Starting phenix.real_space_refine (version: dev) on Mon Dec 12 21:39:21 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3s_10096/12_2022/6s3s_10096.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3s_10096/12_2022/6s3s_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_10096/12_2022/6s3s_10096.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3s_10096/12_2022/6s3s_10096.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3s_10096/12_2022/6s3s_10096.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3s_10096/12_2022/6s3s_10096.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 8.53, per 1000 atoms: 0.69 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: 5.80 Conformation dependent library (CDL) restraints added in 1.8 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: 0.42 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: 3.38 Time building geometry restraints manager: 6.13 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 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. 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: 0.870 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: 4.570 Check model and map are aligned: 0.180 Convert atoms to be neutral: 0.100 Process input model: 36.350 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 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 % 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 *********************** 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 : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 356 average time/residue: 0.2268 time to fit residues: 116.1992 Evaluate side-chains 227 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 1.611 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1028 time to fit residues: 2.1719 ------------------------------------------------------------------------------- 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: 6.9990 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: 5.9990 chunk 137 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 ** 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 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN ** 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: 0.8199 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 12580 Z= 0.235 Angle : 0.783 12.431 17066 Z= 0.385 Chirality : 0.046 0.173 2102 Planarity : 0.006 0.102 2069 Dihedral : 5.647 64.528 1616 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.37 % Favored : 94.38 % Rotamer Outliers : 0.29 % 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: -1.16 (0.21), residues: 1547 helix: -0.07 (0.14), residues: 1231 sheet: None (None), residues: 0 loop : -3.25 (0.34), residues: 316 *********************** 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 351 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 347 time to evaluate : 1.563 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 outliers start: 4 outliers final: 0 residues processed: 350 average time/residue: 0.2171 time to fit residues: 111.5969 Evaluate side-chains 247 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.488 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9527 ------------------------------------------------------------------------------- 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: 7.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 30.0000 chunk 93 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 chunk 46 optimal weight: 0.0040 chunk 110 optimal weight: 3.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN ** 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 251 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 12580 Z= 0.222 Angle : 0.755 10.929 17066 Z= 0.366 Chirality : 0.044 0.200 2102 Planarity : 0.005 0.095 2069 Dihedral : 5.534 63.047 1616 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.37 % Favored : 94.38 % Rotamer Outliers : 0.22 % 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: -0.43 (0.21), residues: 1547 helix: 0.46 (0.15), residues: 1233 sheet: None (None), residues: 0 loop : -3.13 (0.35), residues: 314 *********************** 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 334 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 331 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 331 average time/residue: 0.2206 time to fit residues: 107.1378 Evaluate side-chains 236 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.494 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9781 ------------------------------------------------------------------------------- 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: 10.0000 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 65 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 137 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN C 175 GLN C 180 GLN ** 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** H 39 GLN H 45 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 12580 Z= 0.214 Angle : 0.760 8.663 17066 Z= 0.366 Chirality : 0.044 0.171 2102 Planarity : 0.005 0.092 2069 Dihedral : 5.425 61.749 1616 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.37 % Favored : 94.38 % Rotamer Outliers : 0.29 % 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: 0.03 (0.22), residues: 1547 helix: 0.77 (0.15), residues: 1243 sheet: None (None), residues: 0 loop : -3.06 (0.36), residues: 304 *********************** 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 331 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 327 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 327 average time/residue: 0.2143 time to fit residues: 103.4927 Evaluate side-chains 241 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 1.553 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9649 ------------------------------------------------------------------------------- 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: 4.9990 chunk 82 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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** ** E 141 ASN ** 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 262 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 12580 Z= 0.232 Angle : 0.750 11.275 17066 Z= 0.367 Chirality : 0.044 0.186 2102 Planarity : 0.005 0.088 2069 Dihedral : 5.384 61.397 1616 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.75 % Favored : 93.99 % Rotamer Outliers : 0.00 % 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: 0.32 (0.22), residues: 1547 helix: 1.00 (0.15), residues: 1237 sheet: None (None), residues: 0 loop : -3.00 (0.34), residues: 310 *********************** 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 323 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.2131 time to fit residues: 102.0305 Evaluate side-chains 244 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.534 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0451 ------------------------------------------------------------------------------- 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: 6.9990 chunk 131 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 141 ASN ** 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 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 12580 Z= 0.306 Angle : 0.794 9.636 17066 Z= 0.390 Chirality : 0.045 0.230 2102 Planarity : 0.005 0.093 2069 Dihedral : 5.432 62.606 1616 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.08 % Favored : 93.67 % Rotamer Outliers : 0.00 % 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: 0.49 (0.22), residues: 1547 helix: 1.12 (0.15), residues: 1235 sheet: None (None), residues: 0 loop : -2.88 (0.35), residues: 312 *********************** 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 301 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.2173 time to fit residues: 98.0173 Evaluate side-chains 234 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.441 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0200 ------------------------------------------------------------------------------- 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: 20.0000 chunk 16 optimal weight: 0.0870 chunk 83 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- 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 141 ASN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 12580 Z= 0.303 Angle : 0.799 9.385 17066 Z= 0.390 Chirality : 0.046 0.210 2102 Planarity : 0.005 0.093 2069 Dihedral : 5.386 63.328 1616 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.08 % Favored : 93.67 % Rotamer Outliers : 0.00 % 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: 0.58 (0.22), residues: 1547 helix: 1.16 (0.15), residues: 1238 sheet: None (None), residues: 0 loop : -2.80 (0.36), residues: 309 *********************** 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 293 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.2236 time to fit residues: 99.0235 Evaluate side-chains 229 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.497 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9829 ------------------------------------------------------------------------------- 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: 5.9990 chunk 58 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 43 optimal weight: 0.0770 chunk 28 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 overall best weight: 0.9742 ------------------------------------------------------------------------------- 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 141 ASN ** 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 71 GLN H 45 ASN H 86 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: 0.8152 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12580 Z= 0.214 Angle : 0.798 13.369 17066 Z= 0.387 Chirality : 0.045 0.189 2102 Planarity : 0.005 0.088 2069 Dihedral : 5.288 60.610 1616 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.82 % Favored : 93.92 % Rotamer Outliers : 0.14 % 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: 0.67 (0.22), residues: 1547 helix: 1.20 (0.15), residues: 1238 sheet: None (None), residues: 0 loop : -2.65 (0.36), residues: 309 *********************** 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 309 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 307 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 308 average time/residue: 0.2097 time to fit residues: 96.2554 Evaluate side-chains 237 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.584 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0576 ------------------------------------------------------------------------------- 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: 20.0000 chunk 127 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 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** E 141 ASN ** 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 71 GLN H 39 GLN ** 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: 0.8202 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 12580 Z= 0.286 Angle : 0.827 11.773 17066 Z= 0.401 Chirality : 0.046 0.190 2102 Planarity : 0.005 0.091 2069 Dihedral : 5.341 61.877 1616 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.08 % Favored : 93.67 % Rotamer Outliers : 0.00 % 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: 0.66 (0.22), residues: 1547 helix: 1.23 (0.15), residues: 1234 sheet: None (None), residues: 0 loop : -2.77 (0.35), residues: 313 *********************** 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 304 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2054 time to fit residues: 94.3214 Evaluate side-chains 232 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.514 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0134 ------------------------------------------------------------------------------- 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: 0.9990 chunk 68 optimal weight: 5.9990 chunk 99 optimal weight: 30.0000 chunk 150 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 92 optimal weight: 0.0470 chunk 73 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 127 optimal weight: 0.0470 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 141 ASN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN G 71 GLN I 39 GLN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 12580 Z= 0.224 Angle : 0.815 11.967 17066 Z= 0.395 Chirality : 0.045 0.191 2102 Planarity : 0.005 0.087 2069 Dihedral : 5.269 59.004 1616 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.11 % Favored : 94.63 % Rotamer Outliers : 0.00 % 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: 0.60 (0.22), residues: 1547 helix: 1.21 (0.15), residues: 1233 sheet: None (None), residues: 0 loop : -2.87 (0.34), residues: 314 ********************** 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 307 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.2077 time to fit residues: 96.0974 Evaluate side-chains 238 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.541 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9214 ------------------------------------------------------------------------------- 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: 0.9990 chunk 110 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 105 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 141 ASN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.059982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.049701 restraints weight = 59049.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.051098 restraints weight = 35905.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.052118 restraints weight = 25160.989| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 12580 Z= 0.226 Angle : 0.813 11.431 17066 Z= 0.394 Chirality : 0.045 0.212 2102 Planarity : 0.005 0.088 2069 Dihedral : 5.197 58.786 1616 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.62 % Favored : 94.18 % Rotamer Outliers : 0.00 % 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: 0.73 (0.22), residues: 1547 helix: 1.31 (0.15), residues: 1236 sheet: None (None), residues: 0 loop : -2.95 (0.35), residues: 311 =============================================================================== Job complete usr+sys time: 2520.59 seconds wall clock time: 46 minutes 37.00 seconds (2797.00 seconds total)