Starting phenix.real_space_refine on Tue Jan 13 23:51:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tr3_26080/01_2026/7tr3_26080.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tr3_26080/01_2026/7tr3_26080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tr3_26080/01_2026/7tr3_26080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tr3_26080/01_2026/7tr3_26080.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tr3_26080/01_2026/7tr3_26080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tr3_26080/01_2026/7tr3_26080.map" } resolution = 3.9 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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 8 5.49 5 Mg 1 5.21 5 S 65 5.16 5 C 6361 2.51 5 N 1790 2.21 5 O 1997 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10222 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3381 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 20, 'TRANS': 409} Chain: "K" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3257 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 14, 'TRANS': 403} 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} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'SR6': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.49, per 1000 atoms: 0.24 Number of scatterers: 10222 At special positions: 0 Unit cell: (110.466, 114.798, 82.308, 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 65 16.00 P 8 15.00 Mg 1 11.99 O 1997 8.00 N 1790 7.00 C 6361 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: 0.97 Conformation dependent library (CDL) restraints added in 500.4 milliseconds 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 8 sheets defined 44.5% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.504A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A 52 " --> pdb=" O PHE A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 52' Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.318A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.890A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 162 removed outlier: 4.148A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.757A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.712A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 3.917A pdb=" N ASN A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.685A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.897A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 398 removed outlier: 3.782A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.102A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 4.281A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 removed outlier: 3.790A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 removed outlier: 3.525A pdb=" N GLU B 45 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG B 46 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE B 47 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASN B 48 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 58 removed outlier: 3.670A pdb=" N ASN B 57 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS B 58 " --> pdb=" O THR B 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 54 through 58' Processing helix chain 'B' and resid 70 through 78 removed outlier: 3.864A pdb=" N SER B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 removed outlier: 3.679A pdb=" N GLY B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 125 removed outlier: 3.917A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 removed outlier: 3.948A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 190 removed outlier: 4.305A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.565A pdb=" N ASN B 226 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N HIS B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA B 231 " --> pdb=" O HIS B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 4.140A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 237 through 242' Processing helix chain 'B' and resid 249 through 257 removed outlier: 3.544A pdb=" N LEU B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.767A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP B 295 " --> pdb=" O GLN B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'B' and resid 322 through 337 removed outlier: 4.248A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU B 328 " --> pdb=" O LYS B 324 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET B 330 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN B 337 " --> pdb=" O VAL B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 382 removed outlier: 3.946A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 391 removed outlier: 3.986A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 removed outlier: 3.518A pdb=" N GLY B 400 " --> pdb=" O HIS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 425 removed outlier: 3.893A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 54 removed outlier: 3.820A pdb=" N ARG K 42 " --> pdb=" O ALA K 38 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE K 46 " --> pdb=" O ARG K 42 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN K 48 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP K 49 " --> pdb=" O LYS K 45 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP K 50 " --> pdb=" O ILE K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 128 removed outlier: 3.661A pdb=" N LYS K 126 " --> pdb=" O ASN K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 166 removed outlier: 4.093A pdb=" N ASN K 164 " --> pdb=" O GLN K 160 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR K 166 " --> pdb=" O TYR K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 174 removed outlier: 3.542A pdb=" N LEU K 174 " --> pdb=" O LEU K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 196 Processing helix chain 'K' and resid 204 through 219 Processing helix chain 'K' and resid 235 through 238 Processing helix chain 'K' and resid 274 through 287 Processing helix chain 'K' and resid 347 through 372 removed outlier: 3.796A pdb=" N ILE K 356 " --> pdb=" O GLU K 352 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP K 372 " --> pdb=" O ASN K 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 374 through 378 removed outlier: 4.148A pdb=" N ASN K 377 " --> pdb=" O ARG K 374 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 390 Processing helix chain 'K' and resid 390 through 396 removed outlier: 3.910A pdb=" N GLY K 395 " --> pdb=" O LYS K 391 " (cutoff:3.500A) Processing helix chain 'K' and resid 412 through 425 removed outlier: 3.675A pdb=" N THR K 416 " --> pdb=" O HIS K 412 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 7.256A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 356 removed outlier: 3.567A pdb=" N LYS A 352 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A 356 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 90 through 91 removed outlier: 7.902A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B 136 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.720A pdb=" N ASP B 31 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER B 35 " --> pdb=" O ASP B 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 269 through 270 removed outlier: 4.279A pdb=" N PHE B 367 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 30 through 32 Processing sheet with id=AA7, first strand: chain 'K' and resid 106 through 107 removed outlier: 3.604A pdb=" N ASN K 107 " --> pdb=" O ILE K 115 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE K 115 " --> pdb=" O ASN K 107 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 223 through 233 removed outlier: 6.532A pdb=" N THR K 180 " --> pdb=" O VAL K 401 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 1017 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: 1.48 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1740 1.30 - 1.43: 2643 1.43 - 1.56: 5913 1.56 - 1.69: 27 1.69 - 1.82: 102 Bond restraints: 10425 Sorted by residual: bond pdb=" C2 SR6 B 502 " pdb=" C3 SR6 B 502 " ideal model delta sigma weight residual 1.526 1.320 0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C13 SR6 B 502 " pdb=" N3 SR6 B 502 " ideal model delta sigma weight residual 1.366 1.539 -0.173 2.00e-02 2.50e+03 7.52e+01 bond pdb=" C5 SR6 B 502 " pdb=" N1 SR6 B 502 " ideal model delta sigma weight residual 1.346 1.506 -0.160 2.00e-02 2.50e+03 6.41e+01 bond pdb=" O3A ANP K 501 " pdb=" PB ANP K 501 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C1 SR6 B 502 " pdb=" N1 SR6 B 502 " ideal model delta sigma weight residual 1.464 1.321 0.143 2.00e-02 2.50e+03 5.10e+01 ... (remaining 10420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 13985 3.35 - 6.70: 146 6.70 - 10.05: 11 10.05 - 13.40: 2 13.40 - 16.75: 1 Bond angle restraints: 14145 Sorted by residual: angle pdb=" PB ANP K 501 " pdb=" N3B ANP K 501 " pdb=" PG ANP K 501 " ideal model delta sigma weight residual 126.95 110.20 16.75 3.00e+00 1.11e-01 3.12e+01 angle pdb=" O1B ANP K 501 " pdb=" PB ANP K 501 " pdb=" O2B ANP K 501 " ideal model delta sigma weight residual 120.08 108.50 11.58 3.00e+00 1.11e-01 1.49e+01 angle pdb=" CA PRO A 173 " pdb=" N PRO A 173 " pdb=" CD PRO A 173 " ideal model delta sigma weight residual 112.00 106.62 5.38 1.40e+00 5.10e-01 1.47e+01 angle pdb=" CA SER K 60 " pdb=" C SER K 60 " pdb=" O SER K 60 " ideal model delta sigma weight residual 122.01 118.25 3.76 1.05e+00 9.07e-01 1.28e+01 angle pdb=" CB MET K 113 " pdb=" CG MET K 113 " pdb=" SD MET K 113 " ideal model delta sigma weight residual 112.70 123.21 -10.51 3.00e+00 1.11e-01 1.23e+01 ... (remaining 14140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.56: 5949 28.56 - 57.12: 346 57.12 - 85.68: 37 85.68 - 114.24: 5 114.24 - 142.80: 2 Dihedral angle restraints: 6339 sinusoidal: 2615 harmonic: 3724 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -147.93 -142.80 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -21.84 126.43 1 2.00e+01 2.50e-03 3.83e+01 dihedral pdb=" O3B GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PB GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual -68.92 -178.45 109.53 1 2.00e+01 2.50e-03 3.20e+01 ... (remaining 6336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1278 0.055 - 0.111: 238 0.111 - 0.166: 48 0.166 - 0.222: 1 0.222 - 0.277: 4 Chirality restraints: 1569 Sorted by residual: chirality pdb=" C12 SR6 B 502 " pdb=" C11 SR6 B 502 " pdb=" C16 SR6 B 502 " pdb=" N3 SR6 B 502 " both_signs ideal model delta sigma weight residual False 2.32 2.59 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C3' ANP K 501 " pdb=" C2' ANP K 501 " pdb=" C4' ANP K 501 " pdb=" O3' ANP K 501 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C14 SR6 B 502 " pdb=" C13 SR6 B 502 " pdb=" C20 SR6 B 502 " pdb=" N4 SR6 B 502 " both_signs ideal model delta sigma weight residual False 2.04 2.30 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 1566 not shown) Planarity restraints: 1848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 347 " 0.052 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO A 348 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 348 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 348 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 172 " 0.042 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO A 173 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 376 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" CD GLU B 376 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU B 376 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 376 " 0.014 2.00e-02 2.50e+03 ... (remaining 1845 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 63 2.52 - 3.11: 7855 3.11 - 3.71: 14931 3.71 - 4.30: 19781 4.30 - 4.90: 33620 Nonbonded interactions: 76250 Sorted by model distance: nonbonded pdb=" O3B GTP A 501 " pdb="MG MG A 502 " model vdw 1.919 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.929 2.170 nonbonded pdb=" OE2 GLU A 71 " pdb="MG MG A 502 " model vdw 1.974 2.170 nonbonded pdb=" O1B ANP K 501 " pdb=" O3G ANP K 501 " model vdw 2.059 3.040 nonbonded pdb=" OG1 THR A 292 " pdb=" OH TYR A 319 " model vdw 2.095 3.040 ... (remaining 76245 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: 4.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.760 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 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 0.206 10425 Z= 0.347 Angle : 0.833 16.747 14145 Z= 0.425 Chirality : 0.047 0.277 1569 Planarity : 0.005 0.080 1848 Dihedral : 17.704 142.801 3943 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.50 % Favored : 91.26 % Rotamer: Outliers : 0.36 % Allowed : 18.18 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.83 (0.23), residues: 1282 helix: 0.11 (0.24), residues: 474 sheet: -1.87 (0.37), residues: 178 loop : -2.08 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 241 TYR 0.024 0.001 TYR A 172 PHE 0.016 0.002 PHE K 146 TRP 0.009 0.002 TRP B 344 HIS 0.004 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00691 (10425) covalent geometry : angle 0.83314 (14145) hydrogen bonds : bond 0.15678 ( 351) hydrogen bonds : angle 6.64692 ( 1017) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 169 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 VAL cc_start: 0.7442 (t) cc_final: 0.7169 (t) REVERT: A 84 ARG cc_start: 0.7889 (ttm110) cc_final: 0.7650 (ttm110) REVERT: A 377 MET cc_start: 0.7577 (mmm) cc_final: 0.7001 (ttm) REVERT: B 170 MET cc_start: 0.7409 (tmm) cc_final: 0.6498 (tmm) REVERT: B 258 VAL cc_start: 0.7679 (t) cc_final: 0.7424 (t) REVERT: K 184 TYR cc_start: 0.6615 (OUTLIER) cc_final: 0.5546 (t80) outliers start: 4 outliers final: 1 residues processed: 171 average time/residue: 0.0854 time to fit residues: 21.8919 Evaluate side-chains 158 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 184 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.1980 chunk 55 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 HIS B 256 ASN B 332 ASN K 164 ASN K 412 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.114413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.094338 restraints weight = 17904.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.097644 restraints weight = 9898.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.099945 restraints weight = 6324.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.101559 restraints weight = 4487.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.102652 restraints weight = 3472.084| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10425 Z= 0.156 Angle : 0.610 7.751 14145 Z= 0.306 Chirality : 0.045 0.238 1569 Planarity : 0.005 0.050 1848 Dihedral : 10.493 142.963 1538 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.33 % Allowed : 17.64 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.55 (0.23), residues: 1282 helix: 0.44 (0.24), residues: 464 sheet: -1.80 (0.38), residues: 173 loop : -1.94 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 241 TYR 0.019 0.002 TYR A 172 PHE 0.014 0.002 PHE B 85 TRP 0.011 0.002 TRP A 346 HIS 0.006 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00369 (10425) covalent geometry : angle 0.61009 (14145) hydrogen bonds : bond 0.04090 ( 351) hydrogen bonds : angle 5.20954 ( 1017) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 377 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7290 (ttm) REVERT: B 25 SER cc_start: 0.7803 (OUTLIER) cc_final: 0.7513 (t) REVERT: B 143 THR cc_start: 0.7972 (m) cc_final: 0.7633 (m) REVERT: B 170 MET cc_start: 0.7366 (tmm) cc_final: 0.6382 (tmm) REVERT: K 127 MET cc_start: 0.6152 (mpp) cc_final: 0.5826 (mpp) REVERT: K 184 TYR cc_start: 0.6681 (OUTLIER) cc_final: 0.5490 (t80) REVERT: K 433 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5651 (pp) outliers start: 37 outliers final: 22 residues processed: 190 average time/residue: 0.0858 time to fit residues: 24.2178 Evaluate side-chains 180 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 144 HIS Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 184 TYR Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 406 VAL Chi-restraints excluded: chain K residue 422 TYR Chi-restraints excluded: chain K residue 433 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 77 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 114 optimal weight: 0.0770 chunk 123 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 84 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN B 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.117934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097881 restraints weight = 17804.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.101272 restraints weight = 9792.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.103632 restraints weight = 6208.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.105294 restraints weight = 4393.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.106468 restraints weight = 3349.543| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10425 Z= 0.130 Angle : 0.574 7.534 14145 Z= 0.288 Chirality : 0.044 0.225 1569 Planarity : 0.004 0.042 1848 Dihedral : 9.793 140.624 1537 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.78 % Allowed : 19.26 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.44 (0.23), residues: 1282 helix: 0.59 (0.24), residues: 474 sheet: -1.68 (0.38), residues: 176 loop : -1.99 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 241 TYR 0.018 0.001 TYR A 172 PHE 0.019 0.001 PHE B 212 TRP 0.010 0.002 TRP A 346 HIS 0.005 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00306 (10425) covalent geometry : angle 0.57413 (14145) hydrogen bonds : bond 0.03718 ( 351) hydrogen bonds : angle 4.93146 ( 1017) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.5997 (pmm) cc_final: 0.5769 (pmm) REVERT: A 79 ARG cc_start: 0.7668 (ttp-110) cc_final: 0.7438 (ttm110) REVERT: A 122 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6546 (tt) REVERT: B 2 ARG cc_start: 0.6940 (mtt180) cc_final: 0.6583 (mtt180) REVERT: B 143 THR cc_start: 0.7947 (m) cc_final: 0.7652 (m) REVERT: B 170 MET cc_start: 0.7328 (tmm) cc_final: 0.6313 (tmm) REVERT: K 127 MET cc_start: 0.6048 (mpp) cc_final: 0.5695 (mpp) REVERT: K 184 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.5375 (t80) REVERT: K 223 LYS cc_start: 0.7946 (mttp) cc_final: 0.7500 (mttm) REVERT: K 433 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5635 (pp) outliers start: 42 outliers final: 26 residues processed: 189 average time/residue: 0.0847 time to fit residues: 23.9783 Evaluate side-chains 188 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 144 HIS Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 184 TYR Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 274 SER Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 406 VAL Chi-restraints excluded: chain K residue 422 TYR Chi-restraints excluded: chain K residue 433 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 18 optimal weight: 0.0870 chunk 110 optimal weight: 0.0670 chunk 0 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 127 optimal weight: 0.0970 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.2494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.121541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.101626 restraints weight = 17025.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.105145 restraints weight = 9045.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.107615 restraints weight = 5615.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.109324 restraints weight = 3886.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.110378 restraints weight = 2929.132| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10425 Z= 0.100 Angle : 0.534 7.955 14145 Z= 0.267 Chirality : 0.042 0.241 1569 Planarity : 0.004 0.063 1848 Dihedral : 9.239 136.123 1537 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.15 % Allowed : 20.07 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.03 (0.24), residues: 1282 helix: 0.97 (0.25), residues: 474 sheet: -1.21 (0.40), residues: 157 loop : -1.87 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 162 TYR 0.021 0.001 TYR B 36 PHE 0.014 0.001 PHE B 212 TRP 0.014 0.002 TRP B 101 HIS 0.002 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00224 (10425) covalent geometry : angle 0.53404 (14145) hydrogen bonds : bond 0.03103 ( 351) hydrogen bonds : angle 4.60398 ( 1017) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7710 (ttm110) cc_final: 0.7368 (mtt-85) REVERT: A 122 ILE cc_start: 0.6599 (OUTLIER) cc_final: 0.6342 (tt) REVERT: A 254 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7536 (tm-30) REVERT: A 378 LEU cc_start: 0.8072 (mt) cc_final: 0.7832 (mt) REVERT: B 2 ARG cc_start: 0.6828 (mtt180) cc_final: 0.6474 (mtt180) REVERT: B 143 THR cc_start: 0.7800 (m) cc_final: 0.7413 (m) REVERT: B 170 MET cc_start: 0.7169 (tmm) cc_final: 0.6208 (tmm) REVERT: B 300 MET cc_start: 0.8630 (mtp) cc_final: 0.8414 (mtt) REVERT: K 184 TYR cc_start: 0.6210 (OUTLIER) cc_final: 0.5158 (t80) REVERT: K 223 LYS cc_start: 0.7994 (mttp) cc_final: 0.7583 (mtpp) REVERT: K 414 ASP cc_start: 0.6351 (p0) cc_final: 0.6139 (p0) REVERT: K 415 GLU cc_start: 0.6705 (mm-30) cc_final: 0.6455 (mm-30) outliers start: 35 outliers final: 21 residues processed: 195 average time/residue: 0.0872 time to fit residues: 25.4119 Evaluate side-chains 178 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 144 HIS Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 184 TYR Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 406 VAL Chi-restraints excluded: chain K residue 422 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 65 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 103 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 68 optimal weight: 0.1980 chunk 125 optimal weight: 3.9990 chunk 105 optimal weight: 0.0270 chunk 15 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS K 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.117519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.097068 restraints weight = 17859.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.100510 restraints weight = 9655.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.102898 restraints weight = 6099.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.104536 restraints weight = 4302.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.105767 restraints weight = 3300.245| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10425 Z= 0.116 Angle : 0.542 7.630 14145 Z= 0.271 Chirality : 0.043 0.248 1569 Planarity : 0.004 0.064 1848 Dihedral : 9.211 135.328 1537 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.96 % Allowed : 20.70 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.99 (0.24), residues: 1282 helix: 0.92 (0.25), residues: 481 sheet: -1.19 (0.40), residues: 161 loop : -1.80 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 241 TYR 0.009 0.001 TYR A 172 PHE 0.025 0.001 PHE B 81 TRP 0.015 0.002 TRP B 101 HIS 0.004 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00268 (10425) covalent geometry : angle 0.54163 (14145) hydrogen bonds : bond 0.03281 ( 351) hydrogen bonds : angle 4.60225 ( 1017) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6251 (OUTLIER) cc_final: 0.6039 (mtp) REVERT: A 82 THR cc_start: 0.7545 (p) cc_final: 0.7335 (t) REVERT: A 84 ARG cc_start: 0.7729 (ttm110) cc_final: 0.7467 (mtt-85) REVERT: A 98 ASP cc_start: 0.8125 (p0) cc_final: 0.7654 (p0) REVERT: A 122 ILE cc_start: 0.6732 (OUTLIER) cc_final: 0.6478 (tt) REVERT: A 378 LEU cc_start: 0.8118 (mt) cc_final: 0.7899 (mt) REVERT: B 2 ARG cc_start: 0.6712 (mtt180) cc_final: 0.6155 (mtt180) REVERT: B 143 THR cc_start: 0.7798 (m) cc_final: 0.7418 (m) REVERT: B 170 MET cc_start: 0.7175 (tmm) cc_final: 0.6219 (tmm) REVERT: K 184 TYR cc_start: 0.6268 (OUTLIER) cc_final: 0.5162 (t80) outliers start: 44 outliers final: 31 residues processed: 194 average time/residue: 0.0880 time to fit residues: 25.4838 Evaluate side-chains 192 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 144 HIS Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 184 TYR Chi-restraints excluded: chain K residue 274 SER Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 406 VAL Chi-restraints excluded: chain K residue 422 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 0.0030 chunk 88 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN K 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.114384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.094993 restraints weight = 18249.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.098196 restraints weight = 10090.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.100454 restraints weight = 6443.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.102066 restraints weight = 4559.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.103200 restraints weight = 3501.598| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10425 Z= 0.229 Angle : 0.670 7.819 14145 Z= 0.337 Chirality : 0.048 0.242 1569 Planarity : 0.005 0.066 1848 Dihedral : 9.626 134.916 1537 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 4.50 % Allowed : 21.15 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.46 (0.23), residues: 1282 helix: 0.44 (0.24), residues: 473 sheet: -1.29 (0.39), residues: 176 loop : -2.01 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 79 TYR 0.019 0.002 TYR A 172 PHE 0.023 0.002 PHE B 85 TRP 0.011 0.003 TRP B 397 HIS 0.010 0.002 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00541 (10425) covalent geometry : angle 0.67026 (14145) hydrogen bonds : bond 0.04323 ( 351) hydrogen bonds : angle 5.00029 ( 1017) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7865 (ptp90) cc_final: 0.7564 (ptp-170) REVERT: A 82 THR cc_start: 0.7477 (p) cc_final: 0.7234 (t) REVERT: A 84 ARG cc_start: 0.7877 (ttm110) cc_final: 0.7522 (mtt-85) REVERT: A 344 VAL cc_start: 0.7029 (OUTLIER) cc_final: 0.6754 (m) REVERT: A 378 LEU cc_start: 0.8168 (mt) cc_final: 0.7925 (mt) REVERT: B 258 VAL cc_start: 0.7688 (t) cc_final: 0.7407 (t) REVERT: B 294 PHE cc_start: 0.7236 (t80) cc_final: 0.7002 (t80) REVERT: K 113 MET cc_start: 0.7080 (ppp) cc_final: 0.6683 (ppp) REVERT: K 184 TYR cc_start: 0.6452 (OUTLIER) cc_final: 0.5127 (t80) REVERT: K 433 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.5761 (pp) outliers start: 50 outliers final: 38 residues processed: 197 average time/residue: 0.0812 time to fit residues: 24.4044 Evaluate side-chains 201 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 144 HIS Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 184 TYR Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 263 SER Chi-restraints excluded: chain K residue 274 SER Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 406 VAL Chi-restraints excluded: chain K residue 433 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 69 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 96 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 105 optimal weight: 0.3980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.115669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.096168 restraints weight = 17894.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.099508 restraints weight = 9735.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.101756 restraints weight = 6141.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.103387 restraints weight = 4325.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.104610 restraints weight = 3292.842| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10425 Z= 0.136 Angle : 0.599 11.120 14145 Z= 0.298 Chirality : 0.044 0.244 1569 Planarity : 0.005 0.071 1848 Dihedral : 9.376 134.746 1537 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.60 % Allowed : 22.50 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.28 (0.23), residues: 1282 helix: 0.65 (0.24), residues: 478 sheet: -1.33 (0.39), residues: 170 loop : -1.93 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 241 TYR 0.014 0.001 TYR A 172 PHE 0.026 0.001 PHE B 81 TRP 0.013 0.002 TRP B 101 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00320 (10425) covalent geometry : angle 0.59855 (14145) hydrogen bonds : bond 0.03596 ( 351) hydrogen bonds : angle 4.83766 ( 1017) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 THR cc_start: 0.7454 (p) cc_final: 0.7215 (t) REVERT: A 344 VAL cc_start: 0.7009 (OUTLIER) cc_final: 0.6727 (m) REVERT: A 378 LEU cc_start: 0.8112 (mt) cc_final: 0.7895 (mt) REVERT: B 2 ARG cc_start: 0.6638 (mtt180) cc_final: 0.6390 (mtt180) REVERT: B 170 MET cc_start: 0.7363 (tmm) cc_final: 0.6452 (tmm) REVERT: B 258 VAL cc_start: 0.7632 (t) cc_final: 0.7385 (t) REVERT: B 294 PHE cc_start: 0.7234 (t80) cc_final: 0.6943 (t80) REVERT: B 300 MET cc_start: 0.8708 (mtp) cc_final: 0.8425 (mtt) REVERT: K 113 MET cc_start: 0.7069 (ppp) cc_final: 0.6723 (ppp) REVERT: K 146 PHE cc_start: 0.6511 (m-80) cc_final: 0.5936 (m-10) REVERT: K 184 TYR cc_start: 0.6044 (OUTLIER) cc_final: 0.4788 (t80) outliers start: 40 outliers final: 33 residues processed: 192 average time/residue: 0.0790 time to fit residues: 23.2455 Evaluate side-chains 195 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 144 HIS Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 184 TYR Chi-restraints excluded: chain K residue 274 SER Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 406 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 83 optimal weight: 0.1980 chunk 69 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS ** B 52 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 = 0.3769 r_free = 0.3769 target = 0.115058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.095678 restraints weight = 17898.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.098940 restraints weight = 9830.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.101105 restraints weight = 6252.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.102749 restraints weight = 4444.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.103931 restraints weight = 3392.082| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10425 Z= 0.147 Angle : 0.599 8.795 14145 Z= 0.300 Chirality : 0.045 0.261 1569 Planarity : 0.005 0.073 1848 Dihedral : 9.336 134.455 1537 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.32 % Allowed : 22.23 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.29 (0.23), residues: 1282 helix: 0.66 (0.24), residues: 473 sheet: -1.32 (0.39), residues: 178 loop : -1.94 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 241 TYR 0.015 0.001 TYR A 172 PHE 0.022 0.002 PHE B 81 TRP 0.014 0.002 TRP B 101 HIS 0.011 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00346 (10425) covalent geometry : angle 0.59871 (14145) hydrogen bonds : bond 0.03661 ( 351) hydrogen bonds : angle 4.78618 ( 1017) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 THR cc_start: 0.7460 (p) cc_final: 0.7197 (t) REVERT: A 84 ARG cc_start: 0.7765 (ttm110) cc_final: 0.7506 (mtp85) REVERT: A 242 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8668 (tt) REVERT: A 344 VAL cc_start: 0.7047 (OUTLIER) cc_final: 0.6762 (m) REVERT: A 378 LEU cc_start: 0.8169 (mt) cc_final: 0.7937 (mt) REVERT: B 2 ARG cc_start: 0.6590 (mtt180) cc_final: 0.6350 (mtt180) REVERT: B 258 VAL cc_start: 0.7669 (t) cc_final: 0.7395 (t) REVERT: B 294 PHE cc_start: 0.7296 (t80) cc_final: 0.6989 (t80) REVERT: K 146 PHE cc_start: 0.6696 (m-80) cc_final: 0.6068 (m-10) REVERT: K 352 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6726 (mt-10) outliers start: 48 outliers final: 41 residues processed: 199 average time/residue: 0.0836 time to fit residues: 25.0080 Evaluate side-chains 206 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 144 HIS Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 274 SER Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 406 VAL Chi-restraints excluded: chain K residue 422 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 52 optimal weight: 0.3980 chunk 114 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.0770 chunk 96 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 192 HIS K 397 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.117742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.097797 restraints weight = 17752.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.101214 restraints weight = 9686.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.103584 restraints weight = 6119.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.105271 restraints weight = 4302.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.106456 restraints weight = 3274.277| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10425 Z= 0.131 Angle : 0.599 10.117 14145 Z= 0.300 Chirality : 0.044 0.262 1569 Planarity : 0.005 0.076 1848 Dihedral : 9.166 133.865 1535 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.96 % Allowed : 23.04 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.17 (0.24), residues: 1282 helix: 0.77 (0.24), residues: 477 sheet: -1.26 (0.40), residues: 168 loop : -1.90 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 123 TYR 0.013 0.001 TYR A 172 PHE 0.020 0.001 PHE B 81 TRP 0.015 0.002 TRP B 101 HIS 0.020 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00306 (10425) covalent geometry : angle 0.59935 (14145) hydrogen bonds : bond 0.03451 ( 351) hydrogen bonds : angle 4.72912 ( 1017) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 THR cc_start: 0.7398 (p) cc_final: 0.7125 (t) REVERT: A 84 ARG cc_start: 0.7720 (ttm110) cc_final: 0.7508 (mtp85) REVERT: A 242 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8675 (tt) REVERT: A 378 LEU cc_start: 0.8173 (mt) cc_final: 0.7946 (mt) REVERT: B 2 ARG cc_start: 0.6568 (mtt180) cc_final: 0.6324 (mtt180) REVERT: B 8 GLN cc_start: 0.6742 (OUTLIER) cc_final: 0.6267 (mt0) REVERT: B 233 MET cc_start: 0.7342 (ptm) cc_final: 0.7119 (ptm) REVERT: B 258 VAL cc_start: 0.7661 (t) cc_final: 0.7395 (t) REVERT: B 294 PHE cc_start: 0.7247 (t80) cc_final: 0.6930 (t80) REVERT: K 113 MET cc_start: 0.7135 (ppp) cc_final: 0.5296 (mtp) REVERT: K 146 PHE cc_start: 0.6598 (m-80) cc_final: 0.6004 (m-10) REVERT: K 222 THR cc_start: 0.7368 (OUTLIER) cc_final: 0.7101 (p) REVERT: K 352 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6656 (mt-10) outliers start: 44 outliers final: 38 residues processed: 197 average time/residue: 0.0812 time to fit residues: 24.4535 Evaluate side-chains 204 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 144 HIS Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 222 THR Chi-restraints excluded: chain K residue 263 SER Chi-restraints excluded: chain K residue 274 SER Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 406 VAL Chi-restraints excluded: chain K residue 422 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 117 optimal weight: 0.4980 chunk 102 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.116758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.096854 restraints weight = 17678.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.100224 restraints weight = 9722.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.102565 restraints weight = 6174.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.103980 restraints weight = 4371.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.105284 restraints weight = 3418.373| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10425 Z= 0.152 Angle : 0.618 9.764 14145 Z= 0.310 Chirality : 0.045 0.280 1569 Planarity : 0.005 0.078 1848 Dihedral : 9.186 133.538 1535 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 4.05 % Allowed : 23.31 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.24 (0.24), residues: 1282 helix: 0.69 (0.24), residues: 478 sheet: -1.28 (0.40), residues: 170 loop : -1.93 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 241 TYR 0.015 0.001 TYR K 231 PHE 0.021 0.002 PHE B 81 TRP 0.014 0.002 TRP B 101 HIS 0.015 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00357 (10425) covalent geometry : angle 0.61798 (14145) hydrogen bonds : bond 0.03584 ( 351) hydrogen bonds : angle 4.75504 ( 1017) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7801 (ptp90) cc_final: 0.7540 (ptp-170) REVERT: A 82 THR cc_start: 0.7462 (p) cc_final: 0.7187 (t) REVERT: A 84 ARG cc_start: 0.7795 (ttm110) cc_final: 0.7537 (mtp85) REVERT: A 242 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8711 (tt) REVERT: A 378 LEU cc_start: 0.8150 (mt) cc_final: 0.7923 (mt) REVERT: B 2 ARG cc_start: 0.6568 (mtt180) cc_final: 0.6224 (mtt180) REVERT: B 8 GLN cc_start: 0.6703 (OUTLIER) cc_final: 0.6134 (mt0) REVERT: B 233 MET cc_start: 0.7147 (ptm) cc_final: 0.6444 (ptm) REVERT: B 258 VAL cc_start: 0.7687 (t) cc_final: 0.7443 (t) REVERT: B 294 PHE cc_start: 0.7279 (t80) cc_final: 0.6985 (t80) REVERT: K 113 MET cc_start: 0.7146 (ppp) cc_final: 0.5285 (mtp) REVERT: K 222 THR cc_start: 0.7310 (OUTLIER) cc_final: 0.7088 (p) REVERT: K 352 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6774 (mt-10) outliers start: 45 outliers final: 39 residues processed: 196 average time/residue: 0.0811 time to fit residues: 24.1788 Evaluate side-chains 206 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 144 HIS Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 222 THR Chi-restraints excluded: chain K residue 263 SER Chi-restraints excluded: chain K residue 274 SER Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 406 VAL Chi-restraints excluded: chain K residue 422 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 106 optimal weight: 0.4980 chunk 116 optimal weight: 0.0770 chunk 71 optimal weight: 0.9990 chunk 3 optimal weight: 0.0970 chunk 67 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 77 optimal weight: 0.0670 chunk 69 optimal weight: 0.9980 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.121346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.101474 restraints weight = 17226.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.105059 restraints weight = 9257.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.107476 restraints weight = 5748.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.108958 restraints weight = 3991.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.110331 restraints weight = 3071.247| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10425 Z= 0.110 Angle : 0.577 9.421 14145 Z= 0.290 Chirality : 0.043 0.272 1569 Planarity : 0.005 0.079 1848 Dihedral : 8.883 133.730 1535 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.06 % Allowed : 24.39 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.01 (0.24), residues: 1282 helix: 0.92 (0.25), residues: 481 sheet: -1.05 (0.40), residues: 169 loop : -1.88 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 123 TYR 0.010 0.001 TYR K 231 PHE 0.013 0.001 PHE B 81 TRP 0.015 0.002 TRP B 344 HIS 0.003 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00250 (10425) covalent geometry : angle 0.57741 (14145) hydrogen bonds : bond 0.03077 ( 351) hydrogen bonds : angle 4.56874 ( 1017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1854.93 seconds wall clock time: 32 minutes 54.14 seconds (1974.14 seconds total)