Starting phenix.real_space_refine (version: dev) on Fri May 13 13:32:38 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r69_4733/05_2022/6r69_4733.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r69_4733/05_2022/6r69_4733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r69_4733/05_2022/6r69_4733.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r69_4733/05_2022/6r69_4733.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r69_4733/05_2022/6r69_4733.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r69_4733/05_2022/6r69_4733.pdb" } resolution = 3.65 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= -0.000 sd= 0.002 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 GLU 125": "OE1" <-> "OE2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 106": "OD1" <-> "OD2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 125": "OE1" <-> "OE2" Residue "E ASP 128": "OD1" <-> "OD2" Residue "E ASP 197": "OD1" <-> "OD2" Residue "E ASP 230": "OD1" <-> "OD2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 241": "OE1" <-> "OE2" Residue "F ASP 253": "OD1" <-> "OD2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 75": "OD1" <-> "OD2" Residue "J PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 12541 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "B" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "C" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "D" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "E" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "F" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1986 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 16, 'CIS': 1, 'TRANS': 240} Chain: "G" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "H" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "I" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "J" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Time building chain proxies: 7.45, per 1000 atoms: 0.59 Number of scatterers: 12541 At special positions: 0 Unit cell: (105.4, 101.15, 130.9, 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 99 16.00 O 2118 8.00 N 1934 7.00 C 8390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.62 Conformation dependent library (CDL) restraints added in 1.9 seconds 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3094 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 0 sheets defined 81.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 43 through 61 removed outlier: 3.714A pdb=" N PHE A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Proline residue: A 55 - end of helix Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 87 through 101 removed outlier: 3.637A pdb=" N THR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 112 through 119 removed outlier: 3.957A pdb=" N GLU A 118 " --> pdb=" O GLN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 140 Proline residue: A 133 - end of helix removed outlier: 3.556A pdb=" N ARG A 140 " --> pdb=" O ALA A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.806A pdb=" N LEU A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 208 Proline residue: A 172 - end of helix removed outlier: 3.874A pdb=" N GLN A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) Proline residue: A 192 - end of helix removed outlier: 3.525A pdb=" N LEU A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 228 removed outlier: 3.767A pdb=" N LEU A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Proline residue: A 220 - end of helix removed outlier: 4.348A pdb=" N PHE A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 245 removed outlier: 3.628A pdb=" N LEU A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 63 Proline residue: B 55 - end of helix removed outlier: 3.964A pdb=" N LEU B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 77 removed outlier: 3.765A pdb=" N ALA B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 119 removed outlier: 3.598A pdb=" N GLY B 91 " --> pdb=" O GLN B 87 " (cutoff:3.500A) Proline residue: B 103 - end of helix removed outlier: 4.825A pdb=" N GLN B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Proline residue: B 115 - end of helix removed outlier: 3.811A pdb=" N GLU B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 142 Proline residue: B 133 - end of helix removed outlier: 3.688A pdb=" N GLN B 141 " --> pdb=" O PHE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 153 removed outlier: 3.803A pdb=" N LEU B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 165 Processing helix chain 'B' and resid 166 through 205 Proline residue: B 172 - end of helix removed outlier: 4.127A pdb=" N ILE B 191 " --> pdb=" O PHE B 187 " (cutoff:3.500A) Proline residue: B 192 - end of helix Processing helix chain 'B' and resid 217 through 229 removed outlier: 4.061A pdb=" N PHE B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 245 removed outlier: 3.620A pdb=" N LEU B 234 " --> pdb=" O ASP B 230 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL B 236 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER B 245 " --> pdb=" O GLN B 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.743A pdb=" N ILE C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Proline residue: C 55 - end of helix removed outlier: 3.755A pdb=" N THR C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 75 removed outlier: 3.879A pdb=" N ILE C 68 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C 69 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 70 " --> pdb=" O ARG C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 101 Processing helix chain 'C' and resid 101 through 117 removed outlier: 4.766A pdb=" N GLN C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 123 through 140 removed outlier: 4.063A pdb=" N LEU C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN C 132 " --> pdb=" O ASP C 128 " (cutoff:3.500A) Proline residue: C 133 - end of helix removed outlier: 3.555A pdb=" N ALA C 136 " --> pdb=" O GLN C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 154 removed outlier: 3.956A pdb=" N LEU C 147 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA C 154 " --> pdb=" O PHE C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 190 removed outlier: 3.665A pdb=" N LEU C 170 " --> pdb=" O PRO C 166 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 171 " --> pdb=" O MET C 167 " (cutoff:3.500A) Proline residue: C 172 - end of helix removed outlier: 3.609A pdb=" N PHE C 190 " --> pdb=" O GLY C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 208 Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 217 through 228 removed outlier: 4.269A pdb=" N PHE C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE C 226 " --> pdb=" O LYS C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 245 removed outlier: 3.614A pdb=" N LEU C 234 " --> pdb=" O ASP C 230 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 235 " --> pdb=" O GLY C 231 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 236 " --> pdb=" O TRP C 232 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER C 245 " --> pdb=" O GLN C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 62 removed outlier: 3.675A pdb=" N ILE D 48 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR D 52 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Proline residue: D 55 - end of helix removed outlier: 3.994A pdb=" N THR D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 75 Processing helix chain 'D' and resid 87 through 112 Proline residue: D 103 - end of helix Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 127 through 140 Proline residue: D 133 - end of helix Processing helix chain 'D' and resid 143 through 153 removed outlier: 3.637A pdb=" N LEU D 147 " --> pdb=" O ARG D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 190 removed outlier: 3.701A pdb=" N LEU D 171 " --> pdb=" O MET D 167 " (cutoff:3.500A) Proline residue: D 172 - end of helix Processing helix chain 'D' and resid 190 through 208 Processing helix chain 'D' and resid 213 through 228 removed outlier: 3.543A pdb=" N ILE D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) Proline residue: D 220 - end of helix Processing helix chain 'D' and resid 232 through 245 removed outlier: 3.522A pdb=" N VAL D 236 " --> pdb=" O TRP D 232 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE D 243 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR D 244 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER D 245 " --> pdb=" O GLN D 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 63 removed outlier: 4.414A pdb=" N ILE E 48 " --> pdb=" O THR E 44 " (cutoff:3.500A) Proline residue: E 55 - end of helix removed outlier: 3.847A pdb=" N THR E 62 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 63 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 77 removed outlier: 3.809A pdb=" N VAL E 70 " --> pdb=" O ARG E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 117 removed outlier: 4.234A pdb=" N ALA E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) Proline residue: E 103 - end of helix removed outlier: 4.593A pdb=" N GLN E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 124 through 140 Proline residue: E 133 - end of helix Processing helix chain 'E' and resid 143 through 155 removed outlier: 3.949A pdb=" N LEU E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 208 removed outlier: 3.509A pdb=" N LEU E 170 " --> pdb=" O PRO E 166 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU E 171 " --> pdb=" O MET E 167 " (cutoff:3.500A) Proline residue: E 172 - end of helix removed outlier: 3.730A pdb=" N ILE E 191 " --> pdb=" O PHE E 187 " (cutoff:3.500A) Proline residue: E 192 - end of helix removed outlier: 3.589A pdb=" N LEU E 207 " --> pdb=" O VAL E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 228 removed outlier: 4.564A pdb=" N PHE E 221 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS E 222 " --> pdb=" O ALA E 218 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU E 223 " --> pdb=" O LEU E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 245 removed outlier: 3.861A pdb=" N LEU E 234 " --> pdb=" O ASP E 230 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE E 243 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR E 244 " --> pdb=" O ALA E 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 14 removed outlier: 4.248A pdb=" N LEU F 10 " --> pdb=" O SER F 6 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR F 11 " --> pdb=" O GLU F 7 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TRP F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 29 Processing helix chain 'F' and resid 44 through 55 removed outlier: 3.834A pdb=" N ILE F 48 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL F 53 " --> pdb=" O MET F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 89 removed outlier: 3.662A pdb=" N MET F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN F 76 " --> pdb=" O TRP F 72 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE F 78 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU F 79 " --> pdb=" O MET F 75 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN F 89 " --> pdb=" O GLY F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 104 removed outlier: 4.063A pdb=" N VAL F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE F 101 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 141 removed outlier: 3.808A pdb=" N MET F 131 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE F 137 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU F 138 " --> pdb=" O MET F 134 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE F 140 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 157 removed outlier: 3.535A pdb=" N HIS F 155 " --> pdb=" O VAL F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 176 removed outlier: 4.297A pdb=" N GLY F 176 " --> pdb=" O LEU F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 206 removed outlier: 4.097A pdb=" N LEU F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA F 187 " --> pdb=" O GLY F 183 " (cutoff:3.500A) Proline residue: F 189 - end of helix removed outlier: 3.658A pdb=" N GLY F 202 " --> pdb=" O ASN F 198 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN F 205 " --> pdb=" O LEU F 201 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG F 206 " --> pdb=" O GLY F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 212 removed outlier: 3.641A pdb=" N LEU F 211 " --> pdb=" O ALA F 208 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER F 212 " --> pdb=" O PRO F 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 208 through 212' Processing helix chain 'F' and resid 216 through 232 removed outlier: 4.197A pdb=" N THR F 223 " --> pdb=" O PRO F 219 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET F 229 " --> pdb=" O GLY F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 261 removed outlier: 3.573A pdb=" N PHE F 239 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU F 241 " --> pdb=" O ALA F 237 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N HIS F 242 " --> pdb=" O PRO F 238 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Proline residue: F 259 - end of helix Processing helix chain 'G' and resid 2 through 40 removed outlier: 3.585A pdb=" N MET G 7 " --> pdb=" O PRO G 3 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY G 10 " --> pdb=" O VAL G 6 " (cutoff:3.500A) Proline residue: G 23 - end of helix Processing helix chain 'G' and resid 50 through 66 removed outlier: 3.782A pdb=" N VAL G 58 " --> pdb=" O LYS G 54 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE G 63 " --> pdb=" O PHE G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 89 removed outlier: 3.997A pdb=" N LEU G 73 " --> pdb=" O MET G 69 " (cutoff:3.500A) Proline residue: G 85 - end of helix removed outlier: 3.693A pdb=" N ILE G 88 " --> pdb=" O LEU G 84 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY G 89 " --> pdb=" O PRO G 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 40 Proline residue: H 23 - end of helix removed outlier: 3.705A pdb=" N LEU H 38 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA H 40 " --> pdb=" O SER H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 66 removed outlier: 3.631A pdb=" N VAL H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE H 63 " --> pdb=" O PHE H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 84 removed outlier: 4.083A pdb=" N LEU H 73 " --> pdb=" O MET H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 87 No H-bonds generated for 'chain 'H' and resid 85 through 87' Processing helix chain 'I' and resid 2 through 39 Proline residue: I 23 - end of helix Processing helix chain 'I' and resid 50 through 66 removed outlier: 3.531A pdb=" N VAL I 58 " --> pdb=" O LYS I 54 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE I 63 " --> pdb=" O PHE I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 88 Proline residue: I 85 - end of helix removed outlier: 4.104A pdb=" N ILE I 88 " --> pdb=" O LEU I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 38 removed outlier: 4.157A pdb=" N GLY J 10 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS J 15 " --> pdb=" O THR J 11 " (cutoff:3.500A) Proline residue: J 23 - end of helix removed outlier: 3.701A pdb=" N LEU J 38 " --> pdb=" O ILE J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 66 removed outlier: 4.011A pdb=" N LYS J 54 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE J 63 " --> pdb=" O PHE J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 88 removed outlier: 3.815A pdb=" N LEU J 73 " --> pdb=" O MET J 69 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG J 78 " --> pdb=" O LEU J 74 " (cutoff:3.500A) Proline residue: J 85 - end of helix removed outlier: 3.619A pdb=" N ILE J 88 " --> pdb=" O LEU J 84 " (cutoff:3.500A) 788 hydrogen bonds defined for protein. 2349 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: 3.33 Time building geometry restraints manager: 5.90 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: 3717 1.34 - 1.46: 1593 1.46 - 1.57: 7313 1.57 - 1.69: 0 1.69 - 1.81: 197 Bond restraints: 12820 Sorted by residual: bond pdb=" N PHE F 140 " pdb=" CA PHE F 140 " ideal model delta sigma weight residual 1.468 1.451 0.018 1.24e-02 6.50e+03 2.00e+00 bond pdb=" CG1 ILE B 68 " pdb=" CD1 ILE B 68 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.76e+00 bond pdb=" C GLU I 46 " pdb=" O GLU I 46 " ideal model delta sigma weight residual 1.234 1.245 -0.011 8.30e-03 1.45e+04 1.72e+00 bond pdb=" N GLU J 46 " pdb=" CA GLU J 46 " ideal model delta sigma weight residual 1.468 1.452 0.016 1.24e-02 6.50e+03 1.71e+00 bond pdb=" CB TRP C 232 " pdb=" CG TRP C 232 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.64e+00 ... (remaining 12815 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.15: 429 105.15 - 112.36: 6767 112.36 - 119.58: 4115 119.58 - 126.80: 6019 126.80 - 134.02: 146 Bond angle restraints: 17476 Sorted by residual: angle pdb=" C THR J 42 " pdb=" N GLN J 43 " pdb=" CA GLN J 43 " ideal model delta sigma weight residual 120.38 126.95 -6.57 1.46e+00 4.69e-01 2.02e+01 angle pdb=" CA LEU F 150 " pdb=" CB LEU F 150 " pdb=" CG LEU F 150 " ideal model delta sigma weight residual 116.30 101.67 14.63 3.50e+00 8.16e-02 1.75e+01 angle pdb=" C ILE F 159 " pdb=" N GLY F 160 " pdb=" CA GLY F 160 " ideal model delta sigma weight residual 121.41 113.52 7.89 1.96e+00 2.60e-01 1.62e+01 angle pdb=" N PHE B 64 " pdb=" CA PHE B 64 " pdb=" CB PHE B 64 " ideal model delta sigma weight residual 114.27 107.74 6.53 1.64e+00 3.72e-01 1.58e+01 angle pdb=" N PHE D 64 " pdb=" CA PHE D 64 " pdb=" CB PHE D 64 " ideal model delta sigma weight residual 114.17 110.02 4.15 1.14e+00 7.69e-01 1.33e+01 ... (remaining 17471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 6847 17.38 - 34.75: 745 34.75 - 52.13: 114 52.13 - 69.50: 16 69.50 - 86.88: 9 Dihedral angle restraints: 7731 sinusoidal: 2988 harmonic: 4743 Sorted by residual: dihedral pdb=" CA ALA I 41 " pdb=" C ALA I 41 " pdb=" N THR I 42 " pdb=" CA THR I 42 " ideal model delta harmonic sigma weight residual -180.00 -140.71 -39.29 0 5.00e+00 4.00e-02 6.17e+01 dihedral pdb=" CA ALA G 41 " pdb=" C ALA G 41 " pdb=" N THR G 42 " pdb=" CA THR G 42 " ideal model delta harmonic sigma weight residual -180.00 -141.80 -38.20 0 5.00e+00 4.00e-02 5.84e+01 dihedral pdb=" CA LEU F 211 " pdb=" C LEU F 211 " pdb=" N SER F 212 " pdb=" CA SER F 212 " ideal model delta harmonic sigma weight residual 180.00 142.14 37.86 0 5.00e+00 4.00e-02 5.73e+01 ... (remaining 7728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1309 0.035 - 0.070: 610 0.070 - 0.105: 222 0.105 - 0.140: 39 0.140 - 0.175: 9 Chirality restraints: 2189 Sorted by residual: chirality pdb=" CA PRO G 67 " pdb=" N PRO G 67 " pdb=" C PRO G 67 " pdb=" CB PRO G 67 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CG LEU D 223 " pdb=" CB LEU D 223 " pdb=" CD1 LEU D 223 " pdb=" CD2 LEU D 223 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA PRO E 81 " pdb=" N PRO E 81 " pdb=" C PRO E 81 " pdb=" CB PRO E 81 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.00e-01 ... (remaining 2186 not shown) Planarity restraints: 2130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 84 " 0.051 5.00e-02 4.00e+02 7.82e-02 9.79e+00 pdb=" N PRO C 85 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 213 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.13e+00 pdb=" N PRO D 214 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO D 214 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 214 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 84 " 0.046 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO D 85 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 85 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 85 " 0.039 5.00e-02 4.00e+02 ... (remaining 2127 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1146 2.73 - 3.27: 13976 3.27 - 3.82: 19782 3.82 - 4.36: 23427 4.36 - 4.90: 39753 Nonbonded interactions: 98084 Sorted by model distance: nonbonded pdb=" OE1 GLU G 46 " pdb=" OG SER H 50 " model vdw 2.191 2.440 nonbonded pdb=" O ALA D 131 " pdb=" N ARG D 135 " model vdw 2.195 2.520 nonbonded pdb=" OG1 THR D 65 " pdb=" OE1 GLU D 178 " model vdw 2.199 2.440 nonbonded pdb=" O ALA F 83 " pdb=" OG1 THR F 87 " model vdw 2.201 2.440 nonbonded pdb=" O MET C 138 " pdb=" OG1 THR C 142 " model vdw 2.203 2.440 ... (remaining 98079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 8390 2.51 5 N 1934 2.21 5 O 2118 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: 1.320 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: 6.150 Check model and map are aligned: 0.190 Convert atoms to be neutral: 0.110 Process input model: 35.020 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 12820 Z= 0.348 Angle : 0.896 14.628 17476 Z= 0.506 Chirality : 0.045 0.175 2189 Planarity : 0.007 0.078 2130 Dihedral : 14.420 86.876 4637 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.82 % Favored : 89.81 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -3.99 (0.18), residues: 1609 helix: -1.98 (0.12), residues: 1203 sheet: None (None), residues: 0 loop : -4.27 (0.27), residues: 406 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 386 time to evaluate : 1.553 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: 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 outliers start: 2 outliers final: 0 residues processed: 387 average time/residue: 0.2510 time to fit residues: 136.8315 Evaluate side-chains 249 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.500 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 0.9990 chunk 118 optimal weight: 0.0370 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN B 241 GLN C 76 ASN C 184 GLN C 241 GLN D 76 ASN D 87 GLN E 76 ASN F 105 GLN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 HIS F 165 ASN F 249 ASN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 ASN I 71 ASN J 39 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 12820 Z= 0.267 Angle : 0.810 11.186 17476 Z= 0.398 Chirality : 0.045 0.173 2189 Planarity : 0.008 0.096 2130 Dihedral : 6.171 40.857 1695 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.70 % Favored : 91.17 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.21), residues: 1609 helix: -0.47 (0.14), residues: 1244 sheet: None (None), residues: 0 loop : -3.66 (0.31), residues: 365 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 284 time to evaluate : 1.636 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 10 residues processed: 303 average time/residue: 0.2481 time to fit residues: 108.3085 Evaluate side-chains 245 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 235 time to evaluate : 1.417 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1691 time to fit residues: 4.6687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 0.0040 chunk 39 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 48 optimal weight: 0.1980 chunk 114 optimal weight: 6.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.098 12820 Z= 0.224 Angle : 0.793 12.629 17476 Z= 0.382 Chirality : 0.044 0.221 2189 Planarity : 0.007 0.092 2130 Dihedral : 5.868 41.199 1695 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.96 % Favored : 91.92 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.21), residues: 1609 helix: 0.13 (0.15), residues: 1234 sheet: None (None), residues: 0 loop : -3.55 (0.30), residues: 375 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 281 time to evaluate : 1.671 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 6 residues processed: 301 average time/residue: 0.2388 time to fit residues: 105.9046 Evaluate side-chains 242 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 236 time to evaluate : 1.567 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1200 time to fit residues: 3.2897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 151 optimal weight: 0.0040 chunk 135 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN F 143 HIS ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.117 12820 Z= 0.226 Angle : 0.796 10.110 17476 Z= 0.385 Chirality : 0.043 0.181 2189 Planarity : 0.007 0.092 2130 Dihedral : 5.680 41.061 1695 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.71 % Favored : 92.23 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 (0.21), residues: 1609 helix: 0.46 (0.15), residues: 1238 sheet: None (None), residues: 0 loop : -3.49 (0.29), residues: 371 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 268 time to evaluate : 1.649 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 9 residues processed: 285 average time/residue: 0.2337 time to fit residues: 97.9777 Evaluate side-chains 249 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 240 time to evaluate : 2.394 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1293 time to fit residues: 4.2610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 129 optimal weight: 0.0670 chunk 104 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN D 76 ASN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.130 12820 Z= 0.238 Angle : 0.787 11.639 17476 Z= 0.378 Chirality : 0.044 0.198 2189 Planarity : 0.007 0.096 2130 Dihedral : 5.550 40.193 1695 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.39 (0.22), residues: 1609 helix: 0.64 (0.15), residues: 1243 sheet: None (None), residues: 0 loop : -3.36 (0.30), residues: 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 275 time to evaluate : 1.528 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 4 residues processed: 287 average time/residue: 0.2224 time to fit residues: 95.2138 Evaluate side-chains 241 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 237 time to evaluate : 1.564 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1304 time to fit residues: 2.9402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.137 12820 Z= 0.268 Angle : 0.819 12.281 17476 Z= 0.391 Chirality : 0.044 0.249 2189 Planarity : 0.006 0.070 2130 Dihedral : 5.501 39.360 1695 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.20 % Favored : 91.73 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.19 (0.22), residues: 1609 helix: 0.78 (0.15), residues: 1244 sheet: None (None), residues: 0 loop : -3.31 (0.30), residues: 365 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 245 time to evaluate : 1.720 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: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 9 residues processed: 263 average time/residue: 0.2214 time to fit residues: 87.1281 Evaluate side-chains 242 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 233 time to evaluate : 1.574 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1156 time to fit residues: 3.9111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 110 optimal weight: 0.3980 chunk 85 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 151 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.162 12820 Z= 0.281 Angle : 0.819 11.786 17476 Z= 0.395 Chirality : 0.045 0.341 2189 Planarity : 0.007 0.111 2130 Dihedral : 5.453 38.716 1695 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.52 % Favored : 92.42 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.04 (0.22), residues: 1609 helix: 0.85 (0.15), residues: 1258 sheet: None (None), residues: 0 loop : -3.24 (0.32), residues: 351 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 260 time to evaluate : 1.565 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 270 average time/residue: 0.2196 time to fit residues: 88.7327 Evaluate side-chains 243 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 236 time to evaluate : 1.666 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1258 time to fit residues: 3.6542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 0.0570 chunk 118 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.256 12820 Z= 0.335 Angle : 0.868 16.271 17476 Z= 0.419 Chirality : 0.047 0.347 2189 Planarity : 0.007 0.086 2130 Dihedral : 5.475 37.935 1695 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.14 % Favored : 91.73 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.07 (0.22), residues: 1609 helix: 0.88 (0.15), residues: 1269 sheet: None (None), residues: 0 loop : -3.15 (0.33), residues: 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 244 time to evaluate : 1.609 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: 11 outliers final: 5 residues processed: 251 average time/residue: 0.2236 time to fit residues: 84.0710 Evaluate side-chains 238 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 233 time to evaluate : 1.569 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1274 time to fit residues: 3.1289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 84 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.428 12820 Z= 0.355 Angle : 0.898 25.567 17476 Z= 0.436 Chirality : 0.046 0.271 2189 Planarity : 0.007 0.082 2130 Dihedral : 5.445 39.167 1695 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.58 % Favored : 92.36 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1609 helix: 0.92 (0.15), residues: 1279 sheet: None (None), residues: 0 loop : -3.35 (0.32), residues: 330 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 246 time to evaluate : 1.406 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: symmetry clash outliers start: 9 outliers final: 3 residues processed: 253 average time/residue: 0.2168 time to fit residues: 82.4330 Evaluate side-chains 237 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 234 time to evaluate : 1.564 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1128 time to fit residues: 2.6730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.407 12820 Z= 0.375 Angle : 0.960 24.514 17476 Z= 0.469 Chirality : 0.047 0.281 2189 Planarity : 0.007 0.118 2130 Dihedral : 5.442 37.724 1695 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.33 % Favored : 91.61 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.01 (0.22), residues: 1609 helix: 0.87 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -3.36 (0.32), residues: 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 241 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 246 average time/residue: 0.2085 time to fit residues: 77.7126 Evaluate side-chains 236 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 233 time to evaluate : 1.525 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1083 time to fit residues: 2.5785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.078138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.062932 restraints weight = 47829.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.064950 restraints weight = 26184.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.066308 restraints weight = 17525.137| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.174 12820 Z= 0.254 Angle : 0.899 17.413 17476 Z= 0.431 Chirality : 0.046 0.267 2189 Planarity : 0.007 0.100 2130 Dihedral : 5.424 38.792 1695 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.64 % Favored : 92.29 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.08 (0.22), residues: 1609 helix: 0.92 (0.15), residues: 1273 sheet: None (None), residues: 0 loop : -3.31 (0.32), residues: 336 =============================================================================== Job complete usr+sys time: 2514.40 seconds wall clock time: 46 minutes 53.96 seconds (2813.96 seconds total)