Starting phenix.real_space_refine on Tue Sep 24 03:48:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz6_29604/09_2024/8fz6_29604.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz6_29604/09_2024/8fz6_29604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz6_29604/09_2024/8fz6_29604.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz6_29604/09_2024/8fz6_29604.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz6_29604/09_2024/8fz6_29604.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz6_29604/09_2024/8fz6_29604.cif" } resolution = 2.54 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= 0.008 sd= 0.118 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 31480 2.51 5 N 8526 2.21 5 O 9470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 49780 Number of models: 1 Model: "" Number of chains: 30 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: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1971 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 5, 'TRANS': 244} 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: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1584 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} 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: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1971 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 5, 'TRANS': 244} 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: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1584 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} 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} Chain: "c" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 470 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 14, 'TRANS': 50} Chain: "d" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 470 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 14, 'TRANS': 50} Time building chain proxies: 22.87, per 1000 atoms: 0.46 Number of scatterers: 49780 At special positions: 0 Unit cell: (139.104, 144.072, 180.504, 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 9470 8.00 N 8526 7.00 C 31480 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: 9.37 Conformation dependent library (CDL) restraints added in 4.9 seconds 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11772 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 73 sheets defined 39.5% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.59 Creating SS restraints... Processing helix chain 'A' and resid 22 through 34 removed outlier: 3.595A pdb=" N GLU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 33 " --> pdb=" O PHE A 29 " (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 Processing helix chain 'A' and resid 171 through 185 Processing helix chain 'A' and resid 190 through 207 Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.830A 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: 3.895A 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 18 through 30 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 250 Processing helix chain 'D' and resid 16 through 28 Processing helix chain 'D' and resid 56 through 60 removed outlier: 4.069A pdb=" N ARG D 60 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 99 Processing helix chain 'D' and resid 103 through 120 Processing helix chain 'D' and resid 164 through 176 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: 3.704A 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: 4.395A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.974A 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 removed outlier: 3.501A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 206 Processing helix chain 'E' and resid 230 through 240 removed outlier: 4.511A pdb=" N ASP E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 32 removed outlier: 3.603A pdb=" N GLU F 23 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 3.794A 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: 3.742A 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: 4.391A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N SER F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLU F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 4.177A 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 170 through 179 removed outlier: 3.763A pdb=" N LYS G 179 " --> pdb=" O THR G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 202 removed outlier: 3.853A 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: 3.985A pdb=" N SER H 133 " --> pdb=" O SER H 130 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR H 134 " --> pdb=" O GLY H 131 " (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 removed outlier: 3.547A pdb=" N ILE H 194 " --> pdb=" O GLY H 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.541A pdb=" N TYR I 90 " --> pdb=" O MET I 86 " (cutoff:3.500A) 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 79 Processing helix chain 'J' and resid 83 through 98 removed outlier: 3.972A pdb=" N LYS J 98 " --> pdb=" O LEU J 94 " (cutoff:3.500A) 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: 3.979A pdb=" N ARG K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 147 removed outlier: 4.239A pdb=" N LEU K 138 " --> pdb=" O TYR K 134 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 4.923A 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: 3.795A pdb=" N GLN L 89 " --> pdb=" O ASN L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 143 Processing helix chain 'L' and resid 148 through 167 Processing helix chain 'L' and resid 192 through 201 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 Processing helix chain 'N' and resid 57 through 78 removed outlier: 3.593A 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 34 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 Processing helix chain 'O' and resid 171 through 185 removed outlier: 3.736A 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: 4.258A 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: 3.875A pdb=" N SER P 198 " --> pdb=" O THR P 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 232 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 207 through 209 No H-bonds generated for 'chain 'Q' and resid 207 through 209' 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: 4.026A pdb=" N ARG R 60 " --> pdb=" O ARG R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 99 Processing helix chain 'R' and resid 103 through 119 Processing helix chain 'R' and resid 164 through 176 Processing helix chain 'R' and resid 177 through 181 Processing helix chain 'R' and resid 183 through 199 removed outlier: 3.715A pdb=" N GLU R 197 " --> pdb=" O LYS R 193 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 244 Processing helix chain 'S' and resid 21 through 32 removed outlier: 3.731A 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: 4.337A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 4.023A 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 31 removed outlier: 3.569A pdb=" N GLU T 23 " --> pdb=" O ILE T 19 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 99 Processing helix chain 'T' and resid 104 through 118 removed outlier: 3.768A pdb=" N ILE T 118 " --> pdb=" O SER T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 119 through 122 removed outlier: 3.843A pdb=" N ARG T 122 " --> pdb=" O PRO T 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 119 through 122' Processing helix chain 'T' and resid 164 through 180 removed outlier: 4.407A pdb=" N ALA T 168 " --> pdb=" O ARG T 164 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER T 177 " --> pdb=" O GLU T 173 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLU T 178 " --> pdb=" O ARG T 174 " (cutoff:3.500A) removed outlier: 4.211A 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 33 removed outlier: 3.514A pdb=" N GLU U 25 " --> pdb=" O VAL U 21 " (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 170 through 179 removed outlier: 3.724A pdb=" N LYS U 179 " --> pdb=" O THR U 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 180 through 185 removed outlier: 5.560A pdb=" N LYS U 183 " --> pdb=" O LEU U 180 " (cutoff:3.500A) Processing helix chain 'U' and resid 186 through 202 removed outlier: 3.839A 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 removed outlier: 3.563A pdb=" N LYS U 245 " --> pdb=" O LYS U 241 " (cutoff:3.500A) 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: 3.954A 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 49 through 71 Processing helix chain 'W' and resid 75 through 90 removed outlier: 3.508A pdb=" N TYR W 90 " --> pdb=" O MET W 86 " (cutoff:3.500A) 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 79 Processing helix chain 'X' and resid 83 through 98 removed outlier: 3.978A pdb=" N LYS X 98 " --> pdb=" O LEU X 94 " (cutoff:3.500A) 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: 3.834A pdb=" N ARG Y 93 " --> pdb=" O ALA Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 147 removed outlier: 5.089A pdb=" N SER Y 141 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 4.862A 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: 3.830A pdb=" N GLN Z 89 " --> pdb=" O ASN Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 143 removed outlier: 3.531A 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 201 Processing helix chain 'a' and resid 85 through 108 Processing helix chain 'a' and resid 112 through 127 removed outlier: 3.861A pdb=" N ARG a 127 " --> pdb=" O ILE a 123 " (cutoff:3.500A) 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 Processing helix chain 'b' and resid 57 through 78 removed outlier: 3.643A 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 helix chain 'c' and resid 194 through 199 removed outlier: 3.502A pdb=" N LEU c 198 " --> pdb=" O GLY c 194 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP c 199 " --> pdb=" O GLY c 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 194 through 199' Processing helix chain 'c' and resid 211 through 215 Processing helix chain 'd' and resid 194 through 199 removed outlier: 3.802A pdb=" N ASP d 199 " --> pdb=" O GLY d 195 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 169 removed outlier: 5.761A 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 Processing sheet with id=AA6, first strand: chain 'C' and resid 65 through 67 removed outlier: 4.234A pdb=" N LEU C 147 " --> pdb=" O TRP C 159 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLY C 158 " --> pdb=" O ASP D 55 " (cutoff:3.500A) 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: 4.635A pdb=" N GLN E 221 " --> pdb=" O ASN E 225 " (cutoff:3.500A) removed outlier: 4.915A 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: 6.395A 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 65 removed outlier: 3.506A pdb=" N LEU F 132 " --> pdb=" O THR F 147 " (cutoff:3.500A) removed outlier: 3.985A 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 removed outlier: 3.656A pdb=" N GLY G 45 " --> pdb=" O CYS G 42 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 67 through 69 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: 6.847A pdb=" N THR H 20 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR H 25 " --> pdb=" O THR H 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 34 through 36 removed outlier: 4.194A pdb=" N VAL H 111 " --> pdb=" O GLN H 123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 124 through 127 removed outlier: 6.553A pdb=" N ILE I 173 " --> pdb=" O TYR I 189 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU I 175 " --> pdb=" O ARG I 187 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG I 187 " --> pdb=" O LEU I 175 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL I 177 " --> pdb=" O PHE I 185 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N PHE I 185 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N SER I 179 " --> pdb=" O LEU I 183 " (cutoff:3.500A) removed outlier: 5.160A 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: 6.155A pdb=" N GLU I 22 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.371A 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: 3.575A pdb=" N THR I 213 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL J 185 " --> pdb=" O LEU J 200 " (cutoff:3.500A) removed outlier: 5.638A 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: 6.896A pdb=" N PHE J 28 " --> pdb=" O VAL J 35 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 42 through 46 removed outlier: 5.312A pdb=" N LEU J 49 " --> pdb=" O MET J 45 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA J 54 " --> pdb=" O GLU J 106 " (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: 6.651A pdb=" N ALA K 21 " --> pdb=" O MET K 28 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 35 through 39 removed outlier: 6.403A 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 129 removed outlier: 6.758A 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: 6.170A pdb=" N ARG L 180 " --> pdb=" O TRP L 184 " (cutoff:3.500A) removed outlier: 4.796A 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: 6.697A 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 36 removed outlier: 4.424A pdb=" N MET L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 163 through 167 removed outlier: 5.635A pdb=" N THR M 39 " --> pdb=" O ASP M 54 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP M 54 " --> pdb=" O THR M 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.409A pdb=" N GLU M 59 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 71 through 73 removed outlier: 3.803A pdb=" N ASN M 136 " --> pdb=" O PHE M 152 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL M 149 " --> pdb=" O ASP M 161 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 33 through 36 removed outlier: 5.719A pdb=" N ALA N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR N 30 " --> pdb=" O ALA N 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 33 through 36 removed outlier: 5.719A pdb=" N ALA N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR N 30 " --> pdb=" O ALA N 34 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 136 through 138 removed outlier: 6.037A pdb=" N PHE N 187 " --> pdb=" O PRO N 202 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 165 through 169 removed outlier: 5.854A pdb=" N THR O 38 " --> pdb=" O GLN O 53 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN O 53 " --> pdb=" O THR O 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 69 through 71 Processing sheet with id=AE3, first strand: chain 'P' and resid 160 through 163 Processing sheet with id=AE4, first strand: chain 'P' and resid 66 through 67 Processing sheet with id=AE5, first strand: chain 'Q' and resid 161 through 164 Processing sheet with id=AE6, first strand: chain 'Q' and resid 65 through 69 removed outlier: 6.521A pdb=" N MET Q 72 " --> pdb=" O LEU Q 68 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 158 through 161 Processing sheet with id=AE8, first strand: chain 'R' and resid 62 through 64 Processing sheet with id=AE9, first strand: chain 'S' and resid 167 through 170 removed outlier: 4.829A pdb=" N GLN S 221 " --> pdb=" O ASN S 225 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ASN S 225 " --> pdb=" O GLN S 221 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 67 through 71 removed outlier: 6.492A pdb=" N ILE S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 158 through 161 Processing sheet with id=AF3, first strand: chain 'T' and resid 63 through 65 Processing sheet with id=AF4, first strand: chain 'U' and resid 163 through 166 Processing sheet with id=AF5, first strand: chain 'U' and resid 67 through 69 Processing sheet with id=AF6, first strand: chain 'V' and resid 125 through 128 Processing sheet with id=AF7, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.548A pdb=" N THR V 22 " --> pdb=" O ILE V 26 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE V 26 " --> pdb=" O THR V 22 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 34 through 36 Processing sheet with id=AF9, first strand: chain 'W' and resid 124 through 127 removed outlier: 6.941A pdb=" N ILE W 173 " --> pdb=" O PRO W 188 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 20 through 22 removed outlier: 6.174A pdb=" N GLU W 22 " --> pdb=" O VAL W 26 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL W 26 " --> pdb=" O GLU W 22 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.355A pdb=" N ILE W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.355A 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: 6.493A pdb=" N THR X 199 " --> pdb=" O LEU W 212 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU W 214 " --> pdb=" O THR X 197 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR X 197 " --> pdb=" O GLU W 214 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL W 216 " --> pdb=" O ILE X 195 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE X 195 " --> pdb=" O VAL W 216 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL X 185 " --> pdb=" O LEU X 200 " (cutoff:3.500A) removed outlier: 5.591A 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: 6.188A pdb=" N ILE X 30 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 5.319A 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: 3.871A pdb=" N ALA X 54 " --> pdb=" O GLU X 106 " (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: 6.585A pdb=" N ALA Y 21 " --> pdb=" O MET Y 28 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 35 through 39 removed outlier: 6.452A 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 129 removed outlier: 3.544A pdb=" N SER Z 188 " --> pdb=" O LEU Z 176 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS Z 178 " --> pdb=" O ARG Z 186 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ARG Z 186 " --> pdb=" O HIS Z 178 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG Z 180 " --> pdb=" O TRP Z 184 " (cutoff:3.500A) removed outlier: 4.733A 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: 6.692A 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: 6.384A pdb=" N LEU Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N MET Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'a' and resid 163 through 167 removed outlier: 5.565A pdb=" N THR a 39 " --> pdb=" O ASP a 54 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP a 54 " --> pdb=" O THR a 39 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'a' and resid 57 through 59 removed outlier: 6.381A pdb=" N GLU a 59 " --> pdb=" O ILE a 63 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE a 63 " --> pdb=" O GLU a 59 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'a' and resid 71 through 75 removed outlier: 6.499A pdb=" N THR a 78 " --> pdb=" O LEU a 74 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN a 136 " --> pdb=" O PHE a 152 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL a 149 " --> pdb=" O ASP a 161 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'b' and resid 33 through 36 removed outlier: 5.581A pdb=" N ALA b 34 " --> pdb=" O TYR b 30 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR b 30 " --> pdb=" O ALA b 34 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'b' and resid 33 through 36 removed outlier: 5.581A pdb=" N ALA b 34 " --> pdb=" O TYR b 30 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR b 30 " --> pdb=" O ALA b 34 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'b' and resid 136 through 138 removed outlier: 3.613A pdb=" N GLY b 19 " --> pdb=" O PHE b 16 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE b 187 " --> pdb=" O PRO b 202 " (cutoff:3.500A) 2924 hydrogen bonds defined for protein. 8382 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: 18.96 Time building geometry restraints manager: 11.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16470 1.34 - 1.46: 8021 1.46 - 1.57: 25707 1.57 - 1.69: 0 1.69 - 1.81: 500 Bond restraints: 50698 Sorted by residual: bond pdb=" CA ASP O 155 " pdb=" C ASP O 155 " ideal model delta sigma weight residual 1.517 1.528 -0.011 1.02e-02 9.61e+03 1.21e+00 bond pdb=" CB VAL B 132 " pdb=" CG1 VAL B 132 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.43e-01 bond pdb=" CA PRO H 115 " pdb=" C PRO H 115 " ideal model delta sigma weight residual 1.526 1.517 0.009 1.13e-02 7.83e+03 5.76e-01 bond pdb=" CG PRO B 81 " pdb=" CD PRO B 81 " ideal model delta sigma weight residual 1.503 1.477 0.026 3.40e-02 8.65e+02 5.70e-01 bond pdb=" CA ASN K 24 " pdb=" CB ASN K 24 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.69e-02 3.50e+03 5.00e-01 ... (remaining 50693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 67279 1.28 - 2.55: 973 2.55 - 3.83: 209 3.83 - 5.11: 25 5.11 - 6.38: 4 Bond angle restraints: 68490 Sorted by residual: angle pdb=" C GLY M 218 " pdb=" N ASP M 219 " pdb=" CA ASP M 219 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 angle pdb=" C ARG c 219 " pdb=" CA ARG c 219 " pdb=" CB ARG c 219 " ideal model delta sigma weight residual 110.42 116.05 -5.63 1.99e+00 2.53e-01 8.00e+00 angle pdb=" CA SER I 38 " pdb=" C SER I 38 " pdb=" N PRO I 39 " ideal model delta sigma weight residual 117.68 119.66 -1.98 7.10e-01 1.98e+00 7.81e+00 angle pdb=" C GLN J 31 " pdb=" CA GLN J 31 " pdb=" CB GLN J 31 " ideal model delta sigma weight residual 110.42 115.84 -5.42 1.99e+00 2.53e-01 7.43e+00 angle pdb=" CA ILE Q 52 " pdb=" CB ILE Q 52 " pdb=" CG1 ILE Q 52 " ideal model delta sigma weight residual 110.40 114.48 -4.08 1.70e+00 3.46e-01 5.75e+00 ... (remaining 68485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 27105 17.83 - 35.66: 2734 35.66 - 53.50: 576 53.50 - 71.33: 144 71.33 - 89.16: 61 Dihedral angle restraints: 30620 sinusoidal: 12174 harmonic: 18446 Sorted by residual: 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 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 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 -157.56 -22.44 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PHE M 130 " pdb=" C PHE M 130 " pdb=" N PRO M 131 " pdb=" CA PRO M 131 " ideal model delta harmonic sigma weight residual -180.00 -162.12 -17.88 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 30617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 4768 0.029 - 0.058: 1753 0.058 - 0.087: 577 0.087 - 0.116: 493 0.116 - 0.144: 57 Chirality restraints: 7648 Sorted by residual: chirality pdb=" CA ILE I 12 " pdb=" N ILE I 12 " pdb=" C ILE I 12 " pdb=" CB ILE I 12 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA VAL N 11 " pdb=" N VAL N 11 " pdb=" C VAL N 11 " pdb=" CB VAL N 11 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE A 141 " pdb=" N ILE A 141 " pdb=" C ILE A 141 " pdb=" CB ILE A 141 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 7645 not shown) Planarity restraints: 8850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 150 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO B 151 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 151 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 151 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY P 80 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO P 81 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO P 81 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO P 81 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 11 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO D 12 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 12 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 12 " 0.026 5.00e-02 4.00e+02 ... (remaining 8847 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3449 2.74 - 3.28: 47032 3.28 - 3.82: 87366 3.82 - 4.36: 108855 4.36 - 4.90: 183786 Nonbonded interactions: 430488 Sorted by model distance: nonbonded pdb=" O LYS L 7 " pdb=" OH TYR L 143 " model vdw 2.199 3.040 nonbonded pdb=" O LYS Z 7 " pdb=" OH TYR Z 143 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP K 52 " pdb=" OH TYR L 88 " model vdw 2.230 3.040 nonbonded pdb=" OG1 THR S 190 " pdb=" OE1 GLU S 193 " model vdw 2.235 3.040 nonbonded pdb=" O TYR V 138 " pdb=" OG1 THR V 142 " model vdw 2.238 3.040 ... (remaining 430483 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' } ncs_group { reference = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.610 Check model and map are aligned: 0.290 Set scattering table: 0.370 Process input model: 90.210 Find NCS groups from input model: 2.860 Set up NCS constraints: 0.370 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: 0.020 Load rotamer database and sin/cos tables:10.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 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 : 0.002 0.026 50698 Z= 0.150 Angle : 0.430 6.383 68490 Z= 0.236 Chirality : 0.041 0.144 7648 Planarity : 0.004 0.048 8850 Dihedral : 15.521 89.162 18848 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.26 % Allowed : 11.58 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 1.88 (0.10), residues: 6344 helix: 2.52 (0.10), residues: 2340 sheet: 1.24 (0.13), residues: 1510 loop : 0.05 (0.12), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Z 55 HIS 0.004 0.001 HIS T 175 PHE 0.014 0.001 PHE J 69 TYR 0.012 0.001 TYR b 124 ARG 0.002 0.000 ARG V 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 954 time to evaluate : 4.525 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8228 (pttm) cc_final: 0.7865 (mmtm) REVERT: A 193 GLN cc_start: 0.8028 (mt0) cc_final: 0.7510 (mt0) REVERT: A 209 ASP cc_start: 0.7446 (m-30) cc_final: 0.6993 (m-30) REVERT: B 1 MET cc_start: 0.5955 (ttm) cc_final: 0.4675 (pp-130) REVERT: B 58 ASP cc_start: 0.8119 (t0) cc_final: 0.7782 (m-30) REVERT: B 70 LYS cc_start: 0.8707 (mtmt) cc_final: 0.8175 (tmtt) REVERT: C 82 ASP cc_start: 0.8465 (m-30) cc_final: 0.8251 (m-30) REVERT: C 243 GLU cc_start: 0.7313 (mm-30) cc_final: 0.7027 (tp30) REVERT: D 124 ARG cc_start: 0.8884 (ptp-170) cc_final: 0.8640 (ptm160) REVERT: E 9 ASP cc_start: 0.6843 (p0) cc_final: 0.6221 (t0) REVERT: E 14 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8773 (m) REVERT: E 18 GLU cc_start: 0.8324 (mp0) cc_final: 0.8121 (mp0) REVERT: E 186 HIS cc_start: 0.7984 (p90) cc_final: 0.7698 (p90) REVERT: F 51 ARG cc_start: 0.7510 (mtm-85) cc_final: 0.7268 (mtm-85) REVERT: F 203 GLN cc_start: 0.7074 (tp-100) cc_final: 0.6524 (mt0) REVERT: I 147 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8154 (mm-30) REVERT: I 180 LYS cc_start: 0.8291 (pttt) cc_final: 0.7690 (mtpp) REVERT: J 125 ASP cc_start: 0.8876 (p0) cc_final: 0.8577 (p0) REVERT: J 144 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7753 (mp0) REVERT: J 161 GLU cc_start: 0.8053 (mp0) cc_final: 0.7835 (mp0) REVERT: K 49 GLU cc_start: 0.8249 (tt0) cc_final: 0.7846 (tp30) REVERT: K 110 HIS cc_start: 0.7647 (m-70) cc_final: 0.7422 (m-70) REVERT: K 158 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7961 (mt-10) REVERT: L 89 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8373 (mp10) REVERT: L 107 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.8102 (mtt90) REVERT: L 154 ASP cc_start: 0.7827 (m-30) cc_final: 0.7609 (m-30) REVERT: L 198 LYS cc_start: 0.8583 (ttmt) cc_final: 0.8367 (tttp) REVERT: P 1 MET cc_start: 0.5510 (ttm) cc_final: 0.4431 (ptt) REVERT: P 163 MET cc_start: 0.9191 (mtm) cc_final: 0.8856 (mtm) REVERT: P 225 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7390 (mt-10) REVERT: Q 49 ARG cc_start: 0.7741 (mtp85) cc_final: 0.7451 (mtm110) REVERT: Q 149 GLN cc_start: 0.9337 (tt0) cc_final: 0.9128 (tt0) REVERT: R 55 ASP cc_start: 0.8082 (t70) cc_final: 0.7529 (t70) REVERT: R 175 ASN cc_start: 0.8254 (m110) cc_final: 0.7970 (m-40) REVERT: S 232 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7161 (mm-30) REVERT: T 51 ARG cc_start: 0.7399 (mtm-85) cc_final: 0.7117 (ptp-110) REVERT: T 54 SER cc_start: 0.8474 (t) cc_final: 0.8227 (m) REVERT: T 68 ASN cc_start: 0.9449 (m110) cc_final: 0.9219 (m-40) REVERT: T 189 LYS cc_start: 0.8413 (mttm) cc_final: 0.8209 (mttp) REVERT: U 206 LYS cc_start: 0.7767 (tppp) cc_final: 0.7371 (tmtm) REVERT: V 69 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8009 (mt-10) REVERT: V 95 MET cc_start: 0.8540 (mtp) cc_final: 0.8182 (mtt) REVERT: V 185 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8056 (mt-10) REVERT: W 91 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8366 (mm110) REVERT: W 201 ARG cc_start: 0.7150 (mmp-170) cc_final: 0.6868 (ptm160) REVERT: X 26 ARG cc_start: 0.8384 (mtp180) cc_final: 0.8131 (mtp180) REVERT: Y 179 SER cc_start: 0.9205 (p) cc_final: 0.8939 (m) REVERT: Z 117 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7204 (mt-10) REVERT: b 152 GLU cc_start: 0.7662 (tt0) cc_final: 0.7455 (tp30) REVERT: b 195 LYS cc_start: 0.8168 (pptt) cc_final: 0.7638 (ptpt) REVERT: d 197 ASP cc_start: 0.8439 (t70) cc_final: 0.8194 (t70) outliers start: 67 outliers final: 58 residues processed: 1017 average time/residue: 1.5557 time to fit residues: 1912.7070 Evaluate side-chains 772 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 713 time to evaluate : 4.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 19 GLU Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain P residue 42 ASN Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 224 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 230 SER Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain Y residue 2 GLU Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 133 VAL Chi-restraints excluded: chain a residue 227 THR Chi-restraints excluded: chain d residue 252 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 531 optimal weight: 4.9990 chunk 477 optimal weight: 0.9990 chunk 264 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 322 optimal weight: 8.9990 chunk 255 optimal weight: 7.9990 chunk 493 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 300 optimal weight: 7.9990 chunk 367 optimal weight: 3.9990 chunk 572 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 166 ASN B 207 ASN C 123 GLN C 155 ASN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN E 225 ASN I 91 GLN K 65 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 ASN K 193 ASN L 38 ASN L 70 ASN L 119 ASN N 47 ASN N 157 GLN O 33 ASN O 92 GLN Q 123 GLN Q 146 GLN Q 235 GLN S 225 ASN U 64 ASN Y 168 GLN Z 70 ASN b 104 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 50698 Z= 0.294 Angle : 0.551 7.696 68490 Z= 0.301 Chirality : 0.045 0.181 7648 Planarity : 0.005 0.052 8850 Dihedral : 5.506 72.359 7105 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.61 % Allowed : 15.08 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 1.77 (0.10), residues: 6344 helix: 2.36 (0.10), residues: 2376 sheet: 1.21 (0.13), residues: 1534 loop : 0.00 (0.12), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 55 HIS 0.006 0.001 HIS b 89 PHE 0.025 0.002 PHE P 173 TYR 0.017 0.002 TYR U 239 ARG 0.007 0.000 ARG Z 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 703 time to evaluate : 4.496 Fit side-chains REVERT: A 193 GLN cc_start: 0.8070 (mt0) cc_final: 0.7526 (mt0) REVERT: A 209 ASP cc_start: 0.7399 (m-30) cc_final: 0.6945 (m-30) REVERT: B 1 MET cc_start: 0.5865 (ttm) cc_final: 0.4458 (ppp) REVERT: B 189 HIS cc_start: 0.8017 (m-70) cc_final: 0.7817 (m90) REVERT: C 82 ASP cc_start: 0.8683 (m-30) cc_final: 0.8469 (m-30) REVERT: C 243 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6990 (tp30) REVERT: D 226 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6973 (mm-30) REVERT: E 18 GLU cc_start: 0.8373 (mp0) cc_final: 0.8168 (mp0) REVERT: E 186 HIS cc_start: 0.7935 (p90) cc_final: 0.7712 (p90) REVERT: E 239 LYS cc_start: 0.8280 (mttm) cc_final: 0.7832 (mmtm) REVERT: F 203 GLN cc_start: 0.7084 (tp-100) cc_final: 0.6580 (tt0) REVERT: F 217 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7769 (tptt) REVERT: I 180 LYS cc_start: 0.8306 (pttt) cc_final: 0.7742 (mtpt) REVERT: J 144 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7793 (mp0) REVERT: K 110 HIS cc_start: 0.7590 (m-70) cc_final: 0.7386 (m-70) REVERT: K 158 GLU cc_start: 0.8208 (mt-10) cc_final: 0.8001 (mt-10) REVERT: L 107 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.8109 (mtt90) REVERT: L 154 ASP cc_start: 0.7856 (m-30) cc_final: 0.7635 (m-30) REVERT: L 198 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8386 (tttp) REVERT: O 145 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6209 (pm20) REVERT: P 1 MET cc_start: 0.5612 (ttm) cc_final: 0.4480 (ptt) REVERT: P 163 MET cc_start: 0.9098 (mtm) cc_final: 0.8825 (mtm) REVERT: P 225 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7771 (mt-10) REVERT: Q 49 ARG cc_start: 0.7742 (mtp85) cc_final: 0.7346 (mtp85) REVERT: Q 199 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8106 (tttp) REVERT: Q 235 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7626 (tm130) REVERT: R 175 ASN cc_start: 0.8280 (m110) cc_final: 0.8056 (m110) REVERT: R 208 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8417 (mp) REVERT: S 157 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7990 (p0) REVERT: T 51 ARG cc_start: 0.7409 (mtm-85) cc_final: 0.7041 (ptp-110) REVERT: T 189 LYS cc_start: 0.8452 (mttm) cc_final: 0.8231 (mttp) REVERT: U 206 LYS cc_start: 0.7722 (tppp) cc_final: 0.7355 (tmtm) REVERT: V 95 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8221 (mtt) REVERT: V 104 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.8007 (t0) REVERT: V 196 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8102 (mttp) REVERT: V 202 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6272 (mp) REVERT: W 91 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8444 (mm110) REVERT: X 26 ARG cc_start: 0.8450 (mtp180) cc_final: 0.8170 (mtp180) REVERT: c 232 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8592 (mp) outliers start: 139 outliers final: 57 residues processed: 799 average time/residue: 1.4936 time to fit residues: 1454.4158 Evaluate side-chains 753 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 685 time to evaluate : 4.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 208 LYS Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain K residue 2 GLU Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 145 GLU Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 171 LYS Chi-restraints excluded: chain Q residue 199 LYS Chi-restraints excluded: chain Q residue 235 GLN Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 157 ASP Chi-restraints excluded: chain T residue 185 ASN Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 95 MET Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 182 LYS Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 143 THR Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 158 GLU Chi-restraints excluded: chain Z residue 115 ASP Chi-restraints excluded: chain a residue 200 MET Chi-restraints excluded: chain b residue 3 ASN Chi-restraints excluded: chain c residue 232 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 317 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 476 optimal weight: 7.9990 chunk 389 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 573 optimal weight: 10.0000 chunk 619 optimal weight: 9.9990 chunk 510 optimal weight: 2.9990 chunk 568 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 chunk 459 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN E 122 GLN E 224 GLN E 225 ASN H 62 GLN I 91 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN L 38 ASN L 70 ASN L 119 ASN N 81 HIS N 157 GLN O 53 GLN P 166 ASN Q 198 ASN Q 235 GLN S 225 ASN b 104 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 50698 Z= 0.494 Angle : 0.639 8.563 68490 Z= 0.347 Chirality : 0.049 0.236 7648 Planarity : 0.006 0.069 8850 Dihedral : 5.581 54.798 7062 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.48 % Allowed : 15.21 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 1.41 (0.10), residues: 6344 helix: 2.02 (0.10), residues: 2374 sheet: 1.04 (0.13), residues: 1532 loop : -0.17 (0.12), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP L 55 HIS 0.007 0.001 HIS b 89 PHE 0.025 0.002 PHE J 69 TYR 0.019 0.002 TYR U 239 ARG 0.007 0.001 ARG c 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 674 time to evaluate : 4.613 Fit side-chains REVERT: A 193 GLN cc_start: 0.8154 (mt0) cc_final: 0.7527 (mt0) REVERT: A 209 ASP cc_start: 0.7484 (m-30) cc_final: 0.7054 (m-30) REVERT: A 228 ARG cc_start: 0.8480 (ptt90) cc_final: 0.8266 (ptt-90) REVERT: B 1 MET cc_start: 0.5754 (ttm) cc_final: 0.4472 (ppp) REVERT: B 58 ASP cc_start: 0.8546 (t0) cc_final: 0.8082 (m-30) REVERT: B 179 ASN cc_start: 0.8934 (p0) cc_final: 0.8650 (p0) REVERT: C 79 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8508 (mm) REVERT: C 243 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6963 (tp30) REVERT: C 244 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7138 (mt-10) REVERT: D 124 ARG cc_start: 0.8928 (ptp-170) cc_final: 0.8578 (ptm160) REVERT: D 226 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7111 (mm-30) REVERT: E 18 GLU cc_start: 0.8419 (mp0) cc_final: 0.8202 (mp0) REVERT: E 20 ARG cc_start: 0.8677 (mmt90) cc_final: 0.8358 (mtt180) REVERT: E 239 LYS cc_start: 0.8211 (mttm) cc_final: 0.7797 (mmtm) REVERT: F 203 GLN cc_start: 0.7109 (tp-100) cc_final: 0.6747 (tt0) REVERT: F 217 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7695 (tptt) REVERT: I 180 LYS cc_start: 0.8368 (pttt) cc_final: 0.7792 (mtpt) REVERT: I 198 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6158 (mtm180) REVERT: J 31 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8387 (mm110) REVERT: K 110 HIS cc_start: 0.7639 (m-70) cc_final: 0.7404 (m170) REVERT: K 158 GLU cc_start: 0.8254 (mt-10) cc_final: 0.8043 (mt-10) REVERT: L 107 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.8104 (mtt90) REVERT: L 154 ASP cc_start: 0.7864 (m-30) cc_final: 0.7630 (m-30) REVERT: N 102 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8390 (mtpt) REVERT: O 145 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6249 (pm20) REVERT: P 1 MET cc_start: 0.5724 (ttm) cc_final: 0.4503 (ptt) REVERT: P 7 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8551 (m) REVERT: P 148 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8599 (tt0) REVERT: P 163 MET cc_start: 0.9172 (mtm) cc_final: 0.8921 (mtm) REVERT: Q 49 ARG cc_start: 0.7807 (mtp85) cc_final: 0.7403 (mtp85) REVERT: Q 199 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8223 (tttm) REVERT: R 124 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.6928 (ptm-80) REVERT: R 175 ASN cc_start: 0.8337 (m110) cc_final: 0.8094 (m110) REVERT: R 208 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8501 (mp) REVERT: S 157 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8107 (p0) REVERT: S 217 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8774 (tt) REVERT: T 51 ARG cc_start: 0.7388 (mtm-85) cc_final: 0.7077 (ptp-110) REVERT: U 206 LYS cc_start: 0.7807 (tppp) cc_final: 0.7353 (tmtm) REVERT: U 224 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7877 (ttt90) REVERT: V 95 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8220 (mtt) REVERT: V 104 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.8111 (t0) REVERT: V 196 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8151 (mttp) REVERT: V 202 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6306 (mp) REVERT: W 201 ARG cc_start: 0.7282 (mmt180) cc_final: 0.6989 (mmm-85) REVERT: W 215 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8257 (tptp) REVERT: Z 56 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8769 (mt-10) REVERT: a 143 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7864 (mm-30) REVERT: c 201 PHE cc_start: 0.6925 (OUTLIER) cc_final: 0.6172 (p90) REVERT: c 232 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8525 (mp) outliers start: 185 outliers final: 95 residues processed: 805 average time/residue: 1.4620 time to fit residues: 1440.1644 Evaluate side-chains 772 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 654 time to evaluate : 4.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 208 LYS Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 198 ARG Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain K residue 2 GLU Chi-restraints excluded: chain K residue 192 ASP Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 145 GLU Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 148 GLN Chi-restraints excluded: chain P residue 171 LYS Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain Q residue 199 LYS Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 124 ARG Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 157 ASP Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 224 ARG Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 95 MET Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 182 LYS Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain W residue 215 LYS Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 143 THR Chi-restraints excluded: chain Y residue 158 GLU Chi-restraints excluded: chain Z residue 56 GLU Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 115 ASP Chi-restraints excluded: chain Z residue 133 VAL Chi-restraints excluded: chain a residue 143 GLU Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain a residue 198 ARG Chi-restraints excluded: chain a residue 200 MET Chi-restraints excluded: chain b residue 3 ASN Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain c residue 201 PHE Chi-restraints excluded: chain c residue 208 MET Chi-restraints excluded: chain c residue 232 LEU Chi-restraints excluded: chain d residue 252 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 566 optimal weight: 0.6980 chunk 430 optimal weight: 4.9990 chunk 297 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 273 optimal weight: 0.9990 chunk 384 optimal weight: 20.0000 chunk 575 optimal weight: 10.0000 chunk 608 optimal weight: 5.9990 chunk 300 optimal weight: 1.9990 chunk 545 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN B 207 ASN E 224 GLN E 225 ASN H 62 GLN J 162 HIS ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN L 38 ASN L 70 ASN L 119 ASN N 157 GLN O 53 GLN P 166 ASN S 225 ASN W 91 GLN a 179 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 50698 Z= 0.184 Angle : 0.494 7.279 68490 Z= 0.272 Chirality : 0.043 0.196 7648 Planarity : 0.004 0.051 8850 Dihedral : 5.110 59.937 7061 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.46 % Allowed : 16.27 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 1.71 (0.10), residues: 6344 helix: 2.37 (0.10), residues: 2388 sheet: 1.11 (0.13), residues: 1540 loop : -0.08 (0.12), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 55 HIS 0.005 0.001 HIS F 175 PHE 0.022 0.001 PHE W 36 TYR 0.014 0.001 TYR U 239 ARG 0.007 0.000 ARG c 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 698 time to evaluate : 4.459 Fit side-chains REVERT: A 193 GLN cc_start: 0.8078 (mt0) cc_final: 0.7469 (mt0) REVERT: A 209 ASP cc_start: 0.7406 (m-30) cc_final: 0.6944 (m-30) REVERT: B 1 MET cc_start: 0.5871 (ttm) cc_final: 0.4438 (ppp) REVERT: B 58 ASP cc_start: 0.8451 (t0) cc_final: 0.8029 (m-30) REVERT: B 189 HIS cc_start: 0.7944 (m170) cc_final: 0.7735 (m90) REVERT: C 25 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8046 (mtt) REVERT: C 243 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6969 (tp30) REVERT: C 244 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7120 (mt-10) REVERT: E 62 SER cc_start: 0.8724 (OUTLIER) cc_final: 0.8509 (t) REVERT: F 203 GLN cc_start: 0.7079 (tp-100) cc_final: 0.6618 (tt0) REVERT: F 217 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7750 (tttt) REVERT: I 180 LYS cc_start: 0.8281 (pttt) cc_final: 0.7733 (mtpt) REVERT: I 198 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6067 (mtm180) REVERT: J 31 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8359 (mm110) REVERT: J 144 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7809 (mp0) REVERT: K 110 HIS cc_start: 0.7590 (m-70) cc_final: 0.7349 (m170) REVERT: K 158 GLU cc_start: 0.8217 (mt-10) cc_final: 0.8009 (mt-10) REVERT: L 107 ARG cc_start: 0.8367 (mtm-85) cc_final: 0.8105 (mtt90) REVERT: L 154 ASP cc_start: 0.7834 (m-30) cc_final: 0.7609 (m-30) REVERT: N 166 ARG cc_start: 0.8432 (ttt90) cc_final: 0.8214 (ttt-90) REVERT: P 1 MET cc_start: 0.5589 (ttm) cc_final: 0.4473 (ptt) REVERT: P 148 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8546 (tt0) REVERT: P 163 MET cc_start: 0.9058 (mtm) cc_final: 0.8751 (mtm) REVERT: Q 49 ARG cc_start: 0.7729 (mtp85) cc_final: 0.7368 (mtp85) REVERT: Q 199 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8119 (ttpp) REVERT: R 175 ASN cc_start: 0.8255 (m110) cc_final: 0.8025 (m-40) REVERT: R 208 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8433 (mp) REVERT: S 157 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7967 (p0) REVERT: T 51 ARG cc_start: 0.7495 (mtm-85) cc_final: 0.7144 (ptp-110) REVERT: U 206 LYS cc_start: 0.7794 (tppp) cc_final: 0.7350 (tmtm) REVERT: V 95 MET cc_start: 0.8589 (mtp) cc_final: 0.8212 (mtt) REVERT: V 196 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8187 (mtmt) REVERT: V 202 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6199 (mp) REVERT: Y 179 SER cc_start: 0.9109 (p) cc_final: 0.8787 (m) REVERT: Z 56 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8705 (mt-10) REVERT: a 198 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7597 (ttt180) REVERT: a 229 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7341 (mm-30) REVERT: c 201 PHE cc_start: 0.6801 (OUTLIER) cc_final: 0.6113 (p90) REVERT: c 242 ARG cc_start: 0.7928 (mtt180) cc_final: 0.7667 (mtt180) outliers start: 131 outliers final: 63 residues processed: 787 average time/residue: 1.5368 time to fit residues: 1474.4170 Evaluate side-chains 759 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 681 time to evaluate : 4.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain I residue 198 ARG Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain K residue 2 GLU Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain M residue 162 SER Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 148 GLN Chi-restraints excluded: chain P residue 171 LYS Chi-restraints excluded: chain Q residue 199 LYS Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 157 ASP Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain Y residue 158 GLU Chi-restraints excluded: chain Z residue 56 GLU Chi-restraints excluded: chain Z residue 115 ASP Chi-restraints excluded: chain Z residue 133 VAL Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain a residue 198 ARG Chi-restraints excluded: chain a residue 229 GLU Chi-restraints excluded: chain b residue 3 ASN Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain c residue 201 PHE Chi-restraints excluded: chain d residue 252 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 507 optimal weight: 5.9990 chunk 345 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 453 optimal weight: 5.9990 chunk 251 optimal weight: 10.0000 chunk 519 optimal weight: 3.9990 chunk 420 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 310 optimal weight: 0.2980 chunk 546 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN C 177 GLN C 230 GLN E 122 GLN E 224 GLN E 225 ASN H 62 GLN H 71 ASN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN L 38 ASN L 70 ASN L 119 ASN N 157 GLN O 53 GLN P 166 ASN Q 235 GLN S 225 ASN W 91 GLN X 31 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 104 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 50698 Z= 0.351 Angle : 0.569 7.899 68490 Z= 0.310 Chirality : 0.046 0.182 7648 Planarity : 0.005 0.057 8850 Dihedral : 5.325 57.928 7059 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.12 % Allowed : 16.10 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 1.57 (0.10), residues: 6344 helix: 2.23 (0.10), residues: 2380 sheet: 1.03 (0.13), residues: 1542 loop : -0.11 (0.12), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 55 HIS 0.006 0.001 HIS b 89 PHE 0.023 0.002 PHE J 69 TYR 0.018 0.002 TYR Z 66 ARG 0.006 0.000 ARG L 9 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 690 time to evaluate : 4.773 Fit side-chains REVERT: A 193 GLN cc_start: 0.8134 (mt0) cc_final: 0.7534 (mt0) REVERT: A 209 ASP cc_start: 0.7440 (m-30) cc_final: 0.6984 (m-30) REVERT: B 1 MET cc_start: 0.5776 (ttm) cc_final: 0.4449 (ppp) REVERT: B 58 ASP cc_start: 0.8562 (t0) cc_final: 0.8153 (m-30) REVERT: B 189 HIS cc_start: 0.7982 (m170) cc_final: 0.7760 (m90) REVERT: C 25 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8126 (mtt) REVERT: C 243 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6969 (tp30) REVERT: C 244 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7135 (mt-10) REVERT: D 124 ARG cc_start: 0.8951 (ptp-170) cc_final: 0.8573 (ptm160) REVERT: E 62 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8432 (t) REVERT: F 203 GLN cc_start: 0.7063 (tp-100) cc_final: 0.6630 (tt0) REVERT: F 217 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7840 (tptt) REVERT: I 22 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7659 (mt-10) REVERT: I 180 LYS cc_start: 0.8348 (pttt) cc_final: 0.7782 (mtpt) REVERT: I 198 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6101 (mtm180) REVERT: J 31 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8332 (mt0) REVERT: K 41 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8865 (mttp) REVERT: K 110 HIS cc_start: 0.7629 (m-70) cc_final: 0.7368 (m170) REVERT: K 158 GLU cc_start: 0.8228 (mt-10) cc_final: 0.8022 (mt-10) REVERT: L 107 ARG cc_start: 0.8362 (mtm-85) cc_final: 0.8101 (mtt90) REVERT: L 154 ASP cc_start: 0.7870 (m-30) cc_final: 0.7614 (m-30) REVERT: N 166 ARG cc_start: 0.8477 (ttt90) cc_final: 0.8276 (ttt-90) REVERT: O 145 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6062 (pm20) REVERT: P 1 MET cc_start: 0.5710 (ttm) cc_final: 0.4503 (ptt) REVERT: P 7 SER cc_start: 0.8814 (OUTLIER) cc_final: 0.8531 (m) REVERT: P 148 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8569 (tt0) REVERT: P 163 MET cc_start: 0.9130 (mtm) cc_final: 0.8873 (mtm) REVERT: Q 49 ARG cc_start: 0.7778 (mtp85) cc_final: 0.7378 (mtp85) REVERT: Q 199 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8117 (tttm) REVERT: Q 235 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7678 (tm130) REVERT: R 175 ASN cc_start: 0.8350 (m110) cc_final: 0.8094 (m110) REVERT: R 208 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8476 (mp) REVERT: S 157 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8028 (p0) REVERT: S 217 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8729 (tt) REVERT: T 51 ARG cc_start: 0.7430 (mtm-85) cc_final: 0.7100 (ptp-110) REVERT: U 206 LYS cc_start: 0.7804 (tppp) cc_final: 0.7362 (tmtm) REVERT: V 72 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6987 (pp20) REVERT: V 95 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8212 (mtt) REVERT: V 104 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.8028 (t0) REVERT: V 196 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8148 (mttp) REVERT: V 202 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.6274 (mp) REVERT: W 215 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8304 (tptp) REVERT: X 68 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8595 (tptm) REVERT: a 198 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7901 (ttt180) REVERT: c 201 PHE cc_start: 0.6948 (OUTLIER) cc_final: 0.6477 (p90) outliers start: 166 outliers final: 88 residues processed: 804 average time/residue: 1.5224 time to fit residues: 1495.4043 Evaluate side-chains 782 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 670 time to evaluate : 4.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 198 ARG Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain K residue 2 GLU Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain K residue 41 LYS Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 71 LYS Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain M residue 162 SER Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 145 GLU Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 148 GLN Chi-restraints excluded: chain P residue 171 LYS Chi-restraints excluded: chain P residue 224 THR Chi-restraints excluded: chain Q residue 173 SER Chi-restraints excluded: chain Q residue 199 LYS Chi-restraints excluded: chain Q residue 211 VAL Chi-restraints excluded: chain Q residue 235 GLN Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 157 ASP Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 72 GLU Chi-restraints excluded: chain V residue 95 MET Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain W residue 215 LYS Chi-restraints excluded: chain X residue 4 MET Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 68 LYS Chi-restraints excluded: chain X residue 143 THR Chi-restraints excluded: chain Y residue 68 LYS Chi-restraints excluded: chain Y residue 158 GLU Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 115 ASP Chi-restraints excluded: chain Z residue 133 VAL Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain a residue 198 ARG Chi-restraints excluded: chain a residue 200 MET Chi-restraints excluded: chain b residue 3 ASN Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain c residue 201 PHE Chi-restraints excluded: chain c residue 208 MET Chi-restraints excluded: chain d residue 252 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 204 optimal weight: 0.9990 chunk 548 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 357 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 chunk 609 optimal weight: 0.9990 chunk 506 optimal weight: 2.9990 chunk 282 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 chunk 320 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN C 146 GLN E 224 GLN E 225 ASN F 59 HIS H 71 ASN J 162 HIS ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN L 38 ASN L 70 ASN L 119 ASN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 GLN P 166 ASN Q 240 HIS S 225 ASN W 91 GLN X 31 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 50698 Z= 0.144 Angle : 0.471 7.904 68490 Z= 0.259 Chirality : 0.042 0.230 7648 Planarity : 0.004 0.049 8850 Dihedral : 4.876 54.252 7059 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.26 % Allowed : 17.02 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 6344 helix: 2.53 (0.10), residues: 2390 sheet: 1.11 (0.13), residues: 1540 loop : -0.01 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 55 HIS 0.006 0.001 HIS F 175 PHE 0.021 0.001 PHE W 36 TYR 0.014 0.001 TYR U 239 ARG 0.006 0.000 ARG Z 9 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 723 time to evaluate : 4.587 Fit side-chains REVERT: A 193 GLN cc_start: 0.8053 (mt0) cc_final: 0.7486 (mt0) REVERT: A 209 ASP cc_start: 0.7435 (m-30) cc_final: 0.6966 (m-30) REVERT: B 1 MET cc_start: 0.5920 (ttm) cc_final: 0.4487 (ppp) REVERT: B 58 ASP cc_start: 0.8509 (t0) cc_final: 0.8121 (m-30) REVERT: B 70 LYS cc_start: 0.8698 (mtmt) cc_final: 0.8150 (tmtt) REVERT: B 189 HIS cc_start: 0.7932 (m170) cc_final: 0.7724 (m90) REVERT: C 25 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7944 (mtt) REVERT: C 82 ASP cc_start: 0.8601 (m-30) cc_final: 0.8359 (m-30) REVERT: C 243 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6938 (tp30) REVERT: C 244 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7092 (mt-10) REVERT: E 62 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8513 (t) REVERT: F 203 GLN cc_start: 0.7018 (tp-100) cc_final: 0.6585 (tt0) REVERT: F 217 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7727 (tttt) REVERT: I 180 LYS cc_start: 0.8290 (pttt) cc_final: 0.7746 (mtpt) REVERT: I 198 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6193 (mtm180) REVERT: J 31 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8361 (mm110) REVERT: K 110 HIS cc_start: 0.7642 (m-70) cc_final: 0.7383 (m-70) REVERT: K 158 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7987 (mt-10) REVERT: L 107 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.8130 (mtt90) REVERT: L 154 ASP cc_start: 0.7833 (m-30) cc_final: 0.7613 (m-30) REVERT: N 166 ARG cc_start: 0.8415 (ttt90) cc_final: 0.8206 (ttt-90) REVERT: P 1 MET cc_start: 0.5587 (ttm) cc_final: 0.4411 (ptt) REVERT: P 148 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8512 (tt0) REVERT: P 163 MET cc_start: 0.9012 (mtm) cc_final: 0.8731 (mtm) REVERT: Q 49 ARG cc_start: 0.7732 (mtp85) cc_final: 0.7413 (mtp180) REVERT: R 55 ASP cc_start: 0.7842 (t70) cc_final: 0.7429 (t70) REVERT: R 208 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8434 (mp) REVERT: S 217 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8604 (tt) REVERT: T 51 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.7164 (ptp-110) REVERT: U 206 LYS cc_start: 0.7845 (tppp) cc_final: 0.7421 (tmtm) REVERT: U 233 ARG cc_start: 0.7762 (ttp80) cc_final: 0.7526 (ttm-80) REVERT: V 95 MET cc_start: 0.8553 (mtp) cc_final: 0.8174 (mtt) REVERT: V 196 LYS cc_start: 0.8447 (mttp) cc_final: 0.8160 (mtmt) REVERT: V 202 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6152 (mp) REVERT: W 146 MET cc_start: 0.9071 (mtm) cc_final: 0.8826 (mtm) REVERT: X 143 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8567 (m) REVERT: Y 179 SER cc_start: 0.9085 (p) cc_final: 0.8770 (m) REVERT: a 198 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7519 (ttt180) REVERT: c 201 PHE cc_start: 0.6841 (OUTLIER) cc_final: 0.6420 (p90) outliers start: 120 outliers final: 58 residues processed: 806 average time/residue: 1.4928 time to fit residues: 1470.4908 Evaluate side-chains 749 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 679 time to evaluate : 4.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain I residue 198 ARG Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 148 GLN Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 211 VAL Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 143 THR Chi-restraints excluded: chain Y residue 158 GLU Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 115 ASP Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain a residue 198 ARG Chi-restraints excluded: chain a residue 200 MET Chi-restraints excluded: chain b residue 3 ASN Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain c residue 201 PHE Chi-restraints excluded: chain d residue 252 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 587 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 347 optimal weight: 0.8980 chunk 445 optimal weight: 10.0000 chunk 344 optimal weight: 2.9990 chunk 513 optimal weight: 5.9990 chunk 340 optimal weight: 9.9990 chunk 607 optimal weight: 4.9990 chunk 380 optimal weight: 5.9990 chunk 370 optimal weight: 10.0000 chunk 280 optimal weight: 0.9980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN C 177 GLN E 122 GLN E 224 GLN E 225 ASN H 71 ASN I 91 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN L 38 ASN L 62 GLN L 70 ASN L 119 ASN N 157 GLN O 53 GLN P 123 GLN P 166 ASN S 225 ASN ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 31 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 187 GLN b 104 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 50698 Z= 0.291 Angle : 0.542 9.103 68490 Z= 0.294 Chirality : 0.045 0.298 7648 Planarity : 0.005 0.054 8850 Dihedral : 5.113 52.790 7058 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.71 % Allowed : 16.85 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.10), residues: 6344 helix: 2.40 (0.10), residues: 2388 sheet: 1.04 (0.13), residues: 1552 loop : -0.04 (0.12), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 55 HIS 0.006 0.001 HIS b 89 PHE 0.023 0.002 PHE W 36 TYR 0.022 0.002 TYR Z 66 ARG 0.007 0.000 ARG L 9 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 678 time to evaluate : 4.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.8121 (mt0) cc_final: 0.7543 (mt0) REVERT: A 209 ASP cc_start: 0.7445 (m-30) cc_final: 0.6984 (m-30) REVERT: B 1 MET cc_start: 0.5817 (ttm) cc_final: 0.4446 (ppp) REVERT: B 58 ASP cc_start: 0.8558 (t0) cc_final: 0.8146 (m-30) REVERT: B 189 HIS cc_start: 0.7974 (m170) cc_final: 0.7751 (m90) REVERT: C 25 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8053 (mtt) REVERT: C 243 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6940 (tp30) REVERT: C 244 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7135 (mt-10) REVERT: D 170 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6912 (mt-10) REVERT: E 62 SER cc_start: 0.8759 (OUTLIER) cc_final: 0.8525 (t) REVERT: E 239 LYS cc_start: 0.8115 (mttm) cc_final: 0.7712 (mmtm) REVERT: F 203 GLN cc_start: 0.7024 (tp-100) cc_final: 0.6637 (tt0) REVERT: F 217 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7810 (tptt) REVERT: I 180 LYS cc_start: 0.8359 (pttt) cc_final: 0.7779 (mtpt) REVERT: I 198 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6184 (mtm180) REVERT: J 31 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8326 (mt0) REVERT: J 146 MET cc_start: 0.9377 (mtm) cc_final: 0.9146 (mtp) REVERT: K 110 HIS cc_start: 0.7622 (m-70) cc_final: 0.7383 (m-70) REVERT: K 158 GLU cc_start: 0.8211 (mt-10) cc_final: 0.8008 (mt-10) REVERT: L 154 ASP cc_start: 0.7851 (m-30) cc_final: 0.7619 (m-30) REVERT: M 127 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8364 (mtm180) REVERT: N 110 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8553 (mpp) REVERT: N 166 ARG cc_start: 0.8466 (ttt90) cc_final: 0.8246 (ttt-90) REVERT: P 1 MET cc_start: 0.5548 (ttm) cc_final: 0.4453 (ptt) REVERT: P 148 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8563 (tt0) REVERT: P 163 MET cc_start: 0.9101 (mtm) cc_final: 0.8854 (mtm) REVERT: Q 30 HIS cc_start: 0.6856 (m170) cc_final: 0.6588 (m170) REVERT: Q 49 ARG cc_start: 0.7771 (mtp85) cc_final: 0.7392 (mtp180) REVERT: R 175 ASN cc_start: 0.8217 (m-40) cc_final: 0.7943 (m-40) REVERT: R 208 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8486 (mp) REVERT: S 157 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7925 (p0) REVERT: S 217 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8678 (tt) REVERT: T 51 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.7082 (ptp-110) REVERT: U 206 LYS cc_start: 0.7824 (tppp) cc_final: 0.7392 (tmtm) REVERT: U 233 ARG cc_start: 0.7761 (ttp80) cc_final: 0.7521 (ttm-80) REVERT: V 95 MET cc_start: 0.8599 (mtp) cc_final: 0.8214 (mtt) REVERT: V 196 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8155 (mtmt) REVERT: V 202 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6287 (mp) REVERT: X 68 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8595 (tptm) REVERT: X 77 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8495 (mttp) REVERT: Z 91 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8398 (tttm) REVERT: a 143 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7965 (mm-30) REVERT: a 198 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7813 (ttt180) REVERT: c 201 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6652 (p90) outliers start: 144 outliers final: 83 residues processed: 778 average time/residue: 1.5095 time to fit residues: 1434.1868 Evaluate side-chains 774 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 671 time to evaluate : 4.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain I residue 198 ARG Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain K residue 2 GLU Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain L residue 71 LYS Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain M residue 127 ARG Chi-restraints excluded: chain M residue 162 SER Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 148 GLN Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 211 VAL Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 157 ASP Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 180 MET Chi-restraints excluded: chain T residue 185 ASN Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 183 LEU Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 68 LYS Chi-restraints excluded: chain X residue 77 LYS Chi-restraints excluded: chain X residue 143 THR Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 158 GLU Chi-restraints excluded: chain Z residue 91 LYS Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 115 ASP Chi-restraints excluded: chain Z residue 133 VAL Chi-restraints excluded: chain a residue 143 GLU Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain a residue 198 ARG Chi-restraints excluded: chain a residue 200 MET Chi-restraints excluded: chain b residue 3 ASN Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 207 THR Chi-restraints excluded: chain c residue 201 PHE Chi-restraints excluded: chain d residue 252 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 375 optimal weight: 0.7980 chunk 242 optimal weight: 0.0270 chunk 362 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 386 optimal weight: 0.9990 chunk 413 optimal weight: 0.4980 chunk 300 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 477 optimal weight: 2.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN B 207 ASN E 224 GLN E 225 ASN H 71 ASN J 162 HIS ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN L 38 ASN L 70 ASN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 GLN O 53 GLN P 166 ASN S 225 ASN ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 91 GLN X 31 GLN ** X 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 50698 Z= 0.138 Angle : 0.465 8.482 68490 Z= 0.254 Chirality : 0.042 0.304 7648 Planarity : 0.004 0.049 8850 Dihedral : 4.697 55.474 7058 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.88 % Allowed : 17.73 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 1.95 (0.10), residues: 6344 helix: 2.68 (0.10), residues: 2388 sheet: 1.12 (0.13), residues: 1530 loop : 0.04 (0.12), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Z 55 HIS 0.005 0.001 HIS F 175 PHE 0.021 0.001 PHE W 36 TYR 0.014 0.001 TYR O 159 ARG 0.008 0.000 ARG L 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 718 time to evaluate : 4.691 Fit side-chains revert: symmetry clash REVERT: A 193 GLN cc_start: 0.8028 (mt0) cc_final: 0.7459 (mt0) REVERT: A 209 ASP cc_start: 0.7384 (m-30) cc_final: 0.6914 (m-30) REVERT: B 1 MET cc_start: 0.5824 (ttm) cc_final: 0.4623 (pp-130) REVERT: B 58 ASP cc_start: 0.8520 (t0) cc_final: 0.8154 (m-30) REVERT: B 70 LYS cc_start: 0.8693 (mtmt) cc_final: 0.8151 (tmtt) REVERT: B 141 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7201 (pp20) REVERT: C 82 ASP cc_start: 0.8530 (m-30) cc_final: 0.8279 (m-30) REVERT: C 243 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6996 (tp30) REVERT: E 62 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8527 (t) REVERT: E 186 HIS cc_start: 0.7926 (p90) cc_final: 0.7695 (p-80) REVERT: F 203 GLN cc_start: 0.7044 (tp-100) cc_final: 0.6604 (tt0) REVERT: I 147 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8273 (mm-30) REVERT: I 180 LYS cc_start: 0.8264 (pttt) cc_final: 0.7745 (mtpt) REVERT: J 31 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8301 (mm110) REVERT: J 144 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7809 (mp0) REVERT: K 110 HIS cc_start: 0.7616 (m-70) cc_final: 0.7347 (m-70) REVERT: K 154 GLU cc_start: 0.7586 (mp0) cc_final: 0.7299 (mp0) REVERT: K 158 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7973 (mt-10) REVERT: L 154 ASP cc_start: 0.7834 (m-30) cc_final: 0.7629 (m-30) REVERT: N 74 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: N 166 ARG cc_start: 0.8405 (ttt90) cc_final: 0.8191 (ttt-90) REVERT: P 1 MET cc_start: 0.5533 (ttm) cc_final: 0.4347 (ptt) REVERT: P 7 SER cc_start: 0.8773 (OUTLIER) cc_final: 0.8529 (m) REVERT: P 148 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8501 (tt0) REVERT: P 163 MET cc_start: 0.8995 (mtm) cc_final: 0.8740 (mtm) REVERT: Q 30 HIS cc_start: 0.6699 (m170) cc_final: 0.6388 (m90) REVERT: Q 49 ARG cc_start: 0.7720 (mtp85) cc_final: 0.7437 (mtp180) REVERT: Q 200 THR cc_start: 0.8272 (m) cc_final: 0.7955 (m) REVERT: Q 239 LYS cc_start: 0.8182 (mtpp) cc_final: 0.7873 (tmmm) REVERT: R 55 ASP cc_start: 0.7788 (t70) cc_final: 0.7366 (t70) REVERT: R 175 ASN cc_start: 0.8184 (m-40) cc_final: 0.7956 (m-40) REVERT: T 51 ARG cc_start: 0.7488 (mtm-85) cc_final: 0.7168 (ptp-110) REVERT: U 206 LYS cc_start: 0.7864 (tppp) cc_final: 0.7453 (tmtm) REVERT: U 233 ARG cc_start: 0.7760 (ttp80) cc_final: 0.7524 (ttm-80) REVERT: V 196 LYS cc_start: 0.8424 (mttp) cc_final: 0.8146 (mtmt) REVERT: V 202 LEU cc_start: 0.6535 (OUTLIER) cc_final: 0.6156 (mp) REVERT: X 68 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8518 (tptm) REVERT: X 77 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8466 (mttp) REVERT: Y 179 SER cc_start: 0.9084 (p) cc_final: 0.8746 (m) REVERT: a 198 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7492 (ttt180) REVERT: c 201 PHE cc_start: 0.6890 (OUTLIER) cc_final: 0.6608 (p90) REVERT: c 232 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8529 (mp) outliers start: 100 outliers final: 54 residues processed: 788 average time/residue: 1.4878 time to fit residues: 1436.5297 Evaluate side-chains 755 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 691 time to evaluate : 4.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain L residue 71 LYS Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain M residue 162 SER Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 148 GLN Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 211 VAL Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 185 ASN Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 68 LYS Chi-restraints excluded: chain X residue 77 LYS Chi-restraints excluded: chain Y residue 158 GLU Chi-restraints excluded: chain Z residue 32 LYS Chi-restraints excluded: chain Z residue 133 VAL Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain a residue 198 ARG Chi-restraints excluded: chain a residue 200 MET Chi-restraints excluded: chain b residue 3 ASN Chi-restraints excluded: chain b residue 207 THR Chi-restraints excluded: chain c residue 201 PHE Chi-restraints excluded: chain c residue 232 LEU Chi-restraints excluded: chain d residue 252 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 552 optimal weight: 4.9990 chunk 581 optimal weight: 10.0000 chunk 530 optimal weight: 7.9990 chunk 565 optimal weight: 5.9990 chunk 340 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 444 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 511 optimal weight: 5.9990 chunk 535 optimal weight: 10.0000 chunk 563 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN C 177 GLN E 122 GLN E 214 ASN E 224 GLN E 225 ASN H 71 ASN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN L 38 ASN L 70 ASN L 119 ASN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 GLN ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 GLN P 166 ASN P 207 ASN Q 235 GLN S 225 ASN V 106 GLN X 31 GLN Y 110 HIS ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 187 GLN b 104 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 50698 Z= 0.480 Angle : 0.639 9.547 68490 Z= 0.345 Chirality : 0.049 0.356 7648 Planarity : 0.005 0.066 8850 Dihedral : 5.331 51.397 7052 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.39 % Allowed : 17.64 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.10), residues: 6344 helix: 2.17 (0.10), residues: 2378 sheet: 0.98 (0.13), residues: 1536 loop : -0.10 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP E 100 HIS 0.007 0.001 HIS b 89 PHE 0.030 0.002 PHE J 69 TYR 0.024 0.002 TYR Z 66 ARG 0.008 0.001 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 654 time to evaluate : 4.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.8149 (mt0) cc_final: 0.7539 (mt0) REVERT: A 209 ASP cc_start: 0.7445 (m-30) cc_final: 0.6990 (m-30) REVERT: B 1 MET cc_start: 0.5765 (ttm) cc_final: 0.4451 (ppp) REVERT: B 58 ASP cc_start: 0.8658 (t0) cc_final: 0.8252 (m-30) REVERT: C 243 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6930 (tp30) REVERT: C 244 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7148 (mt-10) REVERT: D 208 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8522 (mt) REVERT: E 62 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8466 (t) REVERT: E 239 LYS cc_start: 0.8046 (mttm) cc_final: 0.7667 (mmtm) REVERT: F 203 GLN cc_start: 0.7020 (tp-100) cc_final: 0.6621 (tt0) REVERT: F 217 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7754 (tttt) REVERT: I 180 LYS cc_start: 0.8382 (pttt) cc_final: 0.7821 (mtpt) REVERT: I 198 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6120 (mtm180) REVERT: J 31 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8341 (mt0) REVERT: J 146 MET cc_start: 0.9366 (mtm) cc_final: 0.9132 (mtp) REVERT: K 110 HIS cc_start: 0.7698 (m-70) cc_final: 0.7477 (m-70) REVERT: L 154 ASP cc_start: 0.7876 (m-30) cc_final: 0.7649 (m-30) REVERT: M 127 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8409 (mtm180) REVERT: P 1 MET cc_start: 0.5788 (ttm) cc_final: 0.4541 (ptt) REVERT: P 7 SER cc_start: 0.8813 (OUTLIER) cc_final: 0.8536 (m) REVERT: P 148 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8599 (tt0) REVERT: P 163 MET cc_start: 0.9124 (mtm) cc_final: 0.8903 (mtm) REVERT: Q 30 HIS cc_start: 0.6975 (m170) cc_final: 0.6683 (m170) REVERT: Q 49 ARG cc_start: 0.7795 (mtp85) cc_final: 0.7368 (mtp180) REVERT: Q 239 LYS cc_start: 0.8240 (mtpp) cc_final: 0.7952 (tmmt) REVERT: R 175 ASN cc_start: 0.8267 (m-40) cc_final: 0.7982 (m-40) REVERT: T 51 ARG cc_start: 0.7440 (mtm-85) cc_final: 0.7123 (ptp-110) REVERT: U 6 THR cc_start: 0.3943 (OUTLIER) cc_final: 0.3687 (p) REVERT: U 145 ASP cc_start: 0.7367 (t0) cc_final: 0.6736 (t0) REVERT: U 206 LYS cc_start: 0.7827 (tppp) cc_final: 0.7387 (tmtm) REVERT: U 224 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7871 (ttt90) REVERT: U 233 ARG cc_start: 0.7786 (ttp80) cc_final: 0.7561 (ttm-80) REVERT: V 196 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8172 (mttp) REVERT: V 202 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.6327 (mp) REVERT: W 215 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8336 (tttp) REVERT: X 77 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8514 (mttp) REVERT: Y 49 GLU cc_start: 0.7821 (tt0) cc_final: 0.7556 (tt0) REVERT: c 201 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6852 (p90) outliers start: 127 outliers final: 72 residues processed: 746 average time/residue: 1.4998 time to fit residues: 1369.3681 Evaluate side-chains 727 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 640 time to evaluate : 4.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain I residue 198 ARG Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain K residue 2 GLU Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain L residue 71 LYS Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain M residue 127 ARG Chi-restraints excluded: chain M residue 162 SER Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 148 GLN Chi-restraints excluded: chain P residue 224 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 211 VAL Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 224 ARG Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 196 LYS Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain W residue 215 LYS Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 77 LYS Chi-restraints excluded: chain X residue 143 THR Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 158 GLU Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 133 VAL Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain a residue 198 ARG Chi-restraints excluded: chain a residue 200 MET Chi-restraints excluded: chain b residue 3 ASN Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 207 THR Chi-restraints excluded: chain c residue 201 PHE Chi-restraints excluded: chain d residue 252 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 371 optimal weight: 1.9990 chunk 598 optimal weight: 5.9990 chunk 365 optimal weight: 2.9990 chunk 283 optimal weight: 5.9990 chunk 415 optimal weight: 4.9990 chunk 627 optimal weight: 8.9990 chunk 577 optimal weight: 5.9990 chunk 499 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 386 optimal weight: 0.9990 chunk 306 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN E 224 GLN E 225 ASN H 71 ASN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN L 38 ASN L 70 ASN N 157 GLN O 53 GLN P 166 ASN P 207 ASN S 225 ASN W 91 GLN X 31 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 50698 Z= 0.241 Angle : 0.533 9.829 68490 Z= 0.290 Chirality : 0.044 0.336 7648 Planarity : 0.004 0.054 8850 Dihedral : 5.062 53.843 7052 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.75 % Allowed : 18.45 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.10), residues: 6344 helix: 2.34 (0.10), residues: 2384 sheet: 1.00 (0.13), residues: 1542 loop : -0.04 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 55 HIS 0.006 0.001 HIS F 175 PHE 0.022 0.001 PHE W 36 TYR 0.016 0.001 TYR U 239 ARG 0.008 0.000 ARG L 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12688 Ramachandran restraints generated. 6344 Oldfield, 0 Emsley, 6344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 669 time to evaluate : 4.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.8117 (mt0) cc_final: 0.7537 (mt0) REVERT: A 209 ASP cc_start: 0.7408 (m-30) cc_final: 0.6951 (m-30) REVERT: B 1 MET cc_start: 0.5826 (ttm) cc_final: 0.4443 (ppp) REVERT: B 58 ASP cc_start: 0.8573 (t0) cc_final: 0.8202 (m-30) REVERT: C 79 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8366 (mm) REVERT: C 243 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6968 (tp30) REVERT: C 244 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7084 (mt-10) REVERT: D 208 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8529 (mt) REVERT: E 62 SER cc_start: 0.8739 (OUTLIER) cc_final: 0.8503 (t) REVERT: F 203 GLN cc_start: 0.7003 (tp-100) cc_final: 0.6621 (tt0) REVERT: F 217 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7746 (tttt) REVERT: I 180 LYS cc_start: 0.8363 (pttt) cc_final: 0.7824 (mtpt) REVERT: I 198 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6180 (mtm180) REVERT: J 31 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8326 (mt0) REVERT: J 144 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7811 (mp0) REVERT: J 146 MET cc_start: 0.9368 (mtm) cc_final: 0.9126 (mtp) REVERT: K 110 HIS cc_start: 0.7673 (m-70) cc_final: 0.7438 (m-70) REVERT: L 154 ASP cc_start: 0.7847 (m-30) cc_final: 0.7632 (m-30) REVERT: P 1 MET cc_start: 0.5539 (ttm) cc_final: 0.4455 (ptt) REVERT: P 7 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8534 (m) REVERT: P 148 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8560 (tt0) REVERT: P 163 MET cc_start: 0.9070 (mtm) cc_final: 0.8823 (mtm) REVERT: Q 30 HIS cc_start: 0.6849 (m170) cc_final: 0.6584 (m170) REVERT: Q 49 ARG cc_start: 0.7791 (mtp85) cc_final: 0.7403 (mtp180) REVERT: Q 239 LYS cc_start: 0.8242 (mtpp) cc_final: 0.7926 (tmmm) REVERT: R 175 ASN cc_start: 0.8208 (m-40) cc_final: 0.7954 (m-40) REVERT: T 51 ARG cc_start: 0.7424 (mtm-85) cc_final: 0.7188 (ptp-110) REVERT: U 6 THR cc_start: 0.3921 (OUTLIER) cc_final: 0.3675 (p) REVERT: U 145 ASP cc_start: 0.7405 (t0) cc_final: 0.6833 (t0) REVERT: U 206 LYS cc_start: 0.7851 (tppp) cc_final: 0.7421 (tmtm) REVERT: U 233 ARG cc_start: 0.7768 (ttp80) cc_final: 0.7551 (ttm-80) REVERT: V 196 LYS cc_start: 0.8484 (mttp) cc_final: 0.8172 (mtmt) REVERT: V 202 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6238 (mp) REVERT: X 77 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8489 (mttp) REVERT: X 165 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: X 192 LYS cc_start: 0.8843 (ptmm) cc_final: 0.8471 (tptp) REVERT: Y 153 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7854 (ptm160) REVERT: a 198 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7690 (ttt180) REVERT: c 201 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6931 (p90) outliers start: 93 outliers final: 61 residues processed: 737 average time/residue: 1.5634 time to fit residues: 1416.3926 Evaluate side-chains 732 residues out of total 5318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 656 time to evaluate : 4.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain I residue 198 ARG Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain K residue 2 GLU Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain M residue 162 SER Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 148 GLN Chi-restraints excluded: chain P residue 224 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 211 VAL Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 77 LYS Chi-restraints excluded: chain X residue 143 THR Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 153 ARG Chi-restraints excluded: chain Y residue 158 GLU Chi-restraints excluded: chain Z residue 133 VAL Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain a residue 198 ARG Chi-restraints excluded: chain b residue 3 ASN Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 207 THR Chi-restraints excluded: chain c residue 201 PHE Chi-restraints excluded: chain d residue 252 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 396 optimal weight: 10.0000 chunk 532 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 460 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 500 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 514 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN C 177 GLN E 224 GLN E 225 ASN H 62 GLN H 71 ASN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN L 38 ASN L 70 ASN N 157 GLN ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 166 ASN P 207 ASN S 225 ASN W 91 GLN X 31 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 104 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.119959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.093171 restraints weight = 62354.276| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.59 r_work: 0.2948 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 50698 Z= 0.378 Angle : 0.594 11.057 68490 Z= 0.321 Chirality : 0.047 0.355 7648 Planarity : 0.005 0.057 8850 Dihedral : 5.255 55.337 7052 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.12 % Allowed : 18.15 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.10), residues: 6344 helix: 2.18 (0.10), residues: 2382 sheet: 0.96 (0.13), residues: 1546 loop : -0.11 (0.12), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 55 HIS 0.007 0.001 HIS b 89 PHE 0.024 0.002 PHE J 69 TYR 0.025 0.002 TYR Z 66 ARG 0.008 0.001 ARG L 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20308.31 seconds wall clock time: 347 minutes 53.85 seconds (20873.85 seconds total)