Starting phenix.real_space_refine on Fri Sep 11 02:55:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6e7c_8998/09_2026/6e7c_8998.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e7c_8998/09_2026/6e7c_8998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6e7c_8998/09_2026/6e7c_8998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e7c_8998/09_2026/6e7c_8998.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6e7c_8998/09_2026/6e7c_8998.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6e7c_8998/09_2026/6e7c_8998.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6e7c_8998/09_2026/6e7c_8998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e7c_8998/09_2026/6e7c_8998.map" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.228 sd= 1.115 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 49 5.16 5 C 4259 2.51 5 N 1156 2.21 5 O 1308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6780 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3356 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "A" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3358 Classifications: {'peptide': 428} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.52, per 1000 atoms: 0.22 Number of scatterers: 6780 At special positions: 0 Unit cell: (74, 73, 107, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 49 16.00 P 6 15.00 Mg 2 11.99 O 1308 8.00 N 1156 7.00 C 4259 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 371.5 milliseconds 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1582 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 8 sheets defined 49.9% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'B' and resid 10 through 28 removed outlier: 3.644A pdb=" N GLN B 15 " --> pdb=" O GLN B 11 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.694A pdb=" N VAL B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 69 through 79 removed outlier: 3.967A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 100 removed outlier: 4.157A pdb=" N ASN B 99 " --> pdb=" O GLY B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.832A pdb=" N ASP B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 removed outlier: 3.588A pdb=" N GLY B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.555A pdb=" N LEU B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.556A pdb=" N LEU B 187 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 removed outlier: 3.665A pdb=" N ASP B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 226 through 242 removed outlier: 3.548A pdb=" N ALA B 231 " --> pdb=" O HIS B 227 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET B 233 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N CYS B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 276 through 280 removed outlier: 3.575A pdb=" N GLN B 279 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN B 280 " --> pdb=" O GLY B 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 276 through 280' Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.618A pdb=" N GLN B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.544A pdb=" N GLN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET B 330 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 390 removed outlier: 4.146A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 3.778A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 424 removed outlier: 4.128A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.509A pdb=" N VAL A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 24 " --> pdb=" O CYS A 20 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.663A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 102 through 108 removed outlier: 3.822A pdb=" N TYR A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 129 removed outlier: 4.222A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 3.572A pdb=" N PHE A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.520A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 removed outlier: 3.747A pdb=" N TYR A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.682A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.790A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.763A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 324 through 338 removed outlier: 4.217A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 400 removed outlier: 3.860A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 412 removed outlier: 4.468A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 437 removed outlier: 3.719A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 63 through 66 removed outlier: 8.986A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.501A pdb=" N VAL B 60 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA4, first strand: chain 'B' and resid 199 through 200 removed outlier: 6.771A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 93 removed outlier: 8.381A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE A 5 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 167 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS A 139 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 93 removed outlier: 8.381A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE A 5 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 167 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS A 139 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA8, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.608A pdb=" N ALA A 374 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 378 " --> pdb=" O CYS A 316 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS A 316 " --> pdb=" O LEU A 378 " (cutoff:3.500A) 256 hydrogen bonds defined for protein. 747 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: 0.84 Time building geometry restraints manager: 0.80 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: 2228 1.34 - 1.46: 1131 1.46 - 1.57: 3485 1.57 - 1.69: 10 1.69 - 1.81: 80 Bond restraints: 6934 Sorted by residual: bond pdb=" O3B G2P B 502 " pdb=" PG G2P B 502 " ideal model delta sigma weight residual 1.716 1.603 0.113 2.00e-02 2.50e+03 3.22e+01 bond pdb=" O1A G2P B 502 " pdb=" PA G2P B 502 " ideal model delta sigma weight residual 1.507 1.608 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" O1B G2P B 502 " pdb=" PB G2P B 502 " ideal model delta sigma weight residual 1.510 1.608 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C5 GTP A 502 " pdb=" C6 GTP A 502 " ideal model delta sigma weight residual 1.390 1.479 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C4 G2P B 502 " pdb=" C5 G2P B 502 " ideal model delta sigma weight residual 1.384 1.463 -0.079 2.00e-02 2.50e+03 1.56e+01 ... (remaining 6929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 9235 2.48 - 4.96: 152 4.96 - 7.44: 18 7.44 - 9.92: 8 9.92 - 12.40: 4 Bond angle restraints: 9417 Sorted by residual: angle pdb=" C3A G2P B 502 " pdb=" PA G2P B 502 " pdb=" O5' G2P B 502 " ideal model delta sigma weight residual 99.14 111.54 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" PA G2P B 502 " pdb=" C3A G2P B 502 " pdb=" PB G2P B 502 " ideal model delta sigma weight residual 120.83 108.52 12.31 3.00e+00 1.11e-01 1.68e+01 angle pdb=" O1B GTP A 502 " pdb=" PB GTP A 502 " pdb=" O2B GTP A 502 " ideal model delta sigma weight residual 109.50 120.92 -11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" O1A GTP A 502 " pdb=" PA GTP A 502 " pdb=" O2A GTP A 502 " ideal model delta sigma weight residual 109.50 120.33 -10.83 3.00e+00 1.11e-01 1.30e+01 angle pdb=" C LEU A 217 " pdb=" N ASP A 218 " pdb=" CA ASP A 218 " ideal model delta sigma weight residual 122.82 127.24 -4.42 1.42e+00 4.96e-01 9.68e+00 ... (remaining 9412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.38: 4067 33.38 - 66.77: 40 66.77 - 100.15: 6 100.15 - 133.54: 1 133.54 - 166.92: 3 Dihedral angle restraints: 4117 sinusoidal: 1650 harmonic: 2467 Sorted by residual: dihedral pdb=" C4' GTP A 502 " pdb=" C5' GTP A 502 " pdb=" O5' GTP A 502 " pdb=" PA GTP A 502 " ideal model delta sinusoidal sigma weight residual 260.87 93.95 166.92 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C8 GTP A 502 " pdb=" C1' GTP A 502 " pdb=" N9 GTP A 502 " pdb=" O4' GTP A 502 " ideal model delta sinusoidal sigma weight residual 104.59 -62.13 166.73 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O2G GTP A 502 " pdb=" O3B GTP A 502 " pdb=" PG GTP A 502 " pdb=" PB GTP A 502 " ideal model delta sinusoidal sigma weight residual 177.30 -35.43 -147.27 1 2.00e+01 2.50e-03 4.42e+01 ... (remaining 4114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 600 0.032 - 0.064: 284 0.064 - 0.096: 82 0.096 - 0.128: 53 0.128 - 0.160: 8 Chirality restraints: 1027 Sorted by residual: chirality pdb=" CA ILE B 368 " pdb=" N ILE B 368 " pdb=" C ILE B 368 " pdb=" CB ILE B 368 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA VAL A 324 " pdb=" N VAL A 324 " pdb=" C VAL A 324 " pdb=" CB VAL A 324 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA ASP A 218 " pdb=" N ASP A 218 " pdb=" C ASP A 218 " pdb=" CB ASP A 218 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.34e-01 ... (remaining 1024 not shown) Planarity restraints: 1224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 69 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO B 70 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 70 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 70 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 221 " 0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO A 222 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 222 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 222 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 391 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C ARG B 391 " -0.028 2.00e-02 2.50e+03 pdb=" O ARG B 391 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS B 392 " 0.009 2.00e-02 2.50e+03 ... (remaining 1221 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 56 2.50 - 3.10: 5419 3.10 - 3.70: 10570 3.70 - 4.30: 15925 4.30 - 4.90: 25485 Nonbonded interactions: 57455 Sorted by model distance: nonbonded pdb="MG MG B 501 " pdb=" O2B G2P B 502 " model vdw 1.901 2.170 nonbonded pdb="MG MG A 501 " pdb=" O2G GTP A 502 " model vdw 1.946 2.170 nonbonded pdb="MG MG A 501 " pdb=" O1B GTP A 502 " model vdw 2.028 2.170 nonbonded pdb=" O1A G2P B 502 " pdb=" O1B G2P B 502 " model vdw 2.078 3.040 nonbonded pdb="MG MG B 501 " pdb=" O1G G2P B 502 " model vdw 2.127 2.170 ... (remaining 57450 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 10.990 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.280 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 : 0.007 0.113 6934 Z= 0.292 Angle : 0.847 12.404 9417 Z= 0.408 Chirality : 0.045 0.160 1027 Planarity : 0.005 0.045 1224 Dihedral : 12.401 166.923 2535 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.32 (0.25), residues: 848 helix: -3.40 (0.17), residues: 343 sheet: -3.87 (0.36), residues: 130 loop : -1.67 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 64 TYR 0.017 0.002 TYR B 50 PHE 0.016 0.002 PHE A 169 TRP 0.017 0.003 TRP A 388 HIS 0.011 0.002 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.29 ( 6934) covalent geometry : angle 0.84655 / 0.41 ( 9417) hydrogen bonds : bond 0.30612 / 20.93 ( 245) hydrogen bonds : angle 10.15279 / 7.06 ( 747) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 ILE cc_start: 0.6379 (pt) cc_final: 0.6126 (pt) REVERT: A 188 ILE cc_start: 0.6807 (pp) cc_final: 0.6470 (pt) REVERT: A 285 GLN cc_start: 0.7785 (pm20) cc_final: 0.6562 (mm110) REVERT: A 346 TRP cc_start: 0.6759 (p-90) cc_final: 0.5915 (m-10) REVERT: A 351 PHE cc_start: 0.6785 (m-80) cc_final: 0.6186 (m-80) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.0882 time to fit residues: 22.2780 Evaluate side-chains 120 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 HIS ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN A 356 ASN A 358 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.144250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.123433 restraints weight = 9693.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.127917 restraints weight = 5151.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.131000 restraints weight = 3327.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.133141 restraints weight = 2409.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.134573 restraints weight = 1882.260| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 6934 Z= 0.164 Angle : 0.684 8.161 9417 Z= 0.351 Chirality : 0.047 0.157 1027 Planarity : 0.005 0.043 1224 Dihedral : 11.967 171.117 946 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.78 % Allowed : 10.40 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.26), residues: 848 helix: -1.77 (0.24), residues: 364 sheet: -3.10 (0.41), residues: 123 loop : -1.71 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 320 TYR 0.010 0.001 TYR B 159 PHE 0.031 0.002 PHE A 255 TRP 0.027 0.002 TRP B 344 HIS 0.009 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 6934) covalent geometry : angle 0.68399 / 0.35 ( 9417) hydrogen bonds : bond 0.04533 / 3.13 ( 245) hydrogen bonds : angle 5.63542 / 3.93 ( 747) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 MET cc_start: 0.8336 (mmp) cc_final: 0.7896 (mmp) REVERT: B 200 TYR cc_start: 0.6990 (m-10) cc_final: 0.6664 (m-10) REVERT: B 247 ASN cc_start: 0.8277 (m-40) cc_final: 0.7727 (m-40) REVERT: A 90 GLU cc_start: 0.6929 (tt0) cc_final: 0.6527 (tp30) REVERT: A 188 ILE cc_start: 0.6030 (pp) cc_final: 0.5655 (pt) REVERT: A 192 HIS cc_start: 0.7801 (t-90) cc_final: 0.7463 (t-170) REVERT: A 285 GLN cc_start: 0.7671 (pm20) cc_final: 0.6598 (mm110) REVERT: A 351 PHE cc_start: 0.7297 (m-80) cc_final: 0.6878 (m-80) REVERT: A 380 ASN cc_start: 0.6658 (t0) cc_final: 0.6371 (t0) outliers start: 13 outliers final: 6 residues processed: 157 average time/residue: 0.0787 time to fit residues: 16.4646 Evaluate side-chains 121 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain A residue 80 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 72 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 62 optimal weight: 0.0870 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 11 GLN B 100 ASN B 131 GLN B 195 ASN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN A 358 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.143392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.123708 restraints weight = 9842.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.128121 restraints weight = 5191.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.131127 restraints weight = 3318.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.133196 restraints weight = 2374.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.134641 restraints weight = 1836.506| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6934 Z= 0.127 Angle : 0.636 13.387 9417 Z= 0.319 Chirality : 0.045 0.149 1027 Planarity : 0.005 0.042 1224 Dihedral : 11.517 173.434 946 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.92 % Allowed : 13.41 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.27), residues: 848 helix: -1.23 (0.26), residues: 358 sheet: -2.54 (0.42), residues: 130 loop : -1.35 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 320 TYR 0.011 0.001 TYR A 24 PHE 0.022 0.002 PHE B 167 TRP 0.034 0.002 TRP B 344 HIS 0.008 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 6934) covalent geometry : angle 0.63632 / 0.32 ( 9417) hydrogen bonds : bond 0.03809 / 2.58 ( 245) hydrogen bonds : angle 4.95184 / 3.46 ( 747) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 145 SER cc_start: 0.6817 (m) cc_final: 0.6324 (t) REVERT: B 158 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6728 (tt0) REVERT: B 159 TYR cc_start: 0.7188 (m-80) cc_final: 0.6836 (m-80) REVERT: B 247 ASN cc_start: 0.8101 (m-40) cc_final: 0.7471 (m-40) REVERT: A 188 ILE cc_start: 0.5840 (pp) cc_final: 0.5492 (pt) REVERT: A 192 HIS cc_start: 0.7749 (t-90) cc_final: 0.7435 (t-170) REVERT: A 256 GLN cc_start: 0.7217 (pt0) cc_final: 0.7005 (pt0) REVERT: A 285 GLN cc_start: 0.7628 (pm20) cc_final: 0.6552 (mm110) outliers start: 14 outliers final: 7 residues processed: 151 average time/residue: 0.0746 time to fit residues: 15.5010 Evaluate side-chains 129 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 75 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 105 HIS B 131 GLN B 134 GLN B 226 ASN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN A 380 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.127513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.108584 restraints weight = 10315.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.112461 restraints weight = 5454.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.115208 restraints weight = 3529.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.117070 restraints weight = 2558.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.118359 restraints weight = 2013.292| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6934 Z= 0.233 Angle : 0.719 9.500 9417 Z= 0.362 Chirality : 0.048 0.158 1027 Planarity : 0.005 0.049 1224 Dihedral : 11.178 171.266 946 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.28 % Allowed : 14.64 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.27), residues: 848 helix: -1.05 (0.26), residues: 363 sheet: -2.64 (0.43), residues: 128 loop : -1.40 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 320 TYR 0.011 0.002 TYR B 398 PHE 0.036 0.002 PHE A 255 TRP 0.032 0.003 TRP B 344 HIS 0.007 0.002 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 ( 6934) covalent geometry : angle 0.71943 / 0.36 ( 9417) hydrogen bonds : bond 0.04172 / 2.78 ( 245) hydrogen bonds : angle 5.02099 / 3.49 ( 747) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.6887 (pp) cc_final: 0.6616 (pt) REVERT: A 192 HIS cc_start: 0.7863 (t-90) cc_final: 0.7606 (t-170) REVERT: A 313 MET cc_start: 0.7218 (mtt) cc_final: 0.6729 (mtt) REVERT: A 339 ARG cc_start: 0.7195 (mmp-170) cc_final: 0.6886 (mmp80) outliers start: 24 outliers final: 15 residues processed: 141 average time/residue: 0.0722 time to fit residues: 13.8946 Evaluate side-chains 121 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 380 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 16 optimal weight: 0.3980 chunk 61 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 30 optimal weight: 0.0870 chunk 4 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 8 optimal weight: 0.2980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 GLN B 227 HIS ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.137049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.117820 restraints weight = 10027.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.121939 restraints weight = 5300.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.124645 restraints weight = 3394.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.126708 restraints weight = 2472.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.128160 restraints weight = 1914.491| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6934 Z= 0.117 Angle : 0.638 9.658 9417 Z= 0.313 Chirality : 0.044 0.155 1027 Planarity : 0.004 0.041 1224 Dihedral : 10.689 169.020 946 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.19 % Allowed : 16.01 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.27), residues: 848 helix: -0.72 (0.26), residues: 361 sheet: -2.05 (0.43), residues: 129 loop : -1.47 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 214 TYR 0.016 0.001 TYR A 24 PHE 0.035 0.002 PHE A 255 TRP 0.032 0.002 TRP B 344 HIS 0.007 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 6934) covalent geometry : angle 0.63789 / 0.31 ( 9417) hydrogen bonds : bond 0.03221 / 2.15 ( 245) hydrogen bonds : angle 4.64148 / 3.24 ( 747) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 SER cc_start: 0.6973 (m) cc_final: 0.6386 (t) REVERT: B 247 ASN cc_start: 0.7852 (m-40) cc_final: 0.7167 (m-40) REVERT: B 325 GLU cc_start: 0.7750 (mt-10) cc_final: 0.6885 (mt-10) REVERT: A 188 ILE cc_start: 0.6522 (OUTLIER) cc_final: 0.6260 (pt) REVERT: A 252 LEU cc_start: 0.8314 (tt) cc_final: 0.8091 (mt) REVERT: A 313 MET cc_start: 0.6923 (mtt) cc_final: 0.6707 (mtt) REVERT: A 339 ARG cc_start: 0.7039 (mmp-170) cc_final: 0.6767 (mmp80) REVERT: A 352 LYS cc_start: 0.8063 (mmmt) cc_final: 0.7024 (mmpt) outliers start: 16 outliers final: 11 residues processed: 147 average time/residue: 0.0670 time to fit residues: 13.6410 Evaluate side-chains 133 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 424 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 50 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 63 optimal weight: 0.0010 chunk 79 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 overall best weight: 2.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 GLN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.130159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.111004 restraints weight = 10167.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.114961 restraints weight = 5336.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.117770 restraints weight = 3443.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.119693 restraints weight = 2491.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.121099 restraints weight = 1956.756| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6934 Z= 0.174 Angle : 0.681 10.226 9417 Z= 0.335 Chirality : 0.046 0.184 1027 Planarity : 0.005 0.044 1224 Dihedral : 10.711 168.148 946 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.56 % Allowed : 15.73 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.28), residues: 848 helix: -0.56 (0.27), residues: 360 sheet: -1.83 (0.44), residues: 129 loop : -1.44 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 320 TYR 0.017 0.002 TYR A 103 PHE 0.017 0.002 PHE A 351 TRP 0.032 0.002 TRP B 344 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 ( 6934) covalent geometry : angle 0.68117 / 0.34 ( 9417) hydrogen bonds : bond 0.03573 / 2.40 ( 245) hydrogen bonds : angle 4.74106 / 3.30 ( 747) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: B 139 LEU cc_start: 0.8384 (tp) cc_final: 0.8184 (tp) REVERT: A 188 ILE cc_start: 0.6760 (OUTLIER) cc_final: 0.6521 (pt) outliers start: 26 outliers final: 18 residues processed: 143 average time/residue: 0.0608 time to fit residues: 12.4119 Evaluate side-chains 134 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 424 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 22 optimal weight: 0.0670 chunk 82 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.136404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.117135 restraints weight = 9923.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.121308 restraints weight = 5218.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.124143 restraints weight = 3339.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.126157 restraints weight = 2408.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.127584 restraints weight = 1873.612| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6934 Z= 0.117 Angle : 0.668 12.026 9417 Z= 0.323 Chirality : 0.044 0.147 1027 Planarity : 0.004 0.041 1224 Dihedral : 10.460 165.854 946 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.01 % Allowed : 17.51 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.28), residues: 848 helix: -0.51 (0.27), residues: 364 sheet: -1.58 (0.44), residues: 129 loop : -1.46 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 320 TYR 0.013 0.001 TYR A 24 PHE 0.014 0.002 PHE A 244 TRP 0.050 0.003 TRP B 344 HIS 0.006 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 6934) covalent geometry : angle 0.66766 / 0.32 ( 9417) hydrogen bonds : bond 0.03150 / 2.07 ( 245) hydrogen bonds : angle 4.59049 / 3.23 ( 747) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: B 131 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7328 (mt0) REVERT: B 139 LEU cc_start: 0.8290 (tp) cc_final: 0.8088 (tp) REVERT: B 247 ASN cc_start: 0.7730 (m-40) cc_final: 0.6924 (m-40) REVERT: A 182 VAL cc_start: 0.8097 (m) cc_final: 0.7676 (p) REVERT: A 188 ILE cc_start: 0.6637 (OUTLIER) cc_final: 0.6432 (pt) REVERT: A 302 MET cc_start: 0.7594 (mtp) cc_final: 0.7357 (mtp) REVERT: A 313 MET cc_start: 0.7355 (mtt) cc_final: 0.7052 (mtt) REVERT: A 352 LYS cc_start: 0.7759 (mmmt) cc_final: 0.7094 (mmtt) outliers start: 22 outliers final: 15 residues processed: 141 average time/residue: 0.0599 time to fit residues: 12.0345 Evaluate side-chains 136 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 424 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 43 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** 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 = 0.3876 r_free = 0.3876 target = 0.125653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.104841 restraints weight = 10115.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.109202 restraints weight = 4919.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.112286 restraints weight = 3018.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.114411 restraints weight = 2132.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.115963 restraints weight = 1640.013| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6934 Z= 0.155 Angle : 0.680 10.903 9417 Z= 0.332 Chirality : 0.045 0.146 1027 Planarity : 0.004 0.041 1224 Dihedral : 10.457 163.734 946 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.01 % Allowed : 18.19 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.28), residues: 848 helix: -0.44 (0.27), residues: 364 sheet: -1.45 (0.44), residues: 129 loop : -1.50 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 320 TYR 0.020 0.001 TYR B 159 PHE 0.017 0.002 PHE A 351 TRP 0.030 0.002 TRP B 344 HIS 0.007 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 ( 6934) covalent geometry : angle 0.67995 / 0.33 ( 9417) hydrogen bonds : bond 0.03362 / 2.24 ( 245) hydrogen bonds : angle 4.66170 / 3.27 ( 747) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 247 ASN cc_start: 0.7804 (m-40) cc_final: 0.6822 (m-40) REVERT: B 330 MET cc_start: 0.8329 (mtp) cc_final: 0.7960 (mtp) REVERT: A 35 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7886 (mm-40) REVERT: A 182 VAL cc_start: 0.8496 (m) cc_final: 0.8049 (p) REVERT: A 188 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6888 (pt) REVERT: A 313 MET cc_start: 0.7411 (mtt) cc_final: 0.7056 (mtt) REVERT: A 352 LYS cc_start: 0.7897 (mmmt) cc_final: 0.6851 (mmtt) REVERT: A 370 LYS cc_start: 0.8793 (tttp) cc_final: 0.8563 (tptt) REVERT: A 376 CYS cc_start: 0.8215 (t) cc_final: 0.7908 (t) REVERT: A 377 MET cc_start: 0.8425 (tmm) cc_final: 0.7643 (tmm) outliers start: 22 outliers final: 16 residues processed: 136 average time/residue: 0.0760 time to fit residues: 14.2123 Evaluate side-chains 134 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 424 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 83 optimal weight: 6.9990 chunk 52 optimal weight: 0.0570 chunk 65 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 0.2980 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.136007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.116616 restraints weight = 10122.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.120794 restraints weight = 5349.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.123644 restraints weight = 3439.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.125645 restraints weight = 2487.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.127074 restraints weight = 1945.461| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6934 Z= 0.120 Angle : 0.688 11.096 9417 Z= 0.332 Chirality : 0.044 0.147 1027 Planarity : 0.004 0.041 1224 Dihedral : 10.290 160.960 946 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.33 % Allowed : 19.02 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.28), residues: 848 helix: -0.39 (0.27), residues: 361 sheet: -1.43 (0.43), residues: 129 loop : -1.53 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 320 TYR 0.013 0.001 TYR B 159 PHE 0.013 0.001 PHE A 169 TRP 0.035 0.003 TRP B 344 HIS 0.007 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 6934) covalent geometry : angle 0.68773 / 0.33 ( 9417) hydrogen bonds : bond 0.03046 / 2.04 ( 245) hydrogen bonds : angle 4.54848 / 3.19 ( 747) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 MET cc_start: 0.7810 (mmm) cc_final: 0.7365 (mmp) REVERT: B 247 ASN cc_start: 0.7574 (m-40) cc_final: 0.6745 (m-40) REVERT: B 330 MET cc_start: 0.8017 (mtp) cc_final: 0.7662 (mtp) REVERT: A 182 VAL cc_start: 0.8237 (m) cc_final: 0.7851 (p) REVERT: A 188 ILE cc_start: 0.6732 (OUTLIER) cc_final: 0.6505 (pt) REVERT: A 302 MET cc_start: 0.8011 (mtm) cc_final: 0.7534 (mtp) REVERT: A 313 MET cc_start: 0.7419 (mtt) cc_final: 0.7180 (mtt) REVERT: A 352 LYS cc_start: 0.7824 (mmmt) cc_final: 0.6987 (mmpt) REVERT: A 376 CYS cc_start: 0.7934 (t) cc_final: 0.7669 (t) REVERT: A 377 MET cc_start: 0.8396 (tmm) cc_final: 0.7743 (tmm) outliers start: 17 outliers final: 15 residues processed: 133 average time/residue: 0.0667 time to fit residues: 12.5732 Evaluate side-chains 131 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 424 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 20 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.129215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.110066 restraints weight = 10261.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.114011 restraints weight = 5426.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.116702 restraints weight = 3516.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.118600 restraints weight = 2572.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.119926 restraints weight = 2031.698| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6934 Z= 0.172 Angle : 0.713 11.919 9417 Z= 0.349 Chirality : 0.045 0.145 1027 Planarity : 0.004 0.041 1224 Dihedral : 10.384 158.887 946 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.60 % Allowed : 19.97 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.28), residues: 848 helix: -0.52 (0.27), residues: 369 sheet: -1.44 (0.44), residues: 129 loop : -1.47 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 320 TYR 0.016 0.002 TYR B 159 PHE 0.026 0.002 PHE B 20 TRP 0.039 0.003 TRP B 344 HIS 0.007 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 6934) covalent geometry : angle 0.71340 / 0.35 ( 9417) hydrogen bonds : bond 0.03537 / 2.40 ( 245) hydrogen bonds : angle 4.70918 / 3.30 ( 747) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 170 MET cc_start: 0.7996 (mmm) cc_final: 0.7546 (mmp) REVERT: B 297 LYS cc_start: 0.8846 (tmtt) cc_final: 0.8597 (tmtt) REVERT: B 330 MET cc_start: 0.8192 (mtp) cc_final: 0.7783 (mtp) REVERT: B 350 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8488 (tttp) REVERT: A 182 VAL cc_start: 0.8388 (m) cc_final: 0.7997 (p) REVERT: A 313 MET cc_start: 0.7522 (mtt) cc_final: 0.7137 (mtt) REVERT: A 370 LYS cc_start: 0.8368 (tptt) cc_final: 0.7945 (tttp) REVERT: A 376 CYS cc_start: 0.7995 (t) cc_final: 0.7786 (t) outliers start: 19 outliers final: 15 residues processed: 131 average time/residue: 0.0732 time to fit residues: 13.3335 Evaluate side-chains 130 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 424 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 79 optimal weight: 0.0770 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 81 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.131411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.111848 restraints weight = 10168.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.115876 restraints weight = 5393.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.118674 restraints weight = 3500.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.120658 restraints weight = 2559.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.121944 restraints weight = 2013.518| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 6934 Z= 0.195 Angle : 1.093 59.150 9417 Z= 0.626 Chirality : 0.045 0.178 1027 Planarity : 0.004 0.044 1224 Dihedral : 10.400 158.871 946 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.33 % Allowed : 19.84 % Favored : 77.84 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.28), residues: 848 helix: -0.51 (0.27), residues: 369 sheet: -1.38 (0.44), residues: 129 loop : -1.48 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 320 TYR 0.016 0.001 TYR B 159 PHE 0.018 0.002 PHE B 20 TRP 0.034 0.003 TRP B 344 HIS 0.014 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 ( 6934) covalent geometry : angle 1.09340 / 0.63 ( 9417) hydrogen bonds : bond 0.03583 / 2.39 ( 245) hydrogen bonds : angle 4.70426 / 3.30 ( 747) =============================================================================== Job complete usr+sys time: 1298.02 seconds wall clock time: 23 minutes 11.94 seconds (1391.94 seconds total)