Starting phenix.real_space_refine on Sat Dec 28 03:41:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zth_14960/12_2024/7zth_14960.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zth_14960/12_2024/7zth_14960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zth_14960/12_2024/7zth_14960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zth_14960/12_2024/7zth_14960.map" model { file = "/net/cci-nas-00/data/ceres_data/7zth_14960/12_2024/7zth_14960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zth_14960/12_2024/7zth_14960.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 84 5.49 5 S 18 5.16 5 C 4622 2.51 5 N 1325 2.21 5 O 1571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7620 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2962 Classifications: {'peptide': 360} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2977 Classifications: {'peptide': 362} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 345} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 834 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 847 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Time building chain proxies: 4.97, per 1000 atoms: 0.65 Number of scatterers: 7620 At special positions: 0 Unit cell: (82.677, 90.678, 132.461, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 84 15.00 O 1571 8.00 N 1325 7.00 C 4622 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: 1.68 Conformation dependent library (CDL) restraints added in 889.0 milliseconds 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 6 sheets defined 37.4% alpha, 8.6% beta 12 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 126 through 129 Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.545A pdb=" N ARG A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 190 removed outlier: 4.151A pdb=" N GLN A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 removed outlier: 3.695A pdb=" N LEU A 209 " --> pdb=" O MET A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.554A pdb=" N LYS A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN A 260 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA A 267 " --> pdb=" O HIS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 4.130A pdb=" N VAL A 315 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 316' Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.971A pdb=" N HIS A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN A 332 " --> pdb=" O HIS A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.537A pdb=" N GLN A 346 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 removed outlier: 3.879A pdb=" N ALA A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 381 removed outlier: 4.161A pdb=" N LYS A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 416 removed outlier: 3.895A pdb=" N GLU A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 450 through 463 removed outlier: 4.186A pdb=" N ALA A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 4.361A pdb=" N TYR B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 131 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N MET B 132 " --> pdb=" O PHE B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 156 removed outlier: 3.715A pdb=" N ILE B 155 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 163 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 207 through 211 removed outlier: 3.788A pdb=" N HIS B 211 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.682A pdb=" N ILE B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 232' Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.852A pdb=" N HIS B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 removed outlier: 3.588A pdb=" N MET B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 291 through 296' Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.843A pdb=" N HIS B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU B 329 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.566A pdb=" N GLN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 380 removed outlier: 3.518A pdb=" N TYR B 369 " --> pdb=" O MET B 365 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B 370 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 383 No H-bonds generated for 'chain 'B' and resid 381 through 383' Processing helix chain 'B' and resid 407 through 415 removed outlier: 3.951A pdb=" N LEU B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU B 413 " --> pdb=" O GLN B 409 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.663A pdb=" N ALA B 456 " --> pdb=" O GLU B 452 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 175 Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 219 removed outlier: 3.532A pdb=" N ILE A 197 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 194 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N TYR A 240 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLY A 196 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 239 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 390 removed outlier: 3.544A pdb=" N ILE A 390 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL A 399 " --> pdb=" O ILE A 390 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 215 through 217 removed outlier: 6.914A pdb=" N ILE B 273 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU B 304 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLU B 275 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ALA B 306 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY B 305 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 221 through 222 Processing sheet with id=AA6, first strand: chain 'B' and resid 389 through 390 removed outlier: 3.971A pdb=" N VAL B 399 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE B 439 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR B 423 " --> pdb=" O VAL B 440 " (cutoff:3.500A) 134 hydrogen bonds defined for protein. 381 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1671 1.33 - 1.45: 2151 1.45 - 1.57: 3955 1.57 - 1.69: 164 1.69 - 1.81: 32 Bond restraints: 7973 Sorted by residual: bond pdb=" OP4 LLP B 309 " pdb=" P LLP B 309 " ideal model delta sigma weight residual 1.726 1.536 0.190 2.00e-02 2.50e+03 9.02e+01 bond pdb=" OP4 LLP A 309 " pdb=" P LLP A 309 " ideal model delta sigma weight residual 1.726 1.540 0.186 2.00e-02 2.50e+03 8.67e+01 bond pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 1.273 1.437 -0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " ideal model delta sigma weight residual 1.273 1.432 -0.159 2.00e-02 2.50e+03 6.32e+01 bond pdb=" C4 LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 1.464 1.618 -0.154 2.00e-02 2.50e+03 5.89e+01 ... (remaining 7968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 10570 2.16 - 4.32: 499 4.32 - 6.48: 59 6.48 - 8.64: 14 8.64 - 10.80: 10 Bond angle restraints: 11152 Sorted by residual: angle pdb=" N ILE A 289 " pdb=" CA ILE A 289 " pdb=" C ILE A 289 " ideal model delta sigma weight residual 109.01 100.06 8.95 1.13e+00 7.83e-01 6.28e+01 angle pdb=" C ASP A 277 " pdb=" N TYR A 278 " pdb=" CA TYR A 278 " ideal model delta sigma weight residual 121.54 131.33 -9.79 1.91e+00 2.74e-01 2.62e+01 angle pdb=" CA ILE A 289 " pdb=" C ILE A 289 " pdb=" N PRO A 290 " ideal model delta sigma weight residual 117.00 120.72 -3.72 9.50e-01 1.11e+00 1.54e+01 angle pdb=" C ILE A 105 " pdb=" N ARG A 106 " pdb=" CA ARG A 106 " ideal model delta sigma weight residual 121.54 128.72 -7.18 1.91e+00 2.74e-01 1.42e+01 angle pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " pdb=" C4 LLP B 309 " ideal model delta sigma weight residual 120.09 109.29 10.80 3.00e+00 1.11e-01 1.30e+01 ... (remaining 11147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.96: 3953 29.96 - 59.91: 576 59.91 - 89.87: 27 89.87 - 119.83: 0 119.83 - 149.78: 3 Dihedral angle restraints: 4559 sinusoidal: 2427 harmonic: 2132 Sorted by residual: dihedral pdb=" CA GLY B 286 " pdb=" C GLY B 286 " pdb=" N LYS B 287 " pdb=" CA LYS B 287 " ideal model delta harmonic sigma weight residual 180.00 -136.34 -43.66 0 5.00e+00 4.00e-02 7.63e+01 dihedral pdb=" CA GLY B 177 " pdb=" C GLY B 177 " pdb=" N VAL B 178 " pdb=" CA VAL B 178 " ideal model delta harmonic sigma weight residual 180.00 151.51 28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ASN B 136 " pdb=" C ASN B 136 " pdb=" N HIS B 137 " pdb=" CA HIS B 137 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 4556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1018 0.081 - 0.161: 193 0.161 - 0.241: 8 0.241 - 0.322: 1 0.322 - 0.402: 1 Chirality restraints: 1221 Sorted by residual: chirality pdb=" CB ILE A 446 " pdb=" CA ILE A 446 " pdb=" CG1 ILE A 446 " pdb=" CG2 ILE A 446 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CA ILE A 289 " pdb=" N ILE A 289 " pdb=" C ILE A 289 " pdb=" CB ILE A 289 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CG LEU B 187 " pdb=" CB LEU B 187 " pdb=" CD1 LEU B 187 " pdb=" CD2 LEU B 187 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.97e-01 ... (remaining 1218 not shown) Planarity restraints: 1133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP A 309 " 0.157 2.00e-02 2.50e+03 2.82e-01 7.96e+02 pdb=" NZ LLP A 309 " -0.384 2.00e-02 2.50e+03 pdb=" C4 LLP A 309 " -0.132 2.00e-02 2.50e+03 pdb=" C4' LLP A 309 " 0.359 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 309 " -0.297 2.00e-02 2.50e+03 2.77e-01 7.65e+02 pdb=" NZ LLP B 309 " 0.311 2.00e-02 2.50e+03 pdb=" C4 LLP B 309 " -0.253 2.00e-02 2.50e+03 pdb=" C4' LLP B 309 " 0.240 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 289 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.40e+00 pdb=" N PRO A 290 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " 0.040 5.00e-02 4.00e+02 ... (remaining 1130 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1636 2.78 - 3.31: 6210 3.31 - 3.84: 12588 3.84 - 4.37: 13923 4.37 - 4.90: 22293 Nonbonded interactions: 56650 Sorted by model distance: nonbonded pdb=" OH TYR A 240 " pdb=" OD2 ASP A 276 " model vdw 2.244 3.040 nonbonded pdb=" O SER A 314 " pdb=" OG SER A 314 " model vdw 2.261 3.040 nonbonded pdb=" OE1 GLN A 184 " pdb=" OH TYR A 330 " model vdw 2.268 3.040 nonbonded pdb=" O GLU B 453 " pdb=" OG1 THR B 457 " model vdw 2.290 3.040 nonbonded pdb=" O GLY B 177 " pdb=" OG SER B 318 " model vdw 2.294 3.040 ... (remaining 56645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 105 through 464) } 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: 1.970 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: 2.220 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.570 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 : 0.009 0.190 7973 Z= 0.574 Angle : 1.065 10.797 11152 Z= 0.585 Chirality : 0.060 0.402 1221 Planarity : 0.014 0.282 1133 Dihedral : 23.039 149.781 3191 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 1.24 % Allowed : 15.06 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.31 (0.24), residues: 712 helix: -4.33 (0.17), residues: 232 sheet: -3.13 (0.41), residues: 112 loop : -3.09 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 124 HIS 0.015 0.002 HIS B 113 PHE 0.025 0.004 PHE A 307 TYR 0.028 0.003 TYR B 202 ARG 0.010 0.001 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.792 Fit side-chains REVERT: A 122 GLU cc_start: 0.7871 (mp0) cc_final: 0.6732 (pm20) REVERT: A 138 ARG cc_start: 0.7915 (mtt-85) cc_final: 0.7292 (mtp180) REVERT: A 353 MET cc_start: 0.7643 (mtm) cc_final: 0.7435 (mtm) outliers start: 8 outliers final: 4 residues processed: 91 average time/residue: 0.2740 time to fit residues: 31.9024 Evaluate side-chains 60 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 402 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 0.0670 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 146 GLN A 211 HIS B 211 HIS B 328 HIS B 332 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7973 Z= 0.180 Angle : 0.637 7.957 11152 Z= 0.352 Chirality : 0.043 0.237 1221 Planarity : 0.006 0.059 1133 Dihedral : 24.654 145.674 1750 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.48 % Allowed : 18.63 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.27), residues: 712 helix: -3.12 (0.27), residues: 240 sheet: -2.09 (0.49), residues: 106 loop : -2.86 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 124 HIS 0.010 0.001 HIS B 110 PHE 0.011 0.001 PHE B 109 TYR 0.020 0.001 TYR A 157 ARG 0.003 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.740 Fit side-chains REVERT: A 122 GLU cc_start: 0.7718 (mp0) cc_final: 0.6656 (pm20) REVERT: A 135 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7435 (tp30) REVERT: A 138 ARG cc_start: 0.7913 (mtt-85) cc_final: 0.7371 (mtp180) REVERT: B 110 HIS cc_start: 0.7602 (t-90) cc_final: 0.7251 (t-90) REVERT: B 370 ARG cc_start: 0.7732 (ttm-80) cc_final: 0.7412 (ttm110) outliers start: 16 outliers final: 12 residues processed: 89 average time/residue: 0.1830 time to fit residues: 23.2460 Evaluate side-chains 78 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 0.0770 chunk 71 optimal weight: 10.0000 overall best weight: 2.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN B 110 HIS B 123 GLN B 145 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7973 Z= 0.242 Angle : 0.634 6.350 11152 Z= 0.348 Chirality : 0.044 0.173 1221 Planarity : 0.005 0.055 1133 Dihedral : 24.562 144.114 1748 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.81 % Allowed : 20.34 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.28), residues: 712 helix: -2.67 (0.30), residues: 232 sheet: -1.93 (0.49), residues: 104 loop : -2.69 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 124 HIS 0.005 0.001 HIS B 110 PHE 0.012 0.002 PHE A 307 TYR 0.017 0.002 TYR A 157 ARG 0.002 0.000 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.815 Fit side-chains REVERT: A 122 GLU cc_start: 0.7768 (mp0) cc_final: 0.6697 (pm20) REVERT: A 135 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7326 (tm-30) REVERT: A 138 ARG cc_start: 0.7969 (mtt-85) cc_final: 0.7513 (mtp180) outliers start: 31 outliers final: 21 residues processed: 94 average time/residue: 0.1653 time to fit residues: 22.5962 Evaluate side-chains 82 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.0170 chunk 37 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7973 Z= 0.161 Angle : 0.584 10.007 11152 Z= 0.315 Chirality : 0.041 0.166 1221 Planarity : 0.005 0.054 1133 Dihedral : 24.338 145.129 1748 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.66 % Allowed : 21.43 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.28), residues: 712 helix: -2.33 (0.31), residues: 236 sheet: -1.73 (0.48), residues: 108 loop : -2.50 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 124 HIS 0.011 0.001 HIS B 110 PHE 0.008 0.001 PHE A 307 TYR 0.018 0.001 TYR B 336 ARG 0.001 0.000 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 69 time to evaluate : 0.750 Fit side-chains REVERT: A 122 GLU cc_start: 0.7711 (mp0) cc_final: 0.6676 (pm20) REVERT: A 135 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7389 (tm-30) REVERT: A 138 ARG cc_start: 0.7939 (mtt-85) cc_final: 0.7481 (mtp180) REVERT: A 343 ARG cc_start: 0.8036 (ttt180) cc_final: 0.7540 (ttt180) REVERT: B 281 GLU cc_start: 0.7320 (pm20) cc_final: 0.7034 (pm20) outliers start: 30 outliers final: 18 residues processed: 90 average time/residue: 0.1679 time to fit residues: 21.6607 Evaluate side-chains 79 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 452 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 0.0770 chunk 57 optimal weight: 0.5980 chunk 31 optimal weight: 8.9990 chunk 65 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7973 Z= 0.152 Angle : 0.551 6.848 11152 Z= 0.300 Chirality : 0.040 0.154 1221 Planarity : 0.005 0.054 1133 Dihedral : 24.135 146.725 1748 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.81 % Allowed : 21.58 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.29), residues: 712 helix: -1.96 (0.32), residues: 240 sheet: -1.27 (0.49), residues: 106 loop : -2.19 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 264 HIS 0.007 0.001 HIS B 110 PHE 0.007 0.001 PHE B 307 TYR 0.016 0.001 TYR B 284 ARG 0.002 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.733 Fit side-chains REVERT: A 122 GLU cc_start: 0.7645 (mp0) cc_final: 0.6741 (pm20) REVERT: A 135 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7495 (tm-30) REVERT: A 138 ARG cc_start: 0.7936 (mtt-85) cc_final: 0.7372 (mtp180) REVERT: B 148 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6705 (tp30) outliers start: 31 outliers final: 22 residues processed: 93 average time/residue: 0.1718 time to fit residues: 22.8772 Evaluate side-chains 84 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 19 optimal weight: 0.0870 chunk 77 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 7973 Z= 0.419 Angle : 0.770 9.888 11152 Z= 0.409 Chirality : 0.049 0.245 1221 Planarity : 0.006 0.054 1133 Dihedral : 24.461 145.187 1748 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 6.06 % Allowed : 21.27 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.29), residues: 712 helix: -2.28 (0.31), residues: 237 sheet: -1.57 (0.49), residues: 104 loop : -2.38 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 124 HIS 0.009 0.002 HIS B 110 PHE 0.021 0.003 PHE A 307 TYR 0.017 0.003 TYR B 212 ARG 0.004 0.001 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 60 time to evaluate : 0.776 Fit side-chains REVERT: A 122 GLU cc_start: 0.7756 (mp0) cc_final: 0.6805 (pm20) REVERT: A 135 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7494 (tm-30) REVERT: A 138 ARG cc_start: 0.7948 (mtt-85) cc_final: 0.7339 (mtp180) REVERT: B 148 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6809 (tp30) outliers start: 39 outliers final: 32 residues processed: 92 average time/residue: 0.1668 time to fit residues: 22.2604 Evaluate side-chains 88 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 56 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 443 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7973 Z= 0.224 Angle : 0.641 9.815 11152 Z= 0.343 Chirality : 0.044 0.209 1221 Planarity : 0.005 0.052 1133 Dihedral : 24.352 146.322 1748 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 4.97 % Allowed : 22.36 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.30), residues: 712 helix: -1.99 (0.32), residues: 236 sheet: -1.42 (0.49), residues: 106 loop : -2.24 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 124 HIS 0.009 0.001 HIS B 110 PHE 0.014 0.002 PHE A 307 TYR 0.018 0.002 TYR B 127 ARG 0.002 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 0.711 Fit side-chains REVERT: A 122 GLU cc_start: 0.7639 (mp0) cc_final: 0.6689 (pm20) REVERT: A 135 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7425 (tm-30) REVERT: A 138 ARG cc_start: 0.7963 (mtt-85) cc_final: 0.7340 (mtp180) REVERT: B 148 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6702 (tp30) outliers start: 32 outliers final: 28 residues processed: 87 average time/residue: 0.1648 time to fit residues: 20.8193 Evaluate side-chains 90 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7973 Z= 0.296 Angle : 0.705 12.971 11152 Z= 0.372 Chirality : 0.046 0.203 1221 Planarity : 0.005 0.052 1133 Dihedral : 24.439 146.213 1748 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 5.75 % Allowed : 21.43 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.30), residues: 712 helix: -2.05 (0.32), residues: 236 sheet: -1.43 (0.50), residues: 104 loop : -2.30 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 124 HIS 0.009 0.001 HIS B 110 PHE 0.019 0.002 PHE A 334 TYR 0.017 0.002 TYR A 157 ARG 0.003 0.000 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 63 time to evaluate : 0.765 Fit side-chains REVERT: A 122 GLU cc_start: 0.7672 (mp0) cc_final: 0.6795 (pm20) REVERT: A 135 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 138 ARG cc_start: 0.7970 (mtt-85) cc_final: 0.7320 (mtp180) REVERT: B 148 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6738 (tp30) outliers start: 37 outliers final: 32 residues processed: 91 average time/residue: 0.1668 time to fit residues: 21.8332 Evaluate side-chains 95 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 63 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 383 TYR Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 439 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 22 optimal weight: 0.0670 chunk 64 optimal weight: 8.9990 chunk 67 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 46 optimal weight: 0.4980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7973 Z= 0.159 Angle : 0.596 12.335 11152 Z= 0.317 Chirality : 0.041 0.158 1221 Planarity : 0.005 0.052 1133 Dihedral : 24.167 148.990 1748 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.95 % Allowed : 23.76 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.30), residues: 712 helix: -1.78 (0.32), residues: 247 sheet: -1.13 (0.49), residues: 106 loop : -1.88 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 264 HIS 0.005 0.001 HIS B 110 PHE 0.012 0.001 PHE B 352 TYR 0.015 0.001 TYR A 157 ARG 0.003 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.799 Fit side-chains REVERT: A 114 ILE cc_start: 0.6003 (tt) cc_final: 0.5659 (tt) REVERT: A 122 GLU cc_start: 0.7594 (mp0) cc_final: 0.6730 (pm20) REVERT: A 135 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7520 (tm-30) REVERT: A 138 ARG cc_start: 0.7915 (mtt-85) cc_final: 0.7411 (mtp180) REVERT: A 353 MET cc_start: 0.7406 (mtm) cc_final: 0.7128 (mtm) REVERT: B 148 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6473 (tp30) outliers start: 19 outliers final: 17 residues processed: 85 average time/residue: 0.1669 time to fit residues: 20.5724 Evaluate side-chains 85 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 439 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 79 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7973 Z= 0.215 Angle : 0.631 12.107 11152 Z= 0.333 Chirality : 0.043 0.173 1221 Planarity : 0.005 0.052 1133 Dihedral : 24.202 148.627 1748 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 3.26 % Allowed : 23.76 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.30), residues: 712 helix: -1.75 (0.32), residues: 247 sheet: -1.05 (0.50), residues: 106 loop : -1.87 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 124 HIS 0.006 0.001 HIS B 110 PHE 0.011 0.001 PHE A 307 TYR 0.018 0.002 TYR B 127 ARG 0.002 0.000 ARG B 370 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7597 (mp0) cc_final: 0.6723 (pm20) REVERT: A 135 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7416 (tm-30) REVERT: A 138 ARG cc_start: 0.7948 (mtt-85) cc_final: 0.7275 (mtp180) REVERT: A 353 MET cc_start: 0.7436 (mtm) cc_final: 0.7150 (mtm) REVERT: B 148 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6561 (tp30) outliers start: 21 outliers final: 19 residues processed: 81 average time/residue: 0.1704 time to fit residues: 19.9687 Evaluate side-chains 82 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 439 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 63 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 8 optimal weight: 0.0050 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.4400 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.168698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.133727 restraints weight = 14259.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.135112 restraints weight = 11877.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.136447 restraints weight = 8286.833| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7973 Z= 0.188 Angle : 0.612 11.698 11152 Z= 0.324 Chirality : 0.042 0.184 1221 Planarity : 0.005 0.054 1133 Dihedral : 24.141 149.179 1748 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.11 % Allowed : 23.91 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.30), residues: 712 helix: -1.69 (0.32), residues: 249 sheet: -1.09 (0.49), residues: 105 loop : -1.80 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 124 HIS 0.007 0.001 HIS B 110 PHE 0.009 0.001 PHE A 307 TYR 0.019 0.001 TYR B 127 ARG 0.002 0.000 ARG B 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1520.45 seconds wall clock time: 28 minutes 55.16 seconds (1735.16 seconds total)