Starting phenix.real_space_refine on Mon Sep 23 21:43:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz5_29603/09_2024/8fz5_29603.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz5_29603/09_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_29603/09_2024/8fz5_29603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz5_29603/09_2024/8fz5_29603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz5_29603/09_2024/8fz5_29603.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz5_29603/09_2024/8fz5_29603.cif" } 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. Time to flip 16 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 21.38, per 1000 atoms: 0.44 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 - 3.00 Amino acid : True - 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: 8.60 Conformation dependent library (CDL) restraints added in 4.6 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: 5.13 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: 17.66 Time building geometry restraints manager: 10.33 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: 0.00 - 1.57: 65399 1.57 - 3.14: 1625 3.14 - 4.71: 165 4.71 - 6.28: 28 6.28 - 7.85: 3 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 3.120 nonbonded pdb=" OH TYR T 6 " pdb=" OD2 ASP U 9 " model vdw 2.254 3.040 nonbonded pdb=" O GLY S 160 " pdb=" NH2 ARG T 82 " model vdw 2.254 3.120 nonbonded pdb=" O LYS E 209 " pdb=" ND2 ASN E 214 " model vdw 2.255 3.120 nonbonded pdb=" O GLY E 160 " pdb=" NH2 ARG F 82 " model vdw 2.262 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 1.700 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: 0.040 Extract box with map and model: 1.370 Check model and map are aligned: 0.280 Set scattering table: 0.330 Process input model: 83.550 Find NCS groups from input model: 3.000 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.590 ------------------------------------------------------------------------------- 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 : 4.345 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: 1.7697 time to fit residues: 2003.5997 Evaluate side-chains 741 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 740 time to evaluate : 4.362 ------------------------------------------------------------------------------- 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: 4.9990 chunk 468 optimal weight: 0.0970 chunk 259 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 chunk 315 optimal weight: 10.0000 chunk 250 optimal weight: 5.9990 chunk 484 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 294 optimal weight: 3.9990 chunk 360 optimal weight: 8.9990 chunk 561 optimal weight: 9.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN B 189 HIS B 207 ASN C 51 ASN C 155 ASN D 205 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 S 182 GLN W 209 ASN Y 168 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 49774 Z= 0.270 Angle : 0.571 7.253 67220 Z= 0.317 Chirality : 0.045 0.154 7522 Planarity : 0.005 0.065 8666 Dihedral : 5.178 36.220 6901 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.68 % Allowed : 10.34 % Favored : 87.98 % 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: 1.70 (0.10), residues: 6224 helix: 2.17 (0.10), residues: 2370 sheet: 1.18 (0.12), residues: 1582 loop : 0.02 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Z 55 HIS 0.005 0.001 HIS F 175 PHE 0.023 0.002 PHE W 36 TYR 0.021 0.002 TYR Q 121 ARG 0.006 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 833 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 745 time to evaluate : 4.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8677 (mtmt) cc_final: 0.8435 (pptt) REVERT: B 143 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8283 (tmt170) REVERT: C 209 GLU cc_start: 0.8003 (pm20) cc_final: 0.7427 (pp20) REVERT: C 230 GLN cc_start: 0.7830 (tt0) cc_final: 0.7241 (mt0) REVERT: C 234 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6989 (mt-10) REVERT: D 54 GLN cc_start: 0.8739 (tt0) cc_final: 0.8527 (tp40) REVERT: D 99 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: E 65 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: E 208 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7096 (mm-30) REVERT: F 26 MET cc_start: 0.8730 (mmm) cc_final: 0.8401 (mmm) REVERT: F 180 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7589 (tpt) REVERT: F 204 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7286 (t70) REVERT: F 206 THR cc_start: 0.8492 (m) cc_final: 0.8204 (p) REVERT: G 18 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: G 211 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7224 (mt-10) REVERT: I 9 LYS cc_start: 0.8699 (ptmt) cc_final: 0.8497 (ptmm) REVERT: I 53 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8109 (m-30) REVERT: I 127 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8889 (mmm) REVERT: I 180 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8191 (ptpp) REVERT: L 56 GLU cc_start: 0.9274 (OUTLIER) cc_final: 0.8987 (mt-10) REVERT: L 194 ASP cc_start: 0.8538 (m-30) cc_final: 0.8332 (m-30) REVERT: M 46 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7822 (tp30) REVERT: M 229 GLU cc_start: 0.8226 (mp0) cc_final: 0.7907 (mp0) REVERT: N 110 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8608 (mpp) REVERT: N 198 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7782 (mm-30) REVERT: O 1 MET cc_start: 0.4763 (ttm) cc_final: 0.4063 (mmt) REVERT: P 70 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8450 (pptt) REVERT: Q 1 MET cc_start: 0.6953 (ttt) cc_final: 0.6698 (ttt) REVERT: Q 209 GLU cc_start: 0.7958 (pm20) cc_final: 0.7395 (pp20) REVERT: Q 230 GLN cc_start: 0.7822 (tt0) cc_final: 0.7233 (mt0) REVERT: Q 234 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6989 (mt-10) REVERT: R 54 GLN cc_start: 0.8734 (tt0) cc_final: 0.8522 (tp40) REVERT: R 99 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: S 65 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: S 208 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6511 (mt-10) REVERT: T 26 MET cc_start: 0.8713 (mmm) cc_final: 0.8392 (mmm) REVERT: T 180 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7588 (tpt) REVERT: T 206 THR cc_start: 0.8414 (m) cc_final: 0.8129 (p) REVERT: U 18 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7730 (m-30) REVERT: U 211 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7267 (mt-10) REVERT: W 53 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: W 127 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8891 (mmm) REVERT: W 180 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8191 (ptpp) REVERT: Z 56 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.8978 (mt-10) REVERT: Z 107 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.7461 (mtm110) REVERT: a 46 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7832 (tp30) REVERT: a 229 GLU cc_start: 0.8233 (mp0) cc_final: 0.7930 (mp0) REVERT: b 198 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7713 (mm-30) outliers start: 88 outliers final: 24 residues processed: 793 average time/residue: 1.6211 time to fit residues: 1543.3961 Evaluate side-chains 773 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 724 time to evaluate : 4.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain B residue 143 ARG 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 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 204 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 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 N residue 198 GLU Chi-restraints excluded: chain O residue 240 VAL 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 184 VAL Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain T residue 180 MET 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 311 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 467 optimal weight: 9.9990 chunk 382 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 562 optimal weight: 5.9990 chunk 607 optimal weight: 4.9990 chunk 500 optimal weight: 7.9990 chunk 557 optimal weight: 3.9990 chunk 191 optimal weight: 9.9990 chunk 451 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS B 207 ASN C 155 ASN D 85 ASN D 215 GLN E 182 GLN G 64 ASN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 ASN J 162 HIS N 2 GLN ** O 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 ASN P 189 HIS P 207 ASN Q 155 ASN R 85 ASN S 182 GLN U 33 ASN U 64 ASN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 209 ASN b 2 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 49774 Z= 0.373 Angle : 0.630 8.580 67220 Z= 0.349 Chirality : 0.048 0.161 7522 Planarity : 0.006 0.069 8666 Dihedral : 5.361 37.618 6900 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.26 % Allowed : 10.87 % Favored : 86.87 % 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: 1.59 (0.10), residues: 6224 helix: 2.04 (0.10), residues: 2372 sheet: 1.10 (0.12), residues: 1602 loop : 0.02 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP S 100 HIS 0.005 0.001 HIS T 175 PHE 0.024 0.002 PHE I 36 TYR 0.019 0.002 TYR Q 121 ARG 0.005 0.001 ARG K 170 *********************** 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 846 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 728 time to evaluate : 4.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8448 (pptt) REVERT: C 209 GLU cc_start: 0.7982 (pm20) cc_final: 0.7413 (pp20) REVERT: C 230 GLN cc_start: 0.7823 (tt0) cc_final: 0.7300 (mt0) REVERT: C 234 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6983 (mt-10) REVERT: C 235 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7394 (tp40) REVERT: D 54 GLN cc_start: 0.8761 (tt0) cc_final: 0.8540 (tp40) REVERT: D 71 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8947 (ptp) REVERT: D 99 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: D 163 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7998 (ptp90) REVERT: E 65 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: E 208 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7166 (mm-30) REVERT: E 236 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6931 (mm-30) REVERT: F 26 MET cc_start: 0.8713 (mmm) cc_final: 0.8354 (mmm) REVERT: F 180 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7679 (tpt) REVERT: F 204 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.7132 (t70) REVERT: F 206 THR cc_start: 0.8498 (m) cc_final: 0.8223 (p) REVERT: G 18 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7648 (m-30) REVERT: G 211 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7272 (mt-10) REVERT: I 9 LYS cc_start: 0.8734 (ptmt) cc_final: 0.8518 (ptmm) REVERT: I 53 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: I 127 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8916 (mmm) REVERT: I 180 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8230 (ptpp) REVERT: J 4 MET cc_start: 0.8913 (mmt) cc_final: 0.8273 (mmt) REVERT: L 56 GLU cc_start: 0.9284 (OUTLIER) cc_final: 0.8999 (mt-10) REVERT: M 46 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7841 (tp30) REVERT: N 110 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.8608 (mpp) REVERT: N 198 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7759 (mm-30) REVERT: O 1 MET cc_start: 0.4903 (ttm) cc_final: 0.4170 (mmt) REVERT: P 70 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8446 (pptt) REVERT: P 143 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8334 (tmt170) REVERT: Q 1 MET cc_start: 0.6943 (ttt) cc_final: 0.6647 (ttt) REVERT: Q 209 GLU cc_start: 0.7948 (pm20) cc_final: 0.7391 (pp20) REVERT: Q 230 GLN cc_start: 0.7813 (tt0) cc_final: 0.7290 (mt0) REVERT: Q 234 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6986 (mt-10) REVERT: Q 235 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7389 (tp40) REVERT: R 54 GLN cc_start: 0.8754 (tt0) cc_final: 0.8533 (tp40) REVERT: R 71 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8938 (ptp) REVERT: R 99 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6859 (mp0) REVERT: R 163 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7998 (ptp90) REVERT: S 65 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7567 (mt-10) REVERT: S 208 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6485 (mt-10) REVERT: T 26 MET cc_start: 0.8716 (mmm) cc_final: 0.8364 (mmm) REVERT: T 180 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7673 (tpt) REVERT: T 206 THR cc_start: 0.8426 (m) cc_final: 0.8162 (p) REVERT: U 18 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: U 211 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7286 (mt-10) REVERT: W 53 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8098 (m-30) REVERT: W 127 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8917 (mmm) REVERT: W 180 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8231 (ptpp) REVERT: X 4 MET cc_start: 0.8918 (mmt) cc_final: 0.8271 (mmt) REVERT: Z 56 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.9000 (mt-10) REVERT: a 46 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7878 (tp30) outliers start: 118 outliers final: 42 residues processed: 797 average time/residue: 1.5793 time to fit residues: 1518.9004 Evaluate side-chains 772 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 699 time to evaluate : 4.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 35 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 235 GLN 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 139 VAL Chi-restraints excluded: chain E residue 208 GLU 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 180 MET 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 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 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 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 P residue 143 ARG 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 Q residue 235 GLN 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 208 GLU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 55 LEU 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 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 Z residue 56 GLU Chi-restraints excluded: chain a residue 46 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 555 optimal weight: 8.9990 chunk 422 optimal weight: 5.9990 chunk 291 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 268 optimal weight: 9.9990 chunk 377 optimal weight: 9.9990 chunk 564 optimal weight: 6.9990 chunk 597 optimal weight: 3.9990 chunk 294 optimal weight: 7.9990 chunk 534 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN B 189 HIS C 155 ASN D 215 GLN E 152 GLN E 182 GLN G 64 ASN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 162 HIS O 123 GLN P 189 HIS Q 155 ASN R 215 GLN S 152 GLN S 182 GLN T 183 ASN U 64 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: 0.8940 moved from start: 0.1134 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= 0.234 Angle : 0.544 7.053 67220 Z= 0.303 Chirality : 0.044 0.156 7522 Planarity : 0.005 0.063 8666 Dihedral : 5.069 34.423 6900 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.12 % Allowed : 12.16 % Favored : 85.72 % 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: 1.76 (0.10), residues: 6224 helix: 2.22 (0.10), residues: 2382 sheet: 1.18 (0.12), residues: 1578 loop : 0.07 (0.13), residues: 2264 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 0.016 0.002 TYR b 124 ARG 0.004 0.000 ARG U 224 *********************** 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 843 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 732 time to evaluate : 4.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8686 (mtmt) cc_final: 0.8441 (pptt) REVERT: B 143 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8242 (tmt-80) REVERT: C 52 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7530 (tt) REVERT: C 209 GLU cc_start: 0.7955 (pm20) cc_final: 0.7430 (pp20) REVERT: C 230 GLN cc_start: 0.7822 (tt0) cc_final: 0.7239 (mt0) REVERT: C 234 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6989 (mt-10) REVERT: D 54 GLN cc_start: 0.8737 (tt0) cc_final: 0.8520 (tp40) REVERT: D 71 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8917 (ptp) REVERT: D 99 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: E 65 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: E 208 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7146 (mm-30) REVERT: F 26 MET cc_start: 0.8693 (mmm) cc_final: 0.8335 (mmm) REVERT: F 180 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7662 (tpt) REVERT: F 206 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8219 (p) REVERT: G 18 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7566 (m-30) REVERT: G 211 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7262 (mt-10) REVERT: H 89 ARG cc_start: 0.8132 (ttp-110) cc_final: 0.7910 (ttp-110) REVERT: I 9 LYS cc_start: 0.8677 (ptmt) cc_final: 0.8471 (ptmm) REVERT: I 53 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8092 (m-30) REVERT: I 127 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8928 (mmm) REVERT: I 180 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8193 (ptpp) REVERT: J 31 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8571 (mt0) REVERT: J 78 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7910 (mt-10) REVERT: L 56 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8921 (mt-10) REVERT: M 46 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7819 (tp30) REVERT: N 110 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8621 (mpp) REVERT: N 155 GLU cc_start: 0.7609 (tp30) cc_final: 0.7235 (mm-30) REVERT: O 1 MET cc_start: 0.4952 (ttm) cc_final: 0.4255 (mmt) REVERT: P 70 LYS cc_start: 0.8688 (mtmt) cc_final: 0.8442 (pptt) REVERT: P 143 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8157 (tmt-80) REVERT: Q 1 MET cc_start: 0.6942 (ttt) cc_final: 0.6666 (ttt) REVERT: Q 52 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7612 (tt) REVERT: Q 209 GLU cc_start: 0.7918 (pm20) cc_final: 0.7655 (pm20) REVERT: Q 230 GLN cc_start: 0.7815 (tt0) cc_final: 0.7238 (mt0) REVERT: Q 234 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6990 (mt-10) REVERT: R 54 GLN cc_start: 0.8730 (tt0) cc_final: 0.8512 (tp40) REVERT: R 71 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8908 (ptp) REVERT: R 99 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: R 226 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7322 (mm-30) REVERT: S 65 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7546 (mt-10) REVERT: T 26 MET cc_start: 0.8704 (mmm) cc_final: 0.8362 (mmm) REVERT: T 180 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7632 (tpt) REVERT: T 206 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8172 (p) REVERT: U 18 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7613 (m-30) REVERT: U 170 ARG cc_start: 0.8196 (ptp-170) cc_final: 0.7891 (ptm160) REVERT: U 211 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7254 (mt-10) REVERT: V 89 ARG cc_start: 0.8131 (ttp-110) cc_final: 0.7892 (ttp-170) REVERT: W 53 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: W 127 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8930 (mmm) REVERT: W 180 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8182 (ptpp) REVERT: X 4 MET cc_start: 0.8907 (mmt) cc_final: 0.8285 (mmt) REVERT: X 78 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: Z 56 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8918 (mt-10) REVERT: Z 107 ARG cc_start: 0.7723 (mtm110) cc_final: 0.7219 (mtm110) REVERT: a 46 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7832 (tp30) REVERT: b 47 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8549 (t0) REVERT: b 198 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7709 (mm-30) outliers start: 111 outliers final: 32 residues processed: 793 average time/residue: 1.6080 time to fit residues: 1536.8140 Evaluate side-chains 775 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 710 time to evaluate : 4.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain B residue 143 ARG 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 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 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 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 78 GLU Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain L residue 192 VAL 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 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 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 180 MET Chi-restraints excluded: chain T residue 206 THR 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 78 GLU Chi-restraints excluded: chain Z residue 56 GLU Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain a residue 46 GLU Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain b residue 47 ASN 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: 9.9990 chunk 339 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 444 optimal weight: 6.9990 chunk 246 optimal weight: 9.9990 chunk 509 optimal weight: 8.9990 chunk 412 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 305 optimal weight: 2.9990 chunk 536 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 205 ASN D 215 GLN E 182 GLN F 183 ASN G 64 ASN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 ASN J 162 HIS P 189 HIS Q 155 ASN R 215 GLN S 182 GLN U 64 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: 0.8979 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 49774 Z= 0.479 Angle : 0.683 8.999 67220 Z= 0.377 Chirality : 0.051 0.188 7522 Planarity : 0.006 0.075 8666 Dihedral : 5.482 38.486 6900 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.28 % Allowed : 12.12 % Favored : 85.60 % 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: 1.94 (0.10), residues: 2368 sheet: 1.12 (0.12), residues: 1584 loop : -0.01 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP S 100 HIS 0.006 0.001 HIS K 132 PHE 0.025 0.003 PHE W 36 TYR 0.022 0.003 TYR Y 12 ARG 0.006 0.001 ARG K 170 *********************** 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 821 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 702 time to evaluate : 4.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8411 (pptt) REVERT: C 52 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7643 (tt) REVERT: C 209 GLU cc_start: 0.7968 (pm20) cc_final: 0.7431 (pp20) REVERT: C 230 GLN cc_start: 0.7821 (tt0) cc_final: 0.7311 (mt0) REVERT: C 234 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7025 (mt-10) REVERT: C 235 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7423 (tp40) REVERT: D 54 GLN cc_start: 0.8802 (tt0) cc_final: 0.8562 (tp40) REVERT: D 71 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8958 (ptp) REVERT: D 99 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: D 163 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7973 (ptp90) REVERT: E 20 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7948 (mtp180) REVERT: E 65 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7571 (mt-10) REVERT: E 208 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: E 236 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.7047 (mm-30) REVERT: F 26 MET cc_start: 0.8702 (mmm) cc_final: 0.8324 (mmm) REVERT: F 206 THR cc_start: 0.8517 (m) cc_final: 0.8240 (p) REVERT: G 18 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7680 (m-30) REVERT: G 211 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7244 (mt-10) REVERT: H 89 ARG cc_start: 0.8187 (ttp-110) cc_final: 0.7967 (ttp-110) REVERT: I 9 LYS cc_start: 0.8729 (ptmt) cc_final: 0.8513 (ptmm) REVERT: I 53 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8094 (m-30) REVERT: I 127 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8935 (mmm) REVERT: I 180 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8246 (ptpp) REVERT: J 4 MET cc_start: 0.8905 (mmt) cc_final: 0.8384 (mmt) REVERT: J 158 MET cc_start: 0.9311 (mtm) cc_final: 0.9091 (mtm) REVERT: L 56 GLU cc_start: 0.9291 (OUTLIER) cc_final: 0.9025 (mt-10) REVERT: N 110 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.8591 (mpp) REVERT: N 155 GLU cc_start: 0.7703 (tp30) cc_final: 0.7285 (mm-30) REVERT: N 198 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7734 (mm-30) REVERT: O 1 MET cc_start: 0.4968 (ttm) cc_final: 0.4259 (mmt) REVERT: P 70 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8411 (pptt) REVERT: Q 52 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7641 (tt) REVERT: Q 209 GLU cc_start: 0.7916 (pm20) cc_final: 0.7404 (pp20) REVERT: Q 230 GLN cc_start: 0.7814 (tt0) cc_final: 0.7315 (mt0) REVERT: Q 234 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7031 (mt-10) REVERT: Q 235 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7419 (tp40) REVERT: R 54 GLN cc_start: 0.8798 (tt0) cc_final: 0.8559 (tp40) REVERT: R 71 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8953 (ptp) REVERT: R 99 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: R 163 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7969 (ptp90) REVERT: S 20 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7918 (mtp180) REVERT: S 65 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: S 208 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7113 (mm-30) REVERT: T 26 MET cc_start: 0.8674 (mmm) cc_final: 0.8304 (mmm) REVERT: T 206 THR cc_start: 0.8444 (m) cc_final: 0.8220 (p) REVERT: U 18 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7697 (m-30) REVERT: U 211 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7327 (mt-10) REVERT: V 89 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7955 (ttp-110) REVERT: W 53 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8136 (m-30) REVERT: W 127 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8935 (mmm) REVERT: W 180 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8243 (ptpp) REVERT: Z 56 GLU cc_start: 0.9287 (OUTLIER) cc_final: 0.9019 (mt-10) outliers start: 119 outliers final: 55 residues processed: 770 average time/residue: 1.6121 time to fit residues: 1497.5166 Evaluate side-chains 780 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 696 time to evaluate : 4.327 ------------------------------------------------------------------------------- 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 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 212 GLU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 235 GLN 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 20 ARG 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 F residue 78 THR Chi-restraints excluded: chain F residue 167 SER 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 I residue 213 THR Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 78 GLU 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 177 SER Chi-restraints excluded: chain O residue 240 VAL Chi-restraints excluded: chain P residue 54 SER 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 212 GLU Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain Q residue 235 GLN 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 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 U residue 18 ASP Chi-restraints excluded: chain U residue 55 LEU 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 X residue 78 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 200 optimal weight: 0.8980 chunk 537 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 350 optimal weight: 9.9990 chunk 147 optimal weight: 0.7980 chunk 597 optimal weight: 8.9990 chunk 496 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 197 optimal weight: 0.2980 chunk 313 optimal weight: 5.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- 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 G 64 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 T 183 ASN U 64 ASN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 49774 Z= 0.222 Angle : 0.543 7.187 67220 Z= 0.302 Chirality : 0.044 0.155 7522 Planarity : 0.005 0.063 8666 Dihedral : 5.089 34.411 6900 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.18 % Allowed : 12.56 % Favored : 85.26 % 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: 1.74 (0.10), residues: 6224 helix: 2.21 (0.10), residues: 2382 sheet: 1.18 (0.12), residues: 1580 loop : 0.06 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Z 55 HIS 0.006 0.001 HIS T 175 PHE 0.022 0.002 PHE I 36 TYR 0.016 0.002 TYR b 124 ARG 0.003 0.000 ARG G 224 *********************** 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 843 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 729 time to evaluate : 4.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8689 (mtmt) cc_final: 0.8439 (pptt) REVERT: C 52 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7750 (tt) REVERT: C 209 GLU cc_start: 0.7895 (pm20) cc_final: 0.7640 (pm20) REVERT: C 230 GLN cc_start: 0.7808 (tt0) cc_final: 0.7306 (mt0) REVERT: C 234 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6992 (mt-10) REVERT: C 243 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6986 (mm-30) REVERT: D 54 GLN cc_start: 0.8740 (tt0) cc_final: 0.8518 (tp40) REVERT: D 71 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8919 (ptp) REVERT: D 99 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: D 226 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7254 (mm-30) REVERT: E 65 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7530 (mt-10) REVERT: E 208 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7117 (mm-30) REVERT: F 26 MET cc_start: 0.8694 (mmm) cc_final: 0.8333 (mmm) REVERT: F 206 THR cc_start: 0.8495 (m) cc_final: 0.8233 (p) REVERT: G 18 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7607 (m-30) REVERT: G 211 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7284 (mt-10) REVERT: H 89 ARG cc_start: 0.8150 (ttp-110) cc_final: 0.7931 (ttp-110) REVERT: I 9 LYS cc_start: 0.8671 (ptmt) cc_final: 0.8464 (ptmm) REVERT: I 53 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8084 (m-30) REVERT: I 180 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8198 (ptpp) REVERT: J 31 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8580 (mt0) REVERT: K 118 MET cc_start: 0.9093 (ttm) cc_final: 0.8712 (mtp) REVERT: L 56 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8921 (mt-10) REVERT: N 110 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.8647 (mpp) REVERT: N 155 GLU cc_start: 0.7617 (tp30) cc_final: 0.7247 (mm-30) REVERT: N 198 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7734 (mm-30) REVERT: O 1 MET cc_start: 0.4829 (ttm) cc_final: 0.4182 (mmt) REVERT: P 70 LYS cc_start: 0.8688 (mtmt) cc_final: 0.8439 (pptt) REVERT: Q 52 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7753 (tt) REVERT: Q 209 GLU cc_start: 0.7899 (pm20) cc_final: 0.7633 (pm20) REVERT: Q 230 GLN cc_start: 0.7800 (tt0) cc_final: 0.7287 (mt0) REVERT: Q 234 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6981 (mt-10) REVERT: R 54 GLN cc_start: 0.8740 (tt0) cc_final: 0.8519 (tp40) REVERT: R 71 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8910 (ptp) REVERT: R 99 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6799 (mp0) REVERT: S 65 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7561 (mt-10) REVERT: T 26 MET cc_start: 0.8694 (mmm) cc_final: 0.8340 (mmm) REVERT: T 206 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.8202 (p) REVERT: U 18 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7596 (m-30) REVERT: U 211 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7298 (mt-10) REVERT: V 89 ARG cc_start: 0.8146 (ttp-110) cc_final: 0.7920 (ttp-110) REVERT: W 53 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: W 180 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8191 (ptpp) REVERT: X 4 MET cc_start: 0.8918 (mmt) cc_final: 0.8343 (mmt) REVERT: Y 118 MET cc_start: 0.9077 (ttm) cc_final: 0.8671 (mtp) REVERT: Z 56 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8919 (mt-10) REVERT: b 198 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7696 (mm-30) outliers start: 114 outliers final: 48 residues processed: 801 average time/residue: 1.5756 time to fit residues: 1523.0630 Evaluate side-chains 784 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 714 time to evaluate : 4.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 193 GLN 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 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 208 GLU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 167 SER 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 198 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 180 LYS Chi-restraints excluded: chain I residue 213 THR 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 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 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 177 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 184 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 180 LYS Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 77 LYS Chi-restraints excluded: chain Y residue 86 ARG 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: 7.9990 chunk 67 optimal weight: 9.9990 chunk 340 optimal weight: 6.9990 chunk 436 optimal weight: 8.9990 chunk 338 optimal weight: 10.0000 chunk 503 optimal weight: 1.9990 chunk 333 optimal weight: 0.0030 chunk 595 optimal weight: 20.0000 chunk 372 optimal weight: 2.9990 chunk 363 optimal weight: 20.0000 chunk 275 optimal weight: 2.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- 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 G 64 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 T 183 ASN U 64 ASN ** 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: 0.8946 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 49774 Z= 0.255 Angle : 0.562 7.366 67220 Z= 0.311 Chirality : 0.044 0.160 7522 Planarity : 0.005 0.064 8666 Dihedral : 5.090 34.227 6900 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.95 % Allowed : 13.15 % Favored : 84.90 % 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: 1.76 (0.10), residues: 6224 helix: 2.22 (0.10), residues: 2380 sheet: 1.18 (0.12), residues: 1564 loop : 0.08 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 100 HIS 0.006 0.001 HIS Y 132 PHE 0.022 0.002 PHE I 36 TYR 0.017 0.002 TYR b 124 ARG 0.004 0.000 ARG U 170 *********************** 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 815 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 713 time to evaluate : 4.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8435 (pptt) REVERT: C 52 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7739 (tt) REVERT: C 209 GLU cc_start: 0.7894 (pm20) cc_final: 0.7644 (pm20) REVERT: C 230 GLN cc_start: 0.7812 (tt0) cc_final: 0.7314 (mt0) REVERT: C 234 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6986 (mt-10) REVERT: C 235 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7374 (tp40) REVERT: C 243 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6985 (mm-30) REVERT: D 54 GLN cc_start: 0.8739 (tt0) cc_final: 0.8515 (tp40) REVERT: D 71 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8915 (ptp) REVERT: D 99 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: D 163 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.8005 (ptp90) REVERT: E 20 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7865 (mtp180) REVERT: E 65 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: E 208 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7123 (mm-30) REVERT: F 26 MET cc_start: 0.8710 (mmm) cc_final: 0.8332 (mmm) REVERT: F 206 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8228 (p) REVERT: G 18 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7664 (m-30) REVERT: G 211 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7278 (mt-10) REVERT: H 89 ARG cc_start: 0.8149 (ttp-110) cc_final: 0.7932 (ttp-110) REVERT: I 9 LYS cc_start: 0.8701 (ptmt) cc_final: 0.8494 (ptmm) REVERT: I 53 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8089 (m-30) REVERT: I 180 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8186 (ptpp) REVERT: J 4 MET cc_start: 0.8912 (mmt) cc_final: 0.8320 (mmt) REVERT: J 31 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8560 (mt0) REVERT: L 56 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8918 (mt-10) REVERT: N 155 GLU cc_start: 0.7605 (tp30) cc_final: 0.7247 (mm-30) REVERT: O 1 MET cc_start: 0.4858 (ttm) cc_final: 0.4220 (mmt) REVERT: P 70 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8434 (pptt) REVERT: Q 52 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7738 (tt) REVERT: Q 209 GLU cc_start: 0.7898 (pm20) cc_final: 0.7639 (pm20) REVERT: Q 230 GLN cc_start: 0.7806 (tt0) cc_final: 0.7307 (mt0) REVERT: Q 234 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6977 (mt-10) REVERT: Q 235 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7374 (tp40) REVERT: Q 243 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6991 (mm-30) REVERT: R 54 GLN cc_start: 0.8741 (tt0) cc_final: 0.8518 (tp40) REVERT: R 71 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8907 (ptp) REVERT: R 99 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: R 163 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7963 (ptp90) REVERT: S 65 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7539 (mt-10) REVERT: T 26 MET cc_start: 0.8690 (mmm) cc_final: 0.8324 (mmm) REVERT: T 206 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8218 (p) REVERT: U 18 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: U 211 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7293 (mt-10) REVERT: V 89 ARG cc_start: 0.8147 (ttp-110) cc_final: 0.7920 (ttp-110) REVERT: W 53 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8060 (m-30) REVERT: W 180 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8182 (ptpp) REVERT: X 4 MET cc_start: 0.8912 (mmt) cc_final: 0.8318 (mmt) REVERT: Z 56 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8914 (mt-10) REVERT: b 198 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7695 (mm-30) outliers start: 102 outliers final: 53 residues processed: 781 average time/residue: 1.6609 time to fit residues: 1563.4964 Evaluate side-chains 786 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 707 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 193 GLN 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 212 GLU Chi-restraints excluded: chain C residue 235 GLN 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 20 ARG 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 167 SER 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 180 LYS Chi-restraints excluded: chain I residue 213 THR 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 K residue 86 ARG 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 169 VAL Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain O residue 193 GLN Chi-restraints excluded: chain O residue 240 VAL 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 212 GLU Chi-restraints excluded: chain Q residue 235 GLN 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 177 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 184 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 180 LYS Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 77 LYS Chi-restraints excluded: chain Y residue 86 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 368 optimal weight: 7.9990 chunk 237 optimal weight: 0.7980 chunk 355 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 378 optimal weight: 5.9990 chunk 405 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 468 optimal weight: 0.6980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 203 GLN G 64 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 U 64 ASN ** 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: 0.8928 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 49774 Z= 0.203 Angle : 0.530 7.368 67220 Z= 0.294 Chirality : 0.043 0.156 7522 Planarity : 0.004 0.057 8666 Dihedral : 4.926 32.450 6900 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.93 % Allowed : 13.48 % Favored : 84.59 % 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: 1.86 (0.10), residues: 6224 helix: 2.33 (0.10), residues: 2384 sheet: 1.21 (0.12), residues: 1562 loop : 0.13 (0.13), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 55 HIS 0.010 0.001 HIS K 132 PHE 0.021 0.002 PHE I 36 TYR 0.015 0.001 TYR b 124 ARG 0.004 0.000 ARG U 170 *********************** 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 835 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 734 time to evaluate : 4.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8670 (mtmt) cc_final: 0.8398 (pptt) REVERT: C 52 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7760 (tt) REVERT: C 209 GLU cc_start: 0.7910 (pm20) cc_final: 0.7669 (pm20) REVERT: C 230 GLN cc_start: 0.7815 (tt0) cc_final: 0.7322 (mt0) REVERT: C 234 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6997 (mt-10) REVERT: C 235 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7419 (tp40) REVERT: C 243 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6978 (mm-30) REVERT: D 54 GLN cc_start: 0.8711 (tt0) cc_final: 0.8496 (tp40) REVERT: D 71 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8912 (ptp) REVERT: D 163 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7950 (ptp-170) REVERT: D 226 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7239 (mm-30) REVERT: E 65 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7503 (mt-10) REVERT: E 208 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7112 (mm-30) REVERT: F 26 MET cc_start: 0.8701 (mmm) cc_final: 0.8336 (mmm) REVERT: F 206 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8223 (p) REVERT: G 18 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7615 (m-30) REVERT: G 211 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7222 (mt-10) REVERT: H 89 ARG cc_start: 0.8145 (ttp-110) cc_final: 0.7923 (ttp-110) REVERT: I 53 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8068 (m-30) REVERT: I 180 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8169 (ptpp) REVERT: J 4 MET cc_start: 0.8848 (mmt) cc_final: 0.8221 (mmt) REVERT: J 31 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8546 (mt0) REVERT: K 118 MET cc_start: 0.9049 (ttm) cc_final: 0.8651 (mtp) REVERT: L 56 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8888 (mt-10) REVERT: N 198 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7727 (mm-30) REVERT: O 1 MET cc_start: 0.4860 (ttm) cc_final: 0.4232 (mmt) REVERT: O 188 ASP cc_start: 0.4737 (OUTLIER) cc_final: 0.4480 (m-30) REVERT: P 70 LYS cc_start: 0.8671 (mtmt) cc_final: 0.8398 (pptt) REVERT: Q 52 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7762 (tt) REVERT: Q 209 GLU cc_start: 0.7916 (pm20) cc_final: 0.7668 (pm20) REVERT: Q 230 GLN cc_start: 0.7807 (tt0) cc_final: 0.7318 (mt0) REVERT: Q 234 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6997 (mt-10) REVERT: Q 235 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7430 (tp40) REVERT: Q 243 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6983 (mm-30) REVERT: R 54 GLN cc_start: 0.8691 (tt0) cc_final: 0.8475 (tp40) REVERT: R 71 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8905 (ptp) REVERT: R 163 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7962 (ptp-170) REVERT: S 65 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7535 (mt-10) REVERT: T 26 MET cc_start: 0.8719 (mmm) cc_final: 0.8360 (mmm) REVERT: T 206 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8208 (p) REVERT: U 18 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7649 (m-30) REVERT: U 211 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7286 (mt-10) REVERT: V 89 ARG cc_start: 0.8141 (ttp-110) cc_final: 0.7911 (ttp-110) REVERT: W 53 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: W 180 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8149 (ptpp) REVERT: X 4 MET cc_start: 0.8844 (mmt) cc_final: 0.8249 (mmt) REVERT: Y 118 MET cc_start: 0.9031 (ttm) cc_final: 0.8631 (mtp) REVERT: Z 56 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8885 (mt-10) REVERT: b 110 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8571 (mtm) REVERT: b 198 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7681 (mm-30) outliers start: 101 outliers final: 51 residues processed: 793 average time/residue: 1.6787 time to fit residues: 1619.7779 Evaluate side-chains 795 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 718 time to evaluate : 4.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 193 GLN 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 C residue 235 GLN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 71 MET 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 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 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 198 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 180 LYS Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 31 GLN Chi-restraints excluded: chain K residue 86 ARG 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 169 VAL Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain O residue 188 ASP 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 Q residue 235 GLN Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 71 MET 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 78 THR Chi-restraints excluded: chain T residue 206 THR 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 39 ASP Chi-restraints excluded: chain V residue 198 THR Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 180 LYS Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain Y residue 86 ARG 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 110 MET 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: 9.9990 chunk 520 optimal weight: 7.9990 chunk 555 optimal weight: 5.9990 chunk 334 optimal weight: 9.9990 chunk 241 optimal weight: 9.9990 chunk 435 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 501 optimal weight: 0.9980 chunk 524 optimal weight: 4.9990 chunk 553 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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 16 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 ASN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 ASN J 162 HIS P 189 HIS Q 155 ASN R 215 GLN S 182 GLN T 16 GLN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 49774 Z= 0.399 Angle : 0.647 8.369 67220 Z= 0.356 Chirality : 0.048 0.163 7522 Planarity : 0.006 0.069 8666 Dihedral : 5.319 36.356 6900 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.88 % Allowed : 13.74 % Favored : 84.38 % 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: 1.64 (0.10), residues: 6224 helix: 2.07 (0.10), residues: 2370 sheet: 1.14 (0.12), residues: 1586 loop : 0.07 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 100 HIS 0.017 0.001 HIS Y 132 PHE 0.024 0.003 PHE I 36 TYR 0.021 0.002 TYR W 90 ARG 0.006 0.001 ARG U 170 *********************** 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 802 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 704 time to evaluate : 4.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8398 (pptt) REVERT: C 52 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7780 (tt) REVERT: C 209 GLU cc_start: 0.7911 (pm20) cc_final: 0.7662 (pm20) REVERT: C 230 GLN cc_start: 0.7805 (tt0) cc_final: 0.7297 (mt0) REVERT: C 234 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6983 (mt-10) REVERT: C 235 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7429 (tp40) REVERT: C 243 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6980 (mm-30) REVERT: D 54 GLN cc_start: 0.8774 (tt0) cc_final: 0.8532 (tp40) REVERT: D 71 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8957 (ptp) REVERT: D 99 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: D 163 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.8023 (ptp90) REVERT: E 20 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7899 (mtp180) REVERT: E 65 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: E 208 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7149 (mm-30) REVERT: E 236 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.7045 (mm-30) REVERT: F 26 MET cc_start: 0.8675 (mmm) cc_final: 0.8279 (mmm) REVERT: F 180 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7708 (tpt) REVERT: F 206 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8224 (p) REVERT: G 18 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7707 (m-30) REVERT: G 170 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7637 (ptp-170) REVERT: G 211 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7259 (mt-10) REVERT: H 89 ARG cc_start: 0.8160 (ttp-110) cc_final: 0.7944 (ttp-110) REVERT: I 53 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8107 (m-30) REVERT: I 180 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8223 (ptpp) REVERT: J 4 MET cc_start: 0.8908 (mmt) cc_final: 0.8293 (mmt) REVERT: L 56 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8979 (mt-10) REVERT: N 155 GLU cc_start: 0.7659 (tp30) cc_final: 0.7272 (mm-30) REVERT: N 198 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7737 (mm-30) REVERT: O 1 MET cc_start: 0.4901 (ttm) cc_final: 0.4229 (mmt) REVERT: P 70 LYS cc_start: 0.8712 (mtmt) cc_final: 0.8404 (pptt) REVERT: Q 52 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7779 (tt) REVERT: Q 209 GLU cc_start: 0.7918 (pm20) cc_final: 0.7662 (pm20) REVERT: Q 230 GLN cc_start: 0.7796 (tt0) cc_final: 0.7300 (mt0) REVERT: Q 234 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6974 (mt-10) REVERT: Q 235 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7425 (tp40) REVERT: Q 243 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6985 (mm-30) REVERT: R 54 GLN cc_start: 0.8762 (tt0) cc_final: 0.8521 (tp40) REVERT: R 71 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8950 (ptp) REVERT: R 99 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: R 163 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.8020 (ptp90) REVERT: S 65 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: S 236 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.7034 (mm-30) REVERT: T 26 MET cc_start: 0.8680 (mmm) cc_final: 0.8289 (mmm) REVERT: T 206 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8246 (p) REVERT: U 18 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7730 (m-30) REVERT: U 211 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7318 (mt-10) REVERT: V 89 ARG cc_start: 0.8158 (ttp-110) cc_final: 0.7933 (ttp-110) REVERT: W 53 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8117 (m-30) REVERT: W 180 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8220 (ptpp) REVERT: X 4 MET cc_start: 0.8910 (mmt) cc_final: 0.8310 (mmt) REVERT: Z 56 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.8989 (mt-10) REVERT: b 110 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8575 (mtm) REVERT: b 198 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7707 (mm-30) outliers start: 98 outliers final: 49 residues processed: 767 average time/residue: 1.6312 time to fit residues: 1505.3537 Evaluate side-chains 771 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 691 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 193 GLN 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 212 GLU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 235 GLN 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 20 ARG 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 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 180 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 170 ARG 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 180 LYS Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 86 ARG 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 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 Q residue 235 GLN 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 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 39 ASP Chi-restraints excluded: chain V residue 198 THR Chi-restraints excluded: chain W residue 53 ASP 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 Y residue 86 ARG 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 110 MET 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: 2.9990 chunk 586 optimal weight: 6.9990 chunk 358 optimal weight: 7.9990 chunk 278 optimal weight: 8.9990 chunk 408 optimal weight: 5.9990 chunk 615 optimal weight: 5.9990 chunk 566 optimal weight: 4.9990 chunk 490 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 378 optimal weight: 1.9990 chunk 300 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 ASN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 ASN J 162 HIS P 189 HIS Q 155 ASN R 205 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 49774 Z= 0.338 Angle : 0.616 8.221 67220 Z= 0.340 Chirality : 0.047 0.185 7522 Planarity : 0.005 0.069 8666 Dihedral : 5.263 36.012 6900 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.72 % Allowed : 13.88 % Favored : 84.40 % 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: 1.64 (0.10), residues: 6224 helix: 2.08 (0.10), residues: 2370 sheet: 1.15 (0.12), residues: 1590 loop : 0.05 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 100 HIS 0.015 0.001 HIS Y 132 PHE 0.023 0.002 PHE I 36 TYR 0.018 0.002 TYR b 124 ARG 0.006 0.001 ARG U 170 ********************** 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 791 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 701 time to evaluate : 4.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8446 (pptt) REVERT: C 52 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7836 (tt) REVERT: C 209 GLU cc_start: 0.7909 (pm20) cc_final: 0.7659 (pm20) REVERT: C 230 GLN cc_start: 0.7782 (tt0) cc_final: 0.7279 (mt0) REVERT: C 234 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6978 (mt-10) REVERT: C 235 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7420 (tp40) REVERT: C 243 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6993 (mm-30) REVERT: D 54 GLN cc_start: 0.8770 (tt0) cc_final: 0.8528 (tp40) REVERT: D 71 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8954 (ptp) REVERT: D 99 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: D 163 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.8018 (ptp90) REVERT: E 20 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7885 (mtp180) REVERT: E 65 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7539 (mt-10) REVERT: E 208 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7146 (mm-30) REVERT: E 236 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.7028 (mm-30) REVERT: F 26 MET cc_start: 0.8686 (mmm) cc_final: 0.8299 (mmm) REVERT: F 206 THR cc_start: 0.8498 (OUTLIER) cc_final: 0.8236 (p) REVERT: G 18 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: G 211 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7264 (mt-10) REVERT: H 89 ARG cc_start: 0.8169 (ttp-110) cc_final: 0.7954 (ttp-110) REVERT: I 53 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8103 (m-30) REVERT: I 180 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8217 (ptpp) REVERT: J 4 MET cc_start: 0.8906 (mmt) cc_final: 0.8291 (mmt) REVERT: L 56 GLU cc_start: 0.9270 (OUTLIER) cc_final: 0.8978 (mt-10) REVERT: N 155 GLU cc_start: 0.7645 (tp30) cc_final: 0.7262 (mm-30) REVERT: N 198 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7737 (mm-30) REVERT: O 1 MET cc_start: 0.4842 (ttm) cc_final: 0.4167 (mmt) REVERT: P 70 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8445 (pptt) REVERT: Q 52 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7810 (tt) REVERT: Q 209 GLU cc_start: 0.7917 (pm20) cc_final: 0.7662 (pm20) REVERT: Q 230 GLN cc_start: 0.7773 (tt0) cc_final: 0.7272 (mt0) REVERT: Q 234 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6976 (mt-10) REVERT: Q 235 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7414 (tp40) REVERT: Q 243 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6985 (mm-30) REVERT: R 54 GLN cc_start: 0.8758 (tt0) cc_final: 0.8519 (tp40) REVERT: R 71 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8948 (ptp) REVERT: R 99 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: R 163 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.8014 (ptp90) REVERT: S 20 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7877 (mtp180) REVERT: S 65 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: T 26 MET cc_start: 0.8700 (mmm) cc_final: 0.8319 (mmm) REVERT: U 18 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7734 (m-30) REVERT: U 211 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7320 (mt-10) REVERT: V 89 ARG cc_start: 0.8166 (ttp-110) cc_final: 0.7943 (ttp-110) REVERT: W 53 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8088 (m-30) REVERT: W 180 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8215 (ptpp) REVERT: X 4 MET cc_start: 0.8907 (mmt) cc_final: 0.8305 (mmt) REVERT: Z 56 GLU cc_start: 0.9268 (OUTLIER) cc_final: 0.8986 (mt-10) REVERT: b 110 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8597 (mtm) REVERT: b 198 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7688 (mm-30) outliers start: 90 outliers final: 49 residues processed: 757 average time/residue: 1.6088 time to fit residues: 1461.5782 Evaluate side-chains 778 residues out of total 5224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 701 time to evaluate : 4.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 193 GLN 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 212 GLU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 235 GLN 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 20 ARG 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 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 206 THR 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 180 LYS Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 86 ARG 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 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 Q residue 235 GLN 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 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 T residue 78 THR Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 55 LEU 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 180 LYS Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 77 LYS Chi-restraints excluded: chain Y residue 86 ARG 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 110 MET 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: 5.9990 chunk 522 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 452 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 491 optimal weight: 0.9990 chunk 205 optimal weight: 20.0000 chunk 504 optimal weight: 4.9990 chunk 62 optimal weight: 0.0670 chunk 90 optimal weight: 0.3980 overall best weight: 1.8924 ------------------------------------------------------------------------------- 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 ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 ASN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 ASN J 162 HIS P 189 HIS Q 155 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.130080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102941 restraints weight = 50924.227| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.29 r_work: 0.3121 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 49774 Z= 0.195 Angle : 0.535 8.424 67220 Z= 0.296 Chirality : 0.043 0.173 7522 Planarity : 0.004 0.059 8666 Dihedral : 4.930 32.447 6900 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.55 % Allowed : 14.09 % Favored : 84.36 % 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: 1.84 (0.10), residues: 6224 helix: 2.31 (0.10), residues: 2384 sheet: 1.21 (0.13), residues: 1562 loop : 0.12 (0.13), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Z 55 HIS 0.009 0.001 HIS Y 132 PHE 0.021 0.001 PHE W 36 TYR 0.016 0.001 TYR b 124 ARG 0.004 0.000 ARG O 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21536.66 seconds wall clock time: 368 minutes 48.01 seconds (22128.01 seconds total)