Starting phenix.real_space_refine on Fri Dec 8 04:45:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t08_40938/12_2023/8t08_40938.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t08_40938/12_2023/8t08_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_40938/12_2023/8t08_40938.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t08_40938/12_2023/8t08_40938.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t08_40938/12_2023/8t08_40938.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t08_40938/12_2023/8t08_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-1.21rc1-5172/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: 20.26, per 1000 atoms: 0.37 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: 15.41 Conformation dependent library (CDL) restraints added in 7.1 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: 4.51 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: 19.61 Time building geometry restraints manager: 17.04 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 11.150 Check model and map are aligned: 0.610 Set scattering table: 0.380 Process input model: 107.330 Find NCS groups from input model: 4.010 Set up NCS constraints: 0.480 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:9.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.870 ------------------------------------------------------------------------------- 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 : 4.752 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 6 residues processed: 1013 average time/residue: 1.4202 time to fit residues: 1813.7208 Evaluate side-chains 665 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 659 time to evaluate : 4.721 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 2 average time/residue: 0.4908 time to fit residues: 7.9377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 403 optimal weight: 0.6980 chunk 628 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 I 218 ASN J 145 GLN K 78 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 Z 218 ASN 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 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 56118 Z= 0.212 Angle : 0.581 9.139 75896 Z= 0.310 Chirality : 0.045 0.167 8606 Planarity : 0.004 0.059 9712 Dihedral : 4.572 74.170 7602 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.83 % Allowed : 9.64 % Favored : 88.53 % 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: 1.08 (0.10), residues: 6864 helix: 1.69 (0.10), residues: 2520 sheet: 0.33 (0.12), residues: 1728 loop : 0.18 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 158 HIS 0.010 0.001 HIS X 183 PHE 0.029 0.002 PHE c 129 TYR 0.020 0.001 TYR g 32 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 938 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 828 time to evaluate : 4.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 47 residues processed: 877 average time/residue: 1.3851 time to fit residues: 1547.7254 Evaluate side-chains 709 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 662 time to evaluate : 4.711 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 21 residues processed: 26 average time/residue: 0.6055 time to fit residues: 31.4665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 349 optimal weight: 0.5980 chunk 195 optimal weight: 0.0870 chunk 523 optimal weight: 9.9990 chunk 427 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 629 optimal weight: 10.0000 chunk 680 optimal weight: 5.9990 chunk 560 optimal weight: 9.9990 chunk 624 optimal weight: 4.9990 chunk 214 optimal weight: 10.0000 chunk 505 optimal weight: 9.9990 overall best weight: 2.9364 ------------------------------------------------------------------------------- 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 G 183 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 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 V 114 GLN V 185 ASN W 60 GLN W 166 GLN X 90 ASN X 123 HIS X 183 HIS Y 102 ASN Y 112 ASN ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 170 HIS a 169 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 e 108 ASN f 225 ASN ** f 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 128 ASN ** h 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 227 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 56118 Z= 0.397 Angle : 0.638 8.168 75896 Z= 0.335 Chirality : 0.047 0.158 8606 Planarity : 0.005 0.062 9712 Dihedral : 4.787 43.007 7602 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.15 % Allowed : 11.99 % Favored : 84.87 % 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: 0.79 (0.10), residues: 6864 helix: 1.48 (0.10), residues: 2534 sheet: 0.17 (0.11), residues: 1730 loop : -0.05 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 133 HIS 0.009 0.002 HIS X 123 PHE 0.030 0.002 PHE V 164 TYR 0.027 0.002 TYR J 69 ARG 0.010 0.001 ARG T 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 885 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 696 time to evaluate : 4.876 Fit side-chains outliers start: 189 outliers final: 81 residues processed: 821 average time/residue: 1.3995 time to fit residues: 1463.3565 Evaluate side-chains 725 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 644 time to evaluate : 4.793 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 60 residues processed: 23 average time/residue: 0.7893 time to fit residues: 33.8060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 621 optimal weight: 1.9990 chunk 473 optimal weight: 0.9990 chunk 326 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 300 optimal weight: 7.9990 chunk 422 optimal weight: 0.9980 chunk 631 optimal weight: 0.6980 chunk 668 optimal weight: 5.9990 chunk 330 optimal weight: 0.5980 chunk 598 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 180 GLN E 185 ASN F 31 GLN F 166 GLN G 90 ASN G 183 HIS H 102 ASN H 112 ASN I 86 GLN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 170 HIS K 37 GLN ** 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 180 GLN V 185 ASN W 166 GLN X 90 ASN X 183 HIS Y 102 ASN Y 112 ASN Z 86 GLN ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 170 HIS b 37 GLN ** b 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 137 GLN e 108 ASN f 225 ASN h 95 HIS ** h 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 56118 Z= 0.182 Angle : 0.541 8.157 75896 Z= 0.285 Chirality : 0.043 0.152 8606 Planarity : 0.004 0.056 9712 Dihedral : 4.480 27.854 7602 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.21 % Allowed : 13.79 % Favored : 83.00 % 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: 1.01 (0.10), residues: 6864 helix: 1.71 (0.10), residues: 2534 sheet: 0.31 (0.12), residues: 1666 loop : 0.01 (0.12), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 133 HIS 0.005 0.001 HIS b 133 PHE 0.035 0.002 PHE L 129 TYR 0.022 0.001 TYR a 69 ARG 0.011 0.000 ARG K 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 927 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 734 time to evaluate : 4.771 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 193 outliers final: 86 residues processed: 866 average time/residue: 1.3819 time to fit residues: 1532.2697 Evaluate side-chains 737 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 651 time to evaluate : 4.785 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 67 residues processed: 19 average time/residue: 0.9223 time to fit residues: 31.0097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 557 optimal weight: 9.9990 chunk 379 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 498 optimal weight: 0.5980 chunk 275 optimal weight: 4.9990 chunk 570 optimal weight: 0.9980 chunk 462 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 341 optimal weight: 3.9990 chunk 600 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 E 185 ASN F 60 GLN F 166 GLN G 90 ASN G 183 HIS H 102 ASN H 112 ASN I 86 GLN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 170 HIS ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN N 108 ASN R 209 HIS S 123 GLN T 21 GLN ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 185 ASN W 60 GLN W 166 GLN X 90 ASN X 183 HIS 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 c 141 HIS ** h 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 56118 Z= 0.238 Angle : 0.550 8.998 75896 Z= 0.288 Chirality : 0.044 0.154 8606 Planarity : 0.004 0.073 9712 Dihedral : 4.444 27.457 7602 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.13 % Allowed : 15.17 % Favored : 81.70 % 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: 1.72 (0.10), residues: 2544 sheet: 0.25 (0.12), residues: 1694 loop : -0.01 (0.12), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 133 HIS 0.005 0.001 HIS X 183 PHE 0.030 0.002 PHE E 164 TYR 0.028 0.001 TYR G 201 ARG 0.008 0.000 ARG b 95 *********************** 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 872 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 684 time to evaluate : 4.733 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 188 outliers final: 95 residues processed: 813 average time/residue: 1.3435 time to fit residues: 1404.0148 Evaluate side-chains 748 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 653 time to evaluate : 4.737 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 70 residues processed: 26 average time/residue: 0.6031 time to fit residues: 31.7928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 132 optimal weight: 5.9990 chunk 392 optimal weight: 0.3980 chunk 165 optimal weight: 8.9990 chunk 669 optimal weight: 2.9990 chunk 555 optimal weight: 4.9990 chunk 309 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 351 optimal weight: 0.8980 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 185 ASN E 218 GLN F 60 GLN F 166 GLN G 90 ASN G 183 HIS H 102 ASN H 112 ASN I 59 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 O 225 ASN O 271 GLN S 123 GLN V 185 ASN W 166 GLN X 90 ASN X 183 HIS Y 102 ASN Y 112 ASN Z 59 ASN Z 86 GLN ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 ASN Z 218 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 f 225 ASN f 271 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 56118 Z= 0.248 Angle : 0.552 10.780 75896 Z= 0.287 Chirality : 0.044 0.164 8606 Planarity : 0.004 0.074 9712 Dihedral : 4.430 27.751 7602 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.13 % Allowed : 16.08 % Favored : 80.79 % 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: 0.98 (0.10), residues: 6864 helix: 1.75 (0.10), residues: 2552 sheet: 0.22 (0.12), residues: 1680 loop : -0.04 (0.12), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 133 HIS 0.005 0.001 HIS G 183 PHE 0.032 0.002 PHE E 164 TYR 0.019 0.001 TYR J 69 ARG 0.007 0.000 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 859 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 671 time to evaluate : 4.786 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 188 outliers final: 107 residues processed: 800 average time/residue: 1.3687 time to fit residues: 1408.7928 Evaluate side-chains 734 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 627 time to evaluate : 4.786 Switching outliers to nearest non-outliers outliers start: 107 outliers final: 82 residues processed: 25 average time/residue: 0.8847 time to fit residues: 37.9875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 645 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 381 optimal weight: 1.9990 chunk 488 optimal weight: 6.9990 chunk 378 optimal weight: 0.9980 chunk 563 optimal weight: 0.6980 chunk 373 optimal weight: 2.9990 chunk 666 optimal weight: 0.9980 chunk 417 optimal weight: 0.8980 chunk 406 optimal weight: 0.6980 chunk 307 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN B 123 GLN E 185 ASN E 218 GLN F 166 GLN G 90 ASN G 147 HIS G 183 HIS H 102 ASN H 112 ASN I 86 GLN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 218 ASN ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN S 123 GLN V 185 ASN W 60 GLN W 166 GLN X 90 ASN X 147 HIS X 183 HIS Y 102 ASN Y 112 ASN Z 86 GLN ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 ASN 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: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 56118 Z= 0.177 Angle : 0.531 9.866 75896 Z= 0.278 Chirality : 0.043 0.152 8606 Planarity : 0.004 0.067 9712 Dihedral : 4.312 25.728 7602 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.76 % Allowed : 16.52 % Favored : 80.72 % 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: 1.84 (0.10), residues: 2560 sheet: 0.26 (0.12), residues: 1678 loop : -0.03 (0.12), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 133 HIS 0.005 0.001 HIS G 183 PHE 0.032 0.001 PHE E 164 TYR 0.034 0.001 TYR L 163 ARG 0.008 0.000 ARG P 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 862 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 696 time to evaluate : 4.749 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 166 outliers final: 98 residues processed: 820 average time/residue: 1.3258 time to fit residues: 1402.8104 Evaluate side-chains 754 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 656 time to evaluate : 4.739 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 77 residues processed: 21 average time/residue: 0.8387 time to fit residues: 31.7358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 412 optimal weight: 3.9990 chunk 266 optimal weight: 9.9990 chunk 398 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 424 optimal weight: 3.9990 chunk 454 optimal weight: 9.9990 chunk 329 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 524 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN E 185 ASN F 60 GLN F 166 GLN G 90 ASN G 183 HIS H 102 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 M 68 ASN V 185 ASN V 218 GLN W 166 GLN X 90 ASN X 183 HIS Y 102 ASN Y 112 ASN Z 86 GLN ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 ASN ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 137 GLN c 141 HIS d 68 ASN ** e 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 56118 Z= 0.411 Angle : 0.633 10.881 75896 Z= 0.329 Chirality : 0.047 0.185 8606 Planarity : 0.005 0.060 9712 Dihedral : 4.628 30.650 7602 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.95 % Allowed : 17.27 % Favored : 79.79 % 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: 0.76 (0.10), residues: 6864 helix: 1.54 (0.10), residues: 2562 sheet: 0.08 (0.12), residues: 1710 loop : -0.11 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 133 HIS 0.006 0.001 HIS G 183 PHE 0.034 0.002 PHE E 164 TYR 0.043 0.002 TYR L 163 ARG 0.011 0.001 ARG O 252 *********************** 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 826 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 649 time to evaluate : 4.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 177 outliers final: 113 residues processed: 785 average time/residue: 1.3404 time to fit residues: 1358.8906 Evaluate side-chains 744 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 631 time to evaluate : 4.720 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 90 residues processed: 23 average time/residue: 0.7949 time to fit residues: 33.1887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 606 optimal weight: 6.9990 chunk 638 optimal weight: 5.9990 chunk 582 optimal weight: 0.7980 chunk 621 optimal weight: 2.9990 chunk 374 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 chunk 488 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 561 optimal weight: 0.0470 chunk 587 optimal weight: 0.7980 chunk 619 optimal weight: 0.4980 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN B 123 GLN E 185 ASN F 166 GLN G 90 ASN G 183 HIS H 102 ASN H 112 ASN I 86 GLN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 169 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** R 176 GLN S 123 GLN V 185 ASN W 60 GLN W 166 GLN X 90 ASN X 183 HIS Y 102 ASN Y 112 ASN Z 86 GLN ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 ASN a 173 ASN ** b 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3359 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= 0.175 Angle : 0.545 10.233 75896 Z= 0.284 Chirality : 0.043 0.178 8606 Planarity : 0.004 0.061 9712 Dihedral : 4.349 26.288 7602 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.50 % Allowed : 17.88 % Favored : 79.62 % 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: 1.02 (0.10), residues: 6864 helix: 1.84 (0.10), residues: 2530 sheet: 0.20 (0.12), residues: 1682 loop : -0.03 (0.12), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP c 133 HIS 0.006 0.001 HIS G 183 PHE 0.030 0.001 PHE E 164 TYR 0.040 0.001 TYR c 163 ARG 0.008 0.000 ARG P 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 849 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 699 time to evaluate : 4.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 150 outliers final: 99 residues processed: 830 average time/residue: 1.2968 time to fit residues: 1398.9112 Evaluate side-chains 761 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 662 time to evaluate : 4.721 Switching outliers to nearest non-outliers outliers start: 99 outliers final: 89 residues processed: 12 average time/residue: 1.0048 time to fit residues: 22.8506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 408 optimal weight: 4.9990 chunk 657 optimal weight: 20.0000 chunk 401 optimal weight: 1.9990 chunk 311 optimal weight: 20.0000 chunk 456 optimal weight: 0.7980 chunk 689 optimal weight: 4.9990 chunk 634 optimal weight: 3.9990 chunk 548 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 chunk 424 optimal weight: 2.9990 chunk 336 optimal weight: 1.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN E 185 ASN F 166 GLN G 183 HIS H 102 ASN H 112 ASN ** 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** ** K 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 HIS M 171 ASN R 209 HIS S 30 GLN ** S 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 123 GLN V 185 ASN W 166 GLN X 183 HIS Y 102 ASN Z 86 GLN ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 ASN ** b 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 137 GLN ** h 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 56118 Z= 0.246 Angle : 0.572 10.309 75896 Z= 0.299 Chirality : 0.044 0.207 8606 Planarity : 0.004 0.057 9712 Dihedral : 4.380 26.306 7602 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.11 % Allowed : 18.71 % Favored : 79.17 % 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: 1.81 (0.10), residues: 2526 sheet: 0.21 (0.12), residues: 1700 loop : -0.06 (0.12), residues: 2638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 133 HIS 0.005 0.001 HIS G 183 PHE 0.033 0.002 PHE E 164 TYR 0.025 0.001 TYR K 59 ARG 0.008 0.000 ARG P 50 ********************** 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 810 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 683 time to evaluate : 4.822 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 94 residues processed: 796 average time/residue: 1.3276 time to fit residues: 1368.1058 Evaluate side-chains 747 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 653 time to evaluate : 4.746 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 89 residues processed: 5 average time/residue: 1.2164 time to fit residues: 14.3104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 436 optimal weight: 0.0570 chunk 584 optimal weight: 0.5980 chunk 168 optimal weight: 0.6980 chunk 506 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 549 optimal weight: 0.9990 chunk 230 optimal weight: 5.9990 chunk 564 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 101 optimal weight: 10.0000 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN A 209 HIS B 123 GLN E 185 ASN F 166 GLN G 183 HIS H 102 ASN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 10 GLN ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 HIS L 137 GLN L 141 HIS M 171 ASN R 176 GLN R 209 HIS S 123 GLN V 185 ASN W 166 GLN X 183 HIS Y 102 ASN Y 112 ASN ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 ASN a 169 GLN ** b 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 137 GLN ** h 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.142773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.100033 restraints weight = 80797.352| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.17 r_work: 0.3156 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 56118 Z= 0.171 Angle : 0.549 10.431 75896 Z= 0.287 Chirality : 0.043 0.209 8606 Planarity : 0.004 0.058 9712 Dihedral : 4.258 26.541 7602 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.13 % Allowed : 18.93 % Favored : 78.94 % 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: 1.07 (0.10), residues: 6864 helix: 1.88 (0.10), residues: 2524 sheet: 0.27 (0.12), residues: 1682 loop : -0.02 (0.12), residues: 2658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 133 HIS 0.005 0.001 HIS G 183 PHE 0.031 0.001 PHE E 164 TYR 0.026 0.001 TYR b 59 ARG 0.008 0.000 ARG e 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20777.49 seconds wall clock time: 360 minutes 59.70 seconds (21659.70 seconds total)