Starting phenix.real_space_refine on Sun Apr 7 04:24:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jia_36304/04_2024/8jia_36304_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jia_36304/04_2024/8jia_36304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jia_36304/04_2024/8jia_36304.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jia_36304/04_2024/8jia_36304.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jia_36304/04_2024/8jia_36304_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jia_36304/04_2024/8jia_36304_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 49 5.16 5 C 6045 2.51 5 N 1697 2.21 5 O 1790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 173": "OE1" <-> "OE2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "C GLU 9": "OE1" <-> "OE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9587 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1581 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 9, 'TRANS': 217} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 133 Chain: "B" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1576 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 9, 'TRANS': 215} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 122 Chain: "E" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 1884 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 3, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 6, 'TYR%COO:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 164 Chain: "D" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2227 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 288} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2257 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 288} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.68, per 1000 atoms: 0.59 Number of scatterers: 9587 At special positions: 0 Unit cell: (119.78, 106, 193.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 6 15.00 O 1790 8.00 N 1697 7.00 C 6045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 73 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS C 73 " - pdb=" SG CYS C 78 " distance=2.03 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: 3.78 Conformation dependent library (CDL) restraints added in 2.1 seconds 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 5 sheets defined 45.9% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 76 through 82 removed outlier: 3.815A pdb=" N ARG A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 removed outlier: 3.949A pdb=" N VAL A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA A 103 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 122 Proline residue: A 121 - end of helix Processing helix chain 'A' and resid 124 through 127 No H-bonds generated for 'chain 'A' and resid 124 through 127' Processing helix chain 'A' and resid 142 through 145 No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.590A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.604A pdb=" N ASP A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR A 188 " --> pdb=" O ARG A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 205 No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'B' and resid 39 through 41 No H-bonds generated for 'chain 'B' and resid 39 through 41' Processing helix chain 'B' and resid 43 through 50 removed outlier: 3.659A pdb=" N LEU B 50 " --> pdb=" O PHE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 104 removed outlier: 3.682A pdb=" N VAL B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 142 through 154 removed outlier: 3.875A pdb=" N GLN B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 186 removed outlier: 4.015A pdb=" N ARG B 176 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASP B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 178 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU B 183 " --> pdb=" O MET B 179 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 109 removed outlier: 3.924A pdb=" N ALA E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR E 57 " --> pdb=" O GLN E 53 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU E 61 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N HIS E 62 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU E 66 " --> pdb=" O HIS E 62 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP E 67 " --> pdb=" O SER E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 128 through 195 removed outlier: 3.735A pdb=" N ILE E 132 " --> pdb=" O PRO E 128 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP E 133 " --> pdb=" O GLN E 129 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL E 140 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS E 143 " --> pdb=" O ARG E 139 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN E 186 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU E 187 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN E 195 " --> pdb=" O GLN E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 201 No H-bonds generated for 'chain 'E' and resid 198 through 201' Processing helix chain 'E' and resid 321 through 324 No H-bonds generated for 'chain 'E' and resid 321 through 324' Processing helix chain 'D' and resid 4 through 16 removed outlier: 3.664A pdb=" N ASN D 8 " --> pdb=" O GLY D 4 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU D 9 " --> pdb=" O PHE D 5 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL D 10 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 49 Processing helix chain 'D' and resid 76 through 84 removed outlier: 3.925A pdb=" N ALA D 80 " --> pdb=" O THR D 76 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 109 removed outlier: 3.707A pdb=" N ASP D 104 " --> pdb=" O GLN D 100 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ALA D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE D 107 " --> pdb=" O TYR D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 137 through 140 No H-bonds generated for 'chain 'D' and resid 137 through 140' Processing helix chain 'D' and resid 158 through 198 removed outlier: 3.920A pdb=" N ALA D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL D 165 " --> pdb=" O ARG D 161 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU D 166 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASP D 167 " --> pdb=" O PHE D 163 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL D 192 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL D 194 " --> pdb=" O ASN D 190 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 206 removed outlier: 4.704A pdb=" N ILE D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 243 removed outlier: 3.669A pdb=" N LEU D 218 " --> pdb=" O TRP D 214 " (cutoff:3.500A) Proline residue: D 219 - end of helix removed outlier: 3.839A pdb=" N GLU D 223 " --> pdb=" O PRO D 219 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA D 224 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 237 " --> pdb=" O GLY D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 255 Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 272 through 284 Processing helix chain 'D' and resid 289 through 292 No H-bonds generated for 'chain 'D' and resid 289 through 292' Processing helix chain 'C' and resid 10 through 16 Processing helix chain 'C' and resid 18 through 48 removed outlier: 3.618A pdb=" N ILE C 22 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 76 through 85 removed outlier: 4.072A pdb=" N LYS C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 106 through 109 No H-bonds generated for 'chain 'C' and resid 106 through 109' Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 162 through 198 Processing helix chain 'C' and resid 203 through 209 Processing helix chain 'C' and resid 213 through 246 removed outlier: 3.798A pdb=" N GLN C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Proline residue: C 219 - end of helix removed outlier: 4.220A pdb=" N PHE C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 269 through 286 Proline residue: C 273 - end of helix removed outlier: 4.081A pdb=" N ALA C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR C 286 " --> pdb=" O MET C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 Processing sheet with id= A, first strand: chain 'A' and resid 33 through 35 removed outlier: 7.074A pdb=" N ARG A 208 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU A 221 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 211 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 83 through 86 removed outlier: 7.151A pdb=" N VAL A 160 " --> pdb=" O GLY A 84 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N VAL A 86 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU A 162 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU A 193 " --> pdb=" O ALA A 163 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.590A pdb=" N ARG B 62 " --> pdb=" O THR B 4 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP B 6 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP B 60 " --> pdb=" O ASP B 6 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 83 through 86 removed outlier: 7.063A pdb=" N VAL B 160 " --> pdb=" O GLY B 84 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N VAL B 86 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU B 162 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR B 191 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ALA B 163 " --> pdb=" O THR B 191 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU B 193 " --> pdb=" O ALA B 163 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 91 through 94 removed outlier: 7.134A pdb=" N LYS C 129 " --> pdb=" O LYS C 92 " (cutoff:3.500A) 347 hydrogen bonds defined for protein. 1032 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: 2.31 Time building geometry restraints manager: 4.07 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: 3169 1.34 - 1.46: 1871 1.46 - 1.58: 4586 1.58 - 1.70: 7 1.70 - 1.82: 91 Bond restraints: 9724 Sorted by residual: bond pdb=" CA ASN D 17 " pdb=" CB ASN D 17 " ideal model delta sigma weight residual 1.522 1.551 -0.029 1.27e-02 6.20e+03 5.26e+00 bond pdb=" CA ILE A 23 " pdb=" CB ILE A 23 " ideal model delta sigma weight residual 1.539 1.558 -0.020 1.19e-02 7.06e+03 2.73e+00 bond pdb=" C VAL B 76 " pdb=" N PRO B 77 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.25e-02 6.40e+03 2.58e+00 bond pdb=" CB GLN B 95 " pdb=" CG GLN B 95 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.50e+00 bond pdb=" C VAL A 120 " pdb=" N PRO A 121 " ideal model delta sigma weight residual 1.334 1.347 -0.013 8.40e-03 1.42e+04 2.37e+00 ... (remaining 9719 not shown) Histogram of bond angle deviations from ideal: 99.01 - 107.19: 294 107.19 - 115.38: 5902 115.38 - 123.57: 6778 123.57 - 131.76: 254 131.76 - 139.94: 19 Bond angle restraints: 13247 Sorted by residual: angle pdb=" N VAL E 304 " pdb=" CA VAL E 304 " pdb=" C VAL E 304 " ideal model delta sigma weight residual 113.71 108.30 5.41 9.50e-01 1.11e+00 3.24e+01 angle pdb=" CB MET D 225 " pdb=" CG MET D 225 " pdb=" SD MET D 225 " ideal model delta sigma weight residual 112.70 126.64 -13.94 3.00e+00 1.11e-01 2.16e+01 angle pdb=" C ASP B 89 " pdb=" N PHE B 90 " pdb=" CA PHE B 90 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.00e+01 angle pdb=" N ILE A 185 " pdb=" CA ILE A 185 " pdb=" C ILE A 185 " ideal model delta sigma weight residual 112.35 106.08 6.27 1.41e+00 5.03e-01 1.98e+01 angle pdb=" N VAL D 242 " pdb=" CA VAL D 242 " pdb=" C VAL D 242 " ideal model delta sigma weight residual 113.39 106.88 6.51 1.47e+00 4.63e-01 1.96e+01 ... (remaining 13242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.12: 5412 16.12 - 32.23: 363 32.23 - 48.35: 79 48.35 - 64.47: 24 64.47 - 80.58: 7 Dihedral angle restraints: 5885 sinusoidal: 2067 harmonic: 3818 Sorted by residual: dihedral pdb=" CA LYS C 262 " pdb=" C LYS C 262 " pdb=" N VAL C 263 " pdb=" CA VAL C 263 " ideal model delta harmonic sigma weight residual 180.00 151.21 28.79 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA MET D 206 " pdb=" C MET D 206 " pdb=" N ARG D 207 " pdb=" CA ARG D 207 " ideal model delta harmonic sigma weight residual 180.00 158.78 21.22 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA ILE C 85 " pdb=" C ILE C 85 " pdb=" N GLU C 86 " pdb=" CA GLU C 86 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1137 0.053 - 0.106: 377 0.106 - 0.159: 82 0.159 - 0.212: 20 0.212 - 0.265: 5 Chirality restraints: 1621 Sorted by residual: chirality pdb=" CG LEU D 239 " pdb=" CB LEU D 239 " pdb=" CD1 LEU D 239 " pdb=" CD2 LEU D 239 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB VAL B 76 " pdb=" CA VAL B 76 " pdb=" CG1 VAL B 76 " pdb=" CG2 VAL B 76 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB THR A 167 " pdb=" CA THR A 167 " pdb=" OG1 THR A 167 " pdb=" CG2 THR A 167 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1618 not shown) Planarity restraints: 1710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 110 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.81e+00 pdb=" N PRO C 111 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 111 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 111 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 57 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.40e+00 pdb=" CD GLU D 57 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU D 57 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU D 57 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 223 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.37e+00 pdb=" CD GLU C 223 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU C 223 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU C 223 " 0.011 2.00e-02 2.50e+03 ... (remaining 1707 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2965 2.82 - 3.34: 9334 3.34 - 3.86: 15607 3.86 - 4.38: 17175 4.38 - 4.90: 28621 Nonbonded interactions: 73702 Sorted by model distance: nonbonded pdb=" O LEU E 47 " pdb=" OG1 THR E 363 " model vdw 2.306 2.440 nonbonded pdb=" O ARG C 213 " pdb=" OG1 THR C 216 " model vdw 2.325 2.440 nonbonded pdb=" O ILE C 268 " pdb=" OG1 THR C 272 " model vdw 2.329 2.440 nonbonded pdb=" O GLU C 9 " pdb=" OG1 THR C 12 " model vdw 2.336 2.440 nonbonded pdb=" NH1 ARG C 99 " pdb=" OD1 ASP C 120 " model vdw 2.356 2.520 ... (remaining 73697 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 1 through 2 or (resid 3 and (name N or name CA or name C o \ r name O or name CB )) or resid 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 12 or (resid 13 and (name N or name CA \ or name C or name O or name CB )) or resid 14 through 19 or (resid 20 through 2 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 23 or (resid \ 24 and (name N or name CA or name C or name O or name CB )) or resid 25 or (res \ id 26 and (name N or name CA or name C or name O or name CB )) or resid 27 or (r \ esid 28 through 29 and (name N or name CA or name C or name O or name CB )) or r \ esid 30 through 65 or (resid 66 through 70 and (name N or name CA or name C or n \ ame O or name CB )) or resid 71 through 88 or (resid 89 and (name N or name CA o \ r name C or name O or name CB )) or resid 90 through 92 or (resid 93 through 100 \ and (name N or name CA or name C or name O or name CB )) or resid 101 through 1 \ 24 or (resid 125 and (name N or name CA or name C or name O or name CB )) or res \ id 126 through 133 or (resid 134 through 136 and (name N or name CA or name C or \ name O or name CB )) or resid 137 through 138 or (resid 139 and (name N or name \ CA or name C or name O or name CB )) or resid 140 through 172 or (resid 173 and \ (name N or name CA or name C or name O or name CB )) or resid 174 through 217 o \ r (resid 218 through 219 and (name N or name CA or name C or name O or name CB ) \ ) or resid 220 through 225 or resid 301)) selection = (chain 'B' and (resid 1 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or (resid 30 through 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 34 or (resid 35 through 36 and (na \ me N or name CA or name C or name O or name CB )) or resid 37 through 44 or (res \ id 45 and (name N or name CA or name C or name O or name CB )) or resid 46 throu \ gh 50 or (resid 51 through 55 and (name N or name CA or name C or name O or name \ CB )) or resid 56 through 59 or (resid 60 and (name N or name CA or name C or n \ ame O or name CB )) or resid 61 through 68 or (resid 69 through 70 and (name N o \ r name CA or name C or name O or name CB )) or resid 71 or (resid 72 and (name N \ or name CA or name C or name O or name CB )) or resid 73 or (resid 74 and (name \ N or name CA or name C or name O or name CB )) or resid 75 through 77 or (resid \ 78 and (name N or name CA or name C or name O or name CB )) or resid 79 through \ 94 or (resid 95 through 100 and (name N or name CA or name C or name O or name \ CB )) or resid 101 through 128 or (resid 129 and (name N or name CA or name C or \ name O or name CB )) or resid 130 through 137 or (resid 138 through 139 and (na \ me N or name CA or name C or name O or name CB )) or resid 140 through 156 or (r \ esid 157 and (name N or name CA or name C or name O or name CB )) or resid 158 t \ hrough 175 or (resid 176 and (name N or name CA or name C or name O or name CB ) \ ) or resid 177 through 179 or (resid 180 and (name N or name CA or name C or nam \ e O or name CB )) or resid 181 through 192 or (resid 193 and (name N or name CA \ or name C or name O or name CB )) or resid 194 through 198 or (resid 199 and (na \ me N or name CA or name C or name O or name CB )) or resid 200 through 213 or (r \ esid 214 and (name N or name CA or name C or name O or name CB )) or resid 215 t \ hrough 218 or (resid 219 and (name N or name CA or name C or name O or name CB ) \ ) or resid 220 or (resid 221 through 223 and (name N or name CA or name C or nam \ e O or name CB )) or resid 224 or (resid 225 and (name N or name CA or name C or \ name O or name CB )) or resid 301)) } ncs_group { reference = (chain 'C' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 15 or (resid 16 and (name N or name \ CA or name C or name O or name CB )) or resid 17 through 108 or (resid 109 and \ (name N or name CA or name C or name O or name CB )) or resid 110 through 133 or \ (resid 134 through 135 and (name N or name CA or name C or name O or name CB )) \ or resid 136 or (resid 137 and (name N or name CA or name C or name O or name C \ B )) or resid 138 through 152 or (resid 153 through 155 and (name N or name CA o \ r name C or name O or name CB )) or resid 156 through 219 or (resid 220 and (nam \ e N or name CA or name C or name O or name CB )) or resid 221 through 291 or (re \ sid 292 and (name N or name CA or name C or name O or name CB )) or resid 293 or \ (resid 294 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 5)) selection = (chain 'D' and (resid 1 through 115 or (resid 116 through 117 and (name N or nam \ e CA or name C or name O or name CB )) or resid 118 through 143 or (resid 144 an \ d (name N or name CA or name C or name O or name CB )) or resid 145 through 196 \ or (resid 197 and (name N or name CA or name C or name O or name CB )) or resid \ 198 through 199 or (resid 200 and (name N or name CA or name C or name O or name \ CB )) or resid 201 through 295)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 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: 0.000 Extract box with map and model: 15.010 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 28.510 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 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 0.076 9724 Z= 0.296 Angle : 1.062 13.944 13247 Z= 0.546 Chirality : 0.056 0.265 1621 Planarity : 0.006 0.074 1710 Dihedral : 12.520 80.584 3403 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.15 % Favored : 92.62 % Rotamer: Outliers : 0.33 % Allowed : 0.99 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.20), residues: 1315 helix: -1.72 (0.18), residues: 585 sheet: -2.20 (0.66), residues: 54 loop : -2.50 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 274 HIS 0.016 0.002 HIS B 199 PHE 0.019 0.002 PHE D 110 TYR 0.028 0.002 TYR C 255 ARG 0.010 0.001 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 181 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 CYS cc_start: 0.8601 (t) cc_final: 0.8396 (t) REVERT: B 205 MET cc_start: 0.8013 (mmp) cc_final: 0.7464 (mmp) REVERT: E 52 ARG cc_start: 0.8165 (tpm170) cc_final: 0.7459 (tpp-160) REVERT: E 305 MET cc_start: 0.8275 (tmm) cc_final: 0.7915 (tmm) REVERT: E 358 MET cc_start: 0.6550 (mpp) cc_final: 0.6061 (mpp) REVERT: D 157 GLU cc_start: 0.7976 (pm20) cc_final: 0.7702 (pm20) REVERT: D 160 ASP cc_start: 0.8499 (m-30) cc_final: 0.7963 (t0) REVERT: D 217 GLN cc_start: 0.8793 (pm20) cc_final: 0.8478 (pm20) REVERT: D 252 ASN cc_start: 0.8506 (m110) cc_final: 0.7096 (m-40) REVERT: D 282 MET cc_start: 0.8482 (ppp) cc_final: 0.8203 (ppp) REVERT: C 230 MET cc_start: 0.9007 (tpt) cc_final: 0.8682 (tpp) REVERT: C 255 TYR cc_start: 0.8152 (t80) cc_final: 0.7500 (t80) REVERT: C 262 LYS cc_start: 0.8854 (mmpt) cc_final: 0.8587 (mmtt) REVERT: C 278 LEU cc_start: 0.9308 (tp) cc_final: 0.9107 (tt) outliers start: 3 outliers final: 1 residues processed: 182 average time/residue: 0.2010 time to fit residues: 52.2914 Evaluate side-chains 143 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 4.9990 chunk 98 optimal weight: 0.0010 chunk 54 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 ASN E 117 HIS D 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9724 Z= 0.167 Angle : 0.566 7.001 13247 Z= 0.288 Chirality : 0.040 0.135 1621 Planarity : 0.003 0.039 1710 Dihedral : 7.619 87.851 1478 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.01 % Favored : 93.76 % Rotamer: Outliers : 1.10 % Allowed : 10.11 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.22), residues: 1315 helix: -0.23 (0.21), residues: 616 sheet: -2.47 (0.63), residues: 60 loop : -2.12 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 214 HIS 0.005 0.001 HIS E 189 PHE 0.017 0.001 PHE A 87 TYR 0.008 0.001 TYR C 294 ARG 0.008 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8692 (m-10) cc_final: 0.8444 (m-10) REVERT: A 187 ARG cc_start: 0.8206 (mtm110) cc_final: 0.7994 (mtm-85) REVERT: B 205 MET cc_start: 0.8057 (mmp) cc_final: 0.7656 (mmp) REVERT: E 52 ARG cc_start: 0.8229 (tpm170) cc_final: 0.7510 (tpp-160) REVERT: E 305 MET cc_start: 0.8541 (tmm) cc_final: 0.8266 (tmm) REVERT: D 24 MET cc_start: 0.7875 (ttm) cc_final: 0.7675 (ttm) REVERT: D 160 ASP cc_start: 0.8512 (m-30) cc_final: 0.8090 (t0) REVERT: D 217 GLN cc_start: 0.8634 (pm20) cc_final: 0.8063 (pm20) REVERT: D 248 GLU cc_start: 0.7637 (tp30) cc_final: 0.7323 (tp30) REVERT: D 252 ASN cc_start: 0.8561 (m110) cc_final: 0.7138 (m110) REVERT: D 282 MET cc_start: 0.8424 (ppp) cc_final: 0.7925 (ppp) REVERT: C 214 TRP cc_start: 0.8151 (t-100) cc_final: 0.7928 (t60) REVERT: C 255 TYR cc_start: 0.8529 (t80) cc_final: 0.8136 (t80) REVERT: C 262 LYS cc_start: 0.8842 (mmpt) cc_final: 0.8549 (tppt) REVERT: C 278 LEU cc_start: 0.9376 (tp) cc_final: 0.9123 (tt) outliers start: 10 outliers final: 5 residues processed: 156 average time/residue: 0.2000 time to fit residues: 45.7572 Evaluate side-chains 143 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 138 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 222 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN E 65 GLN E 69 ASN E 188 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9724 Z= 0.370 Angle : 0.718 8.266 13247 Z= 0.372 Chirality : 0.044 0.157 1621 Planarity : 0.004 0.036 1710 Dihedral : 7.490 83.451 1476 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.37 % Favored : 91.41 % Rotamer: Outliers : 2.31 % Allowed : 15.60 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.24), residues: 1315 helix: -0.03 (0.21), residues: 660 sheet: -2.13 (0.63), residues: 70 loop : -1.91 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 274 HIS 0.005 0.001 HIS C 136 PHE 0.021 0.002 PHE C 163 TYR 0.014 0.002 TYR C 294 ARG 0.008 0.001 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8673 (m-10) cc_final: 0.8422 (m-80) REVERT: A 90 PHE cc_start: 0.9136 (m-80) cc_final: 0.8887 (m-80) REVERT: B 2 MET cc_start: 0.3569 (tpt) cc_final: 0.3349 (tpt) REVERT: B 156 ASN cc_start: 0.7575 (t0) cc_final: 0.7372 (t0) REVERT: E 52 ARG cc_start: 0.8382 (tpm170) cc_final: 0.7883 (tpp-160) REVERT: E 305 MET cc_start: 0.7842 (tmm) cc_final: 0.7579 (tmm) REVERT: D 171 ASN cc_start: 0.8231 (p0) cc_final: 0.7905 (p0) REVERT: D 248 GLU cc_start: 0.7704 (tp30) cc_final: 0.7077 (tp30) REVERT: D 252 ASN cc_start: 0.8607 (m110) cc_final: 0.6966 (m110) REVERT: C 54 ASP cc_start: 0.7347 (p0) cc_final: 0.7125 (p0) outliers start: 21 outliers final: 15 residues processed: 136 average time/residue: 0.2025 time to fit residues: 40.0374 Evaluate side-chains 128 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 188 GLN Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain C residue 222 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 chunk 62 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 HIS ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9724 Z= 0.251 Angle : 0.614 9.270 13247 Z= 0.314 Chirality : 0.041 0.157 1621 Planarity : 0.003 0.034 1710 Dihedral : 7.056 74.901 1476 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.69 % Favored : 93.08 % Rotamer: Outliers : 2.75 % Allowed : 18.35 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.25), residues: 1315 helix: 0.32 (0.21), residues: 660 sheet: -1.94 (0.68), residues: 59 loop : -1.83 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 274 HIS 0.004 0.001 HIS C 136 PHE 0.013 0.001 PHE A 66 TYR 0.010 0.001 TYR C 294 ARG 0.005 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8687 (m-10) cc_final: 0.8443 (m-80) REVERT: A 90 PHE cc_start: 0.9112 (m-80) cc_final: 0.8767 (m-80) REVERT: A 145 GLN cc_start: 0.9136 (tt0) cc_final: 0.8753 (tt0) REVERT: A 179 MET cc_start: 0.9091 (mmp) cc_final: 0.8794 (mmp) REVERT: E 52 ARG cc_start: 0.8370 (tpm170) cc_final: 0.7880 (tpp-160) REVERT: E 305 MET cc_start: 0.8315 (tmm) cc_final: 0.8069 (tmm) REVERT: D 144 LYS cc_start: 0.8431 (pptt) cc_final: 0.7936 (mmmt) REVERT: D 202 GLU cc_start: 0.8878 (pm20) cc_final: 0.8490 (pm20) REVERT: D 217 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8191 (pm20) REVERT: D 248 GLU cc_start: 0.7735 (tp30) cc_final: 0.7514 (tp30) outliers start: 25 outliers final: 18 residues processed: 146 average time/residue: 0.1959 time to fit residues: 41.8774 Evaluate side-chains 134 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 217 GLN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 267 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 64 optimal weight: 0.0670 chunk 112 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 HIS D 171 ASN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9724 Z= 0.172 Angle : 0.565 7.275 13247 Z= 0.284 Chirality : 0.040 0.150 1621 Planarity : 0.003 0.049 1710 Dihedral : 6.656 65.243 1476 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.92 % Favored : 92.85 % Rotamer: Outliers : 2.64 % Allowed : 18.68 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.25), residues: 1315 helix: 0.53 (0.21), residues: 662 sheet: -2.09 (0.64), residues: 70 loop : -1.78 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 274 HIS 0.003 0.001 HIS C 136 PHE 0.011 0.001 PHE B 46 TYR 0.010 0.001 TYR C 255 ARG 0.005 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6200 (mm) REVERT: A 87 PHE cc_start: 0.8722 (m-80) cc_final: 0.8497 (m-80) REVERT: A 145 GLN cc_start: 0.9140 (tt0) cc_final: 0.8870 (tt0) REVERT: B 183 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8137 (tm-30) REVERT: E 52 ARG cc_start: 0.8378 (tpm170) cc_final: 0.7874 (tpp-160) REVERT: E 59 GLU cc_start: 0.8414 (pp20) cc_final: 0.8100 (pp20) REVERT: D 144 LYS cc_start: 0.8225 (pptt) cc_final: 0.7735 (mmmt) REVERT: D 160 ASP cc_start: 0.8302 (m-30) cc_final: 0.7486 (t0) REVERT: D 202 GLU cc_start: 0.8793 (pm20) cc_final: 0.8449 (pm20) REVERT: D 223 GLU cc_start: 0.8571 (pm20) cc_final: 0.8245 (pm20) REVERT: D 248 GLU cc_start: 0.7708 (tp30) cc_final: 0.7461 (tp30) outliers start: 24 outliers final: 19 residues processed: 149 average time/residue: 0.1996 time to fit residues: 43.0725 Evaluate side-chains 143 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 267 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 4.9990 chunk 113 optimal weight: 0.0170 chunk 24 optimal weight: 10.0000 chunk 73 optimal weight: 0.0370 chunk 31 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9724 Z= 0.148 Angle : 0.572 8.405 13247 Z= 0.279 Chirality : 0.039 0.153 1621 Planarity : 0.003 0.049 1710 Dihedral : 6.295 59.670 1476 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.31 % Favored : 93.46 % Rotamer: Outliers : 2.53 % Allowed : 20.22 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.25), residues: 1315 helix: 0.75 (0.22), residues: 654 sheet: -1.75 (0.68), residues: 64 loop : -1.83 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 306 HIS 0.002 0.000 HIS C 136 PHE 0.007 0.001 PHE D 110 TYR 0.009 0.001 TYR C 255 ARG 0.004 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6314 (mm) REVERT: A 90 PHE cc_start: 0.9166 (m-80) cc_final: 0.8759 (m-80) REVERT: A 179 MET cc_start: 0.9127 (mmp) cc_final: 0.8875 (mmp) REVERT: A 187 ARG cc_start: 0.8457 (ptp-110) cc_final: 0.8171 (ptp-110) REVERT: B 179 MET cc_start: 0.9100 (mmm) cc_final: 0.8868 (mmm) REVERT: B 183 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8191 (tm-30) REVERT: B 194 MET cc_start: 0.7776 (tpp) cc_final: 0.7373 (tpp) REVERT: B 205 MET cc_start: 0.8269 (mmp) cc_final: 0.7823 (mmp) REVERT: E 52 ARG cc_start: 0.8357 (tpm170) cc_final: 0.7838 (tpp-160) REVERT: E 59 GLU cc_start: 0.8330 (pp20) cc_final: 0.8105 (pp20) REVERT: E 141 MET cc_start: 0.8997 (tpp) cc_final: 0.8729 (tpt) REVERT: E 305 MET cc_start: 0.8053 (tmm) cc_final: 0.7848 (tmm) REVERT: D 160 ASP cc_start: 0.8238 (m-30) cc_final: 0.7433 (t0) REVERT: D 202 GLU cc_start: 0.8731 (pm20) cc_final: 0.8392 (pm20) REVERT: D 217 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8201 (pm20) REVERT: D 223 GLU cc_start: 0.8540 (pm20) cc_final: 0.8151 (pm20) REVERT: C 217 GLN cc_start: 0.8791 (mp10) cc_final: 0.8554 (mp10) outliers start: 23 outliers final: 16 residues processed: 153 average time/residue: 0.1855 time to fit residues: 41.1999 Evaluate side-chains 145 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 217 GLN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 267 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 0.1980 chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 70 optimal weight: 0.0000 chunk 125 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9724 Z= 0.197 Angle : 0.596 10.637 13247 Z= 0.295 Chirality : 0.040 0.170 1621 Planarity : 0.003 0.053 1710 Dihedral : 6.259 58.254 1476 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.15 % Favored : 92.62 % Rotamer: Outliers : 3.30 % Allowed : 19.78 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1315 helix: 0.81 (0.22), residues: 661 sheet: -1.84 (0.68), residues: 67 loop : -1.79 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 214 HIS 0.004 0.001 HIS C 136 PHE 0.011 0.001 PHE C 163 TYR 0.010 0.001 TYR C 265 ARG 0.004 0.000 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 179 MET cc_start: 0.9063 (mmm) cc_final: 0.8857 (mmm) REVERT: B 194 MET cc_start: 0.7937 (tpp) cc_final: 0.7613 (tpp) REVERT: B 205 MET cc_start: 0.8366 (mmp) cc_final: 0.7935 (mmp) REVERT: E 52 ARG cc_start: 0.8371 (tpm170) cc_final: 0.7875 (tpp-160) REVERT: E 59 GLU cc_start: 0.8400 (pp20) cc_final: 0.8137 (pp20) REVERT: D 144 LYS cc_start: 0.8108 (pptt) cc_final: 0.7625 (mmmt) REVERT: D 160 ASP cc_start: 0.8261 (m-30) cc_final: 0.7453 (t0) REVERT: D 202 GLU cc_start: 0.8730 (pm20) cc_final: 0.8431 (pm20) REVERT: D 217 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8615 (pm20) REVERT: C 54 ASP cc_start: 0.6948 (p0) cc_final: 0.6652 (p0) REVERT: C 217 GLN cc_start: 0.8780 (mp10) cc_final: 0.8535 (mp10) outliers start: 30 outliers final: 24 residues processed: 157 average time/residue: 0.1915 time to fit residues: 43.6188 Evaluate side-chains 152 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 217 GLN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 267 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 ASN B 88 GLN B 169 ASN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9724 Z= 0.264 Angle : 0.654 10.363 13247 Z= 0.325 Chirality : 0.042 0.186 1621 Planarity : 0.004 0.053 1710 Dihedral : 6.465 57.962 1476 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.60 % Favored : 92.02 % Rotamer: Outliers : 3.74 % Allowed : 21.21 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.25), residues: 1315 helix: 0.71 (0.22), residues: 664 sheet: -1.92 (0.68), residues: 67 loop : -1.77 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 306 HIS 0.004 0.001 HIS C 136 PHE 0.015 0.001 PHE C 163 TYR 0.008 0.001 TYR B 12 ARG 0.003 0.000 ARG C 243 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 52 ARG cc_start: 0.8373 (tpm170) cc_final: 0.7898 (tpp-160) REVERT: D 144 LYS cc_start: 0.8346 (pptt) cc_final: 0.8078 (mmmt) REVERT: D 202 GLU cc_start: 0.8750 (pm20) cc_final: 0.8484 (pm20) REVERT: D 248 GLU cc_start: 0.7482 (tp30) cc_final: 0.7011 (tp30) REVERT: C 54 ASP cc_start: 0.7465 (p0) cc_final: 0.7167 (p0) REVERT: C 158 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7111 (tp) REVERT: C 217 GLN cc_start: 0.8848 (mp10) cc_final: 0.8591 (mp10) outliers start: 34 outliers final: 29 residues processed: 151 average time/residue: 0.1983 time to fit residues: 43.4708 Evaluate side-chains 146 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 267 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 5.9990 chunk 116 optimal weight: 0.0770 chunk 120 optimal weight: 0.6980 chunk 70 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9724 Z= 0.177 Angle : 0.609 11.888 13247 Z= 0.297 Chirality : 0.040 0.156 1621 Planarity : 0.003 0.058 1710 Dihedral : 6.274 54.688 1476 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.62 % Favored : 93.08 % Rotamer: Outliers : 3.41 % Allowed : 21.98 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1315 helix: 0.81 (0.22), residues: 658 sheet: -1.83 (0.68), residues: 67 loop : -1.73 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 214 HIS 0.003 0.001 HIS C 136 PHE 0.017 0.001 PHE B 46 TYR 0.004 0.001 TYR E 111 ARG 0.003 0.000 ARG C 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8368 (mmp) REVERT: E 52 ARG cc_start: 0.8354 (tpm170) cc_final: 0.7877 (tpp-160) REVERT: E 59 GLU cc_start: 0.8420 (pp20) cc_final: 0.8148 (pp20) REVERT: E 141 MET cc_start: 0.9072 (tpp) cc_final: 0.8840 (tpt) REVERT: E 358 MET cc_start: 0.7091 (mpp) cc_final: 0.6554 (mpp) REVERT: D 202 GLU cc_start: 0.8708 (pm20) cc_final: 0.8453 (pm20) REVERT: D 217 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8225 (pm20) REVERT: D 248 GLU cc_start: 0.7446 (tp30) cc_final: 0.7001 (tp30) REVERT: C 158 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7241 (tp) outliers start: 31 outliers final: 25 residues processed: 151 average time/residue: 0.2004 time to fit residues: 43.4156 Evaluate side-chains 148 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 217 GLN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 282 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.4980 chunk 58 optimal weight: 4.9990 chunk 85 optimal weight: 0.0030 chunk 129 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 9724 Z= 0.244 Angle : 0.931 59.190 13247 Z= 0.519 Chirality : 0.043 0.522 1621 Planarity : 0.004 0.059 1710 Dihedral : 6.274 54.671 1476 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.69 % Favored : 93.00 % Rotamer: Outliers : 3.30 % Allowed : 22.64 % Favored : 74.07 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.25), residues: 1315 helix: 0.80 (0.22), residues: 658 sheet: -1.83 (0.68), residues: 67 loop : -1.72 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 214 HIS 0.003 0.001 HIS C 136 PHE 0.056 0.001 PHE C 254 TYR 0.005 0.001 TYR C 103 ARG 0.013 0.000 ARG C 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8360 (mmp) REVERT: E 52 ARG cc_start: 0.8351 (tpm170) cc_final: 0.7875 (tpp-160) REVERT: E 59 GLU cc_start: 0.8417 (pp20) cc_final: 0.8146 (pp20) REVERT: E 141 MET cc_start: 0.9074 (tpp) cc_final: 0.8822 (tpt) REVERT: E 358 MET cc_start: 0.7089 (mpp) cc_final: 0.6556 (mpp) REVERT: D 202 GLU cc_start: 0.8704 (pm20) cc_final: 0.8448 (pm20) REVERT: D 248 GLU cc_start: 0.7444 (tp30) cc_final: 0.6997 (tp30) outliers start: 30 outliers final: 27 residues processed: 142 average time/residue: 0.1983 time to fit residues: 41.0575 Evaluate side-chains 148 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 217 GLN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 282 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 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 = 0.3450 r_free = 0.3450 target = 0.066521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.052702 restraints weight = 52264.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.053983 restraints weight = 31185.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.054811 restraints weight = 21819.971| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.224 9724 Z= 0.283 Angle : 0.772 24.593 13247 Z= 0.405 Chirality : 0.043 0.522 1621 Planarity : 0.004 0.074 1710 Dihedral : 6.274 54.671 1476 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.69 % Favored : 93.00 % Rotamer: Outliers : 3.08 % Allowed : 22.75 % Favored : 74.18 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.25), residues: 1315 helix: 0.80 (0.22), residues: 658 sheet: -1.83 (0.68), residues: 67 loop : -1.72 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 214 HIS 0.003 0.001 HIS C 136 PHE 0.056 0.001 PHE C 254 TYR 0.005 0.001 TYR C 103 ARG 0.013 0.000 ARG C 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2138.37 seconds wall clock time: 40 minutes 27.58 seconds (2427.58 seconds total)