Starting phenix.real_space_refine on Fri Feb 16 00:43:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3l_10093/02_2024/6s3l_10093.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3l_10093/02_2024/6s3l_10093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3l_10093/02_2024/6s3l_10093.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3l_10093/02_2024/6s3l_10093.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3l_10093/02_2024/6s3l_10093.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3l_10093/02_2024/6s3l_10093.pdb" } resolution = 3.2 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= -0.000 sd= 0.004 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 146 5.16 5 C 9238 2.51 5 N 2113 2.21 5 O 2352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 179": "NH1" <-> "NH2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ASP 201": "OD1" <-> "OD2" Residue "C PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 251": "OD1" <-> "OD2" Residue "E GLU 165": "OE1" <-> "OE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E GLU 207": "OE1" <-> "OE2" Residue "E GLU 232": "OE1" <-> "OE2" Residue "E PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F GLU 77": "OE1" <-> "OE2" Residue "F PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "F ASP 169": "OD1" <-> "OD2" Residue "F PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F ARG 257": "NH1" <-> "NH2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "G PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 82": "OE1" <-> "OE2" Residue "G ARG 83": "NH1" <-> "NH2" Residue "G TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 4": "OE1" <-> "OE2" Residue "H PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H ARG 83": "NH1" <-> "NH2" Residue "H TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 4": "OE1" <-> "OE2" Residue "I PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 82": "OE1" <-> "OE2" Residue "I ARG 83": "NH1" <-> "NH2" Residue "I TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 4": "OE1" <-> "OE2" Residue "J PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 82": "OE1" <-> "OE2" Residue "J ARG 83": "NH1" <-> "NH2" Residue "J TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 29": "NH1" <-> "NH2" Residue "K GLU 32": "OE1" <-> "OE2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "K ASP 68": "OD1" <-> "OD2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K ASP 74": "OD1" <-> "OD2" Residue "K PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 170": "OD1" <-> "OD2" Residue "K ASP 177": "OD1" <-> "OD2" Residue "K ASP 188": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13849 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1482 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 10, 'TRANS': 180} Chain: "B" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1513 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "C" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1520 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain: "D" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1505 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "E" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1493 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 10, 'TRANS': 181} Chain: "F" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1948 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 9, 'TRANS': 241} Chain: "G" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 724 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "H" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 724 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "I" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 724 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "J" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 724 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "K" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1492 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Time building chain proxies: 7.35, per 1000 atoms: 0.53 Number of scatterers: 13849 At special positions: 0 Unit cell: (99.462, 102.75, 133.986, 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 146 16.00 O 2352 8.00 N 2113 7.00 C 9238 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.62 Conformation dependent library (CDL) restraints added in 2.6 seconds 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3380 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 83.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 111 through 117 Processing helix chain 'A' and resid 118 through 133 removed outlier: 4.241A pdb=" N ILE A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 156 Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 179 through 195 removed outlier: 3.799A pdb=" N GLU A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Proline residue: A 188 - end of helix removed outlier: 3.586A pdb=" N PHE A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 210 Processing helix chain 'A' and resid 220 through 244 Proline residue: A 226 - end of helix removed outlier: 3.627A pdb=" N SER A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 262 removed outlier: 3.694A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 283 Processing helix chain 'A' and resid 285 through 293 removed outlier: 4.479A pdb=" N SER A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.737A pdb=" N ILE B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET B 116 " --> pdb=" O MET B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 134 removed outlier: 3.654A pdb=" N ILE B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 156 removed outlier: 3.785A pdb=" N GLY B 146 " --> pdb=" O GLN B 142 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 149 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 167 Processing helix chain 'B' and resid 167 through 174 removed outlier: 3.547A pdb=" N ASN B 173 " --> pdb=" O GLN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 195 removed outlier: 3.531A pdb=" N ASP B 183 " --> pdb=" O ARG B 179 " (cutoff:3.500A) Proline residue: B 188 - end of helix Processing helix chain 'B' and resid 198 through 210 Processing helix chain 'B' and resid 215 through 219 removed outlier: 3.757A pdb=" N VAL B 219 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 243 Proline residue: B 226 - end of helix removed outlier: 3.560A pdb=" N THR B 230 " --> pdb=" O PRO B 226 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 262 removed outlier: 3.792A pdb=" N ILE B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 removed outlier: 3.865A pdb=" N VAL B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 283 removed outlier: 3.562A pdb=" N LYS B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.712A pdb=" N SER B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 117 removed outlier: 4.521A pdb=" N ILE C 114 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 133 Processing helix chain 'C' and resid 140 through 156 Processing helix chain 'C' and resid 156 through 167 removed outlier: 4.126A pdb=" N GLN C 162 " --> pdb=" O PRO C 158 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 174 removed outlier: 3.579A pdb=" N ASN C 173 " --> pdb=" O GLN C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 194 removed outlier: 3.520A pdb=" N MET C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 210 removed outlier: 4.167A pdb=" N THR C 204 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE C 205 " --> pdb=" O ASP C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 219 Processing helix chain 'C' and resid 220 through 245 Proline residue: C 226 - end of helix removed outlier: 3.627A pdb=" N THR C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 245 " --> pdb=" O PHE C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 261 removed outlier: 3.653A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 283 removed outlier: 4.428A pdb=" N PHE C 275 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 293 Processing helix chain 'D' and resid 108 through 117 removed outlier: 3.834A pdb=" N MET D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE D 114 " --> pdb=" O PRO D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 133 Processing helix chain 'D' and resid 140 through 156 Processing helix chain 'D' and resid 156 through 167 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 181 through 197 removed outlier: 3.521A pdb=" N ALA D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) Proline residue: D 188 - end of helix Processing helix chain 'D' and resid 198 through 210 removed outlier: 3.584A pdb=" N THR D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 262 Proline residue: D 226 - end of helix removed outlier: 3.558A pdb=" N THR D 230 " --> pdb=" O PRO D 226 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 245 " --> pdb=" O PHE D 241 " (cutoff:3.500A) Proline residue: D 246 - end of helix Processing helix chain 'D' and resid 272 through 283 removed outlier: 3.704A pdb=" N VAL D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 295 removed outlier: 3.811A pdb=" N ALA D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 116 Processing helix chain 'E' and resid 118 through 134 removed outlier: 3.793A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 156 Processing helix chain 'E' and resid 156 through 167 Processing helix chain 'E' and resid 167 through 173 Processing helix chain 'E' and resid 177 through 197 removed outlier: 3.735A pdb=" N GLN E 186 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU E 187 " --> pdb=" O ASP E 183 " (cutoff:3.500A) Proline residue: E 188 - end of helix removed outlier: 3.837A pdb=" N LYS E 195 " --> pdb=" O ALA E 191 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN E 196 " --> pdb=" O PHE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 208 removed outlier: 3.808A pdb=" N PHE E 205 " --> pdb=" O ASP E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 219 Processing helix chain 'E' and resid 220 through 261 Proline residue: E 226 - end of helix removed outlier: 3.867A pdb=" N SER E 231 " --> pdb=" O ALA E 227 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS E 234 " --> pdb=" O THR E 230 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET E 242 " --> pdb=" O GLN E 238 " (cutoff:3.500A) Proline residue: E 246 - end of helix Processing helix chain 'E' and resid 272 through 283 Processing helix chain 'E' and resid 285 through 295 removed outlier: 3.583A pdb=" N GLY E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 29 removed outlier: 5.914A pdb=" N TRP F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Proline residue: F 18 - end of helix removed outlier: 3.915A pdb=" N VAL F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 53 removed outlier: 3.577A pdb=" N ALA F 48 " --> pdb=" O TYR F 44 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR F 50 " --> pdb=" O GLY F 46 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 107 removed outlier: 3.570A pdb=" N ILE F 74 " --> pdb=" O GLN F 70 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN F 78 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR F 89 " --> pdb=" O MET F 85 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE F 96 " --> pdb=" O LEU F 92 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU F 99 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET F 105 " --> pdb=" O GLN F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 116 Processing helix chain 'F' and resid 124 through 141 removed outlier: 3.551A pdb=" N GLN F 128 " --> pdb=" O PRO F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 158 removed outlier: 3.773A pdb=" N LYS F 146 " --> pdb=" O ASP F 142 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL F 151 " --> pdb=" O MET F 147 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LYS F 156 " --> pdb=" O VAL F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 174 removed outlier: 3.601A pdb=" N ARG F 171 " --> pdb=" O THR F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 209 removed outlier: 3.583A pdb=" N ILE F 179 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 185 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER F 188 " --> pdb=" O SER F 184 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N SER F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY F 191 " --> pdb=" O VAL F 187 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA F 194 " --> pdb=" O SER F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 234 removed outlier: 3.635A pdb=" N LEU F 224 " --> pdb=" O SER F 220 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU F 234 " --> pdb=" O CYS F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 256 removed outlier: 3.614A pdb=" N ILE F 243 " --> pdb=" O THR F 239 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN F 246 " --> pdb=" O GLU F 242 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU F 247 " --> pdb=" O ILE F 243 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE F 252 " --> pdb=" O THR F 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 42 Proline residue: G 27 - end of helix Processing helix chain 'G' and resid 50 through 65 Processing helix chain 'G' and resid 65 through 83 Processing helix chain 'G' and resid 84 through 89 Processing helix chain 'H' and resid 2 through 42 Proline residue: H 27 - end of helix Processing helix chain 'H' and resid 50 through 65 Processing helix chain 'H' and resid 65 through 83 Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'I' and resid 2 through 42 Proline residue: I 27 - end of helix Processing helix chain 'I' and resid 50 through 65 Processing helix chain 'I' and resid 65 through 83 Processing helix chain 'I' and resid 84 through 89 Processing helix chain 'J' and resid 2 through 42 Proline residue: J 27 - end of helix Processing helix chain 'J' and resid 50 through 65 Processing helix chain 'J' and resid 65 through 83 Processing helix chain 'J' and resid 84 through 89 Processing helix chain 'K' and resid 32 through 66 removed outlier: 3.909A pdb=" N VAL K 38 " --> pdb=" O ALA K 34 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU K 39 " --> pdb=" O SER K 35 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU K 46 " --> pdb=" O GLY K 42 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP K 48 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA K 52 " --> pdb=" O TRP K 48 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN K 55 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER K 66 " --> pdb=" O GLN K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 109 removed outlier: 3.579A pdb=" N ILE K 81 " --> pdb=" O LYS K 77 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU K 91 " --> pdb=" O VAL K 87 " (cutoff:3.500A) Proline residue: K 92 - end of helix Processing helix chain 'K' and resid 129 through 138 Processing helix chain 'K' and resid 139 through 167 removed outlier: 3.630A pdb=" N VAL K 153 " --> pdb=" O SER K 149 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET K 154 " --> pdb=" O ILE K 150 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL K 156 " --> pdb=" O LYS K 152 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE K 161 " --> pdb=" O ALA K 157 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR K 162 " --> pdb=" O GLY K 158 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE K 164 " --> pdb=" O ALA K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 173 Processing helix chain 'K' and resid 178 through 200 removed outlier: 3.986A pdb=" N ILE K 183 " --> pdb=" O TYR K 179 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE K 184 " --> pdb=" O PRO K 180 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE K 189 " --> pdb=" O HIS K 185 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU K 191 " --> pdb=" O LEU K 187 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN K 192 " --> pdb=" O ASP K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 219 Proline residue: K 210 - end of helix removed outlier: 3.603A pdb=" N ALA K 217 " --> pdb=" O ILE K 213 " (cutoff:3.500A) 940 hydrogen bonds defined for protein. 2799 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: 4.00 Time building geometry restraints manager: 6.00 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: 4130 1.34 - 1.46: 2410 1.46 - 1.57: 7314 1.57 - 1.69: 0 1.69 - 1.81: 284 Bond restraints: 14138 Sorted by residual: bond pdb=" CA ASN C 161 " pdb=" C ASN C 161 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.72e-02 3.38e+03 5.63e+00 bond pdb=" CB ILE E 289 " pdb=" CG2 ILE E 289 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.94e+00 bond pdb=" CG LEU F 234 " pdb=" CD2 LEU F 234 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.49e+00 bond pdb=" CB VAL F 151 " pdb=" CG2 VAL F 151 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.36e+00 bond pdb=" C PHE A 244 " pdb=" N LEU A 245 " ideal model delta sigma weight residual 1.337 1.308 0.029 1.61e-02 3.86e+03 3.19e+00 ... (remaining 14133 not shown) Histogram of bond angle deviations from ideal: 96.29 - 103.84: 308 103.84 - 111.39: 6260 111.39 - 118.94: 5314 118.94 - 126.50: 7121 126.50 - 134.05: 175 Bond angle restraints: 19178 Sorted by residual: angle pdb=" N MET E 269 " pdb=" CA MET E 269 " pdb=" C MET E 269 " ideal model delta sigma weight residual 114.56 108.01 6.55 1.27e+00 6.20e-01 2.66e+01 angle pdb=" C ASN C 173 " pdb=" N GLU C 174 " pdb=" CA GLU C 174 " ideal model delta sigma weight residual 121.54 130.67 -9.13 1.91e+00 2.74e-01 2.29e+01 angle pdb=" N VAL E 283 " pdb=" CA VAL E 283 " pdb=" C VAL E 283 " ideal model delta sigma weight residual 112.80 107.66 5.14 1.15e+00 7.56e-01 2.00e+01 angle pdb=" C GLN C 137 " pdb=" N THR C 138 " pdb=" CA THR C 138 " ideal model delta sigma weight residual 121.80 131.98 -10.18 2.44e+00 1.68e-01 1.74e+01 angle pdb=" C GLY E 262 " pdb=" N MET E 263 " pdb=" CA MET E 263 " ideal model delta sigma weight residual 121.54 129.27 -7.73 1.91e+00 2.74e-01 1.64e+01 ... (remaining 19173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7545 17.89 - 35.77: 734 35.77 - 53.66: 162 53.66 - 71.54: 38 71.54 - 89.43: 12 Dihedral angle restraints: 8491 sinusoidal: 3331 harmonic: 5160 Sorted by residual: dihedral pdb=" CA THR C 138 " pdb=" C THR C 138 " pdb=" N PRO C 139 " pdb=" CA PRO C 139 " ideal model delta harmonic sigma weight residual 180.00 107.39 72.61 0 5.00e+00 4.00e-02 2.11e+02 dihedral pdb=" CA THR A 138 " pdb=" C THR A 138 " pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta harmonic sigma weight residual -180.00 -122.96 -57.04 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA ILE F 256 " pdb=" C ILE F 256 " pdb=" N ARG F 257 " pdb=" CA ARG F 257 " ideal model delta harmonic sigma weight residual -180.00 -132.33 -47.67 0 5.00e+00 4.00e-02 9.09e+01 ... (remaining 8488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1329 0.041 - 0.081: 791 0.081 - 0.122: 203 0.122 - 0.163: 32 0.163 - 0.204: 4 Chirality restraints: 2359 Sorted by residual: chirality pdb=" CB ILE K 75 " pdb=" CA ILE K 75 " pdb=" CG1 ILE K 75 " pdb=" CG2 ILE K 75 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA THR B 138 " pdb=" N THR B 138 " pdb=" C THR B 138 " pdb=" CB THR B 138 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CG LEU F 133 " pdb=" CB LEU F 133 " pdb=" CD1 LEU F 133 " pdb=" CD2 LEU F 133 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 2356 not shown) Planarity restraints: 2329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 138 " -0.084 5.00e-02 4.00e+02 1.28e-01 2.63e+01 pdb=" N PRO C 139 " 0.222 5.00e-02 4.00e+02 pdb=" CA PRO C 139 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO C 139 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 138 " 0.073 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO A 139 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 169 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO C 170 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 170 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 170 " -0.029 5.00e-02 4.00e+02 ... (remaining 2326 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 144 2.62 - 3.19: 13104 3.19 - 3.76: 21598 3.76 - 4.33: 30500 4.33 - 4.90: 50297 Nonbonded interactions: 115643 Sorted by model distance: nonbonded pdb=" O GLU C 174 " pdb=" N ILE C 176 " model vdw 2.050 2.520 nonbonded pdb=" O GLU D 174 " pdb=" N ILE D 176 " model vdw 2.066 2.520 nonbonded pdb=" O MET I 63 " pdb=" NZ LYS J 11 " model vdw 2.069 2.520 nonbonded pdb=" NH1 ARG B 121 " pdb=" OG SER B 296 " model vdw 2.124 2.520 nonbonded pdb=" O SER C 267 " pdb=" OG SER C 267 " model vdw 2.169 2.440 ... (remaining 115638 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 109 through 299) selection = (chain 'C' and resid 109 through 299) selection = (chain 'D' and resid 109 through 299) selection = (chain 'E' and resid 109 through 299) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.990 Check model and map are aligned: 0.210 Set scattering table: 0.160 Process input model: 38.310 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 0.010 0.067 14138 Z= 0.630 Angle : 0.934 10.179 19178 Z= 0.516 Chirality : 0.051 0.204 2359 Planarity : 0.007 0.128 2329 Dihedral : 15.446 89.429 5111 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.84 % Favored : 93.64 % Rotamer: Outliers : 2.72 % Allowed : 9.96 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.24 % 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: -3.51 (0.17), residues: 1746 helix: -1.85 (0.12), residues: 1410 sheet: None (None), residues: 0 loop : -3.56 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K 48 HIS 0.005 0.002 HIS F 144 PHE 0.027 0.003 PHE K 101 TYR 0.020 0.002 TYR F 244 ARG 0.006 0.001 ARG G 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 370 time to evaluate : 1.532 Fit side-chains REVERT: B 160 PHE cc_start: 0.8387 (m-80) cc_final: 0.8107 (m-10) REVERT: B 187 GLU cc_start: 0.7544 (tp30) cc_final: 0.7254 (tm-30) REVERT: B 190 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8393 (tttt) REVERT: B 208 MET cc_start: 0.6992 (mmm) cc_final: 0.6588 (mmt) REVERT: C 232 GLU cc_start: 0.7627 (tt0) cc_final: 0.7393 (tt0) REVERT: C 251 ASP cc_start: 0.7622 (m-30) cc_final: 0.7408 (m-30) REVERT: D 242 MET cc_start: 0.7868 (mmt) cc_final: 0.7342 (mmm) REVERT: F 249 GLU cc_start: 0.7479 (tt0) cc_final: 0.7266 (tt0) REVERT: G 13 SER cc_start: 0.8649 (OUTLIER) cc_final: 0.8414 (m) REVERT: G 35 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8628 (t) REVERT: H 31 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8448 (tt) REVERT: H 49 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8139 (tp) REVERT: I 14 LEU cc_start: 0.8839 (mm) cc_final: 0.8541 (mt) REVERT: I 35 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8407 (t) REVERT: I 49 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7610 (mp) REVERT: J 49 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7766 (tt) REVERT: J 57 ILE cc_start: 0.9010 (mm) cc_final: 0.8784 (tp) REVERT: K 31 LYS cc_start: 0.8093 (pttt) cc_final: 0.7412 (mttm) REVERT: K 187 LEU cc_start: 0.8836 (mt) cc_final: 0.8588 (mt) outliers start: 42 outliers final: 7 residues processed: 402 average time/residue: 0.2306 time to fit residues: 138.8790 Evaluate side-chains 319 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 305 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 49 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 186 GLN B 212 GLN C 142 GLN C 212 GLN D 142 GLN D 196 GLN E 131 GLN ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 GLN F 121 GLN F 240 HIS G 39 GLN G 86 GLN H 39 GLN H 86 GLN I 39 GLN I 47 GLN I 86 GLN J 39 GLN K 129 ASN K 185 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14138 Z= 0.215 Angle : 0.709 10.622 19178 Z= 0.350 Chirality : 0.042 0.258 2359 Planarity : 0.006 0.113 2329 Dihedral : 6.715 69.646 1839 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.04 % Favored : 94.62 % Rotamer: Outliers : 2.72 % Allowed : 16.95 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % 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: -1.28 (0.20), residues: 1746 helix: -0.27 (0.14), residues: 1411 sheet: None (None), residues: 0 loop : -2.94 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 48 HIS 0.003 0.001 HIS I 67 PHE 0.023 0.002 PHE A 119 TYR 0.011 0.002 TYR K 179 ARG 0.004 0.000 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 335 time to evaluate : 1.611 Fit side-chains revert: symmetry clash REVERT: B 190 LYS cc_start: 0.8660 (ttmm) cc_final: 0.8286 (tttt) REVERT: B 208 MET cc_start: 0.6726 (mmm) cc_final: 0.6467 (mmt) REVERT: B 232 GLU cc_start: 0.7609 (tp30) cc_final: 0.7206 (tt0) REVERT: C 130 ARG cc_start: 0.8716 (ttp-170) cc_final: 0.8494 (ttp80) REVERT: C 156 MET cc_start: 0.8464 (mmm) cc_final: 0.8226 (mmm) REVERT: C 160 PHE cc_start: 0.7522 (m-10) cc_final: 0.7252 (m-10) REVERT: C 200 LYS cc_start: 0.8358 (tmmt) cc_final: 0.8144 (ttpp) REVERT: C 242 MET cc_start: 0.7829 (mmt) cc_final: 0.7154 (mmt) REVERT: D 131 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7898 (mt0) REVERT: D 156 MET cc_start: 0.7790 (mmm) cc_final: 0.7436 (mmm) REVERT: D 194 LEU cc_start: 0.8718 (tp) cc_final: 0.8482 (tp) REVERT: D 242 MET cc_start: 0.7824 (mmt) cc_final: 0.7284 (mmt) REVERT: E 126 MET cc_start: 0.7719 (mmt) cc_final: 0.7052 (mmt) REVERT: E 182 PHE cc_start: 0.8467 (t80) cc_final: 0.8212 (t80) REVERT: E 289 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8549 (mt) REVERT: I 14 LEU cc_start: 0.8786 (mm) cc_final: 0.8478 (mt) REVERT: I 49 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7670 (mp) REVERT: I 80 MET cc_start: 0.7006 (mtm) cc_final: 0.6562 (ptp) REVERT: J 82 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7408 (mt-10) REVERT: K 31 LYS cc_start: 0.7726 (pttt) cc_final: 0.7258 (mttp) outliers start: 42 outliers final: 16 residues processed: 358 average time/residue: 0.2345 time to fit residues: 125.7454 Evaluate side-chains 319 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 299 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 138 optimal weight: 0.0040 chunk 154 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 GLN I 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14138 Z= 0.189 Angle : 0.660 9.446 19178 Z= 0.323 Chirality : 0.041 0.208 2359 Planarity : 0.005 0.106 2329 Dihedral : 5.789 69.594 1825 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.38 % Favored : 94.39 % Rotamer: Outliers : 3.49 % Allowed : 17.98 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.20), residues: 1746 helix: 0.48 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -2.85 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 48 HIS 0.002 0.000 HIS I 67 PHE 0.019 0.001 PHE C 119 TYR 0.013 0.001 TYR E 171 ARG 0.003 0.000 ARG H 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 309 time to evaluate : 1.515 Fit side-chains revert: symmetry clash REVERT: B 174 GLU cc_start: 0.6585 (mt-10) cc_final: 0.6336 (mt-10) REVERT: B 190 LYS cc_start: 0.8693 (ttmm) cc_final: 0.8451 (tttt) REVERT: B 208 MET cc_start: 0.6612 (mmm) cc_final: 0.6409 (mmt) REVERT: B 232 GLU cc_start: 0.7640 (tp30) cc_final: 0.7192 (tt0) REVERT: C 160 PHE cc_start: 0.7510 (m-10) cc_final: 0.7194 (m-10) REVERT: E 114 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7333 (tp) REVERT: E 115 LEU cc_start: 0.7938 (mt) cc_final: 0.7735 (mm) REVERT: E 126 MET cc_start: 0.7736 (mmt) cc_final: 0.7072 (mmt) REVERT: E 182 PHE cc_start: 0.8436 (t80) cc_final: 0.8172 (t80) REVERT: F 87 MET cc_start: 0.7881 (mmm) cc_final: 0.7600 (mmt) REVERT: F 181 PHE cc_start: 0.8320 (m-80) cc_final: 0.8006 (m-80) REVERT: H 83 ARG cc_start: 0.8206 (tpp80) cc_final: 0.7412 (ttm-80) REVERT: I 49 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7631 (mp) REVERT: I 80 MET cc_start: 0.7061 (mtm) cc_final: 0.6590 (ptp) REVERT: K 31 LYS cc_start: 0.7491 (pttt) cc_final: 0.7262 (mttp) outliers start: 54 outliers final: 22 residues processed: 337 average time/residue: 0.2303 time to fit residues: 117.0268 Evaluate side-chains 315 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 291 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 203 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN E 196 GLN K 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14138 Z= 0.200 Angle : 0.647 9.529 19178 Z= 0.315 Chirality : 0.040 0.161 2359 Planarity : 0.005 0.104 2329 Dihedral : 5.474 67.957 1822 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.15 % Favored : 94.62 % Rotamer: Outliers : 3.30 % Allowed : 19.73 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1746 helix: 0.85 (0.14), residues: 1422 sheet: None (None), residues: 0 loop : -2.63 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 48 HIS 0.001 0.000 HIS F 144 PHE 0.020 0.001 PHE C 119 TYR 0.009 0.001 TYR F 244 ARG 0.003 0.000 ARG J 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 298 time to evaluate : 1.730 Fit side-chains revert: symmetry clash REVERT: B 174 GLU cc_start: 0.6590 (mt-10) cc_final: 0.6337 (mt-10) REVERT: B 190 LYS cc_start: 0.8630 (ttmm) cc_final: 0.8414 (tttt) REVERT: B 232 GLU cc_start: 0.7592 (tp30) cc_final: 0.7101 (tt0) REVERT: C 156 MET cc_start: 0.8008 (mmm) cc_final: 0.7485 (mtp) REVERT: C 160 PHE cc_start: 0.7530 (m-10) cc_final: 0.7203 (m-10) REVERT: D 131 GLN cc_start: 0.7920 (tt0) cc_final: 0.7679 (mt0) REVERT: D 259 MET cc_start: 0.8214 (tpp) cc_final: 0.7952 (tpt) REVERT: E 114 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7374 (tp) REVERT: E 182 PHE cc_start: 0.8416 (t80) cc_final: 0.8184 (t80) REVERT: F 87 MET cc_start: 0.7896 (mmm) cc_final: 0.7614 (mmt) REVERT: F 181 PHE cc_start: 0.8313 (m-80) cc_final: 0.8016 (m-80) REVERT: I 49 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7610 (mp) REVERT: I 80 MET cc_start: 0.7050 (mtm) cc_final: 0.6691 (ptp) REVERT: K 152 LYS cc_start: 0.8045 (mtmt) cc_final: 0.7833 (mttt) outliers start: 51 outliers final: 28 residues processed: 328 average time/residue: 0.2226 time to fit residues: 110.4187 Evaluate side-chains 315 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 285 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 68 ASP Chi-restraints excluded: chain K residue 203 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN D 142 GLN ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14138 Z= 0.195 Angle : 0.636 9.353 19178 Z= 0.309 Chirality : 0.040 0.176 2359 Planarity : 0.005 0.104 2329 Dihedral : 5.409 67.303 1822 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.10 % Favored : 94.67 % Rotamer: Outliers : 3.30 % Allowed : 20.31 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1746 helix: 1.09 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -2.58 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 68 HIS 0.001 0.000 HIS F 144 PHE 0.018 0.001 PHE A 119 TYR 0.015 0.001 TYR F 241 ARG 0.002 0.000 ARG I 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 293 time to evaluate : 1.566 Fit side-chains revert: symmetry clash REVERT: B 187 GLU cc_start: 0.7418 (tp30) cc_final: 0.7187 (tm-30) REVERT: B 190 LYS cc_start: 0.8608 (ttmm) cc_final: 0.8408 (tttt) REVERT: B 232 GLU cc_start: 0.7579 (tp30) cc_final: 0.7100 (tt0) REVERT: D 208 MET cc_start: 0.7303 (tpp) cc_final: 0.7087 (tpp) REVERT: D 259 MET cc_start: 0.8196 (tpp) cc_final: 0.7914 (tpt) REVERT: E 114 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7386 (tp) REVERT: E 182 PHE cc_start: 0.8402 (t80) cc_final: 0.8168 (t80) REVERT: F 87 MET cc_start: 0.7887 (mmm) cc_final: 0.7643 (mmt) REVERT: F 181 PHE cc_start: 0.8302 (m-80) cc_final: 0.8034 (m-80) REVERT: I 49 LEU cc_start: 0.7947 (tt) cc_final: 0.7605 (mp) REVERT: I 80 MET cc_start: 0.7044 (mtm) cc_final: 0.6696 (ptp) outliers start: 51 outliers final: 31 residues processed: 323 average time/residue: 0.2281 time to fit residues: 111.2948 Evaluate side-chains 311 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 279 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 68 ASP Chi-restraints excluded: chain K residue 203 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 97 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14138 Z= 0.181 Angle : 0.630 9.108 19178 Z= 0.305 Chirality : 0.040 0.176 2359 Planarity : 0.005 0.103 2329 Dihedral : 5.262 66.170 1820 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.15 % Favored : 94.62 % Rotamer: Outliers : 3.49 % Allowed : 20.25 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.21), residues: 1746 helix: 1.32 (0.14), residues: 1421 sheet: None (None), residues: 0 loop : -2.43 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 68 HIS 0.001 0.000 HIS F 144 PHE 0.018 0.001 PHE C 119 TYR 0.012 0.001 TYR F 241 ARG 0.002 0.000 ARG G 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 287 time to evaluate : 1.558 Fit side-chains revert: symmetry clash REVERT: B 133 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7188 (mpp) REVERT: B 208 MET cc_start: 0.7002 (mmt) cc_final: 0.6452 (mmt) REVERT: B 232 GLU cc_start: 0.7558 (tp30) cc_final: 0.7067 (tt0) REVERT: B 259 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.7085 (mmm) REVERT: D 131 GLN cc_start: 0.7804 (tt0) cc_final: 0.7579 (mt0) REVERT: D 149 LEU cc_start: 0.8466 (tp) cc_final: 0.8229 (mp) REVERT: D 156 MET cc_start: 0.7637 (mmm) cc_final: 0.7192 (mmm) REVERT: D 259 MET cc_start: 0.8168 (tpp) cc_final: 0.7882 (tpt) REVERT: E 114 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7430 (tp) REVERT: F 87 MET cc_start: 0.7861 (mmm) cc_final: 0.7604 (mmt) REVERT: F 181 PHE cc_start: 0.8287 (m-80) cc_final: 0.7999 (m-80) REVERT: H 80 MET cc_start: 0.8009 (mmt) cc_final: 0.7776 (mmt) REVERT: I 49 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7592 (mp) REVERT: I 80 MET cc_start: 0.7019 (mtm) cc_final: 0.6659 (ptp) outliers start: 54 outliers final: 29 residues processed: 317 average time/residue: 0.2202 time to fit residues: 105.9210 Evaluate side-chains 312 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 279 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 137 MET Chi-restraints excluded: chain K residue 203 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14138 Z= 0.198 Angle : 0.639 11.791 19178 Z= 0.308 Chirality : 0.041 0.177 2359 Planarity : 0.005 0.103 2329 Dihedral : 5.242 65.316 1820 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.15 % Favored : 94.62 % Rotamer: Outliers : 3.17 % Allowed : 21.02 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % 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: 1.11 (0.21), residues: 1746 helix: 1.43 (0.14), residues: 1422 sheet: None (None), residues: 0 loop : -2.40 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 286 HIS 0.001 0.000 HIS F 144 PHE 0.018 0.001 PHE A 119 TYR 0.012 0.001 TYR F 241 ARG 0.004 0.000 ARG K 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 291 time to evaluate : 1.656 Fit side-chains revert: symmetry clash REVERT: B 133 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7059 (mpp) REVERT: B 208 MET cc_start: 0.7008 (mmt) cc_final: 0.6436 (mmt) REVERT: B 232 GLU cc_start: 0.7588 (tp30) cc_final: 0.7076 (tt0) REVERT: D 149 LEU cc_start: 0.8516 (tp) cc_final: 0.8260 (mp) REVERT: D 259 MET cc_start: 0.8179 (tpp) cc_final: 0.7859 (tpt) REVERT: E 114 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7425 (tp) REVERT: F 87 MET cc_start: 0.7883 (mmm) cc_final: 0.7636 (mmt) REVERT: H 9 LEU cc_start: 0.8238 (tp) cc_final: 0.7957 (tp) REVERT: I 80 MET cc_start: 0.7078 (mtm) cc_final: 0.6675 (ptp) REVERT: K 137 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6818 (ttp) outliers start: 49 outliers final: 30 residues processed: 318 average time/residue: 0.2373 time to fit residues: 113.9164 Evaluate side-chains 311 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 278 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 137 MET Chi-restraints excluded: chain K residue 203 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14138 Z= 0.203 Angle : 0.649 10.042 19178 Z= 0.312 Chirality : 0.041 0.180 2359 Planarity : 0.005 0.103 2329 Dihedral : 5.228 64.799 1820 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.27 % Favored : 94.50 % Rotamer: Outliers : 3.23 % Allowed : 20.96 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % 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: 1.21 (0.21), residues: 1746 helix: 1.49 (0.14), residues: 1422 sheet: None (None), residues: 0 loop : -2.33 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 68 HIS 0.002 0.000 HIS F 144 PHE 0.017 0.001 PHE C 119 TYR 0.011 0.001 TYR F 241 ARG 0.002 0.000 ARG E 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 282 time to evaluate : 1.565 Fit side-chains revert: symmetry clash REVERT: B 133 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7072 (mpp) REVERT: B 208 MET cc_start: 0.6957 (mmt) cc_final: 0.6410 (mmt) REVERT: B 232 GLU cc_start: 0.7591 (tp30) cc_final: 0.7074 (tt0) REVERT: B 259 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.7106 (mmm) REVERT: D 149 LEU cc_start: 0.8530 (tp) cc_final: 0.8308 (mp) REVERT: D 156 MET cc_start: 0.7558 (mmm) cc_final: 0.7185 (mmm) REVERT: E 114 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7376 (tp) REVERT: F 87 MET cc_start: 0.7892 (mmm) cc_final: 0.7635 (mmt) REVERT: I 80 MET cc_start: 0.7099 (mtm) cc_final: 0.6695 (ptp) REVERT: K 137 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6834 (ttp) outliers start: 50 outliers final: 35 residues processed: 305 average time/residue: 0.2457 time to fit residues: 114.2494 Evaluate side-chains 318 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 279 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 137 MET Chi-restraints excluded: chain K residue 203 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 120 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 GLN ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14138 Z= 0.183 Angle : 0.639 9.706 19178 Z= 0.309 Chirality : 0.040 0.183 2359 Planarity : 0.005 0.102 2329 Dihedral : 5.203 63.945 1820 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.27 % Favored : 94.56 % Rotamer: Outliers : 3.04 % Allowed : 21.09 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % 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: 1.33 (0.21), residues: 1746 helix: 1.57 (0.14), residues: 1422 sheet: None (None), residues: 0 loop : -2.23 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 68 HIS 0.002 0.000 HIS F 144 PHE 0.017 0.001 PHE C 119 TYR 0.011 0.001 TYR F 241 ARG 0.002 0.000 ARG K 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 285 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: B 133 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7123 (mpp) REVERT: B 232 GLU cc_start: 0.7607 (tp30) cc_final: 0.7094 (tt0) REVERT: B 259 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.7087 (mmm) REVERT: B 284 ASP cc_start: 0.8215 (t0) cc_final: 0.7982 (t0) REVERT: D 149 LEU cc_start: 0.8562 (tp) cc_final: 0.8310 (mp) REVERT: D 259 MET cc_start: 0.8070 (tpp) cc_final: 0.7780 (tpt) REVERT: E 114 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7429 (tp) REVERT: F 87 MET cc_start: 0.7835 (mmm) cc_final: 0.7591 (mmt) REVERT: I 80 MET cc_start: 0.7086 (mtm) cc_final: 0.6683 (ptp) REVERT: J 64 PHE cc_start: 0.8186 (t80) cc_final: 0.7902 (t80) REVERT: K 137 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6840 (ttp) REVERT: K 187 LEU cc_start: 0.8439 (mm) cc_final: 0.8197 (mt) outliers start: 47 outliers final: 32 residues processed: 309 average time/residue: 0.2266 time to fit residues: 106.2891 Evaluate side-chains 309 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 273 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 137 MET Chi-restraints excluded: chain K residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 5.9990 chunk 99 optimal weight: 0.0020 chunk 77 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 170 optimal weight: 0.0870 chunk 156 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.5970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN K 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14138 Z= 0.175 Angle : 0.638 9.399 19178 Z= 0.307 Chirality : 0.040 0.179 2359 Planarity : 0.005 0.101 2329 Dihedral : 5.144 62.727 1820 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.21 % Favored : 94.67 % Rotamer: Outliers : 2.33 % Allowed : 22.06 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.21), residues: 1746 helix: 1.71 (0.14), residues: 1415 sheet: None (None), residues: 0 loop : -2.17 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 68 HIS 0.001 0.000 HIS I 67 PHE 0.021 0.001 PHE H 76 TYR 0.011 0.001 TYR F 241 ARG 0.002 0.000 ARG H 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 284 time to evaluate : 1.487 Fit side-chains revert: symmetry clash REVERT: A 193 MET cc_start: 0.7671 (mtt) cc_final: 0.7213 (mtt) REVERT: B 133 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7102 (mpp) REVERT: B 232 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7095 (tt0) REVERT: B 284 ASP cc_start: 0.8215 (t0) cc_final: 0.7987 (t0) REVERT: C 251 ASP cc_start: 0.7547 (m-30) cc_final: 0.7331 (m-30) REVERT: D 149 LEU cc_start: 0.8571 (tp) cc_final: 0.8333 (mp) REVERT: D 259 MET cc_start: 0.8143 (tpp) cc_final: 0.7731 (tpt) REVERT: E 114 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7361 (tp) REVERT: F 87 MET cc_start: 0.7849 (mmm) cc_final: 0.7614 (mmt) REVERT: I 1 MET cc_start: 0.2056 (mtt) cc_final: 0.0630 (mtt) REVERT: I 80 MET cc_start: 0.7041 (mtm) cc_final: 0.6653 (ptp) REVERT: J 64 PHE cc_start: 0.8172 (t80) cc_final: 0.7931 (t80) REVERT: K 137 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6843 (ttp) REVERT: K 187 LEU cc_start: 0.8381 (mm) cc_final: 0.8149 (mt) outliers start: 36 outliers final: 29 residues processed: 300 average time/residue: 0.2199 time to fit residues: 100.5857 Evaluate side-chains 307 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 274 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 137 MET Chi-restraints excluded: chain K residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.0670 chunk 41 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 0.0370 chunk 135 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 119 optimal weight: 0.5980 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.164649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.138194 restraints weight = 15618.315| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.48 r_work: 0.3364 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14138 Z= 0.158 Angle : 0.634 9.388 19178 Z= 0.306 Chirality : 0.040 0.177 2359 Planarity : 0.005 0.100 2329 Dihedral : 5.057 60.907 1820 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.27 % Favored : 94.56 % Rotamer: Outliers : 2.33 % Allowed : 22.06 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % 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: 1.73 (0.21), residues: 1746 helix: 1.87 (0.14), residues: 1409 sheet: None (None), residues: 0 loop : -2.09 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 68 HIS 0.001 0.000 HIS I 67 PHE 0.024 0.001 PHE H 76 TYR 0.011 0.001 TYR E 171 ARG 0.002 0.000 ARG G 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3311.17 seconds wall clock time: 60 minutes 27.39 seconds (3627.39 seconds total)