Starting phenix.real_space_refine on Mon Mar 25 13:49:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz5_29603/03_2024/8fz5_29603.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz5_29603/03_2024/8fz5_29603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz5_29603/03_2024/8fz5_29603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz5_29603/03_2024/8fz5_29603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz5_29603/03_2024/8fz5_29603.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz5_29603/03_2024/8fz5_29603.pdb" } resolution = 2.23 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= 0.007 sd= 0.130 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 304 5.16 5 C 30908 2.51 5 N 8368 2.21 5 O 9312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 208": "OE1" <-> "OE2" Residue "K PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 129": "OD1" <-> "OD2" Residue "Y PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 48892 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1911 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 8, 'TRANS': 236} Chain: "B" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1820 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain: "C" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1979 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 5, 'TRANS': 245} Chain: "D" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1922 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "E" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1805 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 227} Chain: "F" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1873 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "G" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1888 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 5, 'TRANS': 235} Chain: "H" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1519 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain: "I" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1660 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain: "J" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1594 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "K" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1602 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 8, 'TRANS': 190} Chain: "L" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1557 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "M" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1645 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "N" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1671 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 206} Chain: "O" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1911 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 8, 'TRANS': 236} Chain: "P" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1820 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain: "Q" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1979 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 5, 'TRANS': 245} Chain: "R" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1922 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "S" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1805 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 227} Chain: "T" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1873 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "U" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1888 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 5, 'TRANS': 235} Chain: "V" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1519 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain: "W" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1660 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain: "X" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1594 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "Y" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1602 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 8, 'TRANS': 190} Chain: "Z" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1557 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "a" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1645 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "b" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1671 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 206} Time building chain proxies: 24.38, per 1000 atoms: 0.50 Number of scatterers: 48892 At special positions: 0 Unit cell: (176.364, 134.964, 143.244, 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 304 16.00 O 9312 8.00 N 8368 7.00 C 30908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.92 Conformation dependent library (CDL) restraints added in 8.9 seconds 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11572 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 74 sheets defined 40.2% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.04 Creating SS restraints... Processing helix chain 'A' and resid 22 through 35 removed outlier: 3.692A pdb=" N ASN A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 83 through 106 Processing helix chain 'A' and resid 110 through 128 removed outlier: 3.675A pdb=" N TYR A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 removed outlier: 3.601A pdb=" N LYS A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 207 Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.618A pdb=" N ARG A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 31 Processing helix chain 'B' and resid 79 through 102 Processing helix chain 'B' and resid 106 through 124 Processing helix chain 'B' and resid 166 through 178 Processing helix chain 'B' and resid 183 through 199 removed outlier: 3.776A pdb=" N SER B 198 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 18 through 31 Processing helix chain 'C' and resid 79 through 102 Processing helix chain 'C' and resid 106 through 124 Processing helix chain 'C' and resid 167 through 179 Processing helix chain 'C' and resid 185 through 201 Processing helix chain 'C' and resid 229 through 251 Processing helix chain 'D' and resid 16 through 28 Processing helix chain 'D' and resid 55 through 60 removed outlier: 4.117A pdb=" N ARG D 60 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 98 Processing helix chain 'D' and resid 103 through 120 Processing helix chain 'D' and resid 164 through 176 Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 183 through 197 Processing helix chain 'D' and resid 221 through 244 Processing helix chain 'E' and resid 21 through 32 removed outlier: 3.643A pdb=" N LYS E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 81 through 104 removed outlier: 4.321A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 Processing helix chain 'E' and resid 173 through 185 Processing helix chain 'E' and resid 190 through 206 Processing helix chain 'E' and resid 230 through 239 Processing helix chain 'F' and resid 19 through 32 removed outlier: 3.899A pdb=" N GLY F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 100 Processing helix chain 'F' and resid 104 through 118 removed outlier: 3.695A pdb=" N ILE F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 121 No H-bonds generated for 'chain 'F' and resid 119 through 121' Processing helix chain 'F' and resid 164 through 180 removed outlier: 4.292A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLU F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N MET F 180 " --> pdb=" O MET F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 197 Processing helix chain 'F' and resid 229 through 234 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 122 Processing helix chain 'G' and resid 123 through 125 No H-bonds generated for 'chain 'G' and resid 123 through 125' Processing helix chain 'G' and resid 170 through 179 removed outlier: 3.595A pdb=" N LYS G 179 " --> pdb=" O THR G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 202 removed outlier: 3.829A pdb=" N LYS G 192 " --> pdb=" O ARG G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 222 No H-bonds generated for 'chain 'G' and resid 220 through 222' Processing helix chain 'G' and resid 229 through 245 Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 Processing helix chain 'H' and resid 129 through 134 removed outlier: 3.784A pdb=" N SER H 133 " --> pdb=" O SER H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 143 Processing helix chain 'H' and resid 148 through 167 Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 Processing helix chain 'I' and resid 130 through 142 Processing helix chain 'I' and resid 147 through 166 Processing helix chain 'J' and resid 56 through 78 Processing helix chain 'J' and resid 83 through 97 Processing helix chain 'J' and resid 142 through 154 Processing helix chain 'J' and resid 159 through 176 Processing helix chain 'K' and resid 51 through 72 Processing helix chain 'K' and resid 76 through 93 removed outlier: 3.986A pdb=" N ARG K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 147 removed outlier: 5.260A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 171 Processing helix chain 'L' and resid 48 through 71 Processing helix chain 'L' and resid 75 through 89 removed outlier: 3.796A pdb=" N GLN L 89 " --> pdb=" O ASN L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 143 removed outlier: 3.503A pdb=" N ARG L 141 " --> pdb=" O GLY L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 167 Processing helix chain 'L' and resid 192 through 200 Processing helix chain 'M' and resid 85 through 108 Processing helix chain 'M' and resid 112 through 126 Processing helix chain 'M' and resid 169 through 181 Proline residue: M 175 - end of helix Processing helix chain 'M' and resid 195 through 214 removed outlier: 3.646A pdb=" N ARG M 213 " --> pdb=" O SER M 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 78 removed outlier: 3.622A pdb=" N GLY N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 102 Processing helix chain 'N' and resid 141 through 146 Processing helix chain 'N' and resid 146 through 157 Processing helix chain 'N' and resid 161 through 180 Processing helix chain 'N' and resid 209 through 214 Processing helix chain 'O' and resid 22 through 35 removed outlier: 3.678A pdb=" N ASN O 33 " --> pdb=" O PHE O 29 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY O 35 " --> pdb=" O ALA O 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 66 Processing helix chain 'O' and resid 83 through 106 Processing helix chain 'O' and resid 110 through 128 removed outlier: 3.684A pdb=" N TYR O 125 " --> pdb=" O ILE O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 185 removed outlier: 3.604A pdb=" N LYS O 185 " --> pdb=" O LYS O 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 190 through 207 Processing helix chain 'O' and resid 231 through 245 removed outlier: 3.736A pdb=" N ARG O 245 " --> pdb=" O ALA O 241 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 31 Processing helix chain 'P' and resid 79 through 102 Processing helix chain 'P' and resid 106 through 124 Processing helix chain 'P' and resid 166 through 178 Processing helix chain 'P' and resid 183 through 199 removed outlier: 3.779A pdb=" N SER P 198 " --> pdb=" O THR P 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 233 Processing helix chain 'Q' and resid 2 through 6 Processing helix chain 'Q' and resid 18 through 31 Processing helix chain 'Q' and resid 79 through 102 Processing helix chain 'Q' and resid 106 through 124 Processing helix chain 'Q' and resid 167 through 179 Processing helix chain 'Q' and resid 185 through 201 Processing helix chain 'Q' and resid 229 through 251 Processing helix chain 'R' and resid 16 through 28 Processing helix chain 'R' and resid 55 through 60 removed outlier: 4.118A pdb=" N ARG R 60 " --> pdb=" O ARG R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 98 Processing helix chain 'R' and resid 103 through 120 Processing helix chain 'R' and resid 164 through 176 Processing helix chain 'R' and resid 178 through 182 Processing helix chain 'R' and resid 183 through 197 Processing helix chain 'R' and resid 221 through 244 Processing helix chain 'S' and resid 21 through 32 removed outlier: 3.636A pdb=" N LYS S 32 " --> pdb=" O ILE S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 81 through 104 removed outlier: 4.328A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 118 Processing helix chain 'S' and resid 173 through 185 Processing helix chain 'S' and resid 190 through 206 Processing helix chain 'S' and resid 230 through 239 Processing helix chain 'T' and resid 19 through 32 removed outlier: 3.886A pdb=" N GLY T 32 " --> pdb=" O ALA T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 100 Processing helix chain 'T' and resid 104 through 118 removed outlier: 3.688A pdb=" N ILE T 118 " --> pdb=" O SER T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 119 through 121 No H-bonds generated for 'chain 'T' and resid 119 through 121' Processing helix chain 'T' and resid 164 through 180 removed outlier: 4.298A pdb=" N ALA T 168 " --> pdb=" O ARG T 164 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER T 177 " --> pdb=" O GLU T 173 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLU T 178 " --> pdb=" O ARG T 174 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET T 180 " --> pdb=" O MET T 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 197 Processing helix chain 'T' and resid 229 through 234 Processing helix chain 'U' and resid 21 through 34 removed outlier: 3.762A pdb=" N SER U 34 " --> pdb=" O ALA U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 104 Processing helix chain 'U' and resid 108 through 122 Processing helix chain 'U' and resid 123 through 125 No H-bonds generated for 'chain 'U' and resid 123 through 125' Processing helix chain 'U' and resid 170 through 179 removed outlier: 3.593A pdb=" N LYS U 179 " --> pdb=" O THR U 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 186 through 202 removed outlier: 3.816A pdb=" N LYS U 192 " --> pdb=" O ARG U 188 " (cutoff:3.500A) Processing helix chain 'U' and resid 220 through 222 No H-bonds generated for 'chain 'U' and resid 220 through 222' Processing helix chain 'U' and resid 229 through 245 Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 90 Processing helix chain 'V' and resid 129 through 134 removed outlier: 3.786A pdb=" N SER V 133 " --> pdb=" O SER V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 135 through 143 Processing helix chain 'V' and resid 148 through 167 Processing helix chain 'V' and resid 190 through 194 Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 90 Processing helix chain 'W' and resid 130 through 142 Processing helix chain 'W' and resid 147 through 166 Processing helix chain 'X' and resid 56 through 78 Processing helix chain 'X' and resid 83 through 97 Processing helix chain 'X' and resid 142 through 154 Processing helix chain 'X' and resid 159 through 176 Processing helix chain 'Y' and resid 51 through 72 Processing helix chain 'Y' and resid 76 through 93 removed outlier: 3.985A pdb=" N ARG Y 93 " --> pdb=" O ALA Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 147 removed outlier: 5.247A pdb=" N SER Y 141 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 171 Processing helix chain 'Z' and resid 48 through 71 Processing helix chain 'Z' and resid 75 through 89 removed outlier: 3.798A pdb=" N GLN Z 89 " --> pdb=" O ASN Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 143 removed outlier: 3.506A pdb=" N ARG Z 141 " --> pdb=" O GLY Z 137 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 167 Processing helix chain 'Z' and resid 192 through 200 Processing helix chain 'a' and resid 85 through 108 Processing helix chain 'a' and resid 112 through 126 Processing helix chain 'a' and resid 169 through 181 Proline residue: a 175 - end of helix Processing helix chain 'a' and resid 195 through 214 removed outlier: 3.647A pdb=" N ARG a 213 " --> pdb=" O SER a 209 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 78 removed outlier: 3.626A pdb=" N GLY b 78 " --> pdb=" O GLU b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 102 Processing helix chain 'b' and resid 141 through 146 Processing helix chain 'b' and resid 146 through 157 Processing helix chain 'b' and resid 161 through 180 Processing helix chain 'b' and resid 209 through 214 Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 169 removed outlier: 5.541A pdb=" N THR A 38 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 163 Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.680A pdb=" N GLY C 42 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 65 through 67 Processing sheet with id=AA7, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AA8, first strand: chain 'D' and resid 62 through 64 Processing sheet with id=AA9, first strand: chain 'E' and resid 167 through 170 removed outlier: 4.647A pdb=" N GLN E 221 " --> pdb=" O ASN E 225 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASN E 225 " --> pdb=" O GLN E 221 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.325A pdb=" N ILE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AB3, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.608A pdb=" N ILE F 63 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ILE F 74 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N HIS F 65 " --> pdb=" O ILE F 72 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE F 72 " --> pdb=" O HIS F 65 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE F 144 " --> pdb=" O CYS F 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 163 through 166 Processing sheet with id=AB5, first strand: chain 'G' and resid 67 through 71 removed outlier: 6.253A pdb=" N VAL G 74 " --> pdb=" O VAL G 70 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 125 through 128 Processing sheet with id=AB7, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.744A pdb=" N THR H 20 " --> pdb=" O ALA H 27 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.377A pdb=" N ILE H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 124 through 128 removed outlier: 6.054A pdb=" N THR I 2 " --> pdb=" O ASP I 17 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE I 173 " --> pdb=" O TYR I 189 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU I 175 " --> pdb=" O ARG I 187 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ARG I 187 " --> pdb=" O LEU I 175 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL I 177 " --> pdb=" O PHE I 185 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N PHE I 185 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N SER I 179 " --> pdb=" O LEU I 183 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU I 183 " --> pdb=" O SER I 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 20 through 22 removed outlier: 6.709A pdb=" N ALA I 20 " --> pdb=" O ALA I 27 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.351A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 211 through 218 removed outlier: 3.547A pdb=" N THR I 213 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL J 185 " --> pdb=" O LEU J 200 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ALA J 10 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 28 through 30 removed outlier: 6.112A pdb=" N ILE J 30 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N MET J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 42 through 44 removed outlier: 3.829A pdb=" N ALA J 54 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE J 121 " --> pdb=" O THR J 133 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR J 133 " --> pdb=" O ILE J 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 129 through 132 Processing sheet with id=AC7, first strand: chain 'K' and resid 129 through 132 Processing sheet with id=AC8, first strand: chain 'K' and resid 21 through 23 removed outlier: 6.611A pdb=" N SER K 23 " --> pdb=" O GLN K 27 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLN K 27 " --> pdb=" O SER K 23 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 35 through 39 removed outlier: 6.562A pdb=" N ILE K 42 " --> pdb=" O MET K 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 125 through 128 removed outlier: 6.495A pdb=" N HIS L 178 " --> pdb=" O ARG L 186 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ARG L 186 " --> pdb=" O HIS L 178 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG L 180 " --> pdb=" O TRP L 184 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TRP L 184 " --> pdb=" O ARG L 180 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 20 through 22 removed outlier: 6.482A pdb=" N ALA L 20 " --> pdb=" O ALA L 27 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.445A pdb=" N LEU L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 98 through 105 Processing sheet with id=AD5, first strand: chain 'M' and resid 163 through 167 removed outlier: 5.216A pdb=" N THR M 39 " --> pdb=" O ASP M 54 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.359A pdb=" N GLU M 59 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ILE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 71 through 75 removed outlier: 6.410A pdb=" N THR M 78 " --> pdb=" O LEU M 74 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN M 136 " --> pdb=" O PHE M 152 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL M 149 " --> pdb=" O ASP M 161 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 33 through 36 removed outlier: 5.417A pdb=" N ALA N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR N 30 " --> pdb=" O ALA N 34 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 33 through 36 removed outlier: 5.417A pdb=" N ALA N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR N 30 " --> pdb=" O ALA N 34 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 136 through 138 removed outlier: 6.008A pdb=" N PHE N 187 " --> pdb=" O PRO N 202 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 165 through 169 removed outlier: 5.563A pdb=" N THR O 38 " --> pdb=" O GLN O 53 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 69 through 71 Processing sheet with id=AE4, first strand: chain 'P' and resid 160 through 163 Processing sheet with id=AE5, first strand: chain 'P' and resid 66 through 67 Processing sheet with id=AE6, first strand: chain 'Q' and resid 161 through 164 removed outlier: 3.681A pdb=" N GLY Q 42 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 65 through 67 Processing sheet with id=AE8, first strand: chain 'R' and resid 158 through 161 Processing sheet with id=AE9, first strand: chain 'R' and resid 62 through 64 Processing sheet with id=AF1, first strand: chain 'S' and resid 167 through 170 removed outlier: 4.652A pdb=" N GLN S 221 " --> pdb=" O ASN S 225 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASN S 225 " --> pdb=" O GLN S 221 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 67 through 71 removed outlier: 6.325A pdb=" N ILE S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 158 through 161 Processing sheet with id=AF4, first strand: chain 'T' and resid 63 through 67 removed outlier: 6.613A pdb=" N ILE T 63 " --> pdb=" O ILE T 74 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ILE T 74 " --> pdb=" O ILE T 63 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N HIS T 65 " --> pdb=" O ILE T 72 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE T 72 " --> pdb=" O HIS T 65 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE T 144 " --> pdb=" O CYS T 156 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 163 through 166 Processing sheet with id=AF6, first strand: chain 'U' and resid 67 through 71 removed outlier: 6.254A pdb=" N VAL U 74 " --> pdb=" O VAL U 70 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 125 through 128 Processing sheet with id=AF8, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.742A pdb=" N THR V 20 " --> pdb=" O ALA V 27 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.376A pdb=" N ILE V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 124 through 128 removed outlier: 6.054A pdb=" N THR W 2 " --> pdb=" O ASP W 17 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE W 173 " --> pdb=" O TYR W 189 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU W 175 " --> pdb=" O ARG W 187 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ARG W 187 " --> pdb=" O LEU W 175 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL W 177 " --> pdb=" O PHE W 185 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N PHE W 185 " --> pdb=" O VAL W 177 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N SER W 179 " --> pdb=" O LEU W 183 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU W 183 " --> pdb=" O SER W 179 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 20 through 22 removed outlier: 6.708A pdb=" N ALA W 20 " --> pdb=" O ALA W 27 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.351A pdb=" N ILE W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 211 through 218 removed outlier: 3.531A pdb=" N THR W 213 " --> pdb=" O THR X 199 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL X 185 " --> pdb=" O LEU X 200 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ALA X 10 " --> pdb=" O ASP X 25 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 28 through 30 removed outlier: 6.118A pdb=" N ILE X 30 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N MET X 34 " --> pdb=" O ILE X 30 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 42 through 44 removed outlier: 3.838A pdb=" N ALA X 54 " --> pdb=" O GLU X 106 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE X 121 " --> pdb=" O THR X 133 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR X 133 " --> pdb=" O ILE X 121 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 129 through 132 Processing sheet with id=AG8, first strand: chain 'Y' and resid 129 through 132 Processing sheet with id=AG9, first strand: chain 'Y' and resid 21 through 23 removed outlier: 6.610A pdb=" N SER Y 23 " --> pdb=" O GLN Y 27 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLN Y 27 " --> pdb=" O SER Y 23 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 35 through 39 removed outlier: 6.563A pdb=" N ILE Y 42 " --> pdb=" O MET Y 38 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 125 through 128 removed outlier: 6.500A pdb=" N HIS Z 178 " --> pdb=" O ARG Z 186 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ARG Z 186 " --> pdb=" O HIS Z 178 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG Z 180 " --> pdb=" O TRP Z 184 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TRP Z 184 " --> pdb=" O ARG Z 180 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 20 through 22 removed outlier: 6.482A pdb=" N ALA Z 20 " --> pdb=" O ALA Z 27 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.447A pdb=" N LEU Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Z' and resid 98 through 105 Processing sheet with id=AH6, first strand: chain 'a' and resid 163 through 167 removed outlier: 5.218A pdb=" N THR a 39 " --> pdb=" O ASP a 54 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'a' and resid 57 through 59 removed outlier: 6.361A pdb=" N GLU a 59 " --> pdb=" O ILE a 63 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ILE a 63 " --> pdb=" O GLU a 59 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'a' and resid 71 through 75 removed outlier: 6.410A pdb=" N THR a 78 " --> pdb=" O LEU a 74 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN a 136 " --> pdb=" O PHE a 152 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL a 149 " --> pdb=" O ASP a 161 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'b' and resid 33 through 36 removed outlier: 5.415A pdb=" N ALA b 34 " --> pdb=" O TYR b 30 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR b 30 " --> pdb=" O ALA b 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR b 49 " --> pdb=" O VAL b 45 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'b' and resid 33 through 36 removed outlier: 5.415A pdb=" N ALA b 34 " --> pdb=" O TYR b 30 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR b 30 " --> pdb=" O ALA b 34 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'b' and resid 136 through 138 removed outlier: 6.009A pdb=" N PHE b 187 " --> pdb=" O PRO b 202 " (cutoff:3.500A) 2939 hydrogen bonds defined for protein. 8403 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.24 Time building geometry restraints manager: 20.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14045 1.33 - 1.45: 8328 1.45 - 1.57: 26901 1.57 - 1.69: 0 1.69 - 1.81: 500 Bond restraints: 49774 Sorted by residual: bond pdb=" N VAL E 184 " pdb=" CA VAL E 184 " ideal model delta sigma weight residual 1.460 1.499 -0.040 1.21e-02 6.83e+03 1.08e+01 bond pdb=" N VAL S 184 " pdb=" CA VAL S 184 " ideal model delta sigma weight residual 1.460 1.499 -0.040 1.21e-02 6.83e+03 1.08e+01 bond pdb=" N VAL U 190 " pdb=" CA VAL U 190 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.72e+00 bond pdb=" N VAL G 190 " pdb=" CA VAL G 190 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.62e+00 bond pdb=" N VAL G 191 " pdb=" CA VAL G 191 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.44e+00 ... (remaining 49769 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.04: 841 106.04 - 113.04: 26762 113.04 - 120.04: 17296 120.04 - 127.03: 21935 127.03 - 134.03: 386 Bond angle restraints: 67220 Sorted by residual: angle pdb=" N TYR E 185 " pdb=" CA TYR E 185 " pdb=" C TYR E 185 " ideal model delta sigma weight residual 109.25 117.08 -7.83 1.53e+00 4.27e-01 2.62e+01 angle pdb=" N TYR S 185 " pdb=" CA TYR S 185 " pdb=" C TYR S 185 " ideal model delta sigma weight residual 109.76 117.28 -7.52 1.59e+00 3.96e-01 2.24e+01 angle pdb=" N LEU S 181 " pdb=" CA LEU S 181 " pdb=" C LEU S 181 " ideal model delta sigma weight residual 111.28 107.57 3.71 1.09e+00 8.42e-01 1.16e+01 angle pdb=" N LEU E 181 " pdb=" CA LEU E 181 " pdb=" C LEU E 181 " ideal model delta sigma weight residual 111.28 107.66 3.62 1.09e+00 8.42e-01 1.10e+01 angle pdb=" CA SER Y 39 " pdb=" C SER Y 39 " pdb=" O SER Y 39 " ideal model delta sigma weight residual 121.14 117.85 3.29 1.03e+00 9.43e-01 1.02e+01 ... (remaining 67215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 27026 17.88 - 35.76: 2457 35.76 - 53.64: 398 53.64 - 71.52: 114 71.52 - 89.40: 73 Dihedral angle restraints: 30068 sinusoidal: 11944 harmonic: 18124 Sorted by residual: dihedral pdb=" CA GLY X 101 " pdb=" C GLY X 101 " pdb=" N PRO X 102 " pdb=" CA PRO X 102 " ideal model delta harmonic sigma weight residual -180.00 -157.18 -22.82 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLY J 101 " pdb=" C GLY J 101 " pdb=" N PRO J 102 " pdb=" CA PRO J 102 " ideal model delta harmonic sigma weight residual -180.00 -157.28 -22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA VAL R 102 " pdb=" C VAL R 102 " pdb=" N THR R 103 " pdb=" CA THR R 103 " ideal model delta harmonic sigma weight residual 180.00 158.89 21.11 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 30065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 4773 0.039 - 0.077: 1951 0.077 - 0.116: 652 0.116 - 0.154: 138 0.154 - 0.193: 8 Chirality restraints: 7522 Sorted by residual: chirality pdb=" CA VAL U 232 " pdb=" N VAL U 232 " pdb=" C VAL U 232 " pdb=" CB VAL U 232 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" CA VAL G 232 " pdb=" N VAL G 232 " pdb=" C VAL G 232 " pdb=" CB VAL G 232 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.25e-01 chirality pdb=" CA ILE G 220 " pdb=" N ILE G 220 " pdb=" C ILE G 220 " pdb=" CB ILE G 220 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.21e-01 ... (remaining 7519 not shown) Planarity restraints: 8666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY P 80 " -0.043 5.00e-02 4.00e+02 6.63e-02 7.03e+00 pdb=" N PRO P 81 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO P 81 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO P 81 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 80 " -0.043 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO B 81 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 81 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 81 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 121 " 0.015 2.00e-02 2.50e+03 1.50e-02 4.50e+00 pdb=" CG TYR Q 121 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 121 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 121 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 121 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 121 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR Q 121 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR Q 121 " 0.001 2.00e-02 2.50e+03 ... (remaining 8663 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 9859 2.78 - 3.31: 44454 3.31 - 3.84: 87395 3.84 - 4.37: 105559 4.37 - 4.90: 175038 Nonbonded interactions: 422305 Sorted by model distance: nonbonded pdb=" O GLU Q 15 " pdb=" NZ LYS R 28 " model vdw 2.247 2.520 nonbonded pdb=" OH TYR T 6 " pdb=" OD2 ASP U 9 " model vdw 2.254 2.440 nonbonded pdb=" O GLY S 160 " pdb=" NH2 ARG T 82 " model vdw 2.254 2.520 nonbonded pdb=" O LYS E 209 " pdb=" ND2 ASN E 214 " model vdw 2.255 2.520 nonbonded pdb=" O GLY E 160 " pdb=" NH2 ARG F 82 " model vdw 2.262 2.520 ... (remaining 422300 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 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: 0.070 Extract box with map and model: 12.670 Check model and map are aligned: 0.780 Set scattering table: 0.460 Process input model: 123.180 Find NCS groups from input model: 4.640 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:11.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 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 : 0.005 0.076 49774 Z= 0.318 Angle : 0.601 7.854 67220 Z= 0.345 Chirality : 0.046 0.193 7522 Planarity : 0.006 0.066 8666 Dihedral : 14.802 89.404 18496 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.19 % Allowed : 5.67 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.51 (0.10), residues: 6224 helix: 2.01 (0.10), residues: 2346 sheet: 1.14 (0.12), residues: 1564 loop : -0.09 (0.12), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 100 HIS 0.005 0.001 HIS F 175 PHE 0.020 0.002 PHE Y 171 TYR 0.037 0.002 TYR Q 121 ARG 0.007 0.001 ARG T 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 946 time to evaluate : 5.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8456 (pptt) REVERT: C 209 GLU cc_start: 0.7989 (pm20) cc_final: 0.7399 (pp20) REVERT: C 230 GLN cc_start: 0.7902 (tt0) cc_final: 0.7251 (mt0) REVERT: C 234 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6998 (mt-10) REVERT: D 54 GLN cc_start: 0.8755 (tt0) cc_final: 0.8527 (tp40) REVERT: F 26 MET cc_start: 0.8694 (mmm) cc_final: 0.8363 (mmm) REVERT: F 206 THR cc_start: 0.8515 (m) cc_final: 0.8206 (p) REVERT: G 211 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7231 (mt-10) REVERT: I 9 LYS cc_start: 0.8728 (ptmt) cc_final: 0.8527 (ptmm) REVERT: L 194 ASP cc_start: 0.8544 (m-30) cc_final: 0.8321 (m-30) REVERT: M 229 GLU cc_start: 0.8229 (mp0) cc_final: 0.7914 (mp0) REVERT: O 172 GLN cc_start: 0.8572 (pt0) cc_final: 0.8366 (pt0) REVERT: P 70 LYS cc_start: 0.8710 (mtmt) cc_final: 0.8460 (pptt) REVERT: Q 1 MET cc_start: 0.6930 (ttt) cc_final: 0.6686 (ttt) REVERT: Q 209 GLU cc_start: 0.7994 (pm20) cc_final: 0.7403 (pp20) REVERT: Q 230 GLN cc_start: 0.7894 (tt0) cc_final: 0.7243 (mt0) REVERT: Q 234 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6998 (mt-10) REVERT: R 54 GLN cc_start: 0.8749 (tt0) cc_final: 0.8523 (tp40) REVERT: T 26 MET cc_start: 0.8702 (mmm) cc_final: 0.8395 (mmm) REVERT: T 206 THR cc_start: 0.8486 (m) cc_final: 0.8166 (p) REVERT: U 211 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7257 (mt-10) REVERT: W 9 LYS cc_start: 0.8734 (ptmt) cc_final: 0.8532 (ptmm) REVERT: Z 107 ARG cc_start: 0.7874 (mtm-85) cc_final: 0.7487 (mtm110) REVERT: a 229 GLU cc_start: 0.8237 (mp0) cc_final: 0.7933 (mp0) outliers start: 10 outliers final: 1 residues processed: 954 average time/residue: 2.1016 time to fit residues: 2381.2684 Evaluate side-chains 741 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 740 time to evaluate : 5.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 78 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 521 optimal weight: 5.9990 chunk 468 optimal weight: 0.9980 chunk 259 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 315 optimal weight: 10.0000 chunk 250 optimal weight: 3.9990 chunk 484 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 294 optimal weight: 2.9990 chunk 360 optimal weight: 5.9990 chunk 561 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN B 169 ASN B 189 HIS B 207 ASN C 51 ASN C 155 ASN D 215 GLN E 182 GLN E 214 ASN G 33 ASN I 209 ASN J 162 HIS ** O 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 169 ASN P 189 HIS P 207 ASN Q 51 ASN Q 155 ASN Q 166 ASN S 182 GLN W 209 ASN Y 168 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 49774 Z= 0.249 Angle : 0.553 7.173 67220 Z= 0.308 Chirality : 0.044 0.154 7522 Planarity : 0.005 0.065 8666 Dihedral : 5.138 36.203 6901 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.63 % Allowed : 10.30 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.70 (0.10), residues: 6224 helix: 2.19 (0.10), residues: 2378 sheet: 1.12 (0.12), residues: 1608 loop : 0.04 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Z 55 HIS 0.005 0.001 HIS T 175 PHE 0.022 0.002 PHE I 36 TYR 0.020 0.002 TYR Q 121 ARG 0.007 0.000 ARG Z 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 738 time to evaluate : 6.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8439 (pptt) REVERT: C 1 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6185 (tmm) REVERT: C 209 GLU cc_start: 0.7985 (pm20) cc_final: 0.7391 (pp20) REVERT: C 230 GLN cc_start: 0.7823 (tt0) cc_final: 0.7212 (mt0) REVERT: C 234 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6999 (mt-10) REVERT: D 54 GLN cc_start: 0.8702 (tt0) cc_final: 0.8486 (tp40) REVERT: D 99 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: D 226 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7250 (mm-30) REVERT: E 65 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: E 129 ASP cc_start: 0.5661 (OUTLIER) cc_final: 0.5296 (p0) REVERT: E 208 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7094 (mm-30) REVERT: F 26 MET cc_start: 0.8733 (mmm) cc_final: 0.8407 (mmm) REVERT: F 180 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7610 (tpt) REVERT: F 206 THR cc_start: 0.8478 (m) cc_final: 0.8183 (p) REVERT: G 18 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7669 (m-30) REVERT: G 211 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7226 (mt-10) REVERT: I 53 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8113 (m-30) REVERT: I 127 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8893 (mmm) REVERT: I 180 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8189 (ptpp) REVERT: L 56 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8983 (mt-10) REVERT: L 194 ASP cc_start: 0.8540 (m-30) cc_final: 0.8333 (m-30) REVERT: M 229 GLU cc_start: 0.8225 (mp0) cc_final: 0.7909 (mp0) REVERT: N 110 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8609 (mpp) REVERT: N 198 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7787 (mm-30) REVERT: P 70 LYS cc_start: 0.8707 (mtmt) cc_final: 0.8455 (pptt) REVERT: Q 1 MET cc_start: 0.6972 (ttt) cc_final: 0.6699 (ttt) REVERT: Q 209 GLU cc_start: 0.7956 (pm20) cc_final: 0.7372 (pp20) REVERT: Q 230 GLN cc_start: 0.7815 (tt0) cc_final: 0.7202 (mt0) REVERT: Q 234 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6999 (mt-10) REVERT: R 54 GLN cc_start: 0.8696 (tt0) cc_final: 0.8482 (tp40) REVERT: R 99 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: S 65 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: T 26 MET cc_start: 0.8702 (mmm) cc_final: 0.8384 (mmm) REVERT: T 180 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7568 (tpt) REVERT: T 206 THR cc_start: 0.8394 (m) cc_final: 0.8100 (p) REVERT: U 18 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7726 (m-30) REVERT: W 53 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8070 (m-30) REVERT: W 127 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8889 (mmm) REVERT: W 180 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8190 (ptpp) REVERT: Z 56 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.8974 (mt-10) REVERT: Z 107 ARG cc_start: 0.7984 (mtm-85) cc_final: 0.7469 (mtm110) REVERT: a 229 GLU cc_start: 0.8231 (mp0) cc_final: 0.7927 (mp0) REVERT: b 198 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7712 (mm-30) outliers start: 85 outliers final: 28 residues processed: 788 average time/residue: 1.9632 time to fit residues: 1857.0964 Evaluate side-chains 772 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 722 time to evaluate : 5.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 180 LYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain O residue 240 VAL Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 209 LYS Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 198 THR Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain W residue 180 LYS Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain Z residue 56 GLU Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 198 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 311 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 467 optimal weight: 10.0000 chunk 382 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 562 optimal weight: 5.9990 chunk 607 optimal weight: 4.9990 chunk 500 optimal weight: 9.9990 chunk 557 optimal weight: 3.9990 chunk 191 optimal weight: 9.9990 chunk 451 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS B 207 ASN C 155 ASN D 85 ASN D 215 GLN E 182 GLN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 ASN J 162 HIS O 123 GLN P 189 HIS P 207 ASN Q 155 ASN Q 166 ASN R 85 ASN R 215 GLN S 182 GLN U 33 ASN W 209 ASN b 2 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 49774 Z= 0.271 Angle : 0.560 7.544 67220 Z= 0.311 Chirality : 0.045 0.155 7522 Planarity : 0.005 0.066 8666 Dihedral : 5.134 35.963 6900 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.05 % Allowed : 11.39 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.72 (0.10), residues: 6224 helix: 2.21 (0.10), residues: 2378 sheet: 1.13 (0.12), residues: 1606 loop : 0.05 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 100 HIS 0.005 0.001 HIS T 175 PHE 0.022 0.002 PHE I 36 TYR 0.018 0.002 TYR N 124 ARG 0.004 0.000 ARG Z 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 729 time to evaluate : 6.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8678 (mtmt) cc_final: 0.8438 (pptt) REVERT: B 143 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8205 (tmt-80) REVERT: C 1 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6271 (tmm) REVERT: C 209 GLU cc_start: 0.7985 (pm20) cc_final: 0.7405 (pp20) REVERT: C 230 GLN cc_start: 0.7787 (tt0) cc_final: 0.7285 (mt0) REVERT: C 234 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7004 (mt-10) REVERT: D 54 GLN cc_start: 0.8730 (tt0) cc_final: 0.8517 (tp40) REVERT: D 71 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8935 (ptp) REVERT: D 99 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: D 163 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7695 (ptp90) REVERT: E 65 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: E 129 ASP cc_start: 0.5659 (OUTLIER) cc_final: 0.5284 (p0) REVERT: E 208 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7107 (mm-30) REVERT: F 26 MET cc_start: 0.8694 (mmm) cc_final: 0.8344 (mmm) REVERT: F 180 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7695 (tpt) REVERT: F 206 THR cc_start: 0.8462 (m) cc_final: 0.8181 (p) REVERT: G 18 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7625 (m-30) REVERT: G 211 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7213 (mt-10) REVERT: I 53 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8086 (m-30) REVERT: I 127 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8920 (mmm) REVERT: I 180 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8195 (ptpp) REVERT: J 31 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8582 (mt0) REVERT: L 56 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8947 (mt-10) REVERT: L 194 ASP cc_start: 0.8544 (m-30) cc_final: 0.8343 (m-30) REVERT: M 46 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7821 (tp30) REVERT: M 229 GLU cc_start: 0.8214 (mp0) cc_final: 0.7892 (mp0) REVERT: N 110 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.8633 (mpp) REVERT: N 155 GLU cc_start: 0.7635 (tp30) cc_final: 0.7231 (mm-30) REVERT: P 70 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8442 (pptt) REVERT: P 143 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8222 (tmt-80) REVERT: Q 1 MET cc_start: 0.6934 (ttt) cc_final: 0.6635 (ttt) REVERT: Q 209 GLU cc_start: 0.7993 (pm20) cc_final: 0.7403 (pp20) REVERT: Q 230 GLN cc_start: 0.7779 (tt0) cc_final: 0.7271 (mt0) REVERT: Q 234 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7006 (mt-10) REVERT: R 54 GLN cc_start: 0.8723 (tt0) cc_final: 0.8511 (tp40) REVERT: R 71 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8933 (ptp) REVERT: R 99 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: R 163 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7698 (ptp90) REVERT: S 65 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: S 208 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6447 (mt-10) REVERT: T 26 MET cc_start: 0.8688 (mmm) cc_final: 0.8348 (mmm) REVERT: T 180 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7642 (tpt) REVERT: T 206 THR cc_start: 0.8374 (m) cc_final: 0.8116 (p) REVERT: U 18 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7646 (m-30) REVERT: U 170 ARG cc_start: 0.8189 (ptp-170) cc_final: 0.7879 (ptm160) REVERT: U 211 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: W 53 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8061 (m-30) REVERT: W 127 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8921 (mmm) REVERT: W 180 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8193 (ptpp) REVERT: Z 56 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8965 (mt-10) REVERT: Z 107 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7401 (mtm110) REVERT: a 46 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7839 (tp30) REVERT: a 229 GLU cc_start: 0.8220 (mp0) cc_final: 0.7909 (mp0) REVERT: b 198 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7737 (mm-30) outliers start: 107 outliers final: 37 residues processed: 789 average time/residue: 1.9216 time to fit residues: 1824.6617 Evaluate side-chains 784 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 715 time to evaluate : 5.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 209 LYS Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 180 LYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 31 GLN Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 240 VAL Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain R residue 163 ARG Chi-restraints excluded: chain R residue 166 LYS Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 184 VAL Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain U residue 211 GLU Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain V residue 198 THR Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain W residue 180 LYS Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 77 LYS Chi-restraints excluded: chain Z residue 56 GLU Chi-restraints excluded: chain a residue 46 GLU Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 198 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 555 optimal weight: 9.9990 chunk 422 optimal weight: 8.9990 chunk 291 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 268 optimal weight: 9.9990 chunk 377 optimal weight: 10.0000 chunk 564 optimal weight: 7.9990 chunk 597 optimal weight: 4.9990 chunk 294 optimal weight: 8.9990 chunk 534 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS B 207 ASN C 155 ASN D 215 GLN E 182 GLN ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 ASN J 162 HIS N 2 GLN O 128 ASN P 189 HIS P 207 ASN Q 155 ASN Q 166 ASN R 215 GLN S 182 GLN ** T 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 209 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 49774 Z= 0.460 Angle : 0.669 9.113 67220 Z= 0.370 Chirality : 0.050 0.185 7522 Planarity : 0.006 0.076 8666 Dihedral : 5.472 39.280 6900 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.35 % Allowed : 12.10 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.52 (0.10), residues: 6224 helix: 1.96 (0.10), residues: 2366 sheet: 1.15 (0.12), residues: 1580 loop : -0.05 (0.12), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP E 100 HIS 0.006 0.001 HIS U 111 PHE 0.025 0.003 PHE I 36 TYR 0.021 0.003 TYR K 12 ARG 0.005 0.001 ARG Y 170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 714 time to evaluate : 5.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8471 (pptt) REVERT: C 1 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6273 (tmm) REVERT: C 209 GLU cc_start: 0.8014 (pm20) cc_final: 0.7434 (pp20) REVERT: C 230 GLN cc_start: 0.7829 (tt0) cc_final: 0.7311 (mt0) REVERT: C 234 GLU cc_start: 0.7291 (mt-10) cc_final: 0.7017 (mt-10) REVERT: D 54 GLN cc_start: 0.8793 (tt0) cc_final: 0.8555 (tp40) REVERT: D 71 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8959 (ptp) REVERT: D 99 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: D 163 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7829 (ptp90) REVERT: E 65 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7590 (mt-10) REVERT: E 129 ASP cc_start: 0.5630 (OUTLIER) cc_final: 0.5086 (p0) REVERT: E 208 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7154 (mm-30) REVERT: E 236 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6976 (mm-30) REVERT: F 26 MET cc_start: 0.8697 (mmm) cc_final: 0.8332 (mmm) REVERT: F 204 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7143 (t70) REVERT: F 206 THR cc_start: 0.8491 (m) cc_final: 0.8210 (p) REVERT: G 18 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7679 (m-30) REVERT: G 211 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7280 (mt-10) REVERT: I 53 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8092 (m-30) REVERT: I 127 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8928 (mmm) REVERT: I 180 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8249 (ptpp) REVERT: J 4 MET cc_start: 0.8818 (mmt) cc_final: 0.8158 (mmt) REVERT: L 9 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7952 (ttp-170) REVERT: L 56 GLU cc_start: 0.9292 (OUTLIER) cc_final: 0.9026 (mt-10) REVERT: L 194 ASP cc_start: 0.8539 (m-30) cc_final: 0.8338 (m-30) REVERT: N 110 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8601 (mpp) REVERT: N 198 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7745 (mm-30) REVERT: P 70 LYS cc_start: 0.8740 (mtmt) cc_final: 0.8473 (pptt) REVERT: Q 209 GLU cc_start: 0.8034 (pm20) cc_final: 0.7428 (pp20) REVERT: Q 230 GLN cc_start: 0.7822 (tt0) cc_final: 0.7303 (mt0) REVERT: Q 234 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7016 (mt-10) REVERT: R 54 GLN cc_start: 0.8787 (tt0) cc_final: 0.8549 (tp40) REVERT: R 71 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8947 (ptp) REVERT: R 99 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: R 163 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7897 (ptp90) REVERT: S 20 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7886 (mpp-170) REVERT: S 65 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: S 208 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6477 (mt-10) REVERT: T 26 MET cc_start: 0.8704 (mmm) cc_final: 0.8345 (mmm) REVERT: T 173 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: T 180 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7750 (tpt) REVERT: T 206 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8147 (p) REVERT: U 18 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7720 (m-30) REVERT: U 211 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: W 53 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8121 (m-30) REVERT: W 127 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8929 (mmm) REVERT: W 180 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8247 (ptpp) REVERT: Z 56 GLU cc_start: 0.9287 (OUTLIER) cc_final: 0.9021 (mt-10) outliers start: 123 outliers final: 49 residues processed: 786 average time/residue: 1.9345 time to fit residues: 1826.0580 Evaluate side-chains 786 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 706 time to evaluate : 5.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 209 LYS Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 180 LYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 177 ARG Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 234 GLU Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 240 VAL Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 212 GLU Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain R residue 163 ARG Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 20 ARG Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 184 VAL Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 173 GLU Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain T residue 206 THR Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 55 LEU Chi-restraints excluded: chain U residue 211 GLU Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain V residue 198 THR Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 89 ARG Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain W residue 180 LYS Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 77 LYS Chi-restraints excluded: chain X residue 177 ARG Chi-restraints excluded: chain Z residue 56 GLU Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain a residue 234 GLU Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 198 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 497 optimal weight: 4.9990 chunk 339 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 444 optimal weight: 8.9990 chunk 246 optimal weight: 6.9990 chunk 509 optimal weight: 5.9990 chunk 412 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 305 optimal weight: 0.7980 chunk 536 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS B 207 ASN C 155 ASN D 85 ASN D 215 GLN E 182 GLN F 183 ASN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 162 HIS P 189 HIS P 207 ASN Q 155 ASN Q 166 ASN R 85 ASN R 215 GLN S 182 GLN T 183 ASN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 49774 Z= 0.241 Angle : 0.550 7.447 67220 Z= 0.306 Chirality : 0.044 0.157 7522 Planarity : 0.005 0.066 8666 Dihedral : 5.150 35.917 6900 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.12 % Allowed : 12.96 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.72 (0.10), residues: 6224 helix: 2.20 (0.10), residues: 2376 sheet: 1.18 (0.12), residues: 1588 loop : 0.02 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Z 55 HIS 0.005 0.001 HIS T 175 PHE 0.021 0.002 PHE W 36 TYR 0.017 0.002 TYR N 124 ARG 0.003 0.000 ARG G 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 729 time to evaluate : 6.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8696 (mtmt) cc_final: 0.8445 (pptt) REVERT: C 1 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6226 (tmm) REVERT: C 52 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7523 (tt) REVERT: C 209 GLU cc_start: 0.7988 (pm20) cc_final: 0.7439 (pp20) REVERT: C 230 GLN cc_start: 0.7770 (tt0) cc_final: 0.7332 (mt0) REVERT: C 234 GLU cc_start: 0.7282 (mt-10) cc_final: 0.7021 (mt-10) REVERT: D 54 GLN cc_start: 0.8744 (tt0) cc_final: 0.8517 (tp40) REVERT: D 71 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8943 (ptp) REVERT: D 99 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: D 163 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7728 (ptp90) REVERT: D 226 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7308 (mm-30) REVERT: E 65 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: E 129 ASP cc_start: 0.5540 (OUTLIER) cc_final: 0.4979 (p0) REVERT: E 208 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7120 (mm-30) REVERT: F 26 MET cc_start: 0.8703 (mmm) cc_final: 0.8340 (mmm) REVERT: F 206 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8198 (p) REVERT: G 18 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: G 211 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7285 (mt-10) REVERT: H 89 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7933 (ttp-110) REVERT: I 53 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8078 (m-30) REVERT: I 127 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8931 (mmm) REVERT: I 180 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8200 (ptpp) REVERT: J 4 MET cc_start: 0.8803 (mmt) cc_final: 0.8182 (mmm) REVERT: J 31 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8575 (mt0) REVERT: L 9 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7920 (ttp-170) REVERT: L 56 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8939 (mt-10) REVERT: L 194 ASP cc_start: 0.8538 (m-30) cc_final: 0.8335 (m-30) REVERT: N 110 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.8610 (mpp) REVERT: N 155 GLU cc_start: 0.7629 (tp30) cc_final: 0.7249 (mm-30) REVERT: N 198 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7734 (mm-30) REVERT: P 70 LYS cc_start: 0.8696 (mtmt) cc_final: 0.8444 (pptt) REVERT: Q 52 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7522 (tt) REVERT: Q 209 GLU cc_start: 0.8000 (pm20) cc_final: 0.7412 (pp20) REVERT: Q 230 GLN cc_start: 0.7761 (tt0) cc_final: 0.7325 (mt0) REVERT: Q 234 GLU cc_start: 0.7292 (mt-10) cc_final: 0.7026 (mt-10) REVERT: R 54 GLN cc_start: 0.8738 (tt0) cc_final: 0.8511 (tp40) REVERT: R 71 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8934 (ptp) REVERT: R 99 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6799 (mp0) REVERT: R 163 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7742 (ptp90) REVERT: R 226 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7338 (mm-30) REVERT: S 65 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7577 (mt-10) REVERT: T 26 MET cc_start: 0.8686 (mmm) cc_final: 0.8336 (mmm) REVERT: T 180 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7652 (tpt) REVERT: T 206 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8139 (p) REVERT: U 18 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: V 89 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7924 (ttp-110) REVERT: W 53 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: W 127 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8935 (mmm) REVERT: W 180 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8200 (ptpp) REVERT: X 4 MET cc_start: 0.8855 (mmt) cc_final: 0.8241 (mmm) REVERT: Z 56 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8937 (mt-10) REVERT: b 198 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7698 (mm-30) outliers start: 111 outliers final: 44 residues processed: 797 average time/residue: 1.9248 time to fit residues: 1846.1564 Evaluate side-chains 787 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 713 time to evaluate : 5.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 209 LYS Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 180 LYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 31 GLN Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 234 GLU Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain O residue 240 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain R residue 163 ARG Chi-restraints excluded: chain R residue 166 LYS Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 184 VAL Chi-restraints excluded: chain S residue 240 ASP Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain T residue 206 THR Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain V residue 198 THR Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain W residue 180 LYS Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 77 LYS Chi-restraints excluded: chain Z residue 56 GLU Chi-restraints excluded: chain a residue 192 VAL Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain a residue 234 GLU Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 198 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 200 optimal weight: 3.9990 chunk 537 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 350 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 597 optimal weight: 5.9990 chunk 496 optimal weight: 7.9990 chunk 276 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 197 optimal weight: 0.1980 chunk 313 optimal weight: 9.9990 overall best weight: 5.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN B 189 HIS C 155 ASN D 215 GLN E 182 GLN F 183 ASN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 162 HIS P 189 HIS Q 155 ASN R 215 GLN S 182 GLN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 49774 Z= 0.405 Angle : 0.638 8.636 67220 Z= 0.353 Chirality : 0.048 0.166 7522 Planarity : 0.006 0.071 8666 Dihedral : 5.391 37.886 6900 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.47 % Allowed : 12.86 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.56 (0.10), residues: 6224 helix: 2.01 (0.10), residues: 2368 sheet: 1.16 (0.12), residues: 1580 loop : -0.04 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP S 100 HIS 0.006 0.001 HIS Y 132 PHE 0.025 0.003 PHE W 36 TYR 0.019 0.002 TYR H 61 ARG 0.006 0.001 ARG X 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 709 time to evaluate : 5.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8461 (pptt) REVERT: C 1 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6274 (tmm) REVERT: C 52 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7648 (tt) REVERT: C 209 GLU cc_start: 0.8008 (pm20) cc_final: 0.7450 (pp20) REVERT: C 230 GLN cc_start: 0.7771 (tt0) cc_final: 0.7245 (mt0) REVERT: C 234 GLU cc_start: 0.7294 (mt-10) cc_final: 0.7027 (mt-10) REVERT: D 54 GLN cc_start: 0.8795 (tt0) cc_final: 0.8555 (tp40) REVERT: D 71 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8948 (ptp) REVERT: D 99 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: D 163 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7843 (ptp90) REVERT: E 65 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7587 (mt-10) REVERT: E 208 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7150 (mm-30) REVERT: E 236 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.7061 (mm-30) REVERT: F 26 MET cc_start: 0.8670 (mmm) cc_final: 0.8296 (mmm) REVERT: F 180 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7805 (tpt) REVERT: F 206 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8216 (p) REVERT: G 18 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: G 211 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7283 (mt-10) REVERT: H 89 ARG cc_start: 0.8153 (ttp-110) cc_final: 0.7929 (ttp-110) REVERT: I 53 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8111 (m-30) REVERT: I 127 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8941 (mmm) REVERT: I 180 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8242 (ptpp) REVERT: J 4 MET cc_start: 0.8824 (mmt) cc_final: 0.8171 (mmt) REVERT: J 158 MET cc_start: 0.9327 (mtm) cc_final: 0.9032 (mtm) REVERT: L 9 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7933 (ttp-170) REVERT: L 56 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.9001 (mt-10) REVERT: L 194 ASP cc_start: 0.8537 (m-30) cc_final: 0.8333 (m-30) REVERT: N 110 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.8610 (mpp) REVERT: N 155 GLU cc_start: 0.7661 (tp30) cc_final: 0.7266 (mm-30) REVERT: N 198 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7731 (mm-30) REVERT: P 70 LYS cc_start: 0.8731 (mtmt) cc_final: 0.8459 (pptt) REVERT: Q 52 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7646 (tt) REVERT: Q 209 GLU cc_start: 0.8032 (pm20) cc_final: 0.7426 (pp20) REVERT: Q 230 GLN cc_start: 0.7761 (tt0) cc_final: 0.7239 (mt0) REVERT: Q 234 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7018 (mt-10) REVERT: R 54 GLN cc_start: 0.8790 (tt0) cc_final: 0.8550 (tp40) REVERT: R 71 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.8938 (ptp) REVERT: R 99 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: R 163 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7853 (ptp90) REVERT: S 65 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7616 (mt-10) REVERT: S 236 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.7039 (mm-30) REVERT: T 26 MET cc_start: 0.8674 (mmm) cc_final: 0.8302 (mmm) REVERT: T 180 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7734 (tpt) REVERT: T 206 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8178 (p) REVERT: U 18 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7671 (m-30) REVERT: U 211 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: V 89 ARG cc_start: 0.8153 (ttp-110) cc_final: 0.7920 (ttp-110) REVERT: W 53 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8120 (m-30) REVERT: W 127 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8943 (mmm) REVERT: W 180 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8240 (ptpp) REVERT: Z 56 GLU cc_start: 0.9282 (OUTLIER) cc_final: 0.9006 (mt-10) outliers start: 129 outliers final: 60 residues processed: 788 average time/residue: 1.9287 time to fit residues: 1830.1248 Evaluate side-chains 789 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 698 time to evaluate : 5.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 209 LYS Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 180 LYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 234 GLU Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain O residue 240 VAL Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 212 GLU Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain R residue 163 ARG Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 184 VAL Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 240 ASP Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain T residue 206 THR Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 55 LEU Chi-restraints excluded: chain U residue 211 GLU Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain V residue 198 THR Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain W residue 180 LYS Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 77 LYS Chi-restraints excluded: chain Z residue 56 GLU Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain a residue 192 VAL Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain a residue 234 GLU Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 198 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 576 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 340 optimal weight: 7.9990 chunk 436 optimal weight: 0.9980 chunk 338 optimal weight: 6.9990 chunk 503 optimal weight: 0.6980 chunk 333 optimal weight: 0.5980 chunk 595 optimal weight: 9.9990 chunk 372 optimal weight: 7.9990 chunk 363 optimal weight: 20.0000 chunk 275 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS C 155 ASN D 215 GLN E 152 GLN E 182 GLN F 183 ASN H 110 GLN J 162 HIS P 189 HIS Q 155 ASN R 85 ASN R 215 GLN S 152 GLN S 182 GLN T 90 GLN T 183 ASN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 49774 Z= 0.141 Angle : 0.485 6.995 67220 Z= 0.269 Chirality : 0.041 0.143 7522 Planarity : 0.004 0.054 8666 Dihedral : 4.731 31.534 6900 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.49 % Allowed : 13.88 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.93 (0.11), residues: 6224 helix: 2.44 (0.10), residues: 2384 sheet: 1.24 (0.12), residues: 1576 loop : 0.10 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Z 55 HIS 0.006 0.001 HIS T 175 PHE 0.018 0.001 PHE W 36 TYR 0.014 0.001 TYR b 124 ARG 0.004 0.000 ARG G 224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 739 time to evaluate : 6.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8635 (mtmt) cc_final: 0.8331 (pptt) REVERT: C 52 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7650 (tt) REVERT: C 209 GLU cc_start: 0.7909 (pm20) cc_final: 0.7661 (pm20) REVERT: C 230 GLN cc_start: 0.7797 (tt0) cc_final: 0.7241 (mt0) REVERT: C 234 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6989 (mt-10) REVERT: C 243 GLU cc_start: 0.7288 (mm-30) cc_final: 0.7044 (mm-30) REVERT: D 54 GLN cc_start: 0.8651 (tt0) cc_final: 0.8433 (tp40) REVERT: D 163 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7779 (ptp90) REVERT: D 226 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7321 (mm-30) REVERT: E 65 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: E 208 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7082 (mm-30) REVERT: F 26 MET cc_start: 0.8707 (mmm) cc_final: 0.8324 (mmm) REVERT: F 180 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7681 (tpt) REVERT: F 206 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8203 (p) REVERT: G 18 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7598 (m-30) REVERT: G 211 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7236 (mt-10) REVERT: H 89 ARG cc_start: 0.8153 (ttp-110) cc_final: 0.7915 (ttp-110) REVERT: I 53 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8017 (m-30) REVERT: I 127 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8866 (mmm) REVERT: I 180 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8147 (ptpp) REVERT: J 4 MET cc_start: 0.8796 (mmt) cc_final: 0.8201 (mmt) REVERT: K 118 MET cc_start: 0.9036 (ttm) cc_final: 0.8617 (mtp) REVERT: L 56 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8836 (mt-10) REVERT: L 194 ASP cc_start: 0.8535 (m-30) cc_final: 0.8330 (m-30) REVERT: M 212 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8451 (mm-30) REVERT: M 229 GLU cc_start: 0.8198 (mp0) cc_final: 0.7878 (mp0) REVERT: N 198 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7735 (mm-30) REVERT: P 70 LYS cc_start: 0.8635 (mtmt) cc_final: 0.8332 (pptt) REVERT: Q 52 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7648 (tt) REVERT: Q 209 GLU cc_start: 0.7935 (pm20) cc_final: 0.7669 (pm20) REVERT: Q 230 GLN cc_start: 0.7782 (tt0) cc_final: 0.7209 (mt0) REVERT: Q 234 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6988 (mt-10) REVERT: Q 243 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7050 (mm-30) REVERT: R 54 GLN cc_start: 0.8645 (tt0) cc_final: 0.8428 (tp40) REVERT: R 163 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7733 (ptp90) REVERT: R 226 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7312 (mm-30) REVERT: S 65 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7431 (mt-10) REVERT: T 26 MET cc_start: 0.8693 (mmm) cc_final: 0.8321 (mmm) REVERT: T 206 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8174 (p) REVERT: U 18 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7598 (m-30) REVERT: U 170 ARG cc_start: 0.8162 (ptp-170) cc_final: 0.7888 (ptm160) REVERT: V 89 ARG cc_start: 0.8151 (ttp-110) cc_final: 0.7906 (ttp-110) REVERT: W 53 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: W 127 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8870 (mmm) REVERT: W 180 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8147 (ptpp) REVERT: Y 118 MET cc_start: 0.9017 (ttm) cc_final: 0.8595 (mtp) REVERT: Z 56 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8841 (mt-10) REVERT: a 212 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8458 (mm-30) REVERT: a 229 GLU cc_start: 0.8207 (mp0) cc_final: 0.7902 (mp0) REVERT: b 198 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7697 (mm-30) outliers start: 78 outliers final: 26 residues processed: 793 average time/residue: 1.9025 time to fit residues: 1820.1188 Evaluate side-chains 765 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 717 time to evaluate : 6.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 180 LYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 163 ARG Chi-restraints excluded: chain R residue 166 LYS Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 184 VAL Chi-restraints excluded: chain T residue 206 THR Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 190 LEU Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain W residue 180 LYS Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain Z residue 56 GLU Chi-restraints excluded: chain a residue 192 VAL Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 198 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 368 optimal weight: 0.6980 chunk 237 optimal weight: 1.9990 chunk 355 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 378 optimal weight: 9.9990 chunk 405 optimal weight: 9.9990 chunk 294 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 468 optimal weight: 9.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS C 155 ASN C 166 ASN D 215 GLN E 182 GLN I 209 ASN J 162 HIS P 189 HIS Q 155 ASN Q 166 ASN R 215 GLN S 182 GLN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 209 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 49774 Z= 0.263 Angle : 0.556 7.637 67220 Z= 0.307 Chirality : 0.044 0.159 7522 Planarity : 0.005 0.063 8666 Dihedral : 5.023 33.815 6900 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.63 % Allowed : 14.26 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.87 (0.10), residues: 6224 helix: 2.35 (0.10), residues: 2378 sheet: 1.19 (0.12), residues: 1582 loop : 0.12 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 100 HIS 0.005 0.001 HIS Y 132 PHE 0.023 0.002 PHE W 36 TYR 0.017 0.002 TYR b 124 ARG 0.004 0.000 ARG U 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 720 time to evaluate : 6.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8444 (pptt) REVERT: B 180 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6253 (mp0) REVERT: C 52 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7695 (tt) REVERT: C 209 GLU cc_start: 0.7969 (pm20) cc_final: 0.7733 (pm20) REVERT: C 230 GLN cc_start: 0.7835 (tt0) cc_final: 0.7272 (mt0) REVERT: C 234 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7013 (mt-10) REVERT: C 243 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6982 (mm-30) REVERT: D 54 GLN cc_start: 0.8738 (tt0) cc_final: 0.8511 (tp40) REVERT: D 163 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7744 (ptp90) REVERT: D 226 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7314 (mm-30) REVERT: E 65 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: E 129 ASP cc_start: 0.5430 (OUTLIER) cc_final: 0.4863 (p0) REVERT: E 208 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7111 (mm-30) REVERT: F 26 MET cc_start: 0.8685 (mmm) cc_final: 0.8311 (mmm) REVERT: F 206 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8221 (p) REVERT: G 18 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: G 211 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7256 (mt-10) REVERT: H 89 ARG cc_start: 0.8154 (ttp-110) cc_final: 0.7923 (ttp-110) REVERT: I 53 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8082 (m-30) REVERT: I 127 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8921 (mmm) REVERT: I 180 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8177 (ptpp) REVERT: J 4 MET cc_start: 0.8833 (mmt) cc_final: 0.8182 (mmt) REVERT: J 158 MET cc_start: 0.9345 (mtm) cc_final: 0.8961 (mtm) REVERT: L 56 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8920 (mt-10) REVERT: L 194 ASP cc_start: 0.8546 (m-30) cc_final: 0.8342 (m-30) REVERT: N 110 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8575 (mpp) REVERT: N 198 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7724 (mm-30) REVERT: P 70 LYS cc_start: 0.8696 (mtmt) cc_final: 0.8440 (pptt) REVERT: Q 52 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7697 (tt) REVERT: Q 209 GLU cc_start: 0.7943 (pm20) cc_final: 0.7687 (pm20) REVERT: Q 230 GLN cc_start: 0.7827 (tt0) cc_final: 0.7256 (mt0) REVERT: Q 234 GLU cc_start: 0.7299 (mt-10) cc_final: 0.7012 (mt-10) REVERT: Q 243 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6986 (mm-30) REVERT: R 54 GLN cc_start: 0.8731 (tt0) cc_final: 0.8506 (tp40) REVERT: R 163 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7748 (ptp90) REVERT: R 226 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7355 (mm-30) REVERT: S 65 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: T 26 MET cc_start: 0.8703 (mmm) cc_final: 0.8334 (mmm) REVERT: T 206 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8179 (p) REVERT: U 18 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7638 (m-30) REVERT: V 89 ARG cc_start: 0.8154 (ttp-110) cc_final: 0.7915 (ttp-110) REVERT: W 53 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8053 (m-30) REVERT: W 127 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8923 (mmm) REVERT: W 180 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8177 (ptpp) REVERT: Z 56 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8917 (mt-10) REVERT: a 229 GLU cc_start: 0.8184 (mp0) cc_final: 0.7920 (mp0) REVERT: b 198 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7682 (mm-30) outliers start: 85 outliers final: 38 residues processed: 775 average time/residue: 1.9107 time to fit residues: 1782.1771 Evaluate side-chains 773 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 711 time to evaluate : 5.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 209 LYS Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 180 LYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain O residue 193 GLN Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 148 ASP Chi-restraints excluded: chain R residue 163 ARG Chi-restraints excluded: chain R residue 166 LYS Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 184 VAL Chi-restraints excluded: chain T residue 206 THR Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain W residue 180 LYS Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain Z residue 56 GLU Chi-restraints excluded: chain a residue 192 VAL Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 198 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 541 optimal weight: 7.9990 chunk 570 optimal weight: 7.9990 chunk 520 optimal weight: 7.9990 chunk 555 optimal weight: 4.9990 chunk 334 optimal weight: 9.9990 chunk 241 optimal weight: 5.9990 chunk 435 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 501 optimal weight: 5.9990 chunk 524 optimal weight: 3.9990 chunk 553 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS C 155 ASN C 166 ASN D 215 GLN E 182 GLN F 203 GLN I 209 ASN J 162 HIS P 189 HIS Q 155 ASN Q 166 ASN R 215 GLN S 182 GLN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 209 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 49774 Z= 0.378 Angle : 0.628 8.571 67220 Z= 0.347 Chirality : 0.048 0.160 7522 Planarity : 0.005 0.070 8666 Dihedral : 5.294 36.911 6900 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.78 % Allowed : 14.28 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.67 (0.10), residues: 6224 helix: 2.13 (0.10), residues: 2368 sheet: 1.18 (0.12), residues: 1582 loop : 0.02 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP S 100 HIS 0.020 0.001 HIS Y 132 PHE 0.023 0.002 PHE W 36 TYR 0.021 0.002 TYR I 90 ARG 0.012 0.001 ARG G 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 705 time to evaluate : 5.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8457 (pptt) REVERT: B 180 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6359 (mp0) REVERT: C 52 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7660 (tt) REVERT: C 209 GLU cc_start: 0.7994 (pm20) cc_final: 0.7435 (pp20) REVERT: C 230 GLN cc_start: 0.7834 (tt0) cc_final: 0.7242 (mt0) REVERT: C 234 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6962 (mt-10) REVERT: C 243 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6978 (mm-30) REVERT: D 54 GLN cc_start: 0.8775 (tt0) cc_final: 0.8531 (tp40) REVERT: D 71 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.8948 (ptp) REVERT: D 99 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: D 163 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7827 (ptt90) REVERT: E 65 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: E 208 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7157 (mm-30) REVERT: F 26 MET cc_start: 0.8671 (mmm) cc_final: 0.8278 (mmm) REVERT: F 206 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8210 (p) REVERT: G 18 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7750 (m-30) REVERT: G 211 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7266 (mt-10) REVERT: H 89 ARG cc_start: 0.8177 (ttp-110) cc_final: 0.7949 (ttp-110) REVERT: I 53 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8102 (m-30) REVERT: I 127 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8928 (mmm) REVERT: I 180 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8223 (ptpp) REVERT: K 118 MET cc_start: 0.9158 (ttm) cc_final: 0.8710 (mtp) REVERT: L 56 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.8986 (mt-10) REVERT: N 110 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.8581 (mpp) REVERT: N 155 GLU cc_start: 0.7639 (tp30) cc_final: 0.7269 (mm-30) REVERT: N 198 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7727 (mm-30) REVERT: P 70 LYS cc_start: 0.8721 (mtmt) cc_final: 0.8456 (pptt) REVERT: Q 52 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7745 (tt) REVERT: Q 209 GLU cc_start: 0.7996 (pm20) cc_final: 0.7742 (pm20) REVERT: Q 230 GLN cc_start: 0.7825 (tt0) cc_final: 0.7239 (mt0) REVERT: Q 234 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6961 (mt-10) REVERT: Q 243 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6984 (mm-30) REVERT: R 54 GLN cc_start: 0.8769 (tt0) cc_final: 0.8525 (tp40) REVERT: R 71 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8937 (ptp) REVERT: R 99 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: R 163 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7753 (ptt90) REVERT: S 65 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7592 (mt-10) REVERT: S 236 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.7052 (mm-30) REVERT: T 26 MET cc_start: 0.8672 (mmm) cc_final: 0.8286 (mmm) REVERT: T 206 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8200 (p) REVERT: U 18 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7758 (m-30) REVERT: V 89 ARG cc_start: 0.8176 (ttp-110) cc_final: 0.7941 (ttp-110) REVERT: W 53 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8100 (m-30) REVERT: W 127 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8931 (mmm) REVERT: W 180 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8223 (ptpp) REVERT: Y 118 MET cc_start: 0.9140 (ttm) cc_final: 0.8691 (mtp) REVERT: Z 56 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.8989 (mt-10) REVERT: b 198 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7685 (mm-30) outliers start: 93 outliers final: 48 residues processed: 766 average time/residue: 1.9510 time to fit residues: 1798.8890 Evaluate side-chains 777 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 701 time to evaluate : 5.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 209 LYS Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 180 LYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain R residue 148 ASP Chi-restraints excluded: chain R residue 163 ARG Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 184 VAL Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 206 THR Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain V residue 198 THR Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain W residue 180 LYS Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 77 LYS Chi-restraints excluded: chain Z residue 56 GLU Chi-restraints excluded: chain a residue 192 VAL Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 198 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 364 optimal weight: 5.9990 chunk 586 optimal weight: 4.9990 chunk 358 optimal weight: 7.9990 chunk 278 optimal weight: 10.0000 chunk 408 optimal weight: 9.9990 chunk 615 optimal weight: 5.9990 chunk 566 optimal weight: 0.6980 chunk 490 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 378 optimal weight: 1.9990 chunk 300 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS B 207 ASN C 155 ASN C 166 ASN D 215 GLN E 182 GLN F 183 ASN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 ASN J 162 HIS P 189 HIS P 207 ASN Q 155 ASN R 215 GLN S 182 GLN T 183 ASN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 209 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 49774 Z= 0.303 Angle : 0.588 8.219 67220 Z= 0.325 Chirality : 0.045 0.160 7522 Planarity : 0.005 0.068 8666 Dihedral : 5.204 36.119 6900 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.61 % Allowed : 14.41 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.69 (0.10), residues: 6224 helix: 2.15 (0.10), residues: 2374 sheet: 1.18 (0.12), residues: 1590 loop : 0.02 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 100 HIS 0.017 0.001 HIS Y 132 PHE 0.022 0.002 PHE W 36 TYR 0.018 0.002 TYR N 124 ARG 0.010 0.001 ARG G 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12448 Ramachandran restraints generated. 6224 Oldfield, 0 Emsley, 6224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 705 time to evaluate : 5.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8713 (mtmt) cc_final: 0.8454 (pptt) REVERT: C 52 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7760 (tt) REVERT: C 209 GLU cc_start: 0.7991 (pm20) cc_final: 0.7754 (pm20) REVERT: C 230 GLN cc_start: 0.7813 (tt0) cc_final: 0.7237 (mt0) REVERT: C 234 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6973 (mt-10) REVERT: C 243 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6991 (mm-30) REVERT: D 54 GLN cc_start: 0.8756 (tt0) cc_final: 0.8518 (tp40) REVERT: D 71 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8943 (ptp) REVERT: D 99 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6820 (mp0) REVERT: D 163 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7770 (ptp90) REVERT: E 65 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: E 129 ASP cc_start: 0.5572 (OUTLIER) cc_final: 0.5327 (p0) REVERT: E 208 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7161 (mm-30) REVERT: F 26 MET cc_start: 0.8696 (mmm) cc_final: 0.8310 (mmm) REVERT: F 206 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8207 (p) REVERT: G 18 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: G 211 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7269 (mt-10) REVERT: H 89 ARG cc_start: 0.8189 (ttp-110) cc_final: 0.7961 (ttp-110) REVERT: I 53 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8092 (m-30) REVERT: I 127 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8929 (mmm) REVERT: I 180 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8217 (ptpp) REVERT: K 118 MET cc_start: 0.9157 (ttm) cc_final: 0.8738 (mtp) REVERT: L 56 GLU cc_start: 0.9254 (OUTLIER) cc_final: 0.8955 (mt-10) REVERT: N 110 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8589 (mpp) REVERT: N 155 GLU cc_start: 0.7636 (tp30) cc_final: 0.7265 (mm-30) REVERT: N 198 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7738 (mm-30) REVERT: P 70 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8453 (pptt) REVERT: Q 52 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7759 (tt) REVERT: Q 209 GLU cc_start: 0.7991 (pm20) cc_final: 0.7738 (pm20) REVERT: Q 230 GLN cc_start: 0.7805 (tt0) cc_final: 0.7232 (mt0) REVERT: Q 234 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6972 (mt-10) REVERT: Q 243 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6981 (mm-30) REVERT: R 54 GLN cc_start: 0.8758 (tt0) cc_final: 0.8517 (tp40) REVERT: R 71 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8932 (ptp) REVERT: R 99 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: R 163 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7752 (ptp90) REVERT: S 65 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7583 (mt-10) REVERT: T 26 MET cc_start: 0.8702 (mmm) cc_final: 0.8327 (mmm) REVERT: T 206 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8202 (p) REVERT: U 18 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7673 (m-30) REVERT: U 170 ARG cc_start: 0.8166 (ptp-170) cc_final: 0.7960 (ptm160) REVERT: V 89 ARG cc_start: 0.8188 (ttp-110) cc_final: 0.7953 (ttp-110) REVERT: W 53 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8089 (m-30) REVERT: W 127 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8931 (mmm) REVERT: W 180 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8220 (ptpp) REVERT: X 158 MET cc_start: 0.9310 (mtm) cc_final: 0.9003 (mtm) REVERT: Y 118 MET cc_start: 0.9138 (ttm) cc_final: 0.8719 (mtp) REVERT: Z 56 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.8972 (mt-10) REVERT: b 198 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7686 (mm-30) outliers start: 84 outliers final: 46 residues processed: 764 average time/residue: 1.9794 time to fit residues: 1831.1733 Evaluate side-chains 774 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 701 time to evaluate : 5.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 209 LYS Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 180 LYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain R residue 148 ASP Chi-restraints excluded: chain R residue 163 ARG Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 184 VAL Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 206 THR Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain V residue 190 LEU Chi-restraints excluded: chain V residue 198 THR Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain W residue 180 LYS Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain Z residue 56 GLU Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain a residue 192 VAL Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 198 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 389 optimal weight: 7.9990 chunk 522 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 452 optimal weight: 3.9990 chunk 72 optimal weight: 0.0170 chunk 136 optimal weight: 9.9990 chunk 491 optimal weight: 0.9980 chunk 205 optimal weight: 0.4980 chunk 504 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS C 155 ASN D 215 GLN E 182 GLN F 183 ASN I 209 ASN J 162 HIS P 189 HIS Q 155 ASN Q 166 ASN R 215 GLN S 182 GLN T 183 ASN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 209 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.102244 restraints weight = 50791.476| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.28 r_work: 0.3111 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 49774 Z= 0.220 Angle : 0.541 8.077 67220 Z= 0.299 Chirality : 0.043 0.158 7522 Planarity : 0.004 0.064 8666 Dihedral : 5.017 33.918 6900 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.57 % Allowed : 14.47 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.83 (0.10), residues: 6224 helix: 2.30 (0.10), residues: 2378 sheet: 1.26 (0.13), residues: 1558 loop : 0.06 (0.13), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Z 55 HIS 0.012 0.001 HIS Y 132 PHE 0.021 0.002 PHE W 36 TYR 0.017 0.002 TYR Y 117 ARG 0.009 0.000 ARG G 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24989.73 seconds wall clock time: 439 minutes 7.87 seconds (26347.87 seconds total)