Starting phenix.real_space_refine on Fri Feb 14 04:12:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8idc_35363/02_2025/8idc_35363.cif Found real_map, /net/cci-nas-00/data/ceres_data/8idc_35363/02_2025/8idc_35363.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/cci-nas-00/data/ceres_data/8idc_35363/02_2025/8idc_35363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8idc_35363/02_2025/8idc_35363.map" model { file = "/net/cci-nas-00/data/ceres_data/8idc_35363/02_2025/8idc_35363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8idc_35363/02_2025/8idc_35363.cif" } 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 6143 2.51 5 N 1711 2.21 5 O 1798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9701 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1585 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 9, 'TRANS': 217} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 157 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: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2056 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 286} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASP:plan': 5, 'GLU:plan': 6, 'TYR%COO:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 97 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 Time building chain proxies: 7.46, per 1000 atoms: 0.77 Number of scatterers: 9701 At special positions: 0 Unit cell: (124.02, 108.12, 196.1, 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 49 16.00 O 1798 8.00 N 1711 7.00 C 6143 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 - 3.00 Amino acid : True - 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: 2.11 Conformation dependent library (CDL) restraints added in 1.3 seconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2502 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 53.7% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 43 through 50 removed outlier: 3.757A pdb=" N LEU A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 82 removed outlier: 3.972A pdb=" N LYS A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.729A pdb=" N ALA A 105 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 removed outlier: 4.225A pdb=" N ASN A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 144 through 154 Processing helix chain 'A' and resid 171 through 188 removed outlier: 4.064A pdb=" N ARG A 176 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASP A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 188 " --> pdb=" O ARG A 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 41 removed outlier: 3.546A pdb=" N SER B 41 " --> pdb=" O PRO B 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 38 through 41' Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 97 through 108 removed outlier: 3.622A pdb=" N LEU B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.721A pdb=" N ILE B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 112 through 117' Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.720A pdb=" N VAL B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL B 127 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 removed outlier: 3.978A pdb=" N ALA B 149 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 175 through 180 removed outlier: 4.061A pdb=" N ASP B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 187 removed outlier: 3.535A pdb=" N ILE B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 112 removed outlier: 3.672A pdb=" N GLU E 70 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR E 110 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR E 111 " --> pdb=" O ALA E 107 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 125 removed outlier: 3.848A pdb=" N THR E 124 " --> pdb=" O ASP E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 193 removed outlier: 3.671A pdb=" N ASP E 133 " --> pdb=" O GLN E 129 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL E 140 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS E 143 " --> pdb=" O ARG E 139 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN E 186 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU E 187 " --> pdb=" O VAL E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 205 removed outlier: 3.939A pdb=" N GLN E 197 " --> pdb=" O GLN E 193 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE E 198 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN E 204 " --> pdb=" O VAL E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 216 removed outlier: 3.770A pdb=" N THR E 214 " --> pdb=" O PRO E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 277 removed outlier: 3.602A pdb=" N VAL E 276 " --> pdb=" O ARG E 273 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL E 277 " --> pdb=" O THR E 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 273 through 277' Processing helix chain 'E' and resid 299 through 312 removed outlier: 3.910A pdb=" N VAL E 304 " --> pdb=" O CYS E 300 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN E 310 " --> pdb=" O TRP E 306 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA E 311 " --> pdb=" O ALA E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 323 removed outlier: 3.702A pdb=" N ALA E 323 " --> pdb=" O SER E 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 17 removed outlier: 3.953A pdb=" N LEU D 6 " --> pdb=" O ARG D 2 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL D 10 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 37 removed outlier: 3.927A pdb=" N ILE D 25 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU D 34 " --> pdb=" O ILE D 30 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 54 removed outlier: 3.698A pdb=" N ILE D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 83 removed outlier: 3.908A pdb=" N LEU D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 110 removed outlier: 3.636A pdb=" N ASP D 104 " --> pdb=" O GLN D 100 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ALA D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE D 107 " --> pdb=" O TYR D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 142 Processing helix chain 'D' and resid 159 through 164 Processing helix chain 'D' and resid 164 through 185 removed outlier: 4.130A pdb=" N GLY D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU D 169 " --> pdb=" O VAL D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 199 removed outlier: 3.976A pdb=" N ALA D 189 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 192 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 196 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR D 198 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG D 199 " --> pdb=" O ALA D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 208 removed outlier: 3.672A pdb=" N GLY D 204 " --> pdb=" O ARG D 200 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 220 Processing helix chain 'D' and resid 221 through 247 removed outlier: 3.763A pdb=" N ALA D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR D 229 " --> pdb=" O MET D 225 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET D 230 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 245 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU D 247 " --> pdb=" O ARG D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 252 removed outlier: 3.804A pdb=" N ASN D 252 " --> pdb=" O GLU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 258 removed outlier: 4.175A pdb=" N GLN D 256 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA D 257 " --> pdb=" O GLN D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 293 removed outlier: 3.808A pdb=" N LEU D 277 " --> pdb=" O PRO D 273 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU D 278 " --> pdb=" O TRP D 274 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER D 283 " --> pdb=" O GLY D 279 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY D 284 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR D 286 " --> pdb=" O MET D 282 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 17 removed outlier: 4.586A pdb=" N LEU C 6 " --> pdb=" O ARG C 2 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 7 " --> pdb=" O PHE C 3 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ASN C 8 " --> pdb=" O GLY C 4 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLU C 9 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL C 10 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN C 17 " --> pdb=" O GLY C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 removed outlier: 4.303A pdb=" N LEU C 26 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR C 27 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR C 28 " --> pdb=" O MET C 24 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER C 31 " --> pdb=" O THR C 27 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 52 No H-bonds generated for 'chain 'C' and resid 50 through 52' Processing helix chain 'C' and resid 63 through 67 removed outlier: 3.569A pdb=" N VAL C 66 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 85 removed outlier: 3.841A pdb=" N ILE C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 136 through 144 Processing helix chain 'C' and resid 161 through 164 Processing helix chain 'C' and resid 165 through 189 removed outlier: 3.604A pdb=" N VAL C 179 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 199 removed outlier: 4.156A pdb=" N GLN C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 210 removed outlier: 3.853A pdb=" N ILE C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY C 204 " --> pdb=" O ARG C 200 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG C 207 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 209 " --> pdb=" O ILE C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 217 through 258 removed outlier: 3.951A pdb=" N VAL C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU C 223 " --> pdb=" O PRO C 219 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA C 224 " --> pdb=" O PHE C 220 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASN C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA C 250 " --> pdb=" O PHE C 246 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLN C 253 " --> pdb=" O ASN C 249 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N PHE C 254 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR C 255 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 removed outlier: 3.873A pdb=" N ILE C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C 272 " --> pdb=" O ILE C 268 " (cutoff:3.500A) Proline residue: C 273 - end of helix removed outlier: 3.693A pdb=" N LEU C 278 " --> pdb=" O TRP C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 removed outlier: 4.025A pdb=" N THR C 290 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG C 292 " --> pdb=" O TYR C 288 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 3.579A pdb=" N ARG A 62 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP A 6 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP A 60 " --> pdb=" O ASP A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 86 removed outlier: 4.727A pdb=" N LEU A 193 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 33 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG A 208 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU A 211 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 33 removed outlier: 3.928A pdb=" N VAL B 33 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU B 161 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 328 through 329 removed outlier: 4.432A pdb=" N ALA E 382 " --> pdb=" O VAL E 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 339 through 342 Processing sheet with id=AA6, first strand: chain 'E' and resid 358 through 359 Processing sheet with id=AA7, first strand: chain 'D' and resid 57 through 61 removed outlier: 3.655A pdb=" N VAL D 60 " --> pdb=" O PHE D 126 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER D 125 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AA9, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.996A pdb=" N LYS C 129 " --> pdb=" O LYS C 92 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1185 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: 2.49 Time building geometry restraints manager: 2.51 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: 3296 1.34 - 1.46: 2046 1.46 - 1.58: 4411 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 9844 Sorted by residual: bond pdb=" C VAL B 76 " pdb=" N PRO B 77 " ideal model delta sigma weight residual 1.334 1.353 -0.019 8.40e-03 1.42e+04 5.32e+00 bond pdb=" CA VAL A 127 " pdb=" CB VAL A 127 " ideal model delta sigma weight residual 1.532 1.550 -0.018 1.08e-02 8.57e+03 2.78e+00 bond pdb=" CA ASN D 17 " pdb=" CB ASN D 17 " ideal model delta sigma weight residual 1.526 1.551 -0.025 1.51e-02 4.39e+03 2.70e+00 bond pdb=" C VAL A 120 " pdb=" N PRO A 121 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.23e-02 6.61e+03 2.67e+00 bond pdb=" C THR D 272 " pdb=" N PRO D 273 " ideal model delta sigma weight residual 1.335 1.352 -0.018 1.19e-02 7.06e+03 2.25e+00 ... (remaining 9839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 13064 2.69 - 5.37: 251 5.37 - 8.06: 59 8.06 - 10.75: 19 10.75 - 13.44: 5 Bond angle restraints: 13398 Sorted by residual: angle pdb=" C TYR E 205 " pdb=" CA TYR E 205 " pdb=" CB TYR E 205 " ideal model delta sigma weight residual 116.54 110.13 6.41 1.15e+00 7.56e-01 3.11e+01 angle pdb=" C SER E 344 " pdb=" CA SER E 344 " pdb=" CB SER E 344 " ideal model delta sigma weight residual 116.63 110.61 6.02 1.16e+00 7.43e-01 2.69e+01 angle pdb=" C ALA C 23 " pdb=" N MET C 24 " pdb=" CA MET C 24 " ideal model delta sigma weight residual 120.38 126.98 -6.60 1.37e+00 5.33e-01 2.32e+01 angle pdb=" CB MET A 47 " pdb=" CG MET A 47 " pdb=" SD MET A 47 " ideal model delta sigma weight residual 112.70 126.14 -13.44 3.00e+00 1.11e-01 2.01e+01 angle pdb=" CB MET C 191 " pdb=" CG MET C 191 " pdb=" SD MET C 191 " ideal model delta sigma weight residual 112.70 125.62 -12.92 3.00e+00 1.11e-01 1.86e+01 ... (remaining 13393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.05: 5493 15.05 - 30.09: 350 30.09 - 45.14: 66 45.14 - 60.18: 9 60.18 - 75.23: 3 Dihedral angle restraints: 5921 sinusoidal: 2060 harmonic: 3861 Sorted by residual: dihedral pdb=" CA ILE C 25 " pdb=" C ILE C 25 " pdb=" N LEU C 26 " pdb=" CA LEU C 26 " ideal model delta harmonic sigma weight residual -180.00 -160.72 -19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CB CYS C 73 " pdb=" SG CYS C 73 " pdb=" SG CYS C 78 " pdb=" CB CYS C 78 " ideal model delta sinusoidal sigma weight residual -86.00 -117.64 31.64 1 1.00e+01 1.00e-02 1.43e+01 dihedral pdb=" CA VAL E 183 " pdb=" C VAL E 183 " pdb=" N ARG E 184 " pdb=" CA ARG E 184 " ideal model delta harmonic sigma weight residual 180.00 162.23 17.77 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 5918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1198 0.050 - 0.101: 345 0.101 - 0.151: 77 0.151 - 0.201: 12 0.201 - 0.252: 3 Chirality restraints: 1635 Sorted by residual: chirality pdb=" CB VAL A 63 " pdb=" CA VAL A 63 " pdb=" CG1 VAL A 63 " pdb=" CG2 VAL A 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB VAL A 120 " pdb=" CA VAL A 120 " pdb=" CG1 VAL A 120 " pdb=" CG2 VAL A 120 " 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 VAL A 127 " pdb=" CA VAL A 127 " pdb=" CG1 VAL A 127 " pdb=" CG2 VAL A 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.83 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1632 not shown) Planarity restraints: 1741 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 306 " 0.020 2.00e-02 2.50e+03 1.83e-02 8.36e+00 pdb=" CG TRP E 306 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP E 306 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP E 306 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 306 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 306 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 306 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 306 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 306 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 306 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 371 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.14e+00 pdb=" N PRO E 372 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 372 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 372 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 220 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO E 221 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 221 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 221 " -0.026 5.00e-02 4.00e+02 ... (remaining 1738 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1202 2.76 - 3.29: 9856 3.29 - 3.83: 16243 3.83 - 4.36: 17943 4.36 - 4.90: 29339 Nonbonded interactions: 74583 Sorted by model distance: nonbonded pdb=" O MET D 282 " pdb=" OG1 THR D 286 " model vdw 2.221 3.040 nonbonded pdb=" OE2 GLU E 59 " pdb=" OG SER E 319 " model vdw 2.245 3.040 nonbonded pdb=" OG1 THR E 341 " pdb=" O ILE E 379 " model vdw 2.261 3.040 nonbonded pdb=" O ASN C 17 " pdb=" OG1 THR C 21 " model vdw 2.278 3.040 nonbonded pdb=" NE2 GLN B 88 " pdb=" O GLU B 165 " model vdw 2.315 3.120 ... (remaining 74578 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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 131 or (resid 132 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)) 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 )))) } 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: 4.090 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.140 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 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 : 0.004 0.050 9844 Z= 0.246 Angle : 1.016 13.435 13398 Z= 0.514 Chirality : 0.051 0.252 1635 Planarity : 0.005 0.062 1741 Dihedral : 10.680 75.228 3413 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.92 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -3.33 (0.20), residues: 1330 helix: -1.88 (0.18), residues: 585 sheet: -2.36 (0.61), residues: 70 loop : -2.51 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP E 306 HIS 0.011 0.001 HIS E 317 PHE 0.022 0.001 PHE B 87 TYR 0.029 0.001 TYR A 12 ARG 0.014 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 48 ARG cc_start: 0.9326 (ttm-80) cc_final: 0.9048 (mtp85) REVERT: E 112 MET cc_start: 0.8860 (mpp) cc_final: 0.8651 (mpp) REVERT: E 145 MET cc_start: 0.9170 (tpp) cc_final: 0.8847 (tmm) REVERT: E 305 MET cc_start: 0.8541 (mtm) cc_final: 0.8026 (mmm) REVERT: D 143 MET cc_start: 0.7718 (mmm) cc_final: 0.7461 (mmm) REVERT: D 180 GLN cc_start: 0.9436 (tp-100) cc_final: 0.9201 (tp40) REVERT: D 240 MET cc_start: 0.8940 (mmp) cc_final: 0.8734 (mmm) REVERT: C 39 MET cc_start: 0.8785 (mmp) cc_final: 0.8563 (mmp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1912 time to fit residues: 23.0754 Evaluate side-chains 68 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.7980 chunk 100 optimal weight: 0.0970 chunk 55 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.2980 chunk 53 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.034990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.028543 restraints weight = 136019.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.029036 restraints weight = 94825.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.029330 restraints weight = 72401.066| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9844 Z= 0.148 Angle : 0.617 7.831 13398 Z= 0.306 Chirality : 0.039 0.131 1635 Planarity : 0.004 0.043 1741 Dihedral : 4.224 16.052 1426 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.71 % Favored : 94.06 % Rotamer: Outliers : 0.21 % Allowed : 5.54 % Favored : 94.24 % 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: -2.25 (0.22), residues: 1330 helix: -0.53 (0.21), residues: 588 sheet: -2.47 (0.57), residues: 75 loop : -2.31 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 290 HIS 0.004 0.001 HIS C 136 PHE 0.009 0.001 PHE A 104 TYR 0.010 0.001 TYR D 255 ARG 0.004 0.000 ARG D 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: B 2 MET cc_start: 0.6542 (tpp) cc_final: 0.6123 (tpp) REVERT: E 145 MET cc_start: 0.9179 (tpp) cc_final: 0.8899 (tmm) REVERT: E 380 TYR cc_start: 0.6620 (m-10) cc_final: 0.5127 (t80) REVERT: D 206 MET cc_start: 0.8603 (tmm) cc_final: 0.8314 (tmm) REVERT: D 240 MET cc_start: 0.8955 (mmp) cc_final: 0.8754 (mmm) REVERT: D 282 MET cc_start: 0.9229 (pmm) cc_final: 0.9022 (pmm) REVERT: C 143 MET cc_start: 0.8802 (mmp) cc_final: 0.8559 (mmp) REVERT: C 206 MET cc_start: 0.9249 (pmm) cc_final: 0.9006 (pmm) REVERT: C 282 MET cc_start: 0.8975 (ppp) cc_final: 0.8748 (ppp) outliers start: 2 outliers final: 2 residues processed: 70 average time/residue: 0.1833 time to fit residues: 19.8576 Evaluate side-chains 69 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain C residue 187 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 113 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 19 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN E 100 GLN ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN D 193 GLN C 154 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.033075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.026897 restraints weight = 144347.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.027354 restraints weight = 97824.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.027677 restraints weight = 74242.578| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9844 Z= 0.299 Angle : 0.669 8.083 13398 Z= 0.355 Chirality : 0.040 0.169 1635 Planarity : 0.004 0.033 1741 Dihedral : 4.401 16.296 1426 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.42 % Favored : 91.43 % Rotamer: Outliers : 0.75 % Allowed : 9.38 % Favored : 89.87 % 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: -1.89 (0.23), residues: 1330 helix: -0.20 (0.21), residues: 610 sheet: -2.19 (0.63), residues: 68 loop : -2.22 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 290 HIS 0.009 0.002 HIS E 317 PHE 0.023 0.002 PHE E 152 TYR 0.011 0.001 TYR C 294 ARG 0.006 0.001 ARG B 157 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2 MET cc_start: 0.6499 (tpp) cc_final: 0.6294 (tpp) REVERT: E 145 MET cc_start: 0.9149 (tpp) cc_final: 0.8825 (tmm) REVERT: E 305 MET cc_start: 0.8666 (mtt) cc_final: 0.8340 (mtt) REVERT: D 282 MET cc_start: 0.9385 (pmm) cc_final: 0.9163 (pmm) REVERT: C 24 MET cc_start: 0.8545 (tpp) cc_final: 0.8342 (tpp) outliers start: 7 outliers final: 3 residues processed: 68 average time/residue: 0.1905 time to fit residues: 19.9294 Evaluate side-chains 62 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain C residue 187 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 1 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 121 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** 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 = 0.3129 r_free = 0.3129 target = 0.033893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.027639 restraints weight = 138971.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.028067 restraints weight = 94401.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.028434 restraints weight = 72260.011| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9844 Z= 0.149 Angle : 0.603 10.956 13398 Z= 0.298 Chirality : 0.039 0.132 1635 Planarity : 0.003 0.034 1741 Dihedral : 4.104 15.752 1426 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.32 % Favored : 93.53 % Rotamer: Outliers : 0.43 % Allowed : 11.09 % Favored : 88.49 % 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: -1.66 (0.23), residues: 1330 helix: 0.13 (0.22), residues: 603 sheet: -1.75 (0.64), residues: 68 loop : -2.29 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 274 HIS 0.003 0.001 HIS C 136 PHE 0.014 0.001 PHE B 104 TYR 0.010 0.001 TYR E 380 ARG 0.002 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 145 MET cc_start: 0.8950 (tpp) cc_final: 0.8672 (tmm) REVERT: E 305 MET cc_start: 0.8684 (mtt) cc_final: 0.8237 (mtt) REVERT: D 206 MET cc_start: 0.8825 (ttt) cc_final: 0.8606 (tmm) REVERT: D 240 MET cc_start: 0.8863 (mmm) cc_final: 0.8554 (mmm) REVERT: C 24 MET cc_start: 0.8393 (tpp) cc_final: 0.8078 (tpp) REVERT: C 230 MET cc_start: 0.9304 (mmt) cc_final: 0.8988 (mmp) REVERT: C 282 MET cc_start: 0.9106 (ppp) cc_final: 0.8580 (ppp) outliers start: 4 outliers final: 3 residues processed: 67 average time/residue: 0.1872 time to fit residues: 19.6511 Evaluate side-chains 67 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 187 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 37 optimal weight: 0.0270 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 14 optimal weight: 0.0980 chunk 19 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN E 197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.033004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.026910 restraints weight = 143402.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.027347 restraints weight = 97172.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.027680 restraints weight = 74091.371| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9844 Z= 0.242 Angle : 0.635 8.110 13398 Z= 0.326 Chirality : 0.040 0.162 1635 Planarity : 0.003 0.029 1741 Dihedral : 4.209 15.285 1426 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.57 % Favored : 91.28 % Rotamer: Outliers : 1.07 % Allowed : 12.47 % Favored : 86.46 % 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: -1.62 (0.23), residues: 1330 helix: 0.10 (0.21), residues: 619 sheet: -1.83 (0.68), residues: 64 loop : -2.22 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 290 HIS 0.004 0.001 HIS C 136 PHE 0.018 0.002 PHE E 152 TYR 0.010 0.001 TYR A 12 ARG 0.004 0.000 ARG B 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 145 MET cc_start: 0.9085 (tpp) cc_final: 0.8782 (tmm) REVERT: E 305 MET cc_start: 0.8694 (mtt) cc_final: 0.8284 (mtt) REVERT: D 240 MET cc_start: 0.8886 (mmm) cc_final: 0.8586 (mmm) REVERT: D 282 MET cc_start: 0.9356 (pmm) cc_final: 0.9137 (pmm) REVERT: C 230 MET cc_start: 0.9358 (mmt) cc_final: 0.8982 (mmp) outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 0.1681 time to fit residues: 18.9003 Evaluate side-chains 68 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 187 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 0.0270 chunk 77 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 48 optimal weight: 9.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** 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 = 0.3121 r_free = 0.3121 target = 0.033832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.027572 restraints weight = 138149.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.028046 restraints weight = 93814.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.028380 restraints weight = 71195.925| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9844 Z= 0.145 Angle : 0.612 11.516 13398 Z= 0.296 Chirality : 0.039 0.134 1635 Planarity : 0.003 0.034 1741 Dihedral : 4.003 14.690 1426 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.94 % Favored : 93.91 % Rotamer: Outliers : 1.07 % Allowed : 13.22 % Favored : 85.71 % 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: -1.53 (0.23), residues: 1330 helix: 0.19 (0.21), residues: 628 sheet: -1.66 (0.67), residues: 68 loop : -2.24 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 290 HIS 0.003 0.001 HIS A 67 PHE 0.010 0.001 PHE E 342 TYR 0.020 0.001 TYR E 364 ARG 0.002 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 MET cc_start: 0.2101 (ppp) cc_final: 0.1826 (tmm) REVERT: E 145 MET cc_start: 0.9015 (tpp) cc_final: 0.8702 (tmm) REVERT: E 305 MET cc_start: 0.8761 (mtt) cc_final: 0.8384 (mtt) REVERT: D 240 MET cc_start: 0.8916 (mmm) cc_final: 0.8633 (mmm) REVERT: D 282 MET cc_start: 0.9252 (pmm) cc_final: 0.9015 (pmm) REVERT: C 24 MET cc_start: 0.8580 (tpp) cc_final: 0.8082 (tpp) REVERT: C 230 MET cc_start: 0.9310 (mmt) cc_final: 0.9066 (mmp) outliers start: 10 outliers final: 6 residues processed: 71 average time/residue: 0.1822 time to fit residues: 20.2908 Evaluate side-chains 70 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 206 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 53 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 60 optimal weight: 0.3980 chunk 61 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 117 optimal weight: 0.0970 chunk 102 optimal weight: 0.0770 chunk 84 optimal weight: 0.8980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.034254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.027941 restraints weight = 138416.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.028405 restraints weight = 94788.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.028756 restraints weight = 72485.951| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9844 Z= 0.140 Angle : 0.617 11.957 13398 Z= 0.295 Chirality : 0.039 0.129 1635 Planarity : 0.003 0.031 1741 Dihedral : 3.791 15.613 1426 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.71 % Favored : 94.21 % Rotamer: Outliers : 0.85 % Allowed : 14.18 % Favored : 84.97 % 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: -1.43 (0.23), residues: 1330 helix: 0.37 (0.21), residues: 614 sheet: -1.70 (0.67), residues: 70 loop : -2.25 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 290 HIS 0.002 0.001 HIS E 348 PHE 0.010 0.001 PHE B 104 TYR 0.016 0.001 TYR E 364 ARG 0.002 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 MET cc_start: 0.2339 (ppp) cc_final: 0.2060 (tmm) REVERT: A 48 ARG cc_start: 0.9447 (ttm-80) cc_final: 0.9158 (ttm110) REVERT: E 145 MET cc_start: 0.8976 (tpp) cc_final: 0.8708 (tmm) REVERT: E 305 MET cc_start: 0.8789 (mtt) cc_final: 0.8587 (mtp) REVERT: E 364 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: D 24 MET cc_start: 0.8615 (mtm) cc_final: 0.7861 (pmm) REVERT: D 144 LYS cc_start: 0.8281 (mmtm) cc_final: 0.8072 (mmtm) REVERT: D 240 MET cc_start: 0.8940 (mmm) cc_final: 0.8647 (mmm) REVERT: D 282 MET cc_start: 0.9240 (pmm) cc_final: 0.8904 (pmm) REVERT: C 24 MET cc_start: 0.8501 (tpp) cc_final: 0.8048 (tpp) REVERT: C 230 MET cc_start: 0.9321 (mmt) cc_final: 0.9080 (mmp) outliers start: 8 outliers final: 7 residues processed: 74 average time/residue: 0.2039 time to fit residues: 22.9495 Evaluate side-chains 76 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 364 TYR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 206 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 ASN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.033750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.027498 restraints weight = 141661.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.027965 restraints weight = 96952.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.028301 restraints weight = 73897.707| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9844 Z= 0.182 Angle : 0.618 10.541 13398 Z= 0.304 Chirality : 0.039 0.156 1635 Planarity : 0.003 0.031 1741 Dihedral : 3.818 14.845 1426 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.14 % Favored : 92.78 % Rotamer: Outliers : 0.96 % Allowed : 14.07 % Favored : 84.97 % 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 (0.23), residues: 1330 helix: 0.35 (0.21), residues: 620 sheet: -1.69 (0.67), residues: 70 loop : -2.32 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 290 HIS 0.003 0.001 HIS A 67 PHE 0.010 0.001 PHE E 152 TYR 0.014 0.001 TYR E 364 ARG 0.002 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 MET cc_start: 0.2517 (ppp) cc_final: 0.2289 (tmm) REVERT: E 145 MET cc_start: 0.8968 (tpp) cc_final: 0.8727 (tmm) REVERT: E 305 MET cc_start: 0.8794 (mtt) cc_final: 0.8584 (mtt) REVERT: D 240 MET cc_start: 0.8946 (mmm) cc_final: 0.8694 (mmm) REVERT: C 230 MET cc_start: 0.9312 (mmt) cc_final: 0.9066 (mmp) outliers start: 9 outliers final: 6 residues processed: 73 average time/residue: 0.1825 time to fit residues: 20.5911 Evaluate side-chains 72 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 206 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.0170 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 93 optimal weight: 0.0040 chunk 38 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 overall best weight: 0.5030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.034344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.028032 restraints weight = 137832.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.028456 restraints weight = 95211.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.028829 restraints weight = 73633.415| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9844 Z= 0.149 Angle : 0.658 11.612 13398 Z= 0.313 Chirality : 0.039 0.149 1635 Planarity : 0.003 0.032 1741 Dihedral : 3.782 15.067 1426 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 1.07 % Allowed : 14.71 % Favored : 84.22 % 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: -1.39 (0.23), residues: 1330 helix: 0.43 (0.22), residues: 610 sheet: -1.52 (0.69), residues: 70 loop : -2.27 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 290 HIS 0.002 0.000 HIS A 67 PHE 0.009 0.001 PHE C 61 TYR 0.014 0.001 TYR E 364 ARG 0.002 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 MET cc_start: 0.2562 (ppp) cc_final: 0.2309 (tmm) REVERT: A 48 ARG cc_start: 0.9450 (ttm-80) cc_final: 0.9167 (ttm110) REVERT: E 145 MET cc_start: 0.8981 (tpp) cc_final: 0.8709 (tmm) REVERT: E 305 MET cc_start: 0.8793 (mtt) cc_final: 0.8585 (mtp) REVERT: D 20 MET cc_start: 0.8731 (ttm) cc_final: 0.8347 (ttm) REVERT: D 240 MET cc_start: 0.8956 (mmm) cc_final: 0.8696 (mmm) REVERT: C 24 MET cc_start: 0.8664 (mmt) cc_final: 0.8291 (tpp) REVERT: C 230 MET cc_start: 0.9304 (mmt) cc_final: 0.9054 (mmp) outliers start: 10 outliers final: 8 residues processed: 74 average time/residue: 0.1953 time to fit residues: 21.9022 Evaluate side-chains 76 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 206 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 107 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.0060 chunk 90 optimal weight: 3.9990 chunk 116 optimal weight: 0.0030 chunk 103 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 overall best weight: 0.5408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.034396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.028132 restraints weight = 138471.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.028600 restraints weight = 95971.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.028937 restraints weight = 73850.229| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9844 Z= 0.150 Angle : 0.662 11.578 13398 Z= 0.312 Chirality : 0.039 0.147 1635 Planarity : 0.003 0.032 1741 Dihedral : 3.673 14.872 1426 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 0.85 % Allowed : 14.50 % Favored : 84.65 % 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: -1.36 (0.23), residues: 1330 helix: 0.45 (0.22), residues: 612 sheet: -1.78 (0.67), residues: 76 loop : -2.22 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 290 HIS 0.002 0.000 HIS A 67 PHE 0.009 0.001 PHE B 104 TYR 0.006 0.001 TYR E 343 ARG 0.001 0.000 ARG A 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 MET cc_start: 0.2535 (ppp) cc_final: 0.2285 (tmm) REVERT: A 48 ARG cc_start: 0.9470 (ttm-80) cc_final: 0.9165 (ttm110) REVERT: E 145 MET cc_start: 0.9035 (tpp) cc_final: 0.8728 (tmm) REVERT: E 305 MET cc_start: 0.8793 (mtt) cc_final: 0.8581 (mtt) REVERT: D 144 LYS cc_start: 0.8275 (mmmt) cc_final: 0.7826 (mmtt) REVERT: D 240 MET cc_start: 0.8994 (mmm) cc_final: 0.8751 (mmm) REVERT: C 24 MET cc_start: 0.8767 (mmt) cc_final: 0.8343 (tpp) REVERT: C 230 MET cc_start: 0.9321 (mmt) cc_final: 0.9071 (mmp) outliers start: 8 outliers final: 7 residues processed: 73 average time/residue: 0.1980 time to fit residues: 21.9373 Evaluate side-chains 76 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 206 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 0.0980 chunk 37 optimal weight: 0.0970 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.034538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.028249 restraints weight = 137066.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.028717 restraints weight = 95872.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.029045 restraints weight = 73807.520| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9844 Z= 0.151 Angle : 0.662 11.624 13398 Z= 0.311 Chirality : 0.039 0.154 1635 Planarity : 0.003 0.033 1741 Dihedral : 3.604 14.753 1426 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.79 % Favored : 94.14 % Rotamer: Outliers : 0.75 % Allowed : 14.50 % Favored : 84.75 % 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: -1.34 (0.23), residues: 1330 helix: 0.46 (0.22), residues: 611 sheet: -1.59 (0.67), residues: 74 loop : -2.22 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 290 HIS 0.002 0.000 HIS D 136 PHE 0.009 0.001 PHE B 104 TYR 0.012 0.001 TYR A 12 ARG 0.001 0.000 ARG C 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2866.76 seconds wall clock time: 52 minutes 19.28 seconds (3139.28 seconds total)