Starting phenix.real_space_refine on Fri Mar 15 17:27:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3s_10096/03_2024/6s3s_10096.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3s_10096/03_2024/6s3s_10096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3s_10096/03_2024/6s3s_10096.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3s_10096/03_2024/6s3s_10096.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3s_10096/03_2024/6s3s_10096.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3s_10096/03_2024/6s3s_10096.pdb" } resolution = 4.1 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= 0.001 sd= 0.006 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 138 5.16 5 C 8224 2.51 5 N 1870 2.21 5 O 2089 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 179": "NH1" <-> "NH2" Residue "A PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 201": "OD1" <-> "OD2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 251": "OD1" <-> "OD2" Residue "E PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 116": "OD1" <-> "OD2" Residue "F PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "F ARG 207": "NH1" <-> "NH2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F ARG 257": "NH1" <-> "NH2" Residue "F TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12321 Number of models: 1 Model: "" Number of chains: 10 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: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1520 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain: "E" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1454 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 9, 'TRANS': 177} Chain: "F" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2000 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} 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: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 660 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain breaks: 1 Time building chain proxies: 6.75, per 1000 atoms: 0.55 Number of scatterers: 12321 At special positions: 0 Unit cell: (100.284, 100.284, 123.3, 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 138 16.00 O 2089 8.00 N 1870 7.00 C 8224 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: 5.18 Conformation dependent library (CDL) restraints added in 2.2 seconds 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3008 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 0 sheets defined 83.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 110 through 117 removed outlier: 4.204A pdb=" N ILE A 114 " --> pdb=" O PRO A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 133 removed outlier: 3.616A pdb=" N MET A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 156 Processing helix chain 'A' and resid 156 through 165 Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 177 through 195 removed outlier: 3.534A pdb=" N ALA A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Proline residue: A 188 - end of helix Processing helix chain 'A' and resid 198 through 210 removed outlier: 3.521A pdb=" N GLY A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 262 Proline residue: A 226 - end of helix Proline residue: A 246 - end of helix removed outlier: 3.690A pdb=" N ASP A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 283 removed outlier: 3.791A pdb=" N VAL A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 296 removed outlier: 4.337A pdb=" N SER A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 115 removed outlier: 3.585A pdb=" N LEU B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 133 removed outlier: 3.647A pdb=" N ILE B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 156 removed outlier: 4.165A pdb=" N GLY B 146 " --> pdb=" O GLN B 142 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 149 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 167 Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 179 through 195 removed outlier: 3.872A pdb=" N ASP B 183 " --> pdb=" O ARG B 179 " (cutoff:3.500A) Proline residue: B 188 - end of helix removed outlier: 3.674A pdb=" N LYS B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 209 removed outlier: 3.823A pdb=" N LEU B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 219 removed outlier: 3.536A pdb=" N VAL B 219 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 262 Proline residue: B 226 - end of helix removed outlier: 3.843A pdb=" N THR B 230 " --> pdb=" O PRO B 226 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Proline residue: B 246 - end of helix removed outlier: 4.387A pdb=" N MET B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 removed outlier: 3.523A pdb=" N VAL B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 283 Processing helix chain 'B' and resid 285 through 296 Processing helix chain 'C' and resid 108 through 113 Processing helix chain 'C' and resid 119 through 133 removed outlier: 3.576A pdb=" N VAL C 123 " --> pdb=" O PHE C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 156 Processing helix chain 'C' and resid 156 through 167 removed outlier: 3.710A pdb=" N GLN C 162 " --> pdb=" O PRO C 158 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 172 Processing helix chain 'C' and resid 179 through 185 removed outlier: 3.545A pdb=" N ASP C 183 " --> pdb=" O ARG C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 194 removed outlier: 4.015A pdb=" N MET C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 208 removed outlier: 4.052A pdb=" N THR C 204 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 3.554A 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 261 Proline residue: C 226 - end of helix removed outlier: 4.015A pdb=" N LYS C 234 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C 245 " --> pdb=" O PHE C 241 " (cutoff:3.500A) Proline residue: C 246 - end of helix removed outlier: 3.542A pdb=" N ASP C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 283 Processing helix chain 'C' and resid 285 through 297 Processing helix chain 'D' and resid 108 through 117 removed outlier: 3.655A pdb=" N MET D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE D 114 " --> pdb=" O PRO D 110 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 133 removed outlier: 4.729A pdb=" N ILE D 122 " --> pdb=" O SER D 118 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 123 " --> pdb=" O PHE D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 168 removed outlier: 3.931A pdb=" N ILE D 145 " --> pdb=" O ASN D 141 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY D 146 " --> pdb=" O GLN D 142 " (cutoff:3.500A) Proline residue: D 158 - end of helix Processing helix chain 'D' and resid 169 through 173 Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.504A pdb=" N ALA D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Proline residue: D 188 - end of helix removed outlier: 3.754A pdb=" N LYS D 195 " --> pdb=" O ALA D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 210 removed outlier: 3.906A pdb=" N LEU D 202 " --> pdb=" O ARG D 198 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET D 208 " --> pdb=" O THR D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 219 removed outlier: 3.551A pdb=" N VAL D 219 " --> pdb=" O PRO D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 262 Proline residue: D 226 - end of helix removed outlier: 3.746A pdb=" N THR D 230 " --> pdb=" O PRO D 226 " (cutoff:3.500A) removed outlier: 3.987A 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 271 through 283 removed outlier: 4.427A pdb=" N PHE D 275 " --> pdb=" O VAL D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 297 removed outlier: 3.516A pdb=" N PHE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 133 removed outlier: 3.555A pdb=" N VAL E 124 " --> pdb=" O THR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 167 removed outlier: 3.649A pdb=" N ILE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE E 153 " --> pdb=" O LEU E 149 " (cutoff:3.500A) Proline residue: E 158 - end of helix removed outlier: 3.951A pdb=" N ALA E 167 " --> pdb=" O ILE E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 173 Processing helix chain 'E' and resid 177 through 195 removed outlier: 3.644A pdb=" N GLN E 186 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU E 187 " --> pdb=" O ASP E 183 " (cutoff:3.500A) Proline residue: E 188 - end of helix removed outlier: 3.697A pdb=" N LYS E 195 " --> pdb=" O ALA E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 209 Processing helix chain 'E' and resid 215 through 219 Processing helix chain 'E' and resid 220 through 262 Proline residue: E 226 - end of helix removed outlier: 3.837A 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 267 through 279 removed outlier: 3.675A pdb=" N VAL E 271 " --> pdb=" O SER E 267 " (cutoff:3.500A) Proline residue: E 274 - end of helix Processing helix chain 'E' and resid 285 through 296 removed outlier: 3.525A pdb=" N ILE E 289 " --> pdb=" O GLY E 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 27 Processing helix chain 'F' and resid 38 through 54 removed outlier: 3.575A pdb=" N ARG F 42 " --> pdb=" O PRO F 38 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 107 removed outlier: 3.597A pdb=" N ILE F 74 " --> pdb=" O GLN F 70 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR F 89 " --> pdb=" O MET F 85 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE F 96 " --> pdb=" O LEU F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 116 Processing helix chain 'F' and resid 125 through 141 removed outlier: 3.628A pdb=" N LEU F 132 " --> pdb=" O GLN F 128 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU F 139 " --> pdb=" O THR F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 158 removed outlier: 3.505A pdb=" N LYS F 146 " --> pdb=" O ASP F 142 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE F 155 " --> pdb=" O VAL F 151 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS F 156 " --> pdb=" O VAL F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 175 Processing helix chain 'F' and resid 175 through 208 removed outlier: 5.748A pdb=" N SER F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLY F 191 " --> pdb=" O VAL F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 235 removed outlier: 3.550A pdb=" N SER F 235 " --> pdb=" O TRP F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 256 removed outlier: 4.373A pdb=" N HIS F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE F 252 " --> pdb=" O THR F 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 42 removed outlier: 3.532A pdb=" N SER G 13 " --> pdb=" O LEU G 9 " (cutoff:3.500A) Proline residue: G 27 - end of helix removed outlier: 3.568A pdb=" N THR G 42 " --> pdb=" O PHE G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 65 removed outlier: 3.900A pdb=" N ARG G 54 " --> pdb=" O SER G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 89 removed outlier: 3.813A pdb=" N THR G 70 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU G 84 " --> pdb=" O MET G 80 " (cutoff:3.500A) Proline residue: G 85 - end of helix Processing helix chain 'H' and resid 4 through 42 removed outlier: 3.705A pdb=" N SER H 13 " --> pdb=" O LEU H 9 " (cutoff:3.500A) Proline residue: H 27 - end of helix Processing helix chain 'H' and resid 51 through 65 removed outlier: 3.827A pdb=" N LEU H 62 " --> pdb=" O THR H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 83 removed outlier: 3.825A pdb=" N ILE H 81 " --> pdb=" O PHE H 77 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG H 83 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 89 removed outlier: 3.518A pdb=" N TYR H 89 " --> pdb=" O PRO H 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 43 Proline residue: I 27 - end of helix Processing helix chain 'I' and resid 50 through 65 removed outlier: 3.868A pdb=" N MET I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 89 Proline residue: I 85 - end of helix removed outlier: 3.526A pdb=" N TYR I 89 " --> pdb=" O PRO I 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 39 removed outlier: 3.592A pdb=" N SER J 13 " --> pdb=" O LEU J 9 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA J 23 " --> pdb=" O ILE J 19 " (cutoff:3.500A) Proline residue: J 27 - end of helix Processing helix chain 'J' and resid 51 through 83 removed outlier: 3.595A pdb=" N THR J 58 " --> pdb=" O ARG J 54 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N HIS J 67 " --> pdb=" O MET J 63 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TRP J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 89 removed outlier: 3.669A pdb=" N VAL J 87 " --> pdb=" O ARG J 83 " (cutoff:3.500A) 845 hydrogen bonds defined for protein. 2505 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: 3.75 Time building geometry restraints manager: 5.60 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: 3686 1.34 - 1.46: 2526 1.46 - 1.57: 6099 1.57 - 1.69: 0 1.69 - 1.81: 269 Bond restraints: 12580 Sorted by residual: bond pdb=" C GLU C 187 " pdb=" N PRO C 188 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.20e-02 6.94e+03 4.77e+00 bond pdb=" CA ILE D 176 " pdb=" CB ILE D 176 " ideal model delta sigma weight residual 1.553 1.540 0.013 7.40e-03 1.83e+04 2.95e+00 bond pdb=" CA VAL E 283 " pdb=" C VAL E 283 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.12e-02 7.97e+03 2.40e+00 bond pdb=" C GLN E 166 " pdb=" N ALA E 167 " ideal model delta sigma weight residual 1.332 1.311 0.021 1.40e-02 5.10e+03 2.32e+00 bond pdb=" CA LEU B 266 " pdb=" C LEU B 266 " ideal model delta sigma weight residual 1.532 1.518 0.014 9.60e-03 1.09e+04 2.21e+00 ... (remaining 12575 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.16: 415 106.16 - 113.12: 7082 113.12 - 120.08: 4777 120.08 - 127.03: 4672 127.03 - 133.99: 120 Bond angle restraints: 17066 Sorted by residual: angle pdb=" N GLN C 162 " pdb=" CA GLN C 162 " pdb=" C GLN C 162 " ideal model delta sigma weight residual 113.88 108.61 5.27 1.23e+00 6.61e-01 1.84e+01 angle pdb=" C ASN C 173 " pdb=" N GLU C 174 " pdb=" CA GLU C 174 " ideal model delta sigma weight residual 121.54 128.96 -7.42 1.91e+00 2.74e-01 1.51e+01 angle pdb=" N THR C 138 " pdb=" CA THR C 138 " pdb=" C THR C 138 " ideal model delta sigma weight residual 109.81 117.75 -7.94 2.21e+00 2.05e-01 1.29e+01 angle pdb=" N VAL A 223 " pdb=" CA VAL A 223 " pdb=" C VAL A 223 " ideal model delta sigma weight residual 113.16 107.90 5.26 1.49e+00 4.50e-01 1.25e+01 angle pdb=" C MET E 263 " pdb=" N MET E 264 " pdb=" CA MET E 264 " ideal model delta sigma weight residual 121.54 128.08 -6.54 1.91e+00 2.74e-01 1.17e+01 ... (remaining 17061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 6781 17.47 - 34.93: 633 34.93 - 52.40: 119 52.40 - 69.86: 22 69.86 - 87.33: 9 Dihedral angle restraints: 7564 sinusoidal: 2976 harmonic: 4588 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 180.00 112.92 67.08 0 5.00e+00 4.00e-02 1.80e+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 -130.25 -49.75 0 5.00e+00 4.00e-02 9.90e+01 dihedral pdb=" CA ASN A 173 " pdb=" C ASN A 173 " pdb=" N GLU A 174 " pdb=" CA GLU A 174 " ideal model delta harmonic sigma weight residual -180.00 -144.78 -35.22 0 5.00e+00 4.00e-02 4.96e+01 ... (remaining 7561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1261 0.037 - 0.075: 644 0.075 - 0.112: 173 0.112 - 0.150: 20 0.150 - 0.187: 4 Chirality restraints: 2102 Sorted by residual: chirality pdb=" CB ILE E 128 " pdb=" CA ILE E 128 " pdb=" CG1 ILE E 128 " pdb=" CG2 ILE E 128 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CG LEU C 135 " pdb=" CB LEU C 135 " pdb=" CD1 LEU C 135 " pdb=" CD2 LEU C 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CA LEU B 245 " pdb=" N LEU B 245 " pdb=" C LEU B 245 " pdb=" CB LEU B 245 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.51e-01 ... (remaining 2099 not shown) Planarity restraints: 2069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 138 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO C 139 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO C 139 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 139 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 138 " -0.061 5.00e-02 4.00e+02 9.36e-02 1.40e+01 pdb=" N PRO A 139 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 137 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.27e+00 pdb=" C GLN C 137 " 0.040 2.00e-02 2.50e+03 pdb=" O GLN C 137 " -0.015 2.00e-02 2.50e+03 pdb=" N THR C 138 " -0.014 2.00e-02 2.50e+03 ... (remaining 2066 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 365 2.69 - 3.24: 14500 3.24 - 3.80: 20368 3.80 - 4.35: 25906 4.35 - 4.90: 41670 Nonbonded interactions: 102809 Sorted by model distance: nonbonded pdb=" O LEU B 149 " pdb=" OG1 THR B 152 " model vdw 2.141 2.440 nonbonded pdb=" O ILE C 114 " pdb=" OG1 THR C 117 " model vdw 2.156 2.440 nonbonded pdb=" O LEU E 288 " pdb=" OG SER E 291 " model vdw 2.157 2.440 nonbonded pdb=" O GLU B 232 " pdb=" OG1 THR B 235 " model vdw 2.181 2.440 nonbonded pdb=" O ILE D 289 " pdb=" OG1 THR D 292 " model vdw 2.195 2.440 ... (remaining 102804 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' and resid 113 through 299) selection = (chain 'B' and resid 113 through 299) selection = (chain 'C' and resid 113 through 299) selection = (chain 'D' and resid 113 through 299) selection = chain 'E' } ncs_group { reference = (chain 'G' and (resid 1 through 39 or resid 49 through 89)) selection = (chain 'H' and (resid 1 through 39 or resid 49 through 89)) selection = (chain 'I' and (resid 1 through 39 or resid 49 through 89)) 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 group one per residue 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: 1.150 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: 4.530 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 35.040 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.040 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 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 : 0.007 0.050 12580 Z= 0.425 Angle : 0.871 9.934 17066 Z= 0.487 Chirality : 0.045 0.187 2102 Planarity : 0.005 0.112 2069 Dihedral : 14.287 87.331 4556 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.76 % Favored : 91.86 % Rotamer: Outliers : 0.07 % Allowed : 7.53 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.13 % 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: -3.54 (0.18), residues: 1547 helix: -1.82 (0.13), residues: 1210 sheet: None (None), residues: 0 loop : -3.65 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 286 HIS 0.004 0.002 HIS F 144 PHE 0.022 0.002 PHE B 119 TYR 0.012 0.001 TYR F 241 ARG 0.004 0.000 ARG H 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 355 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8563 (tm-30) REVERT: A 263 MET cc_start: 0.7688 (mtt) cc_final: 0.7396 (mtt) REVERT: B 116 MET cc_start: 0.8254 (mtt) cc_final: 0.8033 (mtm) REVERT: B 183 ASP cc_start: 0.8740 (t0) cc_final: 0.8042 (t0) REVERT: B 193 MET cc_start: 0.8264 (mtp) cc_final: 0.5836 (mtp) REVERT: B 232 GLU cc_start: 0.8324 (tp30) cc_final: 0.7958 (tp30) REVERT: B 261 MET cc_start: 0.8188 (mtm) cc_final: 0.7596 (mtm) REVERT: B 269 MET cc_start: 0.7496 (mmm) cc_final: 0.7289 (tpp) REVERT: B 284 ASP cc_start: 0.8450 (t0) cc_final: 0.8243 (t0) REVERT: C 259 MET cc_start: 0.8416 (mmm) cc_final: 0.7862 (tpp) REVERT: D 116 MET cc_start: 0.7889 (ttm) cc_final: 0.7633 (mmt) REVERT: D 264 MET cc_start: 0.8117 (tmm) cc_final: 0.7896 (tmm) REVERT: D 265 MET cc_start: 0.8369 (tpp) cc_final: 0.6837 (tpp) REVERT: E 138 THR cc_start: 0.8675 (p) cc_final: 0.8414 (p) REVERT: E 142 GLN cc_start: 0.7883 (tt0) cc_final: 0.7680 (tm-30) REVERT: E 174 GLU cc_start: 0.7873 (tp30) cc_final: 0.7605 (tp30) REVERT: E 193 MET cc_start: 0.9014 (mtp) cc_final: 0.8638 (mtm) REVERT: E 245 LEU cc_start: 0.9514 (mt) cc_final: 0.9236 (mt) REVERT: E 264 MET cc_start: 0.7788 (tpp) cc_final: 0.6378 (tpp) REVERT: F 15 TYR cc_start: 0.8181 (m-80) cc_final: 0.6454 (m-10) REVERT: F 25 MET cc_start: 0.8869 (tmm) cc_final: 0.8660 (tmm) REVERT: G 30 LEU cc_start: 0.9491 (mm) cc_final: 0.9161 (tt) REVERT: H 44 ILE cc_start: 0.8684 (mt) cc_final: 0.8480 (mm) REVERT: H 45 ASN cc_start: 0.8346 (t0) cc_final: 0.7383 (t0) REVERT: H 54 ARG cc_start: 0.9006 (ttp-110) cc_final: 0.8691 (mtp-110) REVERT: I 20 MET cc_start: 0.8257 (mtt) cc_final: 0.8002 (mtp) outliers start: 1 outliers final: 1 residues processed: 356 average time/residue: 0.2356 time to fit residues: 121.1007 Evaluate side-chains 235 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 63 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 45 optimal weight: 30.0000 chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN B 164 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN C 142 GLN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 GLN ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 ASN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12580 Z= 0.253 Angle : 0.777 12.106 17066 Z= 0.382 Chirality : 0.046 0.181 2102 Planarity : 0.005 0.101 2069 Dihedral : 5.643 64.464 1616 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.62 % Favored : 94.12 % Rotamer: Outliers : 0.14 % Allowed : 6.73 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.13 % 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: -1.22 (0.21), residues: 1547 helix: -0.11 (0.14), residues: 1236 sheet: None (None), residues: 0 loop : -3.33 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 286 HIS 0.006 0.001 HIS H 67 PHE 0.034 0.002 PHE D 160 TYR 0.012 0.001 TYR F 241 ARG 0.007 0.001 ARG G 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 345 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8552 (ttm170) cc_final: 0.7899 (ttm-80) REVERT: A 131 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8556 (tm-30) REVERT: A 141 ASN cc_start: 0.8444 (m-40) cc_final: 0.8235 (m-40) REVERT: A 232 GLU cc_start: 0.8674 (tp30) cc_final: 0.8193 (mm-30) REVERT: A 259 MET cc_start: 0.9062 (mmm) cc_final: 0.8400 (mmt) REVERT: A 263 MET cc_start: 0.7439 (mtt) cc_final: 0.7044 (mtt) REVERT: B 116 MET cc_start: 0.7936 (mtt) cc_final: 0.7601 (mtm) REVERT: B 269 MET cc_start: 0.7512 (mmm) cc_final: 0.7293 (tpp) REVERT: C 116 MET cc_start: 0.8249 (ptt) cc_final: 0.7850 (tmm) REVERT: D 116 MET cc_start: 0.7934 (ttm) cc_final: 0.7682 (mmt) REVERT: D 232 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8002 (mm-30) REVERT: E 174 GLU cc_start: 0.7867 (tp30) cc_final: 0.7537 (tp30) REVERT: E 264 MET cc_start: 0.7534 (tpp) cc_final: 0.7056 (tpp) REVERT: F 15 TYR cc_start: 0.8187 (m-80) cc_final: 0.7559 (m-10) REVERT: F 98 MET cc_start: 0.8440 (mmt) cc_final: 0.8209 (mmt) REVERT: F 250 GLU cc_start: 0.8459 (pt0) cc_final: 0.8192 (pt0) REVERT: G 20 MET cc_start: 0.8496 (mtm) cc_final: 0.8014 (mtp) REVERT: G 30 LEU cc_start: 0.9511 (mm) cc_final: 0.9100 (tt) REVERT: G 63 MET cc_start: 0.8353 (tpt) cc_final: 0.7855 (tmm) REVERT: H 45 ASN cc_start: 0.8133 (t0) cc_final: 0.7757 (t0) REVERT: H 80 MET cc_start: 0.8913 (mmp) cc_final: 0.8546 (tpp) REVERT: J 25 ILE cc_start: 0.9470 (mm) cc_final: 0.9259 (mm) outliers start: 2 outliers final: 0 residues processed: 346 average time/residue: 0.2134 time to fit residues: 108.8077 Evaluate side-chains 247 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 46 optimal weight: 0.0570 chunk 110 optimal weight: 4.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN F 94 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 12580 Z= 0.216 Angle : 0.745 9.609 17066 Z= 0.362 Chirality : 0.044 0.170 2102 Planarity : 0.005 0.100 2069 Dihedral : 5.477 62.864 1616 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.04 % Favored : 94.70 % Rotamer: Outliers : 0.36 % Allowed : 4.06 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % 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: -0.38 (0.21), residues: 1547 helix: 0.49 (0.15), residues: 1235 sheet: None (None), residues: 0 loop : -3.09 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 68 HIS 0.001 0.001 HIS I 67 PHE 0.028 0.002 PHE B 244 TYR 0.010 0.001 TYR F 170 ARG 0.004 0.000 ARG G 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 336 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASN cc_start: 0.8335 (m-40) cc_final: 0.8133 (m-40) REVERT: A 259 MET cc_start: 0.8936 (mmm) cc_final: 0.8278 (mmt) REVERT: A 263 MET cc_start: 0.7437 (mtt) cc_final: 0.6782 (mtt) REVERT: A 264 MET cc_start: 0.8338 (ttp) cc_final: 0.7769 (ptm) REVERT: B 116 MET cc_start: 0.7846 (mtt) cc_final: 0.7096 (mtm) REVERT: B 269 MET cc_start: 0.7462 (mmm) cc_final: 0.7205 (tpp) REVERT: C 112 MET cc_start: 0.7347 (ptm) cc_final: 0.7107 (ptm) REVERT: C 115 LEU cc_start: 0.9291 (mm) cc_final: 0.8982 (mt) REVERT: C 116 MET cc_start: 0.8411 (ptt) cc_final: 0.8130 (tmm) REVERT: C 126 MET cc_start: 0.8319 (mtm) cc_final: 0.8033 (mtm) REVERT: C 193 MET cc_start: 0.8723 (mtt) cc_final: 0.8513 (mtm) REVERT: C 207 GLU cc_start: 0.8318 (pp20) cc_final: 0.7977 (pp20) REVERT: C 232 GLU cc_start: 0.8715 (tp30) cc_final: 0.8255 (tp30) REVERT: C 263 MET cc_start: 0.8490 (mmt) cc_final: 0.8250 (mmt) REVERT: C 279 LEU cc_start: 0.9324 (tp) cc_final: 0.8777 (mm) REVERT: D 116 MET cc_start: 0.7868 (ttm) cc_final: 0.7621 (mmt) REVERT: E 174 GLU cc_start: 0.7763 (tp30) cc_final: 0.7405 (tp30) REVERT: E 193 MET cc_start: 0.8597 (mtm) cc_final: 0.8366 (mtm) REVERT: E 248 LEU cc_start: 0.9187 (tt) cc_final: 0.8880 (tt) REVERT: E 264 MET cc_start: 0.7625 (tpp) cc_final: 0.7180 (tpp) REVERT: E 276 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8238 (mtmt) REVERT: F 15 TYR cc_start: 0.8176 (m-80) cc_final: 0.7876 (m-10) REVERT: F 25 MET cc_start: 0.8631 (tmm) cc_final: 0.8370 (tmm) REVERT: F 98 MET cc_start: 0.8456 (mmt) cc_final: 0.8153 (mmt) REVERT: G 30 LEU cc_start: 0.9454 (mm) cc_final: 0.9071 (tt) REVERT: G 63 MET cc_start: 0.8438 (tpt) cc_final: 0.7687 (tmm) REVERT: H 45 ASN cc_start: 0.8037 (t0) cc_final: 0.7594 (t0) REVERT: I 47 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8410 (mm-40) REVERT: I 74 MET cc_start: 0.8270 (mmm) cc_final: 0.7759 (tpp) REVERT: I 78 TYR cc_start: 0.8929 (m-80) cc_final: 0.8639 (m-80) REVERT: J 54 ARG cc_start: 0.8738 (mtm110) cc_final: 0.8515 (mtm-85) REVERT: J 57 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8967 (mp) outliers start: 5 outliers final: 0 residues processed: 337 average time/residue: 0.2082 time to fit residues: 104.1125 Evaluate side-chains 246 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 9.9990 chunk 103 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 12580 Z= 0.301 Angle : 0.767 10.024 17066 Z= 0.374 Chirality : 0.045 0.195 2102 Planarity : 0.005 0.095 2069 Dihedral : 5.491 63.686 1616 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.08 % Favored : 93.67 % Rotamer: Outliers : 0.14 % Allowed : 4.20 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % 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: -0.09 (0.22), residues: 1547 helix: 0.71 (0.15), residues: 1238 sheet: None (None), residues: 0 loop : -3.10 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 68 HIS 0.004 0.001 HIS F 144 PHE 0.030 0.002 PHE D 244 TYR 0.009 0.001 TYR F 44 ARG 0.003 0.000 ARG G 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 311 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASN cc_start: 0.8367 (m-40) cc_final: 0.8153 (m-40) REVERT: A 259 MET cc_start: 0.8920 (mmm) cc_final: 0.8375 (mmt) REVERT: A 263 MET cc_start: 0.7642 (mtt) cc_final: 0.7145 (mtt) REVERT: A 277 LEU cc_start: 0.9293 (mt) cc_final: 0.9086 (mt) REVERT: B 193 MET cc_start: 0.7841 (tpp) cc_final: 0.7587 (tpp) REVERT: B 269 MET cc_start: 0.7526 (mmm) cc_final: 0.7308 (tpp) REVERT: B 283 VAL cc_start: 0.8771 (m) cc_final: 0.8299 (m) REVERT: C 116 MET cc_start: 0.8486 (ptt) cc_final: 0.8219 (tmm) REVERT: C 232 GLU cc_start: 0.8709 (tp30) cc_final: 0.8238 (tp30) REVERT: C 263 MET cc_start: 0.8351 (mmt) cc_final: 0.8139 (mmt) REVERT: C 279 LEU cc_start: 0.9355 (tp) cc_final: 0.8773 (mm) REVERT: D 116 MET cc_start: 0.7895 (ttm) cc_final: 0.7670 (mmt) REVERT: D 264 MET cc_start: 0.7894 (tmm) cc_final: 0.7670 (tmm) REVERT: D 265 MET cc_start: 0.8199 (tpp) cc_final: 0.7962 (tpp) REVERT: D 278 MET cc_start: 0.8191 (ttm) cc_final: 0.7844 (ttp) REVERT: E 174 GLU cc_start: 0.7765 (tp30) cc_final: 0.7417 (tp30) REVERT: E 264 MET cc_start: 0.7409 (tpp) cc_final: 0.7075 (tpp) REVERT: F 15 TYR cc_start: 0.7949 (m-80) cc_final: 0.7737 (m-10) REVERT: G 30 LEU cc_start: 0.9468 (mm) cc_final: 0.9090 (tt) REVERT: G 63 MET cc_start: 0.8477 (tpt) cc_final: 0.7795 (tmm) REVERT: H 45 ASN cc_start: 0.8040 (t0) cc_final: 0.7761 (t0) REVERT: H 52 LEU cc_start: 0.8980 (tt) cc_final: 0.8635 (tp) REVERT: H 74 MET cc_start: 0.8821 (mmm) cc_final: 0.8214 (mmm) REVERT: I 74 MET cc_start: 0.8272 (mmm) cc_final: 0.7826 (tpp) REVERT: J 20 MET cc_start: 0.9382 (mtp) cc_final: 0.8860 (mtt) REVERT: J 25 ILE cc_start: 0.9463 (mm) cc_final: 0.9257 (mm) outliers start: 2 outliers final: 0 residues processed: 311 average time/residue: 0.2095 time to fit residues: 96.9202 Evaluate side-chains 240 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN H 45 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 GLN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12580 Z= 0.235 Angle : 0.747 8.875 17066 Z= 0.365 Chirality : 0.044 0.205 2102 Planarity : 0.005 0.094 2069 Dihedral : 5.405 62.715 1616 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.82 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % 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: 0.27 (0.22), residues: 1547 helix: 0.97 (0.15), residues: 1235 sheet: None (None), residues: 0 loop : -2.98 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 68 HIS 0.002 0.001 HIS F 144 PHE 0.017 0.001 PHE B 119 TYR 0.012 0.001 TYR F 44 ARG 0.006 0.000 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8682 (ttm170) cc_final: 0.8344 (ttm-80) REVERT: A 131 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8580 (tm-30) REVERT: A 141 ASN cc_start: 0.8225 (m-40) cc_final: 0.7973 (m-40) REVERT: A 259 MET cc_start: 0.8832 (mmm) cc_final: 0.8347 (mmt) REVERT: A 263 MET cc_start: 0.7721 (mtt) cc_final: 0.7111 (mtt) REVERT: B 193 MET cc_start: 0.7817 (tpp) cc_final: 0.7570 (tpp) REVERT: B 264 MET cc_start: 0.8153 (mtm) cc_final: 0.7712 (mtm) REVERT: B 269 MET cc_start: 0.7456 (mmm) cc_final: 0.7235 (tpp) REVERT: C 115 LEU cc_start: 0.9355 (mm) cc_final: 0.9123 (mt) REVERT: C 156 MET cc_start: 0.8212 (mmm) cc_final: 0.7815 (mmm) REVERT: C 232 GLU cc_start: 0.8695 (tp30) cc_final: 0.8309 (tp30) REVERT: C 259 MET cc_start: 0.8352 (mmm) cc_final: 0.7961 (mmm) REVERT: C 279 LEU cc_start: 0.9326 (tp) cc_final: 0.8791 (mm) REVERT: D 116 MET cc_start: 0.7871 (ttm) cc_final: 0.7626 (mmt) REVERT: E 174 GLU cc_start: 0.7711 (tp30) cc_final: 0.7376 (tp30) REVERT: F 15 TYR cc_start: 0.8231 (m-80) cc_final: 0.7975 (m-10) REVERT: F 102 ILE cc_start: 0.9214 (mt) cc_final: 0.8877 (mt) REVERT: G 30 LEU cc_start: 0.9438 (mm) cc_final: 0.9062 (tt) REVERT: H 45 ASN cc_start: 0.7979 (t0) cc_final: 0.7730 (t0) REVERT: J 57 ILE cc_start: 0.9189 (mp) cc_final: 0.8978 (mp) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.1997 time to fit residues: 97.7995 Evaluate side-chains 244 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 0.0270 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12580 Z= 0.251 Angle : 0.758 11.463 17066 Z= 0.371 Chirality : 0.044 0.196 2102 Planarity : 0.005 0.091 2069 Dihedral : 5.383 62.132 1616 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.08 % Favored : 93.67 % Rotamer: Outliers : 0.07 % Allowed : 2.53 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % 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: 0.41 (0.22), residues: 1547 helix: 1.06 (0.15), residues: 1239 sheet: None (None), residues: 0 loop : -2.94 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 68 HIS 0.003 0.001 HIS F 144 PHE 0.018 0.001 PHE B 160 TYR 0.010 0.001 TYR F 241 ARG 0.005 0.000 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 305 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8731 (ttm170) cc_final: 0.8376 (ttm-80) REVERT: A 141 ASN cc_start: 0.8266 (m-40) cc_final: 0.8010 (m-40) REVERT: A 259 MET cc_start: 0.8808 (mmm) cc_final: 0.8364 (mmt) REVERT: A 263 MET cc_start: 0.7730 (mtt) cc_final: 0.7306 (mtt) REVERT: A 277 LEU cc_start: 0.9238 (mt) cc_final: 0.9026 (mt) REVERT: B 269 MET cc_start: 0.7490 (mmm) cc_final: 0.7285 (tpp) REVERT: C 115 LEU cc_start: 0.9320 (mm) cc_final: 0.8981 (mp) REVERT: C 116 MET cc_start: 0.8313 (ttp) cc_final: 0.8030 (tmm) REVERT: C 156 MET cc_start: 0.8207 (mmm) cc_final: 0.7799 (mmm) REVERT: C 232 GLU cc_start: 0.8711 (tp30) cc_final: 0.8305 (tp30) REVERT: C 264 MET cc_start: 0.8056 (tpp) cc_final: 0.7845 (tpp) REVERT: C 279 LEU cc_start: 0.9319 (tp) cc_final: 0.8795 (mm) REVERT: D 116 MET cc_start: 0.7878 (ttm) cc_final: 0.7658 (mmt) REVERT: E 138 THR cc_start: 0.9027 (p) cc_final: 0.8674 (p) REVERT: E 174 GLU cc_start: 0.7705 (tp30) cc_final: 0.7363 (tp30) REVERT: F 25 MET cc_start: 0.8533 (tmm) cc_final: 0.8296 (tmm) REVERT: F 102 ILE cc_start: 0.9161 (mt) cc_final: 0.8884 (mt) REVERT: F 250 GLU cc_start: 0.8420 (pt0) cc_final: 0.8095 (pt0) REVERT: G 30 LEU cc_start: 0.9447 (mm) cc_final: 0.9046 (tt) REVERT: G 58 THR cc_start: 0.9362 (t) cc_final: 0.9146 (m) REVERT: G 63 MET cc_start: 0.8538 (tpp) cc_final: 0.7732 (tmm) REVERT: H 45 ASN cc_start: 0.8189 (t0) cc_final: 0.7983 (t0) REVERT: H 74 MET cc_start: 0.8724 (mmm) cc_final: 0.8335 (mmm) REVERT: J 57 ILE cc_start: 0.9196 (mp) cc_final: 0.8950 (mp) outliers start: 1 outliers final: 0 residues processed: 306 average time/residue: 0.1983 time to fit residues: 92.1811 Evaluate side-chains 243 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12580 Z= 0.276 Angle : 0.776 10.088 17066 Z= 0.380 Chirality : 0.045 0.205 2102 Planarity : 0.005 0.093 2069 Dihedral : 5.415 62.171 1616 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.82 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.13 % 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: 0.56 (0.22), residues: 1547 helix: 1.20 (0.15), residues: 1230 sheet: None (None), residues: 0 loop : -2.94 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 68 HIS 0.003 0.001 HIS F 144 PHE 0.017 0.002 PHE B 119 TYR 0.009 0.001 TYR F 241 ARG 0.003 0.000 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8663 (ttm170) cc_final: 0.8363 (ttm-80) REVERT: A 242 MET cc_start: 0.7649 (mtm) cc_final: 0.7241 (mtm) REVERT: A 259 MET cc_start: 0.8783 (mmm) cc_final: 0.8350 (mmt) REVERT: A 263 MET cc_start: 0.7748 (mtt) cc_final: 0.7504 (mtt) REVERT: B 193 MET cc_start: 0.8231 (tpp) cc_final: 0.7933 (tpp) REVERT: C 115 LEU cc_start: 0.9332 (mm) cc_final: 0.8992 (mp) REVERT: C 232 GLU cc_start: 0.8712 (tp30) cc_final: 0.8334 (tp30) REVERT: C 279 LEU cc_start: 0.9366 (tp) cc_final: 0.8878 (mm) REVERT: D 116 MET cc_start: 0.7885 (ttm) cc_final: 0.7669 (mmt) REVERT: E 138 THR cc_start: 0.9004 (p) cc_final: 0.8413 (p) REVERT: E 174 GLU cc_start: 0.7719 (tp30) cc_final: 0.7366 (tp30) REVERT: F 25 MET cc_start: 0.8544 (tmm) cc_final: 0.8335 (tmm) REVERT: F 77 GLU cc_start: 0.8740 (tt0) cc_final: 0.8150 (tm-30) REVERT: F 85 MET cc_start: 0.8862 (mtm) cc_final: 0.8654 (mtm) REVERT: F 98 MET cc_start: 0.8901 (mmt) cc_final: 0.8560 (mmm) REVERT: F 102 ILE cc_start: 0.9097 (mt) cc_final: 0.8497 (mt) REVERT: F 114 MET cc_start: 0.8216 (tmm) cc_final: 0.7933 (tmm) REVERT: F 250 GLU cc_start: 0.8405 (pt0) cc_final: 0.8084 (pt0) REVERT: G 18 LEU cc_start: 0.9317 (tt) cc_final: 0.8975 (tt) REVERT: G 30 LEU cc_start: 0.9491 (mm) cc_final: 0.9087 (tt) REVERT: G 58 THR cc_start: 0.9348 (t) cc_final: 0.9102 (m) REVERT: G 63 MET cc_start: 0.8559 (tpp) cc_final: 0.7798 (tmm) REVERT: H 45 ASN cc_start: 0.8214 (t0) cc_final: 0.7970 (t0) REVERT: H 74 MET cc_start: 0.8807 (mmm) cc_final: 0.8373 (mmm) REVERT: J 57 ILE cc_start: 0.9155 (mp) cc_final: 0.8931 (mp) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.1968 time to fit residues: 90.8456 Evaluate side-chains 238 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 0.0170 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN G 71 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12580 Z= 0.244 Angle : 0.792 10.076 17066 Z= 0.383 Chirality : 0.045 0.198 2102 Planarity : 0.005 0.091 2069 Dihedral : 5.406 61.542 1616 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.08 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % 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: 0.64 (0.22), residues: 1547 helix: 1.22 (0.15), residues: 1231 sheet: None (None), residues: 0 loop : -2.77 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 68 HIS 0.002 0.001 HIS F 144 PHE 0.022 0.001 PHE B 150 TYR 0.010 0.001 TYR F 241 ARG 0.003 0.000 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 MET cc_start: 0.8764 (mmm) cc_final: 0.8344 (mmt) REVERT: A 263 MET cc_start: 0.7751 (mtt) cc_final: 0.7496 (mtt) REVERT: A 277 LEU cc_start: 0.9211 (mt) cc_final: 0.8974 (mt) REVERT: B 269 MET cc_start: 0.7546 (tpt) cc_final: 0.7148 (tpp) REVERT: C 115 LEU cc_start: 0.9298 (mm) cc_final: 0.8981 (mt) REVERT: C 208 MET cc_start: 0.8713 (mtp) cc_final: 0.8506 (mmm) REVERT: C 232 GLU cc_start: 0.8698 (tp30) cc_final: 0.8303 (tp30) REVERT: C 259 MET cc_start: 0.8429 (tpp) cc_final: 0.7989 (tpp) REVERT: C 279 LEU cc_start: 0.9324 (tp) cc_final: 0.8853 (mm) REVERT: E 138 THR cc_start: 0.8940 (p) cc_final: 0.8434 (p) REVERT: E 174 GLU cc_start: 0.7762 (tp30) cc_final: 0.7384 (tp30) REVERT: F 25 MET cc_start: 0.8554 (tmm) cc_final: 0.8323 (tmm) REVERT: F 114 MET cc_start: 0.8265 (tmm) cc_final: 0.8047 (tmm) REVERT: F 250 GLU cc_start: 0.8329 (pt0) cc_final: 0.8012 (pt0) REVERT: G 30 LEU cc_start: 0.9472 (mm) cc_final: 0.9064 (tt) REVERT: G 58 THR cc_start: 0.9323 (t) cc_final: 0.9065 (m) REVERT: G 63 MET cc_start: 0.8546 (tpp) cc_final: 0.7770 (tmm) REVERT: H 45 ASN cc_start: 0.8269 (t0) cc_final: 0.7847 (t0) REVERT: H 74 MET cc_start: 0.8764 (mmm) cc_final: 0.8413 (mmm) REVERT: I 74 MET cc_start: 0.8257 (mmm) cc_final: 0.7728 (tpp) REVERT: J 57 ILE cc_start: 0.9100 (mp) cc_final: 0.8873 (mp) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.2044 time to fit residues: 94.5770 Evaluate side-chains 246 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 9.9990 chunk 127 optimal weight: 0.6980 chunk 135 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 41 optimal weight: 0.0980 chunk 122 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN H 39 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12580 Z= 0.239 Angle : 0.799 9.963 17066 Z= 0.388 Chirality : 0.045 0.175 2102 Planarity : 0.005 0.091 2069 Dihedral : 5.415 60.815 1616 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.62 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % 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: 0.61 (0.22), residues: 1547 helix: 1.16 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : -2.81 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 68 HIS 0.002 0.000 HIS F 144 PHE 0.022 0.001 PHE B 192 TYR 0.010 0.001 TYR F 241 ARG 0.003 0.000 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8561 (ttm170) cc_final: 0.8335 (ttm-80) REVERT: A 259 MET cc_start: 0.8701 (mmm) cc_final: 0.8322 (mmt) REVERT: A 263 MET cc_start: 0.7675 (mtt) cc_final: 0.7341 (mtt) REVERT: B 269 MET cc_start: 0.7570 (tpt) cc_final: 0.7150 (tpp) REVERT: C 115 LEU cc_start: 0.9241 (mm) cc_final: 0.8950 (mt) REVERT: C 232 GLU cc_start: 0.8654 (tp30) cc_final: 0.8293 (tp30) REVERT: C 259 MET cc_start: 0.8271 (tpp) cc_final: 0.7909 (tpp) REVERT: C 279 LEU cc_start: 0.9316 (tp) cc_final: 0.8866 (mm) REVERT: D 263 MET cc_start: 0.7901 (mtt) cc_final: 0.7496 (mtt) REVERT: E 138 THR cc_start: 0.8982 (p) cc_final: 0.8466 (p) REVERT: E 174 GLU cc_start: 0.7758 (tp30) cc_final: 0.7369 (tp30) REVERT: E 208 MET cc_start: 0.8200 (mtm) cc_final: 0.7939 (mtt) REVERT: E 264 MET cc_start: 0.8040 (tmm) cc_final: 0.7671 (tmm) REVERT: F 25 MET cc_start: 0.8519 (tmm) cc_final: 0.8299 (tmm) REVERT: F 85 MET cc_start: 0.8848 (mtm) cc_final: 0.8535 (mtm) REVERT: F 98 MET cc_start: 0.8985 (mmt) cc_final: 0.8713 (mmm) REVERT: F 114 MET cc_start: 0.8475 (tmm) cc_final: 0.8105 (tmm) REVERT: F 250 GLU cc_start: 0.8356 (pt0) cc_final: 0.8005 (pt0) REVERT: F 258 LEU cc_start: 0.8770 (tp) cc_final: 0.8568 (tp) REVERT: G 30 LEU cc_start: 0.9475 (mm) cc_final: 0.9050 (tt) REVERT: G 58 THR cc_start: 0.9311 (t) cc_final: 0.9059 (m) REVERT: G 63 MET cc_start: 0.8553 (tpp) cc_final: 0.7782 (tmm) REVERT: H 5 ILE cc_start: 0.8686 (tp) cc_final: 0.7657 (tp) REVERT: H 72 MET cc_start: 0.8787 (pmm) cc_final: 0.8582 (pmm) REVERT: I 59 LEU cc_start: 0.9187 (mt) cc_final: 0.8918 (mt) REVERT: I 74 MET cc_start: 0.8258 (mmm) cc_final: 0.7704 (tpp) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.2060 time to fit residues: 95.4240 Evaluate side-chains 239 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 0.0570 chunk 68 optimal weight: 0.9980 chunk 99 optimal weight: 0.0020 chunk 150 optimal weight: 8.9990 chunk 138 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 127 optimal weight: 0.0980 overall best weight: 0.4308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 12580 Z= 0.218 Angle : 0.808 10.064 17066 Z= 0.388 Chirality : 0.044 0.169 2102 Planarity : 0.005 0.089 2069 Dihedral : 5.360 59.063 1616 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.43 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.07 % 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: 0.68 (0.22), residues: 1547 helix: 1.24 (0.15), residues: 1242 sheet: None (None), residues: 0 loop : -2.84 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 68 HIS 0.002 0.000 HIS J 67 PHE 0.021 0.001 PHE B 192 TYR 0.010 0.001 TYR F 241 ARG 0.008 0.000 ARG I 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8608 (tm-30) REVERT: A 259 MET cc_start: 0.8734 (mmm) cc_final: 0.8298 (mmt) REVERT: A 263 MET cc_start: 0.7696 (mtt) cc_final: 0.7185 (mtt) REVERT: A 277 LEU cc_start: 0.9092 (mt) cc_final: 0.8885 (mt) REVERT: B 269 MET cc_start: 0.7591 (tpt) cc_final: 0.7140 (tpp) REVERT: C 115 LEU cc_start: 0.9277 (mm) cc_final: 0.9002 (mt) REVERT: C 232 GLU cc_start: 0.8625 (tp30) cc_final: 0.8276 (tp30) REVERT: C 259 MET cc_start: 0.8338 (tpp) cc_final: 0.8067 (tpp) REVERT: C 279 LEU cc_start: 0.9311 (tp) cc_final: 0.8858 (mm) REVERT: D 263 MET cc_start: 0.7859 (mtt) cc_final: 0.7368 (mtt) REVERT: D 265 MET cc_start: 0.7980 (ttp) cc_final: 0.7719 (ptm) REVERT: E 138 THR cc_start: 0.8892 (p) cc_final: 0.7710 (p) REVERT: F 25 MET cc_start: 0.8511 (tmm) cc_final: 0.8257 (tmm) REVERT: F 77 GLU cc_start: 0.8758 (tt0) cc_final: 0.8050 (tm-30) REVERT: F 98 MET cc_start: 0.8966 (mmt) cc_final: 0.8589 (mmm) REVERT: F 102 ILE cc_start: 0.8957 (mt) cc_final: 0.8416 (mt) REVERT: F 250 GLU cc_start: 0.8393 (pt0) cc_final: 0.8049 (pt0) REVERT: G 30 LEU cc_start: 0.9457 (mm) cc_final: 0.9035 (tt) REVERT: G 63 MET cc_start: 0.8560 (tpp) cc_final: 0.7829 (tmm) REVERT: H 5 ILE cc_start: 0.8541 (tp) cc_final: 0.7693 (tp) REVERT: H 72 MET cc_start: 0.8746 (pmm) cc_final: 0.8514 (pmm) REVERT: I 4 GLU cc_start: 0.8189 (tp30) cc_final: 0.7716 (tp30) REVERT: I 74 MET cc_start: 0.8244 (mmm) cc_final: 0.7706 (tpp) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.2047 time to fit residues: 97.1502 Evaluate side-chains 250 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 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 = 0.3328 r_free = 0.3328 target = 0.059595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.049615 restraints weight = 59074.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.051073 restraints weight = 34755.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.052091 restraints weight = 23983.636| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 12580 Z= 0.228 Angle : 0.818 10.632 17066 Z= 0.392 Chirality : 0.045 0.208 2102 Planarity : 0.005 0.089 2069 Dihedral : 5.328 58.520 1616 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.49 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.13 % 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: 0.71 (0.23), residues: 1547 helix: 1.30 (0.15), residues: 1228 sheet: None (None), residues: 0 loop : -2.84 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 68 HIS 0.001 0.000 HIS F 144 PHE 0.057 0.002 PHE B 244 TYR 0.009 0.001 TYR F 241 ARG 0.003 0.000 ARG I 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2548.28 seconds wall clock time: 47 minutes 50.43 seconds (2870.43 seconds total)