Starting phenix.real_space_refine on Sat Dec 9 01:52:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8idc_35363/12_2023/8idc_35363.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8idc_35363/12_2023/8idc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8idc_35363/12_2023/8idc_35363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8idc_35363/12_2023/8idc_35363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8idc_35363/12_2023/8idc_35363.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8idc_35363/12_2023/8idc_35363.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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 Residue "D PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.74, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 2.1 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: 1.05 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: 2.46 Time building geometry restraints manager: 3.81 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: 97.86 - 105.46: 187 105.46 - 113.06: 5302 113.06 - 120.66: 4364 120.66 - 128.26: 3498 128.26 - 135.86: 47 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 2.440 nonbonded pdb=" OE2 GLU E 59 " pdb=" OG SER E 319 " model vdw 2.245 2.440 nonbonded pdb=" OG1 THR E 341 " pdb=" O ILE E 379 " model vdw 2.261 2.440 nonbonded pdb=" O ASN C 17 " pdb=" OG1 THR C 21 " model vdw 2.278 2.440 nonbonded pdb=" NE2 GLN B 88 " pdb=" O GLU B 165 " model vdw 2.315 2.520 ... (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 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: 3.420 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: 12.040 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 28.520 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.450 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.208 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1967 time to fit residues: 23.5800 Evaluate side-chains 67 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4021 ------------------------------------------------------------------------------- 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: 3.9990 chunk 100 optimal weight: 0.0870 chunk 55 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- 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 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9844 Z= 0.220 Angle : 0.626 7.977 13398 Z= 0.324 Chirality : 0.039 0.129 1635 Planarity : 0.004 0.041 1741 Dihedral : 4.332 16.698 1426 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.62 % Favored : 93.16 % Rotamer: Outliers : 0.43 % Allowed : 7.78 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.23), residues: 1330 helix: -0.22 (0.22), residues: 595 sheet: -2.44 (0.57), residues: 75 loop : -2.20 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 290 HIS 0.004 0.001 HIS E 317 PHE 0.014 0.001 PHE E 152 TYR 0.023 0.001 TYR D 255 ARG 0.006 0.000 ARG A 48 *********************** 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 fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 1.031 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 69 average time/residue: 0.1767 time to fit residues: 18.8660 Evaluate side-chains 69 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0875 time to fit residues: 2.1119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 0.0070 chunk 129 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- 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 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9844 Z= 0.176 Angle : 0.587 8.120 13398 Z= 0.298 Chirality : 0.038 0.155 1635 Planarity : 0.003 0.035 1741 Dihedral : 4.101 16.282 1426 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.07 % Favored : 92.71 % Rotamer: Outliers : 0.32 % Allowed : 10.66 % Favored : 89.02 % 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: -1.67 (0.23), residues: 1330 helix: 0.16 (0.22), residues: 600 sheet: -2.31 (0.59), residues: 76 loop : -2.24 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 290 HIS 0.003 0.001 HIS D 136 PHE 0.019 0.001 PHE B 104 TYR 0.008 0.001 TYR D 197 ARG 0.004 0.000 ARG A 48 *********************** 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 72 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 71 average time/residue: 0.1933 time to fit residues: 21.3719 Evaluate side-chains 70 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1064 time to fit residues: 1.8502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 chunk 62 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 chunk 114 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN D 101 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9844 Z= 0.133 Angle : 0.593 10.422 13398 Z= 0.286 Chirality : 0.038 0.128 1635 Planarity : 0.003 0.033 1741 Dihedral : 3.889 15.044 1426 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.02 % Favored : 93.76 % Rotamer: Outliers : 0.64 % Allowed : 12.37 % Favored : 86.99 % 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: 0.34 (0.22), residues: 598 sheet: -1.74 (0.63), residues: 68 loop : -2.20 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 290 HIS 0.002 0.001 HIS D 136 PHE 0.016 0.001 PHE B 104 TYR 0.011 0.001 TYR E 380 ARG 0.003 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 74 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 71 average time/residue: 0.1870 time to fit residues: 20.6610 Evaluate side-chains 68 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 1.165 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0952 time to fit residues: 1.9672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9844 Z= 0.257 Angle : 0.650 8.449 13398 Z= 0.336 Chirality : 0.039 0.189 1635 Planarity : 0.003 0.029 1741 Dihedral : 4.164 15.606 1426 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.74 % Favored : 92.03 % Rotamer: Outliers : 0.53 % Allowed : 13.54 % Favored : 85.93 % 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: -1.52 (0.24), residues: 1330 helix: 0.24 (0.22), residues: 615 sheet: -2.21 (0.64), residues: 71 loop : -2.17 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 306 HIS 0.005 0.001 HIS E 317 PHE 0.019 0.002 PHE E 152 TYR 0.009 0.001 TYR C 294 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 66 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 65 average time/residue: 0.1787 time to fit residues: 18.3921 Evaluate side-chains 64 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 1.051 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0853 time to fit residues: 1.9835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 123 optimal weight: 0.1980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9844 Z= 0.160 Angle : 0.618 11.130 13398 Z= 0.302 Chirality : 0.038 0.159 1635 Planarity : 0.003 0.031 1741 Dihedral : 3.960 14.781 1426 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.24 % Favored : 93.53 % Rotamer: Outliers : 0.32 % Allowed : 14.93 % 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: -1.32 (0.24), residues: 1330 helix: 0.52 (0.22), residues: 599 sheet: -1.43 (0.71), residues: 62 loop : -2.22 (0.25), residues: 669 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 0.011 0.001 PHE B 104 TYR 0.011 0.001 TYR E 364 ARG 0.002 0.000 ARG A 48 *********************** 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 65 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 64 average time/residue: 0.1712 time to fit residues: 17.3231 Evaluate side-chains 63 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0867 time to fit residues: 1.6937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 58 optimal weight: 0.0980 chunk 78 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9844 Z= 0.249 Angle : 0.642 9.151 13398 Z= 0.330 Chirality : 0.039 0.190 1635 Planarity : 0.003 0.028 1741 Dihedral : 4.145 14.872 1426 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.97 % Favored : 91.88 % Rotamer: Outliers : 0.96 % Allowed : 15.57 % Favored : 83.48 % 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: -1.45 (0.24), residues: 1330 helix: 0.34 (0.22), residues: 612 sheet: -1.63 (0.68), residues: 64 loop : -2.24 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 290 HIS 0.005 0.001 HIS E 317 PHE 0.016 0.001 PHE E 152 TYR 0.012 0.001 TYR E 364 ARG 0.003 0.000 ARG B 157 *********************** 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 70 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 69 average time/residue: 0.1807 time to fit residues: 19.9493 Evaluate side-chains 64 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0944 time to fit residues: 2.2049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 121 optimal weight: 0.0770 chunk 111 optimal weight: 0.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- 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 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9844 Z= 0.154 Angle : 0.628 9.669 13398 Z= 0.304 Chirality : 0.039 0.181 1635 Planarity : 0.003 0.032 1741 Dihedral : 3.964 14.688 1426 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.02 % Favored : 93.91 % Rotamer: Outliers : 0.32 % Allowed : 15.88 % Favored : 83.80 % 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: -1.31 (0.24), residues: 1330 helix: 0.52 (0.22), residues: 606 sheet: -1.59 (0.70), residues: 64 loop : -2.21 (0.25), residues: 660 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 342 TYR 0.019 0.001 TYR E 364 ARG 0.002 0.000 ARG A 48 *********************** 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 67 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 66 average time/residue: 0.1784 time to fit residues: 18.6374 Evaluate side-chains 65 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0917 time to fit residues: 1.8541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.0980 chunk 121 optimal weight: 0.0770 chunk 71 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 0.0270 chunk 107 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 76 optimal weight: 0.0670 overall best weight: 0.2334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2439 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= 0.143 Angle : 0.650 12.734 13398 Z= 0.309 Chirality : 0.039 0.173 1635 Planarity : 0.003 0.032 1741 Dihedral : 3.783 15.473 1426 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 0.64 % Allowed : 16.31 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.24), residues: 1330 helix: 0.56 (0.22), residues: 596 sheet: -1.95 (0.63), residues: 76 loop : -2.08 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 290 HIS 0.002 0.001 HIS E 348 PHE 0.011 0.001 PHE B 104 TYR 0.018 0.001 TYR E 364 ARG 0.002 0.000 ARG A 48 *********************** 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 70 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 67 average time/residue: 0.1892 time to fit residues: 19.6945 Evaluate side-chains 66 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1156 time to fit residues: 2.1117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 104 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 111 optimal weight: 0.0050 chunk 32 optimal weight: 5.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2519 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= 0.146 Angle : 0.656 11.011 13398 Z= 0.311 Chirality : 0.039 0.193 1635 Planarity : 0.003 0.032 1741 Dihedral : 3.734 16.155 1426 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.29 % Rotamer: Outliers : 0.21 % Allowed : 16.74 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.24), residues: 1330 helix: 0.67 (0.22), residues: 589 sheet: -1.86 (0.64), residues: 76 loop : -2.06 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 290 HIS 0.002 0.000 HIS A 67 PHE 0.010 0.001 PHE B 104 TYR 0.012 0.001 TYR A 12 ARG 0.002 0.000 ARG A 48 ********************** 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 65 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 1.247 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 64 average time/residue: 0.1949 time to fit residues: 19.3908 Evaluate side-chains 65 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0896 time to fit residues: 1.7215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 0.0050 chunk 104 optimal weight: 0.0050 chunk 43 optimal weight: 0.0980 chunk 107 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 overall best weight: 0.6210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 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 = 0.3141 r_free = 0.3141 target = 0.034365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.028141 restraints weight = 138307.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.028581 restraints weight = 95903.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.028920 restraints weight = 73925.706| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 9844 Z= 0.155 Angle : 0.684 14.047 13398 Z= 0.321 Chirality : 0.039 0.193 1635 Planarity : 0.003 0.032 1741 Dihedral : 3.701 16.977 1426 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.79 % Favored : 94.14 % Rotamer: Outliers : 0.11 % Allowed : 16.74 % Favored : 83.16 % 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: -1.20 (0.24), residues: 1330 helix: 0.61 (0.22), residues: 601 sheet: -1.76 (0.64), residues: 76 loop : -2.10 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 290 HIS 0.002 0.000 HIS E 348 PHE 0.011 0.001 PHE B 104 TYR 0.007 0.001 TYR E 343 ARG 0.002 0.000 ARG A 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1807.26 seconds wall clock time: 34 minutes 3.05 seconds (2043.05 seconds total)