Starting phenix.real_space_refine on Thu Feb 15 17:08:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znq_14813/02_2024/7znq_14813.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znq_14813/02_2024/7znq_14813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znq_14813/02_2024/7znq_14813.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znq_14813/02_2024/7znq_14813.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znq_14813/02_2024/7znq_14813.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znq_14813/02_2024/7znq_14813.pdb" } resolution = 3.04 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= 0.001 sd= 0.018 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 Cu 1 5.60 5 Mg 1 5.21 5 S 44 5.16 5 C 8224 2.51 5 N 2255 2.21 5 O 2336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 256": "OE1" <-> "OE2" Residue "Y GLU 11": "OE1" <-> "OE2" Residue "Y GLU 201": "OE1" <-> "OE2" Residue "y GLU 11": "OE1" <-> "OE2" Residue "y GLU 132": "OE1" <-> "OE2" Residue "y GLU 170": "OE1" <-> "OE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "L GLU 35": "OE1" <-> "OE2" Residue "L GLU 104": "OE1" <-> "OE2" Residue "L GLU 138": "OE1" <-> "OE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "L GLU 157": "OE1" <-> "OE2" Residue "L GLU 158": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12862 Number of models: 1 Model: "" Number of chains: 8 Chain: "f" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2367 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 12, 'TRANS': 294} Chain: "F" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2367 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 12, 'TRANS': 294} Chain: "Y" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2030 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 8, 'TRANS': 260} Chain breaks: 1 Chain: "y" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1910 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 8, 'TRANS': 241} Chain breaks: 2 Chain: "D" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3077 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain breaks: 1 Chain: "L" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1108 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11876 SG CYS L 45 34.329 40.988 141.651 1.00 79.98 S ATOM 11899 SG CYS L 48 36.435 41.705 143.966 1.00 89.23 S ATOM 12080 SG CYS L 72 32.929 42.618 145.143 1.00 99.19 S Time building chain proxies: 7.48, per 1000 atoms: 0.58 Number of scatterers: 12862 At special positions: 0 Unit cell: (86.1, 88.56, 193.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Cu 1 28.99 S 44 16.00 Mg 1 11.99 O 2336 8.00 N 2255 7.00 C 8224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.27 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 45 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 72 " 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3006 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 14 sheets defined 47.1% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'f' and resid 40 through 50 Processing helix chain 'f' and resid 72 through 74 No H-bonds generated for 'chain 'f' and resid 72 through 74' Processing helix chain 'f' and resid 90 through 103 removed outlier: 3.502A pdb=" N THR f 94 " --> pdb=" O SER f 90 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU f 95 " --> pdb=" O GLY f 91 " (cutoff:3.500A) Processing helix chain 'f' and resid 105 through 107 No H-bonds generated for 'chain 'f' and resid 105 through 107' Processing helix chain 'f' and resid 108 through 116 Processing helix chain 'f' and resid 125 through 129 Processing helix chain 'f' and resid 130 through 143 Processing helix chain 'f' and resid 160 through 178 removed outlier: 3.572A pdb=" N ARG f 177 " --> pdb=" O ARG f 173 " (cutoff:3.500A) Processing helix chain 'f' and resid 211 through 219 Processing helix chain 'f' and resid 232 through 238 removed outlier: 4.071A pdb=" N GLN f 238 " --> pdb=" O ASP f 234 " (cutoff:3.500A) Processing helix chain 'f' and resid 238 through 243 removed outlier: 3.946A pdb=" N ASP f 242 " --> pdb=" O GLN f 238 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA f 243 " --> pdb=" O ARG f 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 238 through 243' Processing helix chain 'f' and resid 263 through 275 removed outlier: 3.502A pdb=" N LEU f 267 " --> pdb=" O HIS f 263 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG f 269 " --> pdb=" O LEU f 265 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN f 270 " --> pdb=" O VAL f 266 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU f 271 " --> pdb=" O LEU f 267 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY f 275 " --> pdb=" O LEU f 271 " (cutoff:3.500A) Processing helix chain 'f' and resid 286 through 297 Processing helix chain 'F' and resid 40 through 50 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 90 through 103 removed outlier: 3.559A pdb=" N LEU F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 116 removed outlier: 3.847A pdb=" N ASP F 110 " --> pdb=" O LEU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 129 Processing helix chain 'F' and resid 130 through 143 Processing helix chain 'F' and resid 160 through 176 removed outlier: 3.956A pdb=" N GLN F 165 " --> pdb=" O PRO F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 219 removed outlier: 3.591A pdb=" N ARG F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 244 removed outlier: 3.837A pdb=" N ALA F 243 " --> pdb=" O TRP F 240 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY F 244 " --> pdb=" O THR F 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 240 through 244' Processing helix chain 'F' and resid 263 through 274 removed outlier: 3.764A pdb=" N GLU F 274 " --> pdb=" O GLN F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 298 Processing helix chain 'Y' and resid 3 through 16 removed outlier: 3.573A pdb=" N SER Y 13 " --> pdb=" O ARG Y 9 " (cutoff:3.500A) Processing helix chain 'Y' and resid 18 through 43 removed outlier: 3.673A pdb=" N LEU Y 22 " --> pdb=" O ASN Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 74 Proline residue: Y 67 - end of helix Processing helix chain 'Y' and resid 78 through 84 removed outlier: 3.509A pdb=" N GLU Y 83 " --> pdb=" O VAL Y 79 " (cutoff:3.500A) Processing helix chain 'Y' and resid 85 through 93 removed outlier: 4.130A pdb=" N LEU Y 89 " --> pdb=" O GLY Y 85 " (cutoff:3.500A) Processing helix chain 'Y' and resid 97 through 131 removed outlier: 3.677A pdb=" N ALA Y 124 " --> pdb=" O PHE Y 120 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 168 removed outlier: 3.695A pdb=" N LEU Y 139 " --> pdb=" O GLU Y 135 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TRP Y 141 " --> pdb=" O GLY Y 137 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS Y 167 " --> pdb=" O VAL Y 163 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL Y 168 " --> pdb=" O LEU Y 164 " (cutoff:3.500A) Processing helix chain 'Y' and resid 170 through 187 removed outlier: 3.541A pdb=" N VAL Y 186 " --> pdb=" O TRP Y 182 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 201 removed outlier: 3.647A pdb=" N SER Y 200 " --> pdb=" O LEU Y 196 " (cutoff:3.500A) Processing helix chain 'Y' and resid 208 through 215 removed outlier: 3.509A pdb=" N LEU Y 213 " --> pdb=" O PRO Y 210 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU Y 214 " --> pdb=" O TRP Y 211 " (cutoff:3.500A) Processing helix chain 'Y' and resid 216 through 226 removed outlier: 3.781A pdb=" N ARG Y 222 " --> pdb=" O THR Y 218 " (cutoff:3.500A) Processing helix chain 'Y' and resid 232 through 245 removed outlier: 3.911A pdb=" N MET Y 236 " --> pdb=" O GLY Y 233 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY Y 237 " --> pdb=" O SER Y 234 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL Y 238 " --> pdb=" O ALA Y 235 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU Y 239 " --> pdb=" O MET Y 236 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA Y 243 " --> pdb=" O SER Y 240 " (cutoff:3.500A) Processing helix chain 'Y' and resid 248 through 274 removed outlier: 4.271A pdb=" N LEU Y 252 " --> pdb=" O PRO Y 248 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP Y 253 " --> pdb=" O ALA Y 249 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER Y 263 " --> pdb=" O TRP Y 259 " (cutoff:3.500A) Processing helix chain 'y' and resid 3 through 17 removed outlier: 3.890A pdb=" N LYS y 10 " --> pdb=" O ASN y 6 " (cutoff:3.500A) Processing helix chain 'y' and resid 18 through 42 Processing helix chain 'y' and resid 51 through 75 Proline residue: y 67 - end of helix removed outlier: 3.561A pdb=" N ALA y 74 " --> pdb=" O ALA y 70 " (cutoff:3.500A) Processing helix chain 'y' and resid 78 through 84 Processing helix chain 'y' and resid 85 through 93 removed outlier: 3.817A pdb=" N LEU y 89 " --> pdb=" O GLY y 85 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR y 92 " --> pdb=" O MET y 88 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR y 93 " --> pdb=" O LEU y 89 " (cutoff:3.500A) Processing helix chain 'y' and resid 96 through 131 removed outlier: 4.197A pdb=" N ALA y 123 " --> pdb=" O GLY y 119 " (cutoff:3.500A) Processing helix chain 'y' and resid 136 through 168 removed outlier: 3.538A pdb=" N TRP y 141 " --> pdb=" O GLY y 137 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY y 166 " --> pdb=" O TYR y 162 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS y 167 " --> pdb=" O VAL y 163 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL y 168 " --> pdb=" O LEU y 164 " (cutoff:3.500A) Processing helix chain 'y' and resid 170 through 187 removed outlier: 3.521A pdb=" N ALA y 174 " --> pdb=" O GLU y 170 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL y 186 " --> pdb=" O TRP y 182 " (cutoff:3.500A) Processing helix chain 'y' and resid 187 through 200 Processing helix chain 'y' and resid 208 through 213 Processing helix chain 'y' and resid 216 through 226 removed outlier: 3.520A pdb=" N ILE y 220 " --> pdb=" O ASN y 216 " (cutoff:3.500A) Processing helix chain 'y' and resid 250 through 272 removed outlier: 3.740A pdb=" N SER y 263 " --> pdb=" O TRP y 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.813A pdb=" N THR D 34 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 383 removed outlier: 3.665A pdb=" N ARG D 378 " --> pdb=" O ASP D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 Processing helix chain 'D' and resid 392 through 405 removed outlier: 3.711A pdb=" N GLU D 396 " --> pdb=" O SER D 392 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 34 removed outlier: 3.624A pdb=" N SER L 33 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU L 34 " --> pdb=" O GLN L 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 30 through 34' Processing helix chain 'L' and resid 73 through 82 removed outlier: 3.670A pdb=" N GLY L 79 " --> pdb=" O ALA L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 88 removed outlier: 4.541A pdb=" N LEU L 88 " --> pdb=" O PRO L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 148 removed outlier: 3.842A pdb=" N ALA L 142 " --> pdb=" O GLU L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 173 Processing sheet with id=AA1, first strand: chain 'f' and resid 76 through 79 removed outlier: 3.928A pdb=" N ALA f 208 " --> pdb=" O ILE f 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'f' and resid 246 through 248 removed outlier: 4.225A pdb=" N GLU f 256 " --> pdb=" O ARG f 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 4 through 9 removed outlier: 3.599A pdb=" N VAL F 4 " --> pdb=" O LEU F 26 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU F 22 " --> pdb=" O GLY F 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 76 through 79 removed outlier: 3.876A pdb=" N LEU F 79 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA F 208 " --> pdb=" O ILE F 200 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA F 202 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU F 206 " --> pdb=" O ALA F 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 246 through 248 removed outlier: 3.818A pdb=" N ARG F 248 " --> pdb=" O GLU F 256 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER F 228 " --> pdb=" O ASP F 279 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP F 279 " --> pdb=" O SER F 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 50 through 51 removed outlier: 6.285A pdb=" N GLY D 50 " --> pdb=" O VAL D 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 56 through 58 removed outlier: 6.748A pdb=" N PHE D 56 " --> pdb=" O LEU D 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 94 through 96 removed outlier: 6.955A pdb=" N LEU D 95 " --> pdb=" O ARG D 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 133 through 134 removed outlier: 6.307A pdb=" N VAL D 134 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE D 184 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N MET D 209 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE D 186 " --> pdb=" O MET D 209 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA D 229 " --> pdb=" O GLY D 205 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS D 207 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET D 231 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET D 209 " --> pdb=" O MET D 231 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR D 228 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ASN D 254 " --> pdb=" O TYR D 228 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU D 230 " --> pdb=" O ASN D 254 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA D 287 " --> pdb=" O TYR D 249 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE D 310 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE D 289 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU D 312 " --> pdb=" O PHE D 289 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N TYR D 291 " --> pdb=" O LEU D 312 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU D 308 " --> pdb=" O GLN D 332 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LYS D 334 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE D 310 " --> pdb=" O LYS D 334 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 146 through 148 removed outlier: 3.837A pdb=" N ARG D 178 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL D 177 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE D 199 " --> pdb=" O ARG D 222 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 170 through 173 removed outlier: 6.013A pdb=" N ASN D 192 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE D 217 " --> pdb=" O ASN D 192 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU D 194 " --> pdb=" O ILE D 217 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 242 through 244 removed outlier: 6.278A pdb=" N SER D 243 " --> pdb=" O SER D 267 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 69 through 71 Processing sheet with id=AB5, first strand: chain 'L' and resid 134 through 136 597 hydrogen bonds defined for protein. 1704 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.65 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3290 1.33 - 1.45: 2380 1.45 - 1.57: 7358 1.57 - 1.69: 1 1.69 - 1.81: 75 Bond restraints: 13104 Sorted by residual: bond pdb=" C ILE y 51 " pdb=" N PRO y 52 " ideal model delta sigma weight residual 1.337 1.377 -0.040 1.24e-02 6.50e+03 1.03e+01 bond pdb=" N ASN D 361 " pdb=" CA ASN D 361 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.31e-02 5.83e+03 6.69e+00 bond pdb=" N CYS L 48 " pdb=" CA CYS L 48 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.28e-02 6.10e+03 5.95e+00 bond pdb=" N MET L 129 " pdb=" CA MET L 129 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.68e+00 bond pdb=" N MET L 50 " pdb=" CA MET L 50 " ideal model delta sigma weight residual 1.453 1.484 -0.031 1.31e-02 5.83e+03 5.45e+00 ... (remaining 13099 not shown) Histogram of bond angle deviations from ideal: 97.19 - 104.95: 215 104.95 - 112.71: 6903 112.71 - 120.47: 5522 120.47 - 128.23: 5017 128.23 - 135.99: 121 Bond angle restraints: 17778 Sorted by residual: angle pdb=" C ASP D 359 " pdb=" CA ASP D 359 " pdb=" CB ASP D 359 " ideal model delta sigma weight residual 112.09 102.56 9.53 1.43e+00 4.89e-01 4.45e+01 angle pdb=" CA GLU y 201 " pdb=" CB GLU y 201 " pdb=" CG GLU y 201 " ideal model delta sigma weight residual 114.10 125.95 -11.85 2.00e+00 2.50e-01 3.51e+01 angle pdb=" N GLU L 76 " pdb=" CA GLU L 76 " pdb=" C GLU L 76 " ideal model delta sigma weight residual 113.23 106.20 7.03 1.24e+00 6.50e-01 3.21e+01 angle pdb=" CA LEU D 89 " pdb=" CB LEU D 89 " pdb=" CG LEU D 89 " ideal model delta sigma weight residual 116.30 135.99 -19.69 3.50e+00 8.16e-02 3.17e+01 angle pdb=" CA ARG L 66 " pdb=" CB ARG L 66 " pdb=" CG ARG L 66 " ideal model delta sigma weight residual 114.10 123.31 -9.21 2.00e+00 2.50e-01 2.12e+01 ... (remaining 17773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 6661 16.56 - 33.11: 814 33.11 - 49.67: 228 49.67 - 66.22: 46 66.22 - 82.78: 9 Dihedral angle restraints: 7758 sinusoidal: 3048 harmonic: 4710 Sorted by residual: dihedral pdb=" CA ASP D 182 " pdb=" C ASP D 182 " pdb=" N GLY D 183 " pdb=" CA GLY D 183 " ideal model delta harmonic sigma weight residual 180.00 -154.24 -25.76 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA GLN f 108 " pdb=" C GLN f 108 " pdb=" N VAL f 109 " pdb=" CA VAL f 109 " ideal model delta harmonic sigma weight residual -180.00 -158.71 -21.29 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" C ASP D 182 " pdb=" N ASP D 182 " pdb=" CA ASP D 182 " pdb=" CB ASP D 182 " ideal model delta harmonic sigma weight residual -122.60 -133.00 10.40 0 2.50e+00 1.60e-01 1.73e+01 ... (remaining 7755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1826 0.084 - 0.168: 199 0.168 - 0.251: 10 0.251 - 0.335: 3 0.335 - 0.419: 1 Chirality restraints: 2039 Sorted by residual: chirality pdb=" CB ILE D 72 " pdb=" CA ILE D 72 " pdb=" CG1 ILE D 72 " pdb=" CG2 ILE D 72 " both_signs ideal model delta sigma weight residual False 2.64 3.06 -0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA GLU y 201 " pdb=" N GLU y 201 " pdb=" C GLU y 201 " pdb=" CB GLU y 201 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE D 147 " pdb=" CA ILE D 147 " pdb=" CG1 ILE D 147 " pdb=" CG2 ILE D 147 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 2036 not shown) Planarity restraints: 2282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 109 " -0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C VAL D 109 " 0.066 2.00e-02 2.50e+03 pdb=" O VAL D 109 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE D 110 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 226 " -0.016 2.00e-02 2.50e+03 3.13e-02 9.78e+00 pdb=" C THR D 226 " 0.054 2.00e-02 2.50e+03 pdb=" O THR D 226 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY D 227 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET y 66 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.05e+00 pdb=" N PRO y 67 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO y 67 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO y 67 " -0.040 5.00e-02 4.00e+02 ... (remaining 2279 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 42 2.45 - 3.06: 7383 3.06 - 3.68: 19170 3.68 - 4.29: 27835 4.29 - 4.90: 47590 Nonbonded interactions: 102020 Sorted by model distance: nonbonded pdb=" OE1 GLU L 76 " pdb="ZN ZN L 201 " model vdw 1.840 2.230 nonbonded pdb=" OD1 ASP D 359 " pdb="MG MG D 501 " model vdw 1.887 2.170 nonbonded pdb=" OE2 GLU L 76 " pdb="ZN ZN L 201 " model vdw 2.010 2.230 nonbonded pdb=" OD1 ASN D 361 " pdb="MG MG D 501 " model vdw 2.015 2.170 nonbonded pdb=" SD MET D 231 " pdb="CU CU D 502 " model vdw 2.038 2.600 ... (remaining 102015 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 'F' selection = chain 'f' } ncs_group { reference = (chain 'Y' and (resid 2 through 43 or resid 51 through 227 or resid 245 through \ 275)) selection = chain 'y' } 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 individual isotropic 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: 8.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.700 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 37.610 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 0.053 13104 Z= 0.283 Angle : 0.903 19.693 17778 Z= 0.485 Chirality : 0.051 0.419 2039 Planarity : 0.006 0.071 2282 Dihedral : 15.839 82.777 4752 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.00 % Favored : 93.70 % Rotamer: Outliers : 0.22 % Allowed : 20.62 % Favored : 79.15 % Cbeta Deviations : 0.07 % 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: -2.57 (0.18), residues: 1650 helix: -0.97 (0.16), residues: 703 sheet: -1.80 (0.34), residues: 207 loop : -2.35 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP y 211 HIS 0.006 0.001 HIS F 37 PHE 0.021 0.001 PHE y 146 TYR 0.012 0.001 TYR D 204 ARG 0.014 0.000 ARG L 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: F 16 MET cc_start: 0.8610 (pmm) cc_final: 0.8207 (pmm) REVERT: D 89 LEU cc_start: 0.8828 (tt) cc_final: 0.8448 (mt) REVERT: D 390 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7750 (mmm) REVERT: L 171 GLN cc_start: 0.8464 (tm-30) cc_final: 0.7832 (tm-30) outliers start: 3 outliers final: 2 residues processed: 135 average time/residue: 0.2882 time to fit residues: 55.4541 Evaluate side-chains 129 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain L residue 63 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 13104 Z= 0.438 Angle : 0.639 9.781 17778 Z= 0.325 Chirality : 0.044 0.208 2039 Planarity : 0.004 0.058 2282 Dihedral : 5.026 51.701 1815 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.27 % Favored : 94.30 % Rotamer: Outliers : 3.34 % Allowed : 19.81 % Favored : 76.85 % 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: -1.12 (0.20), residues: 1650 helix: 0.84 (0.19), residues: 701 sheet: -1.83 (0.35), residues: 226 loop : -2.00 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP y 211 HIS 0.006 0.001 HIS f 186 PHE 0.021 0.002 PHE y 120 TYR 0.017 0.002 TYR D 204 ARG 0.006 0.000 ARG f 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 119 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 224 ARG cc_start: 0.8849 (ttp-110) cc_final: 0.8643 (ttp80) REVERT: Y 82 ASP cc_start: 0.8900 (t70) cc_final: 0.8698 (t0) REVERT: Y 138 MET cc_start: 0.7762 (tmm) cc_final: 0.7484 (tmm) REVERT: y 201 GLU cc_start: 0.8632 (pm20) cc_final: 0.8333 (pm20) REVERT: L 43 ASP cc_start: 0.8295 (m-30) cc_final: 0.8082 (m-30) outliers start: 45 outliers final: 32 residues processed: 152 average time/residue: 0.2715 time to fit residues: 58.6432 Evaluate side-chains 145 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 113 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 126 VAL Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain f residue 191 VAL Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 88 MET Chi-restraints excluded: chain Y residue 112 LEU Chi-restraints excluded: chain Y residue 169 ASN Chi-restraints excluded: chain Y residue 229 PHE Chi-restraints excluded: chain Y residue 244 ASP Chi-restraints excluded: chain y residue 129 LEU Chi-restraints excluded: chain y residue 138 MET Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain y residue 274 ARG Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 141 ASP Chi-restraints excluded: chain L residue 153 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 123 optimal weight: 0.0970 chunk 101 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 149 optimal weight: 0.2980 chunk 161 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 147 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 196 ASN ** D 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 HIS L 96 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13104 Z= 0.122 Angle : 0.483 9.058 17778 Z= 0.245 Chirality : 0.040 0.145 2039 Planarity : 0.003 0.048 2282 Dihedral : 4.213 25.467 1809 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.94 % Favored : 95.76 % Rotamer: Outliers : 2.15 % Allowed : 21.59 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1650 helix: 1.70 (0.20), residues: 699 sheet: -1.64 (0.36), residues: 211 loop : -1.72 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 253 HIS 0.004 0.000 HIS f 37 PHE 0.026 0.001 PHE y 120 TYR 0.006 0.001 TYR L 118 ARG 0.007 0.000 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 125 time to evaluate : 1.490 Fit side-chains revert: symmetry clash REVERT: f 224 ARG cc_start: 0.8839 (ttp-110) cc_final: 0.8522 (ttp80) REVERT: Y 82 ASP cc_start: 0.8923 (t70) cc_final: 0.8623 (t0) REVERT: Y 207 GLU cc_start: 0.5837 (tp30) cc_final: 0.5556 (tp30) REVERT: D 426 LYS cc_start: 0.9052 (mtmm) cc_final: 0.8638 (mmtm) REVERT: L 70 LYS cc_start: 0.8826 (mtmt) cc_final: 0.8617 (mtmt) REVERT: L 155 ARG cc_start: 0.9006 (mmm-85) cc_final: 0.8714 (mmm-85) outliers start: 29 outliers final: 20 residues processed: 147 average time/residue: 0.2557 time to fit residues: 54.3366 Evaluate side-chains 139 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 229 PHE Chi-restraints excluded: chain y residue 138 MET Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 141 ASP Chi-restraints excluded: chain L residue 170 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 158 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 196 ASN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 13104 Z= 0.427 Angle : 0.620 10.645 17778 Z= 0.312 Chirality : 0.044 0.187 2039 Planarity : 0.004 0.044 2282 Dihedral : 4.566 28.509 1809 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.45 % Favored : 94.18 % Rotamer: Outliers : 4.53 % Allowed : 19.96 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.21), residues: 1650 helix: 1.70 (0.20), residues: 703 sheet: -1.71 (0.36), residues: 226 loop : -1.68 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 352 HIS 0.005 0.001 HIS F 97 PHE 0.017 0.002 PHE Y 157 TYR 0.017 0.002 TYR D 204 ARG 0.007 0.000 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 114 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: f 224 ARG cc_start: 0.8842 (ttp-110) cc_final: 0.8497 (ttp80) REVERT: F 57 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: F 224 ARG cc_start: 0.9313 (ttp-170) cc_final: 0.8754 (tmm-80) REVERT: Y 207 GLU cc_start: 0.6080 (tp30) cc_final: 0.5807 (tp30) REVERT: y 213 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9411 (mp) REVERT: D 218 ASP cc_start: 0.8477 (t0) cc_final: 0.8208 (t0) REVERT: D 426 LYS cc_start: 0.9014 (mtmm) cc_final: 0.8594 (mmtm) outliers start: 61 outliers final: 42 residues processed: 159 average time/residue: 0.2602 time to fit residues: 59.4743 Evaluate side-chains 158 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 114 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 84 THR Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 126 VAL Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain f residue 184 CYS Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 112 LEU Chi-restraints excluded: chain Y residue 169 ASN Chi-restraints excluded: chain Y residue 229 PHE Chi-restraints excluded: chain y residue 129 LEU Chi-restraints excluded: chain y residue 138 MET Chi-restraints excluded: chain y residue 158 LEU Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain y residue 213 LEU Chi-restraints excluded: chain y residue 274 ARG Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 141 ASP Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 170 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 196 ASN ** D 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13104 Z= 0.169 Angle : 0.501 9.963 17778 Z= 0.254 Chirality : 0.040 0.158 2039 Planarity : 0.003 0.042 2282 Dihedral : 4.237 25.492 1809 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.00 % Favored : 95.70 % Rotamer: Outliers : 2.89 % Allowed : 21.88 % Favored : 75.22 % 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: 0.05 (0.21), residues: 1650 helix: 2.14 (0.20), residues: 704 sheet: -1.58 (0.35), residues: 226 loop : -1.62 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Y 253 HIS 0.002 0.000 HIS f 37 PHE 0.014 0.001 PHE y 120 TYR 0.008 0.001 TYR F 86 ARG 0.008 0.000 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 121 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 38 ASN cc_start: 0.8678 (m-40) cc_final: 0.8447 (m110) REVERT: f 224 ARG cc_start: 0.8831 (ttp-110) cc_final: 0.8453 (ttp80) REVERT: Y 11 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8246 (mm-30) REVERT: Y 207 GLU cc_start: 0.6024 (tp30) cc_final: 0.5760 (tp30) REVERT: Y 236 MET cc_start: 0.8230 (mpp) cc_final: 0.7772 (mpp) REVERT: D 218 ASP cc_start: 0.8475 (t0) cc_final: 0.8259 (t0) REVERT: D 426 LYS cc_start: 0.8982 (mtmm) cc_final: 0.8555 (mmtm) REVERT: L 43 ASP cc_start: 0.8234 (m-30) cc_final: 0.8016 (m-30) REVERT: L 65 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.9044 (tmtt) REVERT: L 155 ARG cc_start: 0.9041 (mmm-85) cc_final: 0.8799 (mmm-85) outliers start: 39 outliers final: 29 residues processed: 149 average time/residue: 0.2540 time to fit residues: 55.0054 Evaluate side-chains 148 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 84 THR Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 146 PHE Chi-restraints excluded: chain Y residue 229 PHE Chi-restraints excluded: chain y residue 138 MET Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 141 ASP Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 170 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 31 optimal weight: 0.0980 chunk 93 optimal weight: 0.3980 chunk 39 optimal weight: 6.9990 chunk 158 optimal weight: 20.0000 chunk 131 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN ** D 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13104 Z= 0.246 Angle : 0.530 13.083 17778 Z= 0.266 Chirality : 0.041 0.164 2039 Planarity : 0.003 0.041 2282 Dihedral : 4.225 26.301 1809 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.21 % Favored : 94.48 % Rotamer: Outliers : 4.01 % Allowed : 21.22 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1650 helix: 2.20 (0.20), residues: 704 sheet: -1.55 (0.37), residues: 206 loop : -1.53 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP y 211 HIS 0.003 0.001 HIS f 37 PHE 0.013 0.001 PHE Y 157 TYR 0.011 0.001 TYR D 204 ARG 0.010 0.000 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 118 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 57 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: Y 207 GLU cc_start: 0.6007 (tp30) cc_final: 0.5722 (tp30) REVERT: D 218 ASP cc_start: 0.8458 (t0) cc_final: 0.8174 (t0) REVERT: D 426 LYS cc_start: 0.8974 (mtmm) cc_final: 0.8549 (mmtm) REVERT: L 65 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.9089 (tmtt) outliers start: 54 outliers final: 43 residues processed: 160 average time/residue: 0.2358 time to fit residues: 56.0800 Evaluate side-chains 161 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 116 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 84 THR Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 283 HIS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 146 PHE Chi-restraints excluded: chain Y residue 229 PHE Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain y residue 129 LEU Chi-restraints excluded: chain y residue 138 MET Chi-restraints excluded: chain y residue 158 LEU Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 141 ASP Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 170 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 115 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 158 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 96 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13104 Z= 0.184 Angle : 0.508 14.313 17778 Z= 0.254 Chirality : 0.040 0.158 2039 Planarity : 0.003 0.040 2282 Dihedral : 4.112 25.245 1809 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.36 % Favored : 95.33 % Rotamer: Outliers : 4.15 % Allowed : 21.14 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.22), residues: 1650 helix: 2.36 (0.20), residues: 705 sheet: -1.47 (0.36), residues: 216 loop : -1.48 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP y 211 HIS 0.002 0.000 HIS D 163 PHE 0.012 0.001 PHE Y 157 TYR 0.008 0.001 TYR F 13 ARG 0.011 0.000 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 119 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 38 ASN cc_start: 0.8685 (m110) cc_final: 0.8444 (m-40) REVERT: F 57 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: Y 207 GLU cc_start: 0.5985 (tp30) cc_final: 0.5710 (tp30) REVERT: D 218 ASP cc_start: 0.8468 (t0) cc_final: 0.8213 (t0) REVERT: D 426 LYS cc_start: 0.8981 (mtmm) cc_final: 0.8539 (mmtm) REVERT: L 65 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.9128 (tmtt) REVERT: L 155 ARG cc_start: 0.9035 (mmm-85) cc_final: 0.8832 (mmm-85) outliers start: 56 outliers final: 40 residues processed: 164 average time/residue: 0.2428 time to fit residues: 58.8203 Evaluate side-chains 157 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 115 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 84 THR Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 126 VAL Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 283 HIS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 146 PHE Chi-restraints excluded: chain Y residue 229 PHE Chi-restraints excluded: chain y residue 129 LEU Chi-restraints excluded: chain y residue 138 MET Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 141 ASP Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 170 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 31 optimal weight: 0.0270 chunk 30 optimal weight: 9.9990 chunk 100 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 13104 Z= 0.160 Angle : 0.511 14.796 17778 Z= 0.252 Chirality : 0.040 0.187 2039 Planarity : 0.003 0.044 2282 Dihedral : 4.000 25.132 1809 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.03 % Favored : 94.67 % Rotamer: Outliers : 3.26 % Allowed : 22.26 % Favored : 74.48 % 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: 0.43 (0.22), residues: 1650 helix: 2.48 (0.20), residues: 705 sheet: -1.47 (0.35), residues: 232 loop : -1.43 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP y 211 HIS 0.002 0.000 HIS D 163 PHE 0.012 0.001 PHE Y 157 TYR 0.009 0.001 TYR F 13 ARG 0.011 0.000 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 121 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: F 57 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: F 224 ARG cc_start: 0.9135 (ttp-170) cc_final: 0.8559 (ttp-170) REVERT: Y 207 GLU cc_start: 0.5937 (tp30) cc_final: 0.5672 (tp30) REVERT: D 112 LEU cc_start: 0.8761 (mt) cc_final: 0.8553 (mt) REVERT: D 218 ASP cc_start: 0.8469 (t0) cc_final: 0.8212 (t0) REVERT: D 426 LYS cc_start: 0.8982 (mtmm) cc_final: 0.8545 (mmtm) REVERT: L 65 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9148 (tmtt) REVERT: L 155 ARG cc_start: 0.9053 (mmm-85) cc_final: 0.8840 (mmm-85) outliers start: 44 outliers final: 37 residues processed: 154 average time/residue: 0.2418 time to fit residues: 55.2098 Evaluate side-chains 159 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 120 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 84 THR Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 126 VAL Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 184 CYS Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 283 HIS Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 146 PHE Chi-restraints excluded: chain Y residue 229 PHE Chi-restraints excluded: chain y residue 129 LEU Chi-restraints excluded: chain y residue 138 MET Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 141 ASP Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 170 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 115 optimal weight: 0.0010 chunk 45 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13104 Z= 0.189 Angle : 0.530 15.633 17778 Z= 0.260 Chirality : 0.041 0.249 2039 Planarity : 0.003 0.052 2282 Dihedral : 4.018 25.232 1809 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.73 % Favored : 94.97 % Rotamer: Outliers : 3.56 % Allowed : 21.96 % Favored : 74.48 % 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: 0.50 (0.22), residues: 1650 helix: 2.51 (0.20), residues: 706 sheet: -1.46 (0.36), residues: 212 loop : -1.36 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP y 211 HIS 0.002 0.001 HIS D 163 PHE 0.013 0.001 PHE Y 157 TYR 0.009 0.001 TYR F 13 ARG 0.013 0.000 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 123 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 57 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: Y 207 GLU cc_start: 0.5921 (tp30) cc_final: 0.5651 (tp30) REVERT: D 112 LEU cc_start: 0.8782 (mt) cc_final: 0.8567 (mt) REVERT: D 218 ASP cc_start: 0.8466 (t0) cc_final: 0.8194 (t0) REVERT: D 426 LYS cc_start: 0.8976 (mtmm) cc_final: 0.8534 (mmtm) REVERT: L 65 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.9173 (tmtt) outliers start: 48 outliers final: 39 residues processed: 158 average time/residue: 0.2383 time to fit residues: 55.6084 Evaluate side-chains 162 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 121 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 84 THR Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 126 VAL Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 184 CYS Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 232 GLU Chi-restraints excluded: chain f residue 283 HIS Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 146 PHE Chi-restraints excluded: chain Y residue 229 PHE Chi-restraints excluded: chain y residue 129 LEU Chi-restraints excluded: chain y residue 138 MET Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 141 ASP Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 163 optimal weight: 8.9990 chunk 150 optimal weight: 0.4980 chunk 130 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13104 Z= 0.142 Angle : 0.515 15.816 17778 Z= 0.252 Chirality : 0.040 0.234 2039 Planarity : 0.003 0.055 2282 Dihedral : 3.871 24.672 1809 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.73 % Favored : 94.97 % Rotamer: Outliers : 3.19 % Allowed : 22.26 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.22), residues: 1650 helix: 2.64 (0.20), residues: 706 sheet: -1.40 (0.35), residues: 232 loop : -1.32 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP D 98 HIS 0.002 0.000 HIS D 163 PHE 0.011 0.001 PHE Y 157 TYR 0.011 0.001 TYR F 13 ARG 0.014 0.000 ARG L 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 124 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 57 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: Y 207 GLU cc_start: 0.5853 (tp30) cc_final: 0.5588 (tp30) REVERT: D 218 ASP cc_start: 0.8467 (t0) cc_final: 0.8224 (t0) REVERT: D 426 LYS cc_start: 0.8971 (mtmm) cc_final: 0.8545 (mmtm) REVERT: L 65 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.9164 (tmtt) outliers start: 43 outliers final: 34 residues processed: 156 average time/residue: 0.2473 time to fit residues: 56.7934 Evaluate side-chains 155 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 84 THR Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 126 VAL Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 232 GLU Chi-restraints excluded: chain f residue 283 HIS Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 146 PHE Chi-restraints excluded: chain Y residue 229 PHE Chi-restraints excluded: chain y residue 64 PHE Chi-restraints excluded: chain y residue 129 LEU Chi-restraints excluded: chain y residue 138 MET Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 141 ASP Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 54 optimal weight: 30.0000 chunk 133 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 196 ASN ** F 283 HIS ** 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 = 0.3577 r_free = 0.3577 target = 0.092728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.058790 restraints weight = 27222.886| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.17 r_work: 0.2755 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 13104 Z= 0.460 Angle : 0.663 16.127 17778 Z= 0.326 Chirality : 0.045 0.245 2039 Planarity : 0.004 0.094 2282 Dihedral : 4.417 26.592 1809 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.94 % Favored : 93.70 % Rotamer: Outliers : 3.26 % Allowed : 22.33 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1650 helix: 2.24 (0.20), residues: 705 sheet: -1.85 (0.36), residues: 220 loop : -1.43 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 352 HIS 0.004 0.001 HIS f 97 PHE 0.016 0.002 PHE Y 143 TYR 0.018 0.002 TYR D 204 ARG 0.014 0.000 ARG L 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2536.22 seconds wall clock time: 47 minutes 38.57 seconds (2858.57 seconds total)