 241 " --> pdb=" O SER f 237 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN f 244 " --> pdb=" O ASP f 240 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP f 245 " --> pdb=" O LEU f 241 " (cutoff:3.500A) Processing helix chain 'f' and resid 249 through 263 removed outlier: 3.661A pdb=" N ARG f 259 " --> pdb=" O GLU f 255 " (cutoff:3.500A) Processing helix chain 'f' and resid 268 through 273 removed outlier: 4.248A pdb=" N SER f 272 " --> pdb=" O GLY f 269 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 12 No H-bonds generated for 'chain 'g' and resid 10 through 12' Processing helix chain 'g' and resid 13 through 26 Processing helix chain 'g' and resid 94 through 102 Processing helix chain 'g' and resid 102 through 111 removed outlier: 3.543A pdb=" N PHE g 106 " --> pdb=" O ILE g 102 " (cutoff:3.500A) Processing helix chain 'g' and resid 183 through 193 removed outlier: 3.761A pdb=" N LYS g 187 " --> pdb=" O GLN g 183 " (cutoff:3.500A) Processing helix chain 'g' and resid 217 through 231 Processing helix chain 'g' and resid 246 through 254 removed outlier: 4.224A pdb=" N TYR g 253 " --> pdb=" O GLN g 250 " (cutoff:3.500A) Processing helix chain 'h' and resid 90 through 108 removed outlier: 3.555A pdb=" N LEU h 99 " --> pdb=" O HIS h 95 " (cutoff:3.500A) Processing helix chain 'h' and resid 121 through 139 Processing helix chain 'h' and resid 179 through 192 removed outlier: 3.572A pdb=" N MET h 183 " --> pdb=" O PHE h 179 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN h 185 " --> pdb=" O ALA h 181 " (cutoff:3.500A) Proline residue: h 186 - end of helix removed outlier: 3.833A pdb=" N VAL h 191 " --> pdb=" O LEU h 187 " (cutoff:3.500A) Processing helix chain 'h' and resid 194 through 198 Processing helix chain 'h' and resid 202 through 221 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 73 removed outlier: 3.692A pdb=" N ILE A 154 " --> pdb=" O TYR A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.691A pdb=" N GLY B 42 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU B 211 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.629A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 133 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 224 through 225 removed outlier: 5.199A pdb=" N ASP I 212 " --> pdb=" O GLU I 208 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLU I 208 " --> pdb=" O ASP I 212 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN I 218 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL I 202 " --> pdb=" O ASN I 218 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR I 31 " --> pdb=" O ASP I 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 162 through 165 removed outlier: 3.682A pdb=" N GLY C 43 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 66 through 70 removed outlier: 3.635A pdb=" N LEU C 69 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU C 148 " --> pdb=" O TRP C 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 161 through 164 removed outlier: 4.016A pdb=" N GLU D 211 " --> pdb=" O CYS D 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 71 through 77 Processing sheet with id=AB1, first strand: chain 'E' and resid 169 through 172 removed outlier: 3.641A pdb=" N GLN E 218 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 71 removed outlier: 5.901A pdb=" N ILE E 67 " --> pdb=" O MET E 78 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET E 78 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU E 69 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N CYS E 76 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP E 148 " --> pdb=" O GLY E 152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 65 removed outlier: 3.668A pdb=" N ASN F 152 " --> pdb=" O GLN F 148 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 162 through 164 Processing sheet with id=AB6, first strand: chain 'G' and resid 68 through 71 removed outlier: 6.522A pdb=" N ILE G 74 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP G 158 " --> pdb=" O MET G 150 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 49 through 51 removed outlier: 5.972A pdb=" N GLN I 51 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL I 55 " --> pdb=" O GLN I 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 63 through 67 removed outlier: 6.478A pdb=" N ILE I 70 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR I 126 " --> pdb=" O ALA I 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 241 through 247 removed outlier: 4.117A pdb=" N LYS I 243 " --> pdb=" O TYR J 199 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL J 195 " --> pdb=" O VAL I 247 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA J 185 " --> pdb=" O LEU J 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 43 through 45 Processing sheet with id=AC2, first strand: chain 'K' and resid 130 through 133 removed outlier: 4.069A pdb=" N ILE K 4 " --> pdb=" O HIS K 133 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL K 181 " --> pdb=" O VAL K 192 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP K 185 " --> pdb=" O GLY K 188 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 25 through 26 removed outlier: 3.657A pdb=" N ILE L 87 " --> pdb=" O VAL L 255 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU L 252 " --> pdb=" O HIS L 263 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 35 through 39 removed outlier: 3.646A pdb=" N LEU K 38 " --> pdb=" O THR K 42 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR K 42 " --> pdb=" O LEU K 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 174 through 180 Processing sheet with id=AC6, first strand: chain 'M' and resid 155 through 159 removed outlier: 5.660A pdb=" N THR M 30 " --> pdb=" O ASP M 45 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 48 through 50 removed outlier: 6.669A pdb=" N THR M 50 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ILE M 54 " --> pdb=" O THR M 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 63 through 66 removed outlier: 5.728A pdb=" N ILE M 69 " --> pdb=" O CYS M 65 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN M 74 " --> pdb=" O HIS M 127 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR M 128 " --> pdb=" O PHE M 144 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER M 143 " --> pdb=" O GLU M 151 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 17 through 18 removed outlier: 4.222A pdb=" N GLY N 66 " --> pdb=" O LEU N 18 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE N 60 " --> pdb=" O VAL N 56 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 17 through 18 removed outlier: 4.222A pdb=" N GLY N 66 " --> pdb=" O LEU N 18 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 143 through 147 removed outlier: 3.656A pdb=" N GLY N 30 " --> pdb=" O PHE N 27 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 39 through 41 removed outlier: 3.575A pdb=" N ASN N 47 " --> pdb=" O THR N 39 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR N 41 " --> pdb=" O ILE N 45 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE N 45 " --> pdb=" O THR N 41 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 35 through 37 removed outlier: 3.612A pdb=" N THR O 77 " --> pdb=" O LYS O 35 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS O 75 " --> pdb=" O GLU O 37 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N SER O 70 " --> pdb=" O SER O 126 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N SER O 126 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY O 72 " --> pdb=" O ILE O 124 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER O 134 " --> pdb=" O PRO O 123 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE O 165 " --> pdb=" O LYS O 215 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LEU O 217 " --> pdb=" O ILE O 165 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL O 167 " --> pdb=" O LEU O 217 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ALA O 219 " --> pdb=" O VAL O 167 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY O 169 " --> pdb=" O ALA O 219 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 193 through 194 Processing sheet with id=AD6, first strand: chain 'P' and resid 30 through 34 removed outlier: 5.349A pdb=" N TYR P 32 " --> pdb=" O TYR P 74 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR P 74 " --> pdb=" O TYR P 32 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU P 34 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N CYS P 3 " --> pdb=" O PHE P 81 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE P 83 " --> pdb=" O CYS P 3 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL P 5 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLN P 85 " --> pdb=" O VAL P 5 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU P 4 " --> pdb=" O CYS P 116 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TRP P 118 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU P 6 " --> pdb=" O TRP P 118 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N SER P 120 " --> pdb=" O LEU P 6 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE P 115 " --> pdb=" O SER P 204 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 66 through 69 removed outlier: 5.405A pdb=" N LEU Q 67 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR Q 63 " --> pdb=" O LEU Q 67 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 66 through 69 removed outlier: 5.405A pdb=" N LEU Q 67 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR Q 63 " --> pdb=" O LEU Q 67 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 174 through 176 removed outlier: 5.706A pdb=" N PHE Q 228 " --> pdb=" O ASN Q 244 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN Q 244 " --> pdb=" O PHE Q 228 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 168 through 171 Processing sheet with id=AE2, first strand: chain 'R' and resid 72 through 73 removed outlier: 3.692A pdb=" N ILE R 154 " --> pdb=" O TYR R 166 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 161 through 164 removed outlier: 3.691A pdb=" N GLY S 42 " --> pdb=" O ALA S 39 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU S 211 " --> pdb=" O LEU S 238 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 65 through 68 removed outlier: 6.630A pdb=" N ILE S 71 " --> pdb=" O LEU S 67 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER S 133 " --> pdb=" O SER S 76 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 224 through 225 removed outlier: 5.200A pdb=" N ASP Z 212 " --> pdb=" O GLU Z 208 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLU Z 208 " --> pdb=" O ASP Z 212 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN Z 218 " --> pdb=" O VAL Z 202 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL Z 202 " --> pdb=" O ASN Z 218 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR Z 31 " --> pdb=" O ASP Z 46 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'T' and resid 162 through 165 removed outlier: 3.683A pdb=" N GLY T 43 " --> pdb=" O ALA T 40 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 66 through 70 removed outlier: 3.634A pdb=" N LEU T 69 " --> pdb=" O ILE T 73 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE T 73 " --> pdb=" O LEU T 69 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU T 148 " --> pdb=" O TRP T 160 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'U' and resid 161 through 164 removed outlier: 4.016A pdb=" N GLU U 211 " --> pdb=" O CYS U 46 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'U' and resid 71 through 77 Processing sheet with id=AF1, first strand: chain 'V' and resid 169 through 172 removed outlier: 3.641A pdb=" N GLN V 218 " --> pdb=" O VAL V 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 67 through 71 removed outlier: 5.900A pdb=" N ILE V 67 " --> pdb=" O MET V 78 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET V 78 " --> pdb=" O ILE V 67 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU V 69 " --> pdb=" O CYS V 76 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N CYS V 76 " --> pdb=" O GLU V 69 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP V 148 " --> pdb=" O GLY V 152 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 158 through 161 Processing sheet with id=AF4, first strand: chain 'W' and resid 63 through 65 removed outlier: 3.668A pdb=" N ASN W 152 " --> pdb=" O GLN W 148 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'X' and resid 162 through 164 Processing sheet with id=AF6, first strand: chain 'X' and resid 68 through 71 removed outlier: 6.522A pdb=" N ILE X 74 " --> pdb=" O VAL X 70 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP X 158 " --> pdb=" O MET X 150 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 49 through 51 removed outlier: 5.973A pdb=" N GLN Z 51 " --> pdb=" O VAL Z 55 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL Z 55 " --> pdb=" O GLN Z 51 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 63 through 67 removed outlier: 6.479A pdb=" N ILE Z 70 " --> pdb=" O ILE Z 66 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR Z 126 " --> pdb=" O ALA Z 75 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 241 through 247 removed outlier: 4.109A pdb=" N LYS Z 243 " --> pdb=" O TYR a 199 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL a 195 " --> pdb=" O VAL Z 247 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA a 185 " --> pdb=" O LEU a 200 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'a' and resid 43 through 45 Processing sheet with id=AG2, first strand: chain 'b' and resid 130 through 133 removed outlier: 4.069A pdb=" N ILE b 4 " --> pdb=" O HIS b 133 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL b 181 " --> pdb=" O VAL b 192 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP b 185 " --> pdb=" O GLY b 188 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'b' and resid 25 through 26 removed outlier: 3.657A pdb=" N ILE c 87 " --> pdb=" O VAL c 255 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU c 252 " --> pdb=" O HIS c 263 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'b' and resid 35 through 39 removed outlier: 3.647A pdb=" N LEU b 38 " --> pdb=" O THR b 42 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR b 42 " --> pdb=" O LEU b 38 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'c' and resid 174 through 180 Processing sheet with id=AG6, first strand: chain 'd' and resid 155 through 159 removed outlier: 5.660A pdb=" N THR d 30 " --> pdb=" O ASP d 45 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'd' and resid 48 through 50 removed outlier: 6.669A pdb=" N THR d 50 " --> pdb=" O ILE d 54 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ILE d 54 " --> pdb=" O THR d 50 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'd' and resid 63 through 66 removed outlier: 5.726A pdb=" N ILE d 69 " --> pdb=" O CYS d 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN d 74 " --> pdb=" O HIS d 127 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR d 128 " --> pdb=" O PHE d 144 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER d 143 " --> pdb=" O GLU d 151 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'e' and resid 17 through 18 removed outlier: 4.222A pdb=" N GLY e 66 " --> pdb=" O LEU e 18 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE e 60 " --> pdb=" O VAL e 56 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'e' and resid 17 through 18 removed outlier: 4.222A pdb=" N GLY e 66 " --> pdb=" O LEU e 18 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'e' and resid 143 through 147 removed outlier: 3.656A pdb=" N GLY e 30 " --> pdb=" O PHE e 27 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'e' and resid 39 through 41 removed outlier: 3.575A pdb=" N ASN e 47 " --> pdb=" O THR e 39 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR e 41 " --> pdb=" O ILE e 45 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE e 45 " --> pdb=" O THR e 41 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'f' and resid 35 through 37 removed outlier: 3.612A pdb=" N THR f 77 " --> pdb=" O LYS f 35 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS f 75 " --> pdb=" O GLU f 37 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N SER f 70 " --> pdb=" O SER f 126 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N SER f 126 " --> pdb=" O SER f 70 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY f 72 " --> pdb=" O ILE f 124 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER f 134 " --> pdb=" O PRO f 123 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE f 165 " --> pdb=" O LYS f 215 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU f 217 " --> pdb=" O ILE f 165 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL f 167 " --> pdb=" O LEU f 217 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ALA f 219 " --> pdb=" O VAL f 167 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY f 169 " --> pdb=" O ALA f 219 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'f' and resid 193 through 194 Processing sheet with id=AH6, first strand: chain 'g' and resid 30 through 34 removed outlier: 5.350A pdb=" N TYR g 32 " --> pdb=" O TYR g 74 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR g 74 " --> pdb=" O TYR g 32 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU g 34 " --> pdb=" O VAL g 72 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N CYS g 3 " --> pdb=" O PHE g 81 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE g 83 " --> pdb=" O CYS g 3 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL g 5 " --> pdb=" O ILE g 83 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N GLN g 85 " --> pdb=" O VAL g 5 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU g 4 " --> pdb=" O CYS g 116 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TRP g 118 " --> pdb=" O LEU g 4 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU g 6 " --> pdb=" O TRP g 118 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N SER g 120 " --> pdb=" O LEU g 6 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE g 115 " --> pdb=" O SER g 204 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'h' and resid 66 through 69 removed outlier: 5.405A pdb=" N LEU h 67 " --> pdb=" O TYR h 63 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR h 63 " --> pdb=" O LEU h 67 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'h' and resid 66 through 69 removed outlier: 5.405A pdb=" N LEU h 67 " --> pdb=" O TYR h 63 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR h 63 " --> pdb=" O LEU h 67 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'h' and resid 174 through 176 removed outlier: 5.704A pdb=" N PHE h 228 " --> pdb=" O ASN h 244 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN h 244 " --> pdb=" O PHE h 228 " (cutoff:3.500A) 2992 hydrogen bonds defined for protein. 8472 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: 20.06 Time building geometry restraints manager: 16.93 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: 17965 1.34 - 1.47: 13083 1.47 - 1.59: 24756 1.59 - 1.72: 0 1.72 - 1.84: 314 Bond restraints: 56118 Sorted by residual: bond pdb=" N MET f 1 " pdb=" CA MET f 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N MET O 1 " pdb=" CA MET O 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N LYS T 100 " pdb=" CA LYS T 100 " ideal model delta sigma weight residual 1.458 1.480 -0.023 1.33e-02 5.65e+03 2.98e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N MET W 1 " pdb=" CA MET W 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 ... (remaining 56113 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.31: 1221 106.31 - 113.24: 30712 113.24 - 120.17: 18919 120.17 - 127.09: 24565 127.09 - 134.02: 479 Bond angle restraints: 75896 Sorted by residual: angle pdb=" N ARG Z 217 " pdb=" CA ARG Z 217 " pdb=" C ARG Z 217 " ideal model delta sigma weight residual 110.43 105.90 4.53 1.31e+00 5.83e-01 1.20e+01 angle pdb=" N ARG I 217 " pdb=" CA ARG I 217 " pdb=" C ARG I 217 " ideal model delta sigma weight residual 110.43 105.93 4.50 1.31e+00 5.83e-01 1.18e+01 angle pdb=" N LYS C 100 " pdb=" CA LYS C 100 " pdb=" C LYS C 100 " ideal model delta sigma weight residual 112.54 108.56 3.98 1.22e+00 6.72e-01 1.06e+01 angle pdb=" N LYS T 100 " pdb=" CA LYS T 100 " pdb=" C LYS T 100 " ideal model delta sigma weight residual 112.54 108.63 3.91 1.22e+00 6.72e-01 1.03e+01 angle pdb=" CA ARG I 217 " pdb=" C ARG I 217 " pdb=" O ARG I 217 " ideal model delta sigma weight residual 121.87 118.65 3.22 1.10e+00 8.26e-01 8.59e+00 ... (remaining 75891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 31194 17.90 - 35.81: 2020 35.81 - 53.71: 306 53.71 - 71.61: 78 71.61 - 89.52: 56 Dihedral angle restraints: 33654 sinusoidal: 13338 harmonic: 20316 Sorted by residual: dihedral pdb=" CB CYS W 66 " pdb=" SG CYS W 66 " pdb=" SG CYS W 92 " pdb=" CB CYS W 92 " ideal model delta sinusoidal sigma weight residual 93.00 134.65 -41.65 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CB CYS F 66 " pdb=" SG CYS F 66 " pdb=" SG CYS F 92 " pdb=" CB CYS F 92 " ideal model delta sinusoidal sigma weight residual 93.00 134.65 -41.65 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CA LEU I 4 " pdb=" C LEU I 4 " pdb=" N SER I 5 " pdb=" CA SER I 5 " ideal model delta harmonic sigma weight residual -180.00 -159.06 -20.94 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 33651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 8595 0.154 - 0.307: 5 0.307 - 0.461: 0 0.461 - 0.614: 4 0.614 - 0.768: 2 Chirality restraints: 8606 Sorted by residual: chirality pdb=" CG LEU Z 220 " pdb=" CB LEU Z 220 " pdb=" CD1 LEU Z 220 " pdb=" CD2 LEU Z 220 " both_signs ideal model delta sigma weight residual False -2.59 -1.82 -0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" CG LEU I 220 " pdb=" CB LEU I 220 " pdb=" CD1 LEU I 220 " pdb=" CD2 LEU I 220 " both_signs ideal model delta sigma weight residual False -2.59 -1.82 -0.77 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CB THR b 53 " pdb=" CA THR b 53 " pdb=" OG1 THR b 53 " pdb=" CG2 THR b 53 " both_signs ideal model delta sigma weight residual False 2.55 2.04 0.51 2.00e-01 2.50e+01 6.58e+00 ... (remaining 8603 not shown) Planarity restraints: 9712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 129 " -0.028 2.00e-02 2.50e+03 2.80e-02 1.38e+01 pdb=" CG PHE L 129 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE L 129 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE L 129 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE L 129 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE L 129 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE L 129 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE c 129 " -0.028 2.00e-02 2.50e+03 2.79e-02 1.37e+01 pdb=" CG PHE c 129 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE c 129 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE c 129 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE c 129 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE c 129 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE c 129 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 117 " -0.015 2.00e-02 2.50e+03 2.29e-02 1.05e+01 pdb=" CG TYR d 117 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR d 117 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR d 117 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR d 117 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR d 117 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR d 117 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR d 117 " -0.003 2.00e-02 2.50e+03 ... (remaining 9709 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 586 2.59 - 3.17: 48881 3.17 - 3.75: 84262 3.75 - 4.32: 124313 4.32 - 4.90: 210933 Nonbonded interactions: 468975 Sorted by model distance: nonbonded pdb=" OG SER N 166 " pdb=" OE1 GLU N 169 " model vdw 2.014 2.440 nonbonded pdb=" OG SER e 166 " pdb=" OE1 GLU e 169 " model vdw 2.015 2.440 nonbonded pdb=" O PRO P 172 " pdb=" OG1 THR P 173 " model vdw 2.034 2.440 nonbonded pdb=" O PRO g 172 " pdb=" OG1 THR g 173 " model vdw 2.035 2.440 nonbonded pdb=" O ILE G 4 " pdb=" OH TYR G 26 " model vdw 2.038 2.440 ... (remaining 468970 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'R' } ncs_group { reference = chain 'B' selection = chain 'S' } ncs_group { reference = chain 'C' selection = chain 'T' } ncs_group { reference = chain 'D' selection = chain 'U' } ncs_group { reference = chain 'E' selection = chain 'V' } ncs_group { reference = chain 'F' selection = chain 'W' } ncs_group { reference = chain 'G' selection = chain 'X' } ncs_group { reference = chain 'H' selection = chain 'Y' } ncs_group { reference = chain 'I' selection = chain 'Z' } ncs_group { reference = chain 'J' selection = chain 'a' } ncs_group { reference = chain 'K' selection = chain 'b' } ncs_group { reference = chain 'L' selection = chain 'c' } ncs_group { reference = chain 'M' selection = chain 'd' } ncs_group { reference = chain 'N' selection = chain 'e' } ncs_group { reference = chain 'O' selection = chain 'f' } ncs_group { reference = chain 'P' selection = chain 'g' } ncs_group { reference = chain 'Q' selection = chain 'h' } 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=0.00 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 11.120 Check model and map are aligned: 0.620 Set scattering table: 0.380 Process input model: 109.100 Find NCS groups from input model: 4.140 Set up NCS constraints: 0.530 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 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 : 0.003 0.048 56118 Z= 0.174 Angle : 0.465 7.584 75896 Z= 0.251 Chirality : 0.043 0.768 8606 Planarity : 0.004 0.121 9712 Dihedral : 12.796 89.516 20616 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.07 % Allowed : 0.15 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.10), residues: 6864 helix: 1.75 (0.11), residues: 2434 sheet: 0.40 (0.12), residues: 1734 loop : 0.13 (0.12), residues: 2696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 261 HIS 0.003 0.001 HIS Q 95 PHE 0.063 0.001 PHE L 129 TYR 0.049 0.001 TYR d 117 ARG 0.008 0.000 ARG D 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1013 time to evaluate : 4.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 GLU cc_start: 0.8546 (tp30) cc_final: 0.8251 (tp30) REVERT: C 28 SER cc_start: 0.8959 (t) cc_final: 0.8664 (p) REVERT: C 152 ASN cc_start: 0.8111 (m-40) cc_final: 0.7863 (m-40) REVERT: C 156 ASN cc_start: 0.8380 (p0) cc_final: 0.8029 (p0) REVERT: C 165 VAL cc_start: 0.8395 (p) cc_final: 0.8140 (m) REVERT: C 191 GLU cc_start: 0.7271 (mp0) cc_final: 0.7031 (mp0) REVERT: C 236 LYS cc_start: 0.8313 (ttmt) cc_final: 0.7853 (ptpt) REVERT: C 237 ASP cc_start: 0.7785 (m-30) cc_final: 0.7583 (m-30) REVERT: D 6 ARG cc_start: 0.8258 (pmt-80) cc_final: 0.7595 (mtt180) REVERT: H 35 GLN cc_start: 0.8029 (tt0) cc_final: 0.7617 (pt0) REVERT: H 133 MET cc_start: 0.4405 (mmp) cc_final: 0.3776 (mmp) REVERT: I 178 GLU cc_start: 0.8058 (mp0) cc_final: 0.7795 (mp0) REVERT: I 214 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7388 (mm-30) REVERT: I 218 ASN cc_start: 0.7478 (m-40) cc_final: 0.7251 (m110) REVERT: K 148 TYR cc_start: 0.7621 (t80) cc_final: 0.7351 (t80) REVERT: K 156 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7118 (mt-10) REVERT: K 167 GLU cc_start: 0.7892 (mp0) cc_final: 0.7045 (mp0) REVERT: L 148 ARG cc_start: 0.6746 (tpt-90) cc_final: 0.6238 (ttt180) REVERT: M 22 ASN cc_start: 0.7024 (t0) cc_final: 0.6571 (p0) REVERT: M 234 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7188 (mm-30) REVERT: Q 157 ASP cc_start: 0.7422 (m-30) cc_final: 0.7065 (m-30) REVERT: Q 161 ARG cc_start: 0.8749 (mmm160) cc_final: 0.8489 (mtp85) REVERT: Q 190 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7960 (mtmt) REVERT: R 242 GLU cc_start: 0.8489 (tp30) cc_final: 0.8198 (tp30) REVERT: T 28 SER cc_start: 0.8961 (t) cc_final: 0.8664 (p) REVERT: T 152 ASN cc_start: 0.8105 (m-40) cc_final: 0.7851 (m-40) REVERT: T 156 ASN cc_start: 0.8373 (p0) cc_final: 0.8018 (p0) REVERT: T 165 VAL cc_start: 0.8405 (p) cc_final: 0.8147 (m) REVERT: T 191 GLU cc_start: 0.7272 (mp0) cc_final: 0.7011 (mp0) REVERT: T 236 LYS cc_start: 0.8313 (ttmt) cc_final: 0.7849 (ptpt) REVERT: T 237 ASP cc_start: 0.7799 (m-30) cc_final: 0.7576 (m-30) REVERT: U 6 ARG cc_start: 0.8257 (pmt-80) cc_final: 0.7591 (mtt180) REVERT: V 185 ASN cc_start: 0.7919 (m110) cc_final: 0.7716 (m110) REVERT: Y 35 GLN cc_start: 0.8051 (tt0) cc_final: 0.7623 (pt0) REVERT: Y 133 MET cc_start: 0.4402 (mmp) cc_final: 0.3779 (mmp) REVERT: Z 178 GLU cc_start: 0.8111 (mp0) cc_final: 0.7844 (mp0) REVERT: Z 214 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7417 (mm-30) REVERT: Z 218 ASN cc_start: 0.7581 (m-40) cc_final: 0.7357 (m110) REVERT: b 148 TYR cc_start: 0.7546 (t80) cc_final: 0.7284 (t80) REVERT: b 156 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7067 (mt-10) REVERT: b 167 GLU cc_start: 0.7903 (mp0) cc_final: 0.7053 (mp0) REVERT: c 148 ARG cc_start: 0.6756 (tpt-90) cc_final: 0.6229 (ttt180) REVERT: d 22 ASN cc_start: 0.6998 (t0) cc_final: 0.6641 (p0) REVERT: d 234 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7110 (mm-30) REVERT: d 241 ASP cc_start: 0.6376 (p0) cc_final: 0.5712 (p0) REVERT: h 95 HIS cc_start: 0.7767 (t-90) cc_final: 0.7542 (t-90) REVERT: h 157 ASP cc_start: 0.7392 (m-30) cc_final: 0.6917 (m-30) REVERT: h 161 ARG cc_start: 0.8733 (mmm160) cc_final: 0.8474 (mtp85) REVERT: h 190 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7903 (mtmt) outliers start: 4 outliers final: 6 residues processed: 1013 average time/residue: 1.3979 time to fit residues: 1774.9929 Evaluate side-chains 686 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 680 time to evaluate : 5.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain Q residue 70 ASN Chi-restraints excluded: chain S residue 220 ASP Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain h residue 70 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 584 optimal weight: 7.9990 chunk 524 optimal weight: 10.0000 chunk 291 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 353 optimal weight: 0.4980 chunk 280 optimal weight: 0.7980 chunk 542 optimal weight: 9.9990 chunk 209 optimal weight: 8.9990 chunk 329 optimal weight: 3.9990 chunk 403 optimal weight: 0.6980 chunk 628 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS B 123 GLN B 218 ASN C 21 GLN E 100 ASN E 147 HIS E 185 ASN E 218 GLN F 31 GLN F 166 GLN G 21 ASN G 183 HIS H 102 ASN H 112 ASN I 86 GLN I 170 HIS J 145 GLN ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN N 108 ASN O 225 ASN Q 212 ASN ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 209 HIS S 123 GLN S 218 ASN T 21 GLN V 147 HIS V 185 ASN W 31 GLN W 166 GLN X 21 ASN X 183 HIS Y 102 ASN Y 112 ASN Z 86 GLN Z 170 HIS a 145 GLN ** b 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 137 GLN d 74 ASN e 108 ASN f 225 ASN ** h 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 212 ASN ** h 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 56118 Z= 0.229 Angle : 0.577 9.152 75896 Z= 0.308 Chirality : 0.045 0.168 8606 Planarity : 0.004 0.060 9712 Dihedral : 4.831 75.692 7614 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.85 % Allowed : 9.29 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.10), residues: 6864 helix: 1.70 (0.10), residues: 2526 sheet: 0.35 (0.12), residues: 1724 loop : 0.17 (0.12), residues: 2614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 158 HIS 0.009 0.001 HIS X 183 PHE 0.029 0.002 PHE L 83 TYR 0.019 0.001 TYR J 96 ARG 0.008 0.001 ARG b 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 830 time to evaluate : 5.738 Fit side-chains revert: symmetry clash REVERT: A 39 ASN cc_start: 0.8393 (t0) cc_final: 0.8190 (t0) REVERT: A 121 MET cc_start: 0.9155 (mmm) cc_final: 0.8918 (mmm) REVERT: A 158 ASP cc_start: 0.8476 (p0) cc_final: 0.8238 (p0) REVERT: C 152 ASN cc_start: 0.8134 (m-40) cc_final: 0.7891 (m-40) REVERT: C 165 VAL cc_start: 0.8444 (p) cc_final: 0.8224 (m) REVERT: C 194 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8056 (mm) REVERT: D 6 ARG cc_start: 0.8277 (pmt-80) cc_final: 0.7572 (mtt-85) REVERT: D 220 ASP cc_start: 0.8194 (t0) cc_final: 0.7984 (t0) REVERT: G 195 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7451 (mm-40) REVERT: H 35 GLN cc_start: 0.8217 (tt0) cc_final: 0.7840 (pt0) REVERT: I 214 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7425 (mm-30) REVERT: J 169 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7655 (tp40) REVERT: K 148 TYR cc_start: 0.7580 (t80) cc_final: 0.7374 (t80) REVERT: K 156 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7523 (mt-10) REVERT: K 167 GLU cc_start: 0.7924 (mp0) cc_final: 0.6727 (mp0) REVERT: L 145 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6406 (mp0) REVERT: M 22 ASN cc_start: 0.7054 (t0) cc_final: 0.6668 (p0) REVERT: M 166 MET cc_start: 0.5312 (mmm) cc_final: 0.4941 (mmm) REVERT: N 83 GLU cc_start: 0.7594 (tt0) cc_final: 0.7385 (mt-10) REVERT: Q 157 ASP cc_start: 0.7778 (m-30) cc_final: 0.7382 (m-30) REVERT: R 39 ASN cc_start: 0.8389 (t0) cc_final: 0.8185 (t0) REVERT: R 89 ASP cc_start: 0.8700 (m-30) cc_final: 0.8406 (m-30) REVERT: R 121 MET cc_start: 0.9152 (mmm) cc_final: 0.8917 (mmm) REVERT: R 158 ASP cc_start: 0.8485 (p0) cc_final: 0.8276 (p0) REVERT: T 152 ASN cc_start: 0.8128 (m-40) cc_final: 0.7881 (m-40) REVERT: T 156 ASN cc_start: 0.8472 (p0) cc_final: 0.8269 (p0) REVERT: T 165 VAL cc_start: 0.8451 (p) cc_final: 0.8230 (m) REVERT: T 194 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8052 (mm) REVERT: T 236 LYS cc_start: 0.8237 (ttmt) cc_final: 0.7692 (ptmt) REVERT: U 6 ARG cc_start: 0.8276 (pmt-80) cc_final: 0.7568 (mtt-85) REVERT: U 220 ASP cc_start: 0.8195 (t0) cc_final: 0.7986 (t0) REVERT: V 104 ASP cc_start: 0.7217 (m-30) cc_final: 0.6986 (m-30) REVERT: Y 35 GLN cc_start: 0.8212 (tt0) cc_final: 0.7835 (pt0) REVERT: Z 214 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7416 (mm-30) REVERT: a 169 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7653 (tp40) REVERT: b 115 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8161 (mt-10) REVERT: b 148 TYR cc_start: 0.7600 (t80) cc_final: 0.7392 (t80) REVERT: b 156 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7519 (mt-10) REVERT: b 167 GLU cc_start: 0.7916 (mp0) cc_final: 0.6714 (mp0) REVERT: c 145 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6725 (mp0) REVERT: d 22 ASN cc_start: 0.7035 (t0) cc_final: 0.6612 (p0) REVERT: d 166 MET cc_start: 0.5233 (mmm) cc_final: 0.4853 (mmm) REVERT: d 201 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8479 (ttpp) REVERT: d 234 GLU cc_start: 0.7301 (mm-30) cc_final: 0.7018 (mm-30) REVERT: e 83 GLU cc_start: 0.7588 (tt0) cc_final: 0.7381 (mt-10) REVERT: e 162 ARG cc_start: 0.7910 (mtm110) cc_final: 0.7411 (mtm110) REVERT: h 157 ASP cc_start: 0.7735 (m-30) cc_final: 0.7317 (m-30) outliers start: 111 outliers final: 47 residues processed: 885 average time/residue: 1.3593 time to fit residues: 1520.0167 Evaluate side-chains 730 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 676 time to evaluate : 4.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 169 GLN Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain P residue 124 MET Chi-restraints excluded: chain Q residue 70 ASN Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Q residue 240 THR Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain S residue 103 GLU Chi-restraints excluded: chain S residue 187 ASP Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 186 VAL Chi-restraints excluded: chain T residue 194 LEU Chi-restraints excluded: chain U residue 14 ASP Chi-restraints excluded: chain V residue 78 MET Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 114 SER Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 169 GLN Chi-restraints excluded: chain b residue 153 THR Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 175 MET Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 201 LYS Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain f residue 31 CYS Chi-restraints excluded: chain g residue 124 MET Chi-restraints excluded: chain h residue 70 ASN Chi-restraints excluded: chain h residue 240 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 349 optimal weight: 0.9990 chunk 195 optimal weight: 0.8980 chunk 523 optimal weight: 5.9990 chunk 427 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 629 optimal weight: 7.9990 chunk 680 optimal weight: 5.9990 chunk 560 optimal weight: 10.0000 chunk 624 optimal weight: 4.9990 chunk 214 optimal weight: 9.9990 chunk 505 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN B 123 GLN E 114 GLN E 185 ASN F 31 GLN F 60 GLN F 166 GLN G 90 ASN G 123 HIS H 102 ASN H 112 ASN I 86 GLN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 170 HIS J 169 GLN K 37 GLN K 78 GLN ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN M 171 ASN N 108 ASN O 225 ASN P 128 ASN Q 95 HIS Q 227 ASN S 30 GLN S 123 GLN V 114 GLN V 185 ASN W 60 GLN W 166 GLN X 90 ASN X 123 HIS Y 102 ASN Y 112 ASN ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 170 HIS a 169 GLN b 37 GLN b 78 GLN ** b 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 137 GLN d 171 ASN e 108 ASN f 225 ASN ** f 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 128 ASN h 95 HIS h 227 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 56118 Z= 0.372 Angle : 0.620 8.141 75896 Z= 0.326 Chirality : 0.047 0.187 8606 Planarity : 0.005 0.061 9712 Dihedral : 4.846 42.897 7610 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.98 % Allowed : 12.05 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: 0.86 (0.10), residues: 6864 helix: 1.54 (0.10), residues: 2528 sheet: 0.23 (0.12), residues: 1728 loop : -0.03 (0.12), residues: 2608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 133 HIS 0.008 0.001 HIS G 123 PHE 0.030 0.002 PHE a 124 TYR 0.021 0.002 TYR J 96 ARG 0.011 0.001 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 727 time to evaluate : 5.366 Fit side-chains revert: symmetry clash REVERT: A 41 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.7459 (p0) REVERT: A 48 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6859 (mttp) REVERT: A 148 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7481 (pt0) REVERT: A 158 ASP cc_start: 0.8627 (p0) cc_final: 0.8368 (p0) REVERT: A 222 ASP cc_start: 0.8380 (t0) cc_final: 0.8075 (t0) REVERT: C 152 ASN cc_start: 0.8362 (m-40) cc_final: 0.8118 (m-40) REVERT: C 165 VAL cc_start: 0.8673 (p) cc_final: 0.8422 (m) REVERT: C 194 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8063 (mm) REVERT: C 233 GLN cc_start: 0.8068 (tm-30) cc_final: 0.7830 (tm-30) REVERT: D 5 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8083 (t0) REVERT: D 6 ARG cc_start: 0.8319 (pmt-80) cc_final: 0.7578 (mtt-85) REVERT: E 100 ASN cc_start: 0.8745 (t0) cc_final: 0.8532 (t0) REVERT: E 134 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6891 (mtm) REVERT: E 185 ASN cc_start: 0.7548 (m-40) cc_final: 0.7276 (m110) REVERT: G 68 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7457 (mp10) REVERT: G 184 PRO cc_start: 0.7656 (Cg_endo) cc_final: 0.7172 (Cg_exo) REVERT: H 35 GLN cc_start: 0.8203 (tt0) cc_final: 0.7895 (pt0) REVERT: H 133 MET cc_start: 0.4699 (mmp) cc_final: 0.4333 (mmp) REVERT: I 214 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7389 (mm-30) REVERT: J 103 TYR cc_start: 0.8753 (m-80) cc_final: 0.8498 (m-80) REVERT: J 126 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8113 (tp) REVERT: K 156 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7566 (mt-10) REVERT: K 167 GLU cc_start: 0.7265 (mp0) cc_final: 0.6787 (mp0) REVERT: K 195 PHE cc_start: 0.4693 (m-10) cc_final: 0.4179 (m-80) REVERT: L 145 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6300 (mp0) REVERT: M 241 ASP cc_start: 0.6592 (p0) cc_final: 0.6372 (p0) REVERT: N 124 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7976 (pttp) REVERT: O 47 TYR cc_start: 0.5821 (m-80) cc_final: 0.5598 (m-80) REVERT: Q 102 ASP cc_start: 0.7304 (m-30) cc_final: 0.7081 (m-30) REVERT: Q 157 ASP cc_start: 0.7886 (m-30) cc_final: 0.7380 (m-30) REVERT: R 41 ASN cc_start: 0.7829 (OUTLIER) cc_final: 0.7450 (p0) REVERT: R 48 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6846 (mttp) REVERT: R 111 ASP cc_start: 0.8570 (m-30) cc_final: 0.8366 (m-30) REVERT: R 148 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7484 (pt0) REVERT: R 158 ASP cc_start: 0.8628 (p0) cc_final: 0.8367 (p0) REVERT: T 152 ASN cc_start: 0.8319 (m-40) cc_final: 0.8092 (m-40) REVERT: T 165 VAL cc_start: 0.8679 (p) cc_final: 0.8430 (m) REVERT: T 194 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8059 (mm) REVERT: T 233 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7649 (tm-30) REVERT: T 237 ASP cc_start: 0.7716 (m-30) cc_final: 0.7356 (m-30) REVERT: U 5 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8084 (t0) REVERT: U 6 ARG cc_start: 0.8317 (pmt-80) cc_final: 0.7578 (mtt-85) REVERT: V 134 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.6895 (mtm) REVERT: X 68 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7455 (mp10) REVERT: X 184 PRO cc_start: 0.7660 (Cg_endo) cc_final: 0.7181 (Cg_exo) REVERT: Y 35 GLN cc_start: 0.8198 (tt0) cc_final: 0.7893 (pt0) REVERT: Y 133 MET cc_start: 0.4676 (mmp) cc_final: 0.4309 (mmp) REVERT: Z 214 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7393 (mm-30) REVERT: a 103 TYR cc_start: 0.8754 (m-80) cc_final: 0.8505 (m-80) REVERT: a 126 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8105 (tp) REVERT: a 162 ASP cc_start: 0.8471 (m-30) cc_final: 0.8185 (m-30) REVERT: a 169 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7701 (tp40) REVERT: b 115 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8169 (mt-10) REVERT: b 156 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7545 (mt-10) REVERT: b 167 GLU cc_start: 0.7257 (mp0) cc_final: 0.6797 (mp0) REVERT: b 195 PHE cc_start: 0.4540 (m-10) cc_final: 0.4074 (m-80) REVERT: c 145 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6390 (mp0) REVERT: d 234 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6912 (mm-30) REVERT: h 157 ASP cc_start: 0.7769 (m-30) cc_final: 0.7292 (m-30) outliers start: 179 outliers final: 74 residues processed: 832 average time/residue: 1.3506 time to fit residues: 1423.5142 Evaluate side-chains 735 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 641 time to evaluate : 4.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 195 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain Q residue 70 ASN Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 200 LYS Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 41 ASN Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain R residue 231 ASP Chi-restraints excluded: chain R residue 240 ASN Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain S residue 187 ASP Chi-restraints excluded: chain S residue 220 ASP Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 70 ASN Chi-restraints excluded: chain T residue 186 VAL Chi-restraints excluded: chain T residue 194 LEU Chi-restraints excluded: chain T residue 200 THR Chi-restraints excluded: chain U residue 5 ASP Chi-restraints excluded: chain U residue 14 ASP Chi-restraints excluded: chain U residue 40 ASN Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain V residue 134 MET Chi-restraints excluded: chain V residue 218 GLN Chi-restraints excluded: chain X residue 68 GLN Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 221 THR Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 114 SER Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 169 GLN Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain b residue 153 THR Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 180 THR Chi-restraints excluded: chain c residue 195 THR Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 136 ASP Chi-restraints excluded: chain d residue 199 VAL Chi-restraints excluded: chain d residue 201 LYS Chi-restraints excluded: chain d residue 226 VAL Chi-restraints excluded: chain e residue 63 CYS Chi-restraints excluded: chain e residue 70 ASP Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain f residue 31 CYS Chi-restraints excluded: chain h residue 70 ASN Chi-restraints excluded: chain h residue 80 ASP Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain h residue 200 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 621 optimal weight: 0.0050 chunk 473 optimal weight: 2.9990 chunk 326 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 300 optimal weight: 7.9990 chunk 422 optimal weight: 0.9980 chunk 631 optimal weight: 0.0270 chunk 668 optimal weight: 7.9990 chunk 330 optimal weight: 1.9990 chunk 598 optimal weight: 7.9990 chunk 180 optimal weight: 0.9980 overall best weight: 0.5852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN B 123 GLN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN F 31 GLN F 166 GLN G 90 ASN H 102 ASN H 112 ASN I 86 GLN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN N 108 ASN O 225 ASN S 30 GLN S 123 GLN ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 185 ASN W 166 GLN X 90 ASN Y 102 ASN Y 112 ASN Z 86 GLN ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 170 HIS Z 194 ASN ** b 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 137 GLN d 114 HIS e 108 ASN f 225 ASN ** h 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 56118 Z= 0.165 Angle : 0.531 8.320 75896 Z= 0.279 Chirality : 0.043 0.153 8606 Planarity : 0.004 0.056 9712 Dihedral : 4.535 38.805 7610 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.65 % Allowed : 13.79 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.10), residues: 6864 helix: 1.75 (0.10), residues: 2540 sheet: 0.39 (0.12), residues: 1674 loop : 0.01 (0.12), residues: 2650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 133 HIS 0.005 0.001 HIS b 133 PHE 0.031 0.001 PHE c 129 TYR 0.022 0.001 TYR G 201 ARG 0.009 0.000 ARG b 171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 762 time to evaluate : 4.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 MET cc_start: 0.9352 (tpp) cc_final: 0.9151 (ttt) REVERT: A 148 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7444 (pt0) REVERT: A 158 ASP cc_start: 0.8543 (p0) cc_final: 0.8256 (p0) REVERT: A 222 ASP cc_start: 0.8387 (t0) cc_final: 0.8076 (t0) REVERT: C 114 ARG cc_start: 0.8848 (tpp80) cc_final: 0.8567 (tpp-160) REVERT: C 152 ASN cc_start: 0.8264 (m-40) cc_final: 0.8015 (m-40) REVERT: C 194 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8033 (mm) REVERT: C 233 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7715 (tm-30) REVERT: C 237 ASP cc_start: 0.7689 (m-30) cc_final: 0.7410 (m-30) REVERT: D 6 ARG cc_start: 0.8196 (pmt-80) cc_final: 0.7367 (mtt-85) REVERT: D 55 GLN cc_start: 0.8947 (mt0) cc_final: 0.8607 (tt0) REVERT: D 220 ASP cc_start: 0.8082 (t0) cc_final: 0.7865 (t0) REVERT: G 68 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7435 (mp10) REVERT: G 184 PRO cc_start: 0.7837 (Cg_endo) cc_final: 0.7398 (Cg_exo) REVERT: H 35 GLN cc_start: 0.8195 (tt0) cc_final: 0.7975 (pt0) REVERT: H 120 GLU cc_start: 0.8488 (mp0) cc_final: 0.8239 (mp0) REVERT: H 133 MET cc_start: 0.4456 (mmp) cc_final: 0.4132 (mmp) REVERT: H 141 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8333 (mttp) REVERT: I 214 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7365 (mm-30) REVERT: K 156 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7545 (mt-10) REVERT: K 167 GLU cc_start: 0.7234 (mp0) cc_final: 0.6882 (mp0) REVERT: K 195 PHE cc_start: 0.4614 (m-10) cc_final: 0.4059 (m-80) REVERT: L 145 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.5994 (mp0) REVERT: M 234 GLU cc_start: 0.7283 (mm-30) cc_final: 0.7056 (mm-30) REVERT: N 124 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7953 (pttp) REVERT: Q 137 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8001 (ttt90) REVERT: Q 157 ASP cc_start: 0.7887 (m-30) cc_final: 0.7457 (m-30) REVERT: Q 234 ASP cc_start: 0.6974 (t0) cc_final: 0.6588 (t0) REVERT: R 89 ASP cc_start: 0.8765 (m-30) cc_final: 0.8471 (m-30) REVERT: R 112 MET cc_start: 0.9348 (tpp) cc_final: 0.9141 (ttt) REVERT: R 148 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7447 (pt0) REVERT: R 158 ASP cc_start: 0.8544 (p0) cc_final: 0.8242 (p0) REVERT: T 114 ARG cc_start: 0.8850 (tpp80) cc_final: 0.8572 (tpp-160) REVERT: T 152 ASN cc_start: 0.8229 (m-40) cc_final: 0.7992 (m-40) REVERT: T 194 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8032 (mm) REVERT: U 6 ARG cc_start: 0.8194 (pmt-80) cc_final: 0.7366 (mtt-85) REVERT: U 220 ASP cc_start: 0.8079 (t0) cc_final: 0.7850 (t0) REVERT: V 53 ARG cc_start: 0.7696 (ttm-80) cc_final: 0.7313 (ttm110) REVERT: X 68 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7429 (mp10) REVERT: X 184 PRO cc_start: 0.7843 (Cg_endo) cc_final: 0.7405 (Cg_exo) REVERT: Y 35 GLN cc_start: 0.8196 (tt0) cc_final: 0.7987 (pt0) REVERT: Y 120 GLU cc_start: 0.8489 (mp0) cc_final: 0.8245 (mp0) REVERT: Y 133 MET cc_start: 0.4406 (mmp) cc_final: 0.4149 (mmp) REVERT: Z 214 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7344 (mm-30) REVERT: a 162 ASP cc_start: 0.8489 (m-30) cc_final: 0.8227 (m-30) REVERT: b 156 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7543 (mt-10) REVERT: b 167 GLU cc_start: 0.7225 (mp0) cc_final: 0.6885 (mp0) REVERT: b 195 PHE cc_start: 0.4487 (m-10) cc_final: 0.4008 (m-80) REVERT: c 145 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6516 (mp0) REVERT: d 201 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8520 (mttp) REVERT: d 234 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6867 (mm-30) REVERT: f 57 MET cc_start: 0.7786 (mmm) cc_final: 0.7379 (mmt) REVERT: h 137 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7992 (ttt90) REVERT: h 157 ASP cc_start: 0.7842 (m-30) cc_final: 0.7462 (m-30) outliers start: 159 outliers final: 54 residues processed: 860 average time/residue: 1.3242 time to fit residues: 1446.8620 Evaluate side-chains 748 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 681 time to evaluate : 4.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 141 LYS Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain K residue 172 MET Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain O residue 8 ASP Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain Q residue 70 ASN Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 137 ARG Chi-restraints excluded: chain Q residue 196 SER Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain S residue 187 ASP Chi-restraints excluded: chain S residue 216 ASP Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 194 LEU Chi-restraints excluded: chain T residue 200 THR Chi-restraints excluded: chain U residue 14 ASP Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain X residue 68 GLN Chi-restraints excluded: chain X residue 76 CYS Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 114 SER Chi-restraints excluded: chain b residue 172 MET Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 175 MET Chi-restraints excluded: chain c residue 180 THR Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 136 ASP Chi-restraints excluded: chain d residue 201 LYS Chi-restraints excluded: chain e residue 63 CYS Chi-restraints excluded: chain e residue 70 ASP Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain e residue 165 MET Chi-restraints excluded: chain f residue 8 ASP Chi-restraints excluded: chain f residue 31 CYS Chi-restraints excluded: chain h residue 70 ASN Chi-restraints excluded: chain h residue 98 ARG Chi-restraints excluded: chain h residue 137 ARG Chi-restraints excluded: chain h residue 200 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 557 optimal weight: 10.0000 chunk 379 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 498 optimal weight: 0.3980 chunk 275 optimal weight: 4.9990 chunk 570 optimal weight: 0.9980 chunk 462 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 341 optimal weight: 0.9980 chunk 600 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS B 123 GLN C 21 GLN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN E 185 ASN F 60 GLN F 166 GLN G 90 ASN H 102 ASN H 112 ASN I 86 GLN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 ASN ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN R 209 HIS S 123 GLN T 21 GLN ** U 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 180 GLN V 185 ASN W 60 GLN W 166 GLN X 90 ASN Y 102 ASN Y 112 ASN Z 86 GLN Z 114 GLN Z 170 HIS ** b 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 137 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 56118 Z= 0.238 Angle : 0.547 9.162 75896 Z= 0.286 Chirality : 0.044 0.216 8606 Planarity : 0.004 0.071 9712 Dihedral : 4.445 29.048 7606 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.96 % Allowed : 14.95 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: 0.99 (0.10), residues: 6864 helix: 1.70 (0.10), residues: 2568 sheet: 0.30 (0.12), residues: 1696 loop : -0.03 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 133 HIS 0.004 0.001 HIS K 133 PHE 0.031 0.002 PHE E 164 TYR 0.020 0.001 TYR J 96 ARG 0.010 0.000 ARG a 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 713 time to evaluate : 5.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6723 (mttp) REVERT: A 112 MET cc_start: 0.9375 (tpp) cc_final: 0.9132 (ttt) REVERT: A 148 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7462 (pt0) REVERT: A 158 ASP cc_start: 0.8592 (p0) cc_final: 0.8299 (p0) REVERT: A 222 ASP cc_start: 0.8473 (t0) cc_final: 0.8081 (t0) REVERT: C 114 ARG cc_start: 0.8864 (tpp80) cc_final: 0.8584 (tpp-160) REVERT: C 152 ASN cc_start: 0.8267 (m-40) cc_final: 0.8030 (m-40) REVERT: C 194 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8003 (mm) REVERT: C 233 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7687 (tm-30) REVERT: D 6 ARG cc_start: 0.8005 (pmt-80) cc_final: 0.7143 (mtt-85) REVERT: D 107 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: G 68 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7432 (mp10) REVERT: G 98 SER cc_start: 0.8513 (t) cc_final: 0.8306 (t) REVERT: G 118 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8743 (mp10) REVERT: G 184 PRO cc_start: 0.7808 (Cg_endo) cc_final: 0.7380 (Cg_exo) REVERT: H 120 GLU cc_start: 0.8526 (mp0) cc_final: 0.8279 (mp0) REVERT: H 133 MET cc_start: 0.4568 (mmp) cc_final: 0.4281 (mmp) REVERT: H 141 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8315 (mttp) REVERT: I 214 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7355 (mm-30) REVERT: K 156 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7627 (mt-10) REVERT: K 195 PHE cc_start: 0.4788 (m-10) cc_final: 0.4238 (m-80) REVERT: L 145 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.5995 (mp0) REVERT: M 51 ASP cc_start: 0.7710 (m-30) cc_final: 0.7024 (t0) REVERT: M 234 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6917 (mm-30) REVERT: N 124 LYS cc_start: 0.8256 (pttm) cc_final: 0.7954 (pttp) REVERT: O 47 TYR cc_start: 0.5965 (m-80) cc_final: 0.5760 (m-80) REVERT: O 122 PHE cc_start: 0.6760 (m-80) cc_final: 0.5989 (m-80) REVERT: Q 137 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.8057 (ttt90) REVERT: Q 157 ASP cc_start: 0.7940 (m-30) cc_final: 0.7658 (m-30) REVERT: Q 234 ASP cc_start: 0.7038 (t0) cc_final: 0.6625 (t0) REVERT: R 48 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6704 (mttp) REVERT: R 112 MET cc_start: 0.9374 (tpp) cc_final: 0.9126 (ttt) REVERT: R 148 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7461 (pt0) REVERT: R 158 ASP cc_start: 0.8593 (p0) cc_final: 0.8299 (p0) REVERT: T 39 MET cc_start: 0.8929 (ttp) cc_final: 0.8710 (ttp) REVERT: T 114 ARG cc_start: 0.8870 (tpp80) cc_final: 0.8599 (tpp-160) REVERT: T 152 ASN cc_start: 0.8235 (m-40) cc_final: 0.8026 (m-40) REVERT: T 194 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8006 (mm) REVERT: T 233 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7486 (tm-30) REVERT: T 237 ASP cc_start: 0.7719 (m-30) cc_final: 0.7167 (m-30) REVERT: U 6 ARG cc_start: 0.8003 (pmt-80) cc_final: 0.7145 (mtt-85) REVERT: U 107 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8236 (tm-30) REVERT: X 68 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7439 (mp10) REVERT: X 98 SER cc_start: 0.8513 (t) cc_final: 0.8307 (t) REVERT: X 118 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8743 (mp10) REVERT: X 184 PRO cc_start: 0.7813 (Cg_endo) cc_final: 0.7383 (Cg_exo) REVERT: Y 86 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8327 (mmt) REVERT: Y 120 GLU cc_start: 0.8527 (mp0) cc_final: 0.8278 (mp0) REVERT: Y 133 MET cc_start: 0.4569 (mmp) cc_final: 0.4285 (mmp) REVERT: Y 141 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8473 (mttp) REVERT: Z 214 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7332 (mm-30) REVERT: b 156 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7653 (mt-10) REVERT: b 195 PHE cc_start: 0.4830 (m-10) cc_final: 0.4266 (m-80) REVERT: c 145 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6469 (mp0) REVERT: d 51 ASP cc_start: 0.7803 (m-30) cc_final: 0.7295 (t0) REVERT: d 201 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8571 (mttp) REVERT: d 234 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6948 (mm-30) REVERT: e 64 ARG cc_start: 0.7144 (mtm110) cc_final: 0.6877 (mtm110) REVERT: e 124 LYS cc_start: 0.8244 (pttm) cc_final: 0.7946 (pttp) REVERT: f 122 PHE cc_start: 0.6787 (m-80) cc_final: 0.5941 (m-80) REVERT: h 137 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8052 (ttt90) REVERT: h 157 ASP cc_start: 0.7888 (m-30) cc_final: 0.7523 (m-30) REVERT: h 234 ASP cc_start: 0.6994 (t0) cc_final: 0.6583 (t0) outliers start: 178 outliers final: 83 residues processed: 824 average time/residue: 1.3258 time to fit residues: 1391.4862 Evaluate side-chains 778 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 675 time to evaluate : 4.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 32 CYS Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 141 LYS Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain O residue 8 ASP Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 137 ARG Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 196 SER Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain R residue 231 ASP Chi-restraints excluded: chain S residue 187 ASP Chi-restraints excluded: chain S residue 216 ASP Chi-restraints excluded: chain S residue 220 ASP Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 70 ASN Chi-restraints excluded: chain T residue 194 LEU Chi-restraints excluded: chain T residue 200 THR Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain U residue 14 ASP Chi-restraints excluded: chain U residue 32 CYS Chi-restraints excluded: chain U residue 107 GLU Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain V residue 78 MET Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 68 GLN Chi-restraints excluded: chain X residue 76 CYS Chi-restraints excluded: chain X residue 118 GLN Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Y residue 86 MET Chi-restraints excluded: chain Y residue 141 LYS Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 114 SER Chi-restraints excluded: chain a residue 138 VAL Chi-restraints excluded: chain b residue 153 THR Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 180 THR Chi-restraints excluded: chain c residue 195 THR Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 136 ASP Chi-restraints excluded: chain d residue 201 LYS Chi-restraints excluded: chain e residue 63 CYS Chi-restraints excluded: chain e residue 70 ASP Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 178 LEU Chi-restraints excluded: chain f residue 8 ASP Chi-restraints excluded: chain f residue 31 CYS Chi-restraints excluded: chain h residue 80 ASP Chi-restraints excluded: chain h residue 98 ARG Chi-restraints excluded: chain h residue 137 ARG Chi-restraints excluded: chain h residue 169 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 225 optimal weight: 7.9990 chunk 602 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 392 optimal weight: 0.9990 chunk 165 optimal weight: 7.9990 chunk 669 optimal weight: 3.9990 chunk 555 optimal weight: 5.9990 chunk 309 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 351 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN B 123 GLN E 185 ASN E 218 GLN F 60 GLN F 166 GLN G 90 ASN H 102 ASN H 112 ASN ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 ASN ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN N 108 ASN O 271 GLN R 27 GLN R 41 ASN S 123 GLN V 185 ASN W 166 GLN X 90 ASN Y 102 ASN Y 112 ASN Z 86 GLN a 169 GLN ** b 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 137 GLN f 225 ASN f 271 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 56118 Z= 0.363 Angle : 0.595 8.751 75896 Z= 0.311 Chirality : 0.046 0.216 8606 Planarity : 0.004 0.074 9712 Dihedral : 4.588 29.856 7602 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.21 % Allowed : 15.73 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: 0.89 (0.10), residues: 6864 helix: 1.66 (0.10), residues: 2536 sheet: 0.20 (0.12), residues: 1704 loop : -0.09 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 133 HIS 0.006 0.001 HIS X 147 PHE 0.031 0.002 PHE V 164 TYR 0.023 0.002 TYR c 163 ARG 0.007 0.001 ARG g 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 680 time to evaluate : 5.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6712 (mttp) REVERT: A 121 MET cc_start: 0.9189 (mmm) cc_final: 0.8896 (mmm) REVERT: A 148 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7462 (pt0) REVERT: A 158 ASP cc_start: 0.8632 (p0) cc_final: 0.8337 (p0) REVERT: C 114 ARG cc_start: 0.8893 (tpp80) cc_final: 0.8631 (tpp-160) REVERT: C 152 ASN cc_start: 0.8341 (m-40) cc_final: 0.8117 (m-40) REVERT: C 194 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8097 (mm) REVERT: C 213 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.8095 (t80) REVERT: C 233 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7786 (tm-30) REVERT: C 237 ASP cc_start: 0.7871 (m-30) cc_final: 0.7596 (m-30) REVERT: D 6 ARG cc_start: 0.8043 (pmt-80) cc_final: 0.7080 (mtt180) REVERT: D 53 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7444 (mtpp) REVERT: D 107 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8216 (tm-30) REVERT: G 44 ASP cc_start: 0.7214 (p0) cc_final: 0.6609 (p0) REVERT: G 68 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7434 (mp10) REVERT: G 98 SER cc_start: 0.8536 (t) cc_final: 0.8329 (t) REVERT: G 118 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8719 (mp10) REVERT: G 184 PRO cc_start: 0.7807 (Cg_endo) cc_final: 0.7381 (Cg_exo) REVERT: G 237 GLN cc_start: 0.8734 (mm-40) cc_final: 0.7713 (pt0) REVERT: H 35 GLN cc_start: 0.8342 (pt0) cc_final: 0.8088 (pt0) REVERT: H 120 GLU cc_start: 0.8565 (mp0) cc_final: 0.8343 (mp0) REVERT: H 133 MET cc_start: 0.4635 (mmp) cc_final: 0.4313 (mmp) REVERT: H 141 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8490 (mttp) REVERT: I 51 GLN cc_start: 0.6353 (OUTLIER) cc_final: 0.5584 (tm-30) REVERT: I 214 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7338 (mm-30) REVERT: J 169 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7599 (mm-40) REVERT: K 156 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7746 (mt-10) REVERT: K 195 PHE cc_start: 0.4920 (m-10) cc_final: 0.4356 (m-80) REVERT: L 145 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6160 (mp0) REVERT: M 51 ASP cc_start: 0.7838 (m-30) cc_final: 0.7158 (t0) REVERT: M 228 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6926 (pmtt) REVERT: N 124 LYS cc_start: 0.8324 (pttm) cc_final: 0.7999 (pttp) REVERT: O 57 MET cc_start: 0.7906 (mmm) cc_final: 0.7314 (mmt) REVERT: Q 137 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8111 (ttt90) REVERT: Q 157 ASP cc_start: 0.7995 (m-30) cc_final: 0.7678 (m-30) REVERT: Q 234 ASP cc_start: 0.7220 (t0) cc_final: 0.7017 (t0) REVERT: R 48 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6714 (mttp) REVERT: R 121 MET cc_start: 0.9191 (mmm) cc_final: 0.8897 (mmm) REVERT: R 148 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7478 (pt0) REVERT: R 158 ASP cc_start: 0.8609 (p0) cc_final: 0.8336 (p0) REVERT: T 39 MET cc_start: 0.8944 (ttp) cc_final: 0.8726 (ttp) REVERT: T 114 ARG cc_start: 0.8906 (tpp80) cc_final: 0.8634 (tpp-160) REVERT: T 194 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8094 (mm) REVERT: T 213 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.8124 (t80) REVERT: U 6 ARG cc_start: 0.8041 (pmt-80) cc_final: 0.7079 (mtt180) REVERT: U 107 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8221 (tm-30) REVERT: X 44 ASP cc_start: 0.7215 (p0) cc_final: 0.6609 (p0) REVERT: X 68 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7435 (mp10) REVERT: X 98 SER cc_start: 0.8543 (t) cc_final: 0.8334 (t) REVERT: X 118 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8717 (mp10) REVERT: X 184 PRO cc_start: 0.7810 (Cg_endo) cc_final: 0.7384 (Cg_exo) REVERT: X 237 GLN cc_start: 0.8736 (mm-40) cc_final: 0.7712 (pt0) REVERT: Y 35 GLN cc_start: 0.8373 (pt0) cc_final: 0.8052 (pt0) REVERT: Y 86 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8357 (mmt) REVERT: Y 133 MET cc_start: 0.4633 (mmp) cc_final: 0.4320 (mmp) REVERT: Y 141 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8593 (mttp) REVERT: Z 51 GLN cc_start: 0.6318 (OUTLIER) cc_final: 0.5492 (tm-30) REVERT: Z 214 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7337 (mm-30) REVERT: b 156 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7713 (mt-10) REVERT: b 195 PHE cc_start: 0.4869 (m-10) cc_final: 0.4294 (m-80) REVERT: c 145 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: d 51 ASP cc_start: 0.7849 (m-30) cc_final: 0.7197 (t0) REVERT: d 201 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8580 (mttp) REVERT: d 234 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7037 (mm-30) REVERT: e 64 ARG cc_start: 0.7229 (mtm110) cc_final: 0.6969 (mtm110) REVERT: e 124 LYS cc_start: 0.8256 (pttm) cc_final: 0.7952 (pttp) REVERT: f 57 MET cc_start: 0.7933 (mmm) cc_final: 0.7338 (mmt) REVERT: h 137 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8107 (ttt90) REVERT: h 157 ASP cc_start: 0.7956 (m-30) cc_final: 0.7640 (m-30) outliers start: 193 outliers final: 112 residues processed: 813 average time/residue: 1.3356 time to fit residues: 1379.1436 Evaluate side-chains 778 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 639 time to evaluate : 4.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 32 CYS Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 141 LYS Chi-restraints excluded: chain I residue 51 GLN Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 169 GLN Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 149 ARG Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 137 GLN Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 177 CYS Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain O residue 8 ASP Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 137 ARG Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 196 SER Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain R residue 231 ASP Chi-restraints excluded: chain S residue 187 ASP Chi-restraints excluded: chain S residue 216 ASP Chi-restraints excluded: chain S residue 220 ASP Chi-restraints excluded: chain S residue 227 ILE Chi-restraints excluded: chain S residue 231 LYS Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 70 ASN Chi-restraints excluded: chain T residue 194 LEU Chi-restraints excluded: chain T residue 200 THR Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain T residue 213 PHE Chi-restraints excluded: chain U residue 14 ASP Chi-restraints excluded: chain U residue 32 CYS Chi-restraints excluded: chain U residue 107 GLU Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain V residue 78 MET Chi-restraints excluded: chain V residue 218 GLN Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 68 GLN Chi-restraints excluded: chain X residue 76 CYS Chi-restraints excluded: chain X residue 118 GLN Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Y residue 86 MET Chi-restraints excluded: chain Y residue 141 LYS Chi-restraints excluded: chain Z residue 51 GLN Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 114 SER Chi-restraints excluded: chain a residue 138 VAL Chi-restraints excluded: chain b residue 103 LEU Chi-restraints excluded: chain b residue 149 ARG Chi-restraints excluded: chain b residue 153 THR Chi-restraints excluded: chain c residue 137 GLN Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 180 THR Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 136 ASP Chi-restraints excluded: chain d residue 147 VAL Chi-restraints excluded: chain d residue 201 LYS Chi-restraints excluded: chain e residue 41 THR Chi-restraints excluded: chain e residue 63 CYS Chi-restraints excluded: chain e residue 70 ASP Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 178 LEU Chi-restraints excluded: chain f residue 8 ASP Chi-restraints excluded: chain f residue 31 CYS Chi-restraints excluded: chain f residue 149 MET Chi-restraints excluded: chain h residue 80 ASP Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 98 ARG Chi-restraints excluded: chain h residue 137 ARG Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain h residue 208 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 645 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 381 optimal weight: 1.9990 chunk 488 optimal weight: 6.9990 chunk 378 optimal weight: 0.8980 chunk 563 optimal weight: 0.5980 chunk 373 optimal weight: 2.9990 chunk 666 optimal weight: 2.9990 chunk 417 optimal weight: 0.9990 chunk 406 optimal weight: 0.8980 chunk 307 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 41 ASN A 176 GLN B 123 GLN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN E 218 GLN F 166 GLN G 90 ASN G 147 HIS H 102 ASN H 112 ASN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 ASN ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN O 271 GLN R 176 GLN S 123 GLN T 233 GLN ** U 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 185 ASN W 60 GLN W 166 GLN X 90 ASN X 147 HIS Y 102 ASN Y 112 ASN Z 86 GLN Z 114 GLN a 169 GLN a 173 ASN ** b 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 137 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 56118 Z= 0.199 Angle : 0.539 9.546 75896 Z= 0.283 Chirality : 0.043 0.193 8606 Planarity : 0.004 0.068 9712 Dihedral : 4.416 26.627 7602 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.90 % Allowed : 16.35 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: 0.95 (0.10), residues: 6864 helix: 1.73 (0.10), residues: 2556 sheet: 0.23 (0.12), residues: 1692 loop : -0.08 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 133 HIS 0.004 0.001 HIS b 133 PHE 0.032 0.001 PHE E 164 TYR 0.033 0.001 TYR c 163 ARG 0.012 0.000 ARG g 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 696 time to evaluate : 4.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6710 (mttp) REVERT: A 148 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: A 158 ASP cc_start: 0.8552 (p0) cc_final: 0.8251 (p0) REVERT: A 222 ASP cc_start: 0.8494 (t0) cc_final: 0.8080 (t0) REVERT: C 114 ARG cc_start: 0.8851 (tpp80) cc_final: 0.8578 (tpp-160) REVERT: C 152 ASN cc_start: 0.8266 (m-40) cc_final: 0.8034 (m-40) REVERT: C 194 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8036 (mm) REVERT: C 233 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7722 (tm-30) REVERT: C 234 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7383 (pt0) REVERT: C 237 ASP cc_start: 0.7897 (m-30) cc_final: 0.7582 (m-30) REVERT: D 6 ARG cc_start: 0.8037 (pmt-80) cc_final: 0.7143 (mtt180) REVERT: G 44 ASP cc_start: 0.7051 (p0) cc_final: 0.6455 (p0) REVERT: G 98 SER cc_start: 0.8522 (t) cc_final: 0.8316 (t) REVERT: G 118 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8759 (mp10) REVERT: G 184 PRO cc_start: 0.7839 (Cg_endo) cc_final: 0.7427 (Cg_exo) REVERT: G 237 GLN cc_start: 0.8694 (mm-40) cc_final: 0.7676 (pt0) REVERT: H 35 GLN cc_start: 0.8393 (pt0) cc_final: 0.8113 (pt0) REVERT: H 120 GLU cc_start: 0.8539 (mp0) cc_final: 0.8291 (mp0) REVERT: H 141 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8434 (mttp) REVERT: I 214 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7315 (mm-30) REVERT: J 11 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8582 (tp) REVERT: J 169 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.6970 (mp10) REVERT: K 156 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7671 (mt-10) REVERT: K 195 PHE cc_start: 0.4668 (m-10) cc_final: 0.4174 (m-80) REVERT: L 145 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6026 (mp0) REVERT: M 51 ASP cc_start: 0.7745 (m-30) cc_final: 0.7113 (t0) REVERT: M 228 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6988 (pmtt) REVERT: N 124 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7954 (pttp) REVERT: O 57 MET cc_start: 0.7874 (mmm) cc_final: 0.7375 (mmt) REVERT: O 122 PHE cc_start: 0.6860 (m-80) cc_final: 0.6327 (m-80) REVERT: Q 137 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8104 (ttt90) REVERT: Q 157 ASP cc_start: 0.7902 (m-30) cc_final: 0.7604 (m-30) REVERT: R 48 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6710 (mttp) REVERT: R 148 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7447 (pt0) REVERT: R 158 ASP cc_start: 0.8551 (p0) cc_final: 0.8270 (p0) REVERT: T 39 MET cc_start: 0.8928 (ttp) cc_final: 0.8711 (ttp) REVERT: T 114 ARG cc_start: 0.8853 (tpp80) cc_final: 0.8581 (tpp-160) REVERT: T 194 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8030 (mm) REVERT: T 237 ASP cc_start: 0.7893 (m-30) cc_final: 0.7610 (m-30) REVERT: U 6 ARG cc_start: 0.8023 (pmt-80) cc_final: 0.7151 (mtt180) REVERT: X 44 ASP cc_start: 0.7053 (p0) cc_final: 0.6456 (p0) REVERT: X 98 SER cc_start: 0.8519 (t) cc_final: 0.8312 (t) REVERT: X 118 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8758 (mp10) REVERT: X 184 PRO cc_start: 0.7839 (Cg_endo) cc_final: 0.7426 (Cg_exo) REVERT: X 237 GLN cc_start: 0.8696 (mm-40) cc_final: 0.7682 (pt0) REVERT: Y 35 GLN cc_start: 0.8392 (pt0) cc_final: 0.8115 (pt0) REVERT: Y 120 GLU cc_start: 0.8513 (mp0) cc_final: 0.8302 (mp0) REVERT: Y 141 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8513 (mttp) REVERT: Z 214 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7312 (mm-30) REVERT: b 156 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7668 (mt-10) REVERT: b 195 PHE cc_start: 0.4766 (m-10) cc_final: 0.4232 (m-80) REVERT: c 145 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6614 (mp0) REVERT: d 51 ASP cc_start: 0.7769 (m-30) cc_final: 0.7161 (t0) REVERT: d 201 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8591 (mttp) REVERT: e 124 LYS cc_start: 0.8258 (pttm) cc_final: 0.7959 (pttp) REVERT: f 57 MET cc_start: 0.7881 (mmm) cc_final: 0.7384 (mmt) REVERT: f 122 PHE cc_start: 0.6968 (m-80) cc_final: 0.6371 (m-80) REVERT: h 137 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8101 (ttt90) REVERT: h 157 ASP cc_start: 0.7862 (m-30) cc_final: 0.7543 (m-30) outliers start: 174 outliers final: 93 residues processed: 819 average time/residue: 1.3103 time to fit residues: 1365.8070 Evaluate side-chains 781 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 668 time to evaluate : 4.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 32 CYS Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 141 LYS Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 169 GLN Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain L residue 138 CYS Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain O residue 149 MET Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 137 ARG Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 196 SER Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain S residue 187 ASP Chi-restraints excluded: chain S residue 216 ASP Chi-restraints excluded: chain S residue 227 ILE Chi-restraints excluded: chain S residue 231 LYS Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 70 ASN Chi-restraints excluded: chain T residue 194 LEU Chi-restraints excluded: chain T residue 200 THR Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain U residue 14 ASP Chi-restraints excluded: chain U residue 32 CYS Chi-restraints excluded: chain U residue 40 ASN Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 76 CYS Chi-restraints excluded: chain X residue 118 GLN Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 141 LYS Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 138 VAL Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 153 THR Chi-restraints excluded: chain b residue 167 GLU Chi-restraints excluded: chain c residue 138 CYS Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 180 THR Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 136 ASP Chi-restraints excluded: chain d residue 201 LYS Chi-restraints excluded: chain e residue 63 CYS Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain f residue 31 CYS Chi-restraints excluded: chain f residue 149 MET Chi-restraints excluded: chain f residue 276 ILE Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 98 ARG Chi-restraints excluded: chain h residue 137 ARG Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain h residue 196 SER Chi-restraints excluded: chain h residue 208 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 412 optimal weight: 10.0000 chunk 266 optimal weight: 5.9990 chunk 398 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 424 optimal weight: 3.9990 chunk 454 optimal weight: 10.0000 chunk 329 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 524 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN B 123 GLN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN F 60 GLN F 166 GLN G 90 ASN H 102 ASN H 112 ASN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 ASN ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 ASN O 225 ASN S 123 GLN T 177 GLN ** U 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 185 ASN V 218 GLN W 166 GLN X 90 ASN Y 102 ASN Y 112 ASN Z 86 GLN Z 114 GLN a 173 ASN ** b 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 68 ASN ** e 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 225 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 56118 Z= 0.382 Angle : 0.615 9.833 75896 Z= 0.321 Chirality : 0.046 0.214 8606 Planarity : 0.004 0.061 9712 Dihedral : 4.652 30.227 7602 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.10 % Allowed : 16.90 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.78 (0.10), residues: 6864 helix: 1.59 (0.10), residues: 2542 sheet: 0.11 (0.12), residues: 1710 loop : -0.15 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 133 HIS 0.005 0.001 HIS d 114 PHE 0.034 0.002 PHE V 164 TYR 0.039 0.002 TYR c 163 ARG 0.009 0.001 ARG g 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 668 time to evaluate : 4.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6702 (mttp) REVERT: A 148 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7480 (pt0) REVERT: A 158 ASP cc_start: 0.8631 (p0) cc_final: 0.8348 (p0) REVERT: A 221 ASN cc_start: 0.7976 (m110) cc_final: 0.7374 (p0) REVERT: A 222 ASP cc_start: 0.8490 (t0) cc_final: 0.8122 (t0) REVERT: C 114 ARG cc_start: 0.8910 (tpp80) cc_final: 0.8644 (tpp-160) REVERT: C 152 ASN cc_start: 0.8385 (m-40) cc_final: 0.8164 (m-40) REVERT: C 194 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8124 (mm) REVERT: C 233 GLN cc_start: 0.8068 (tm-30) cc_final: 0.7784 (tm-30) REVERT: C 234 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7344 (pt0) REVERT: D 6 ARG cc_start: 0.8151 (pmt-80) cc_final: 0.7135 (mtt180) REVERT: D 53 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7516 (mtpp) REVERT: D 107 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8211 (tm-30) REVERT: G 44 ASP cc_start: 0.7271 (p0) cc_final: 0.6591 (p0) REVERT: G 118 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8744 (mp10) REVERT: G 184 PRO cc_start: 0.7607 (Cg_endo) cc_final: 0.7212 (Cg_exo) REVERT: G 190 ARG cc_start: 0.8205 (mmm160) cc_final: 0.7970 (mmm160) REVERT: H 35 GLN cc_start: 0.8446 (pt0) cc_final: 0.8233 (pt0) REVERT: H 120 GLU cc_start: 0.8577 (mp0) cc_final: 0.8334 (mp0) REVERT: H 141 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8568 (mttp) REVERT: I 214 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7325 (mm-30) REVERT: J 11 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8825 (tp) REVERT: K 156 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7724 (mt-10) REVERT: K 195 PHE cc_start: 0.4812 (m-10) cc_final: 0.4292 (m-80) REVERT: L 145 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6129 (mp0) REVERT: M 51 ASP cc_start: 0.7791 (m-30) cc_final: 0.7151 (t0) REVERT: M 228 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6895 (pmtt) REVERT: N 110 ASP cc_start: 0.7642 (m-30) cc_final: 0.7412 (m-30) REVERT: N 124 LYS cc_start: 0.8312 (pttm) cc_final: 0.7996 (pttp) REVERT: O 57 MET cc_start: 0.7878 (mmm) cc_final: 0.7364 (mmt) REVERT: Q 157 ASP cc_start: 0.7973 (m-30) cc_final: 0.7701 (m-30) REVERT: R 48 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6705 (mttp) REVERT: R 148 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7456 (pt0) REVERT: R 158 ASP cc_start: 0.8631 (p0) cc_final: 0.8347 (p0) REVERT: T 39 MET cc_start: 0.8958 (ttp) cc_final: 0.8733 (ttp) REVERT: T 114 ARG cc_start: 0.8914 (tpp80) cc_final: 0.8647 (tpp-160) REVERT: T 194 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8118 (mm) REVERT: U 6 ARG cc_start: 0.8151 (pmt-80) cc_final: 0.7135 (mtt180) REVERT: U 107 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8209 (tm-30) REVERT: X 44 ASP cc_start: 0.7317 (p0) cc_final: 0.6638 (p0) REVERT: X 118 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8745 (mp10) REVERT: X 184 PRO cc_start: 0.7608 (Cg_endo) cc_final: 0.7216 (Cg_exo) REVERT: X 190 ARG cc_start: 0.8138 (mmm160) cc_final: 0.7908 (mmm160) REVERT: Y 35 GLN cc_start: 0.8445 (pt0) cc_final: 0.8235 (pt0) REVERT: Z 214 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7329 (mm-30) REVERT: a 11 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8808 (tp) REVERT: b 156 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7691 (mt-10) REVERT: b 195 PHE cc_start: 0.4801 (m-10) cc_final: 0.4285 (m-80) REVERT: c 145 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: d 51 ASP cc_start: 0.7809 (m-30) cc_final: 0.7192 (t0) REVERT: d 201 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8582 (mttp) REVERT: e 124 LYS cc_start: 0.8241 (pttm) cc_final: 0.7946 (pttp) REVERT: f 57 MET cc_start: 0.7903 (mmm) cc_final: 0.7442 (mmt) REVERT: f 122 PHE cc_start: 0.7087 (m-80) cc_final: 0.6564 (m-80) REVERT: h 157 ASP cc_start: 0.7930 (m-30) cc_final: 0.7605 (m-30) outliers start: 186 outliers final: 112 residues processed: 808 average time/residue: 1.3463 time to fit residues: 1378.9038 Evaluate side-chains 756 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 625 time to evaluate : 4.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 32 CYS Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 141 LYS Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 149 ARG Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 138 CYS Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 195 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 219 ASP Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain O residue 8 ASP Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain O residue 149 MET Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 196 SER Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain R residue 231 ASP Chi-restraints excluded: chain S residue 187 ASP Chi-restraints excluded: chain S residue 216 ASP Chi-restraints excluded: chain S residue 220 ASP Chi-restraints excluded: chain S residue 227 ILE Chi-restraints excluded: chain S residue 231 LYS Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 70 ASN Chi-restraints excluded: chain T residue 194 LEU Chi-restraints excluded: chain T residue 200 THR Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain U residue 14 ASP Chi-restraints excluded: chain U residue 32 CYS Chi-restraints excluded: chain U residue 40 ASN Chi-restraints excluded: chain U residue 107 GLU Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 76 CYS Chi-restraints excluded: chain X residue 118 GLN Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Y residue 141 LYS Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 131 ASP Chi-restraints excluded: chain a residue 138 VAL Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 103 LEU Chi-restraints excluded: chain b residue 149 ARG Chi-restraints excluded: chain b residue 153 THR Chi-restraints excluded: chain c residue 138 CYS Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 180 THR Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 136 ASP Chi-restraints excluded: chain d residue 147 VAL Chi-restraints excluded: chain d residue 199 VAL Chi-restraints excluded: chain d residue 201 LYS Chi-restraints excluded: chain d residue 219 ASP Chi-restraints excluded: chain e residue 63 CYS Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain f residue 8 ASP Chi-restraints excluded: chain f residue 31 CYS Chi-restraints excluded: chain h residue 80 ASP Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 98 ARG Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain h residue 196 SER Chi-restraints excluded: chain h residue 208 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 606 optimal weight: 5.9990 chunk 638 optimal weight: 1.9990 chunk 582 optimal weight: 0.9980 chunk 621 optimal weight: 1.9990 chunk 374 optimal weight: 5.9990 chunk 270 optimal weight: 1.9990 chunk 488 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 561 optimal weight: 7.9990 chunk 587 optimal weight: 0.0470 chunk 619 optimal weight: 3.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN B 123 GLN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN F 166 GLN G 90 ASN H 102 ASN I 86 GLN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 ASN ** I 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN R 41 ASN S 123 GLN ** U 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 185 ASN W 60 GLN W 166 GLN X 90 ASN Y 102 ASN Z 86 GLN Z 114 GLN ** b 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 56118 Z= 0.211 Angle : 0.553 10.238 75896 Z= 0.290 Chirality : 0.044 0.190 8606 Planarity : 0.004 0.062 9712 Dihedral : 4.440 26.460 7602 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.71 % Allowed : 17.28 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: 0.93 (0.10), residues: 6864 helix: 1.76 (0.10), residues: 2546 sheet: 0.17 (0.12), residues: 1686 loop : -0.10 (0.12), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 133 HIS 0.004 0.001 HIS b 133 PHE 0.046 0.001 PHE c 129 TYR 0.042 0.001 TYR L 163 ARG 0.009 0.000 ARG g 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 677 time to evaluate : 4.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6720 (mttp) REVERT: A 148 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7483 (pt0) REVERT: A 158 ASP cc_start: 0.8564 (p0) cc_final: 0.8281 (p0) REVERT: A 221 ASN cc_start: 0.7996 (m110) cc_final: 0.7407 (p0) REVERT: C 114 ARG cc_start: 0.8855 (tpp80) cc_final: 0.8584 (tpp-160) REVERT: C 152 ASN cc_start: 0.8304 (m-40) cc_final: 0.8068 (m-40) REVERT: C 194 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8057 (mm) REVERT: C 233 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7641 (tm-30) REVERT: D 6 ARG cc_start: 0.8056 (pmt-80) cc_final: 0.7153 (mtt180) REVERT: D 53 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7467 (mtpp) REVERT: G 44 ASP cc_start: 0.7174 (p0) cc_final: 0.6476 (p0) REVERT: G 118 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8756 (mp10) REVERT: G 184 PRO cc_start: 0.7609 (Cg_endo) cc_final: 0.7224 (Cg_exo) REVERT: G 190 ARG cc_start: 0.8195 (mmm160) cc_final: 0.7955 (mmm160) REVERT: G 237 GLN cc_start: 0.8618 (mm-40) cc_final: 0.7696 (pt0) REVERT: H 120 GLU cc_start: 0.8543 (mp0) cc_final: 0.8266 (mp0) REVERT: H 133 MET cc_start: 0.4520 (mmp) cc_final: 0.4130 (mmp) REVERT: H 141 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8495 (mttp) REVERT: I 153 TYR cc_start: 0.9082 (p90) cc_final: 0.8844 (p90) REVERT: I 214 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7299 (mm-30) REVERT: K 195 PHE cc_start: 0.4824 (m-10) cc_final: 0.4239 (m-80) REVERT: L 145 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: M 51 ASP cc_start: 0.7713 (m-30) cc_final: 0.7120 (t0) REVERT: M 228 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6983 (pmtt) REVERT: N 110 ASP cc_start: 0.7620 (m-30) cc_final: 0.7409 (m-30) REVERT: N 124 LYS cc_start: 0.8254 (pttm) cc_final: 0.7967 (pttp) REVERT: O 57 MET cc_start: 0.7835 (mmm) cc_final: 0.7350 (mmt) REVERT: O 122 PHE cc_start: 0.6862 (m-80) cc_final: 0.6067 (m-80) REVERT: Q 106 GLU cc_start: 0.7343 (pp20) cc_final: 0.7010 (tm-30) REVERT: Q 157 ASP cc_start: 0.7935 (m-30) cc_final: 0.7684 (m-30) REVERT: R 48 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6721 (mttp) REVERT: R 148 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7484 (pt0) REVERT: R 158 ASP cc_start: 0.8561 (p0) cc_final: 0.8276 (p0) REVERT: R 221 ASN cc_start: 0.8128 (m110) cc_final: 0.7629 (p0) REVERT: T 39 MET cc_start: 0.8925 (ttp) cc_final: 0.8721 (ttp) REVERT: T 114 ARG cc_start: 0.8860 (tpp80) cc_final: 0.8587 (tpp-160) REVERT: T 194 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8062 (mm) REVERT: U 6 ARG cc_start: 0.8057 (pmt-80) cc_final: 0.7152 (mtt180) REVERT: X 44 ASP cc_start: 0.7167 (p0) cc_final: 0.6480 (p0) REVERT: X 118 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8759 (mp10) REVERT: X 184 PRO cc_start: 0.7615 (Cg_endo) cc_final: 0.7229 (Cg_exo) REVERT: X 190 ARG cc_start: 0.8196 (mmm160) cc_final: 0.7961 (mmm160) REVERT: X 237 GLN cc_start: 0.8620 (mm-40) cc_final: 0.7703 (pt0) REVERT: Y 133 MET cc_start: 0.4544 (mmp) cc_final: 0.4157 (mmp) REVERT: Y 141 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8583 (mttp) REVERT: Z 214 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7305 (mm-30) REVERT: b 156 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7763 (mt-10) REVERT: b 195 PHE cc_start: 0.4776 (m-10) cc_final: 0.4175 (m-80) REVERT: c 145 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: d 51 ASP cc_start: 0.7740 (m-30) cc_final: 0.7267 (t0) REVERT: d 93 TRP cc_start: 0.7779 (m100) cc_final: 0.7478 (m100) REVERT: d 201 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8565 (mttp) REVERT: e 124 LYS cc_start: 0.8260 (pttm) cc_final: 0.7968 (pttp) REVERT: f 57 MET cc_start: 0.7866 (mmm) cc_final: 0.7413 (mmt) REVERT: h 106 GLU cc_start: 0.7353 (pp20) cc_final: 0.7017 (tm-30) REVERT: h 157 ASP cc_start: 0.7924 (m-30) cc_final: 0.7663 (m-30) outliers start: 163 outliers final: 99 residues processed: 798 average time/residue: 1.3118 time to fit residues: 1336.7322 Evaluate side-chains 771 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 657 time to evaluate : 4.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 32 CYS Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 141 LYS Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain L residue 138 CYS Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 195 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 197 GLU Chi-restraints excluded: chain M residue 219 ASP Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain O residue 149 MET Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 196 SER Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain S residue 187 ASP Chi-restraints excluded: chain S residue 200 VAL Chi-restraints excluded: chain S residue 216 ASP Chi-restraints excluded: chain S residue 227 ILE Chi-restraints excluded: chain S residue 231 LYS Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 70 ASN Chi-restraints excluded: chain T residue 178 MET Chi-restraints excluded: chain T residue 194 LEU Chi-restraints excluded: chain T residue 200 THR Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain U residue 14 ASP Chi-restraints excluded: chain U residue 32 CYS Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 76 CYS Chi-restraints excluded: chain X residue 118 GLN Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Y residue 141 LYS Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 138 VAL Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 153 THR Chi-restraints excluded: chain b residue 167 GLU Chi-restraints excluded: chain c residue 138 CYS Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 177 CYS Chi-restraints excluded: chain c residue 180 THR Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 136 ASP Chi-restraints excluded: chain d residue 201 LYS Chi-restraints excluded: chain d residue 219 ASP Chi-restraints excluded: chain e residue 63 CYS Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain f residue 31 CYS Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 98 ARG Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain h residue 196 SER Chi-restraints excluded: chain h residue 208 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 408 optimal weight: 0.7980 chunk 657 optimal weight: 0.3980 chunk 401 optimal weight: 1.9990 chunk 311 optimal weight: 30.0000 chunk 456 optimal weight: 9.9990 chunk 689 optimal weight: 4.9990 chunk 634 optimal weight: 20.0000 chunk 548 optimal weight: 0.1980 chunk 57 optimal weight: 0.8980 chunk 424 optimal weight: 0.5980 chunk 336 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS B 123 GLN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN F 60 GLN F 166 GLN G 90 ASN H 102 ASN H 112 ASN I 86 GLN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 ASN ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 GLN J 173 ASN K 10 GLN ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 HIS R 209 HIS ** U 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 185 ASN V 218 GLN W 166 GLN X 90 ASN Y 102 ASN Y 112 ASN Z 86 GLN Z 114 GLN a 169 GLN a 173 ASN ** b 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 56118 Z= 0.163 Angle : 0.544 11.118 75896 Z= 0.284 Chirality : 0.043 0.221 8606 Planarity : 0.004 0.060 9712 Dihedral : 4.279 26.505 7602 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.21 % Allowed : 17.85 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.10), residues: 6864 helix: 1.88 (0.10), residues: 2544 sheet: 0.25 (0.12), residues: 1680 loop : -0.05 (0.13), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP c 133 HIS 0.005 0.000 HIS b 133 PHE 0.047 0.001 PHE c 129 TYR 0.018 0.001 TYR h 128 ARG 0.016 0.000 ARG b 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 736 time to evaluate : 4.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8751 (m-30) cc_final: 0.8454 (m-30) REVERT: A 148 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7422 (pt0) REVERT: A 158 ASP cc_start: 0.8540 (p0) cc_final: 0.8230 (p0) REVERT: A 221 ASN cc_start: 0.8026 (m110) cc_final: 0.7440 (p0) REVERT: A 222 ASP cc_start: 0.8493 (t0) cc_final: 0.8157 (t0) REVERT: C 114 ARG cc_start: 0.8836 (tpp80) cc_final: 0.8557 (tpp-160) REVERT: C 152 ASN cc_start: 0.8215 (m-40) cc_final: 0.8002 (m-40) REVERT: C 194 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8048 (mm) REVERT: C 233 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7372 (tm-30) REVERT: C 237 ASP cc_start: 0.7859 (m-30) cc_final: 0.7279 (m-30) REVERT: D 6 ARG cc_start: 0.7983 (pmt-80) cc_final: 0.7110 (mtt180) REVERT: D 53 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7406 (mtpp) REVERT: D 143 ASP cc_start: 0.7966 (p0) cc_final: 0.7493 (t0) REVERT: D 220 ASP cc_start: 0.8011 (t0) cc_final: 0.7794 (t0) REVERT: F 118 LYS cc_start: 0.8485 (mtmm) cc_final: 0.8262 (tptp) REVERT: G 44 ASP cc_start: 0.7232 (p0) cc_final: 0.6554 (p0) REVERT: G 184 PRO cc_start: 0.7803 (Cg_endo) cc_final: 0.7453 (Cg_exo) REVERT: G 241 ASP cc_start: 0.7941 (m-30) cc_final: 0.7572 (p0) REVERT: H 120 GLU cc_start: 0.8477 (mp0) cc_final: 0.8180 (mp0) REVERT: H 133 MET cc_start: 0.4486 (mmp) cc_final: 0.4091 (mmp) REVERT: H 141 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8372 (mttp) REVERT: I 51 GLN cc_start: 0.6483 (OUTLIER) cc_final: 0.5597 (tm-30) REVERT: I 148 THR cc_start: 0.9080 (p) cc_final: 0.8879 (t) REVERT: I 214 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7259 (mm-30) REVERT: K 195 PHE cc_start: 0.4754 (m-10) cc_final: 0.4049 (m-80) REVERT: M 51 ASP cc_start: 0.7700 (m-30) cc_final: 0.7245 (t0) REVERT: N 110 ASP cc_start: 0.7583 (m-30) cc_final: 0.7353 (m-30) REVERT: N 124 LYS cc_start: 0.8279 (pttm) cc_final: 0.7997 (pttp) REVERT: O 57 MET cc_start: 0.7800 (mmm) cc_final: 0.7317 (mmt) REVERT: Q 106 GLU cc_start: 0.7313 (pp20) cc_final: 0.7016 (tm-30) REVERT: Q 157 ASP cc_start: 0.7943 (m-30) cc_final: 0.7720 (m-30) REVERT: R 89 ASP cc_start: 0.8756 (m-30) cc_final: 0.8457 (m-30) REVERT: R 148 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7405 (pt0) REVERT: R 158 ASP cc_start: 0.8546 (p0) cc_final: 0.8239 (p0) REVERT: R 221 ASN cc_start: 0.8083 (m110) cc_final: 0.7597 (p0) REVERT: T 114 ARG cc_start: 0.8839 (tpp80) cc_final: 0.8560 (tpp-160) REVERT: T 178 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7501 (ppp) REVERT: T 194 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8040 (mm) REVERT: U 6 ARG cc_start: 0.7986 (pmt-80) cc_final: 0.7115 (mtt180) REVERT: W 118 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8309 (tptp) REVERT: X 44 ASP cc_start: 0.7227 (p0) cc_final: 0.6543 (p0) REVERT: X 184 PRO cc_start: 0.7806 (Cg_endo) cc_final: 0.7457 (Cg_exo) REVERT: X 241 ASP cc_start: 0.7984 (m-30) cc_final: 0.7584 (p0) REVERT: Y 133 MET cc_start: 0.4511 (mmp) cc_final: 0.4115 (mmp) REVERT: Y 141 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8490 (mttp) REVERT: Z 214 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7259 (mm-30) REVERT: a 19 ASP cc_start: 0.7334 (t70) cc_final: 0.6946 (OUTLIER) REVERT: b 195 PHE cc_start: 0.4724 (m-10) cc_final: 0.4023 (m-80) REVERT: c 145 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6591 (mp0) REVERT: d 51 ASP cc_start: 0.7738 (m-30) cc_final: 0.7288 (t0) REVERT: d 93 TRP cc_start: 0.7794 (m100) cc_final: 0.7538 (m100) REVERT: d 201 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8586 (mttp) REVERT: e 124 LYS cc_start: 0.8267 (pttm) cc_final: 0.7971 (pttp) REVERT: f 57 MET cc_start: 0.7820 (mmm) cc_final: 0.7325 (mmt) REVERT: h 65 SER cc_start: 0.8653 (m) cc_final: 0.8362 (t) REVERT: h 106 GLU cc_start: 0.7324 (pp20) cc_final: 0.6979 (tm-30) REVERT: h 157 ASP cc_start: 0.7951 (m-30) cc_final: 0.7709 (m-30) outliers start: 133 outliers final: 86 residues processed: 840 average time/residue: 1.2530 time to fit residues: 1355.8584 Evaluate side-chains 760 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 664 time to evaluate : 4.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 32 CYS Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 141 LYS Chi-restraints excluded: chain I residue 51 GLN Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain L residue 138 CYS Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 195 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 219 ASP Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 196 SER Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain S residue 187 ASP Chi-restraints excluded: chain S residue 200 VAL Chi-restraints excluded: chain S residue 216 ASP Chi-restraints excluded: chain S residue 227 ILE Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 178 MET Chi-restraints excluded: chain T residue 194 LEU Chi-restraints excluded: chain T residue 200 THR Chi-restraints excluded: chain U residue 14 ASP Chi-restraints excluded: chain U residue 32 CYS Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 76 CYS Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Y residue 141 LYS Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 131 ASP Chi-restraints excluded: chain a residue 138 VAL Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 153 THR Chi-restraints excluded: chain b residue 167 GLU Chi-restraints excluded: chain c residue 138 CYS Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 177 CYS Chi-restraints excluded: chain c residue 180 THR Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 136 ASP Chi-restraints excluded: chain d residue 147 VAL Chi-restraints excluded: chain d residue 197 GLU Chi-restraints excluded: chain d residue 201 LYS Chi-restraints excluded: chain d residue 219 ASP Chi-restraints excluded: chain d residue 226 VAL Chi-restraints excluded: chain e residue 70 ASP Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain f residue 31 CYS Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain h residue 208 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 436 optimal weight: 2.9990 chunk 584 optimal weight: 8.9990 chunk 168 optimal weight: 0.4980 chunk 506 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 549 optimal weight: 0.7980 chunk 230 optimal weight: 4.9990 chunk 564 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 209 HIS ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN C 177 GLN E 185 ASN F 166 GLN H 102 ASN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 ASN ** I 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 HIS ** Q 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 209 HIS ** S 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 123 GLN T 152 ASN V 185 ASN W 60 GLN W 166 GLN Y 102 ASN ** b 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.140473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.097350 restraints weight = 80918.203| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.16 r_work: 0.3113 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 56118 Z= 0.291 Angle : 0.589 11.070 75896 Z= 0.307 Chirality : 0.045 0.213 8606 Planarity : 0.004 0.063 9712 Dihedral : 4.374 28.669 7602 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.20 % Allowed : 18.83 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: 0.99 (0.10), residues: 6864 helix: 1.80 (0.10), residues: 2538 sheet: 0.22 (0.12), residues: 1694 loop : -0.06 (0.13), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP c 133 HIS 0.004 0.001 HIS K 133 PHE 0.048 0.002 PHE c 129 TYR 0.022 0.002 TYR b 59 ARG 0.015 0.001 ARG b 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20351.98 seconds wall clock time: 353 minutes 49.00 seconds (21229.00 seconds total)