Starting phenix.real_space_refine on Fri Aug 22 20:18:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u65_41944/08_2025/8u65_41944.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u65_41944/08_2025/8u65_41944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u65_41944/08_2025/8u65_41944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u65_41944/08_2025/8u65_41944.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u65_41944/08_2025/8u65_41944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u65_41944/08_2025/8u65_41944.map" } resolution = 3.01 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 4827 2.51 5 N 1325 2.21 5 O 1438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7636 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3785 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 458} Chain breaks: 2 Chain: "A" Number of atoms: 3765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3765 Classifications: {'peptide': 482} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 455} Chain breaks: 3 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.20, per 1000 atoms: 0.29 Number of scatterers: 7636 At special positions: 0 Unit cell: (120.888, 80.811, 101.178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1438 8.00 N 1325 7.00 C 4827 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 375 " - pdb=" SG CYS B 379 " distance=2.02 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 438.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 45.3% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'B' and resid 2 through 15 removed outlier: 3.608A pdb=" N VAL B 11 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN B 15 " --> pdb=" O VAL B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 54 Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 72 through 83 Processing helix chain 'B' and resid 135 through 145 Processing helix chain 'B' and resid 148 through 164 Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 294 through 341 removed outlier: 3.564A pdb=" N SER B 341 " --> pdb=" O MET B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 350 Processing helix chain 'B' and resid 352 through 361 removed outlier: 3.541A pdb=" N LEU B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP B 358 " --> pdb=" O GLN B 354 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 394 removed outlier: 3.978A pdb=" N ILE B 385 " --> pdb=" O GLU B 381 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET B 393 " --> pdb=" O HIS B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 removed outlier: 4.033A pdb=" N ALA B 414 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 416 " --> pdb=" O GLU B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 removed outlier: 3.764A pdb=" N SER B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 480 Processing helix chain 'B' and resid 488 through 512 Processing helix chain 'A' and resid 3 through 15 removed outlier: 3.544A pdb=" N ALA A 8 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASN A 15 " --> pdb=" O VAL A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 removed outlier: 3.785A pdb=" N VAL A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.559A pdb=" N LEU A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.163A pdb=" N VAL A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 148 through 165 removed outlier: 3.717A pdb=" N GLY A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 294 through 341 removed outlier: 4.039A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 337 " --> pdb=" O GLN A 333 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 341 " --> pdb=" O MET A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.871A pdb=" N LEU A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 345 through 349' Processing helix chain 'A' and resid 352 through 361 removed outlier: 3.822A pdb=" N LEU A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 389 through 394 removed outlier: 4.182A pdb=" N MET A 393 " --> pdb=" O HIS A 389 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 389 through 394' Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.710A pdb=" N SER A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 481 Processing helix chain 'A' and resid 488 through 503 removed outlier: 3.504A pdb=" N LEU A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 512 removed outlier: 4.282A pdb=" N ALA A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 27 removed outlier: 3.695A pdb=" N GLN B 64 " --> pdb=" O ILE B 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 27 removed outlier: 6.588A pdb=" N THR B 35 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL B 46 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU B 33 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU B 101 " --> pdb=" O GLN B 120 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU B 93 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 198 through 199 removed outlier: 6.061A pdb=" N VAL B 182 " --> pdb=" O ARG B 173 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG B 173 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 184 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TRP B 280 " --> pdb=" O PHE B 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 373 through 376 removed outlier: 3.735A pdb=" N GLY B 364 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 434 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 26 through 27 removed outlier: 3.642A pdb=" N ILE A 27 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 228 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 231 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL A 46 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A 42 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR A 35 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL A 46 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU A 33 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU A 101 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 198 through 199 removed outlier: 7.026A pdb=" N ILE A 171 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLU A 185 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL A 169 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TRP A 280 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU A 273 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU A 282 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL A 271 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER A 284 " --> pdb=" O MET A 269 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N MET A 269 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 374 through 377 removed outlier: 3.521A pdb=" N VAL A 365 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A 425 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 423 " --> pdb=" O TRP A 437 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1047 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: 1.39 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1409 1.32 - 1.45: 1884 1.45 - 1.57: 4422 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 7793 Sorted by residual: bond pdb=" C PRO B 410 " pdb=" N PRO B 411 " ideal model delta sigma weight residual 1.339 1.395 -0.056 3.40e-02 8.65e+02 2.69e+00 bond pdb=" CB ASN A 49 " pdb=" CG ASN A 49 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 9.91e-01 bond pdb=" CB LYS B 56 " pdb=" CG LYS B 56 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.29e-01 bond pdb=" CB GLU B 369 " pdb=" CG GLU B 369 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.34e-01 bond pdb=" CA ASN A 49 " pdb=" CB ASN A 49 " ideal model delta sigma weight residual 1.529 1.542 -0.014 1.64e-02 3.72e+03 6.88e-01 ... (remaining 7788 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 10293 1.51 - 3.01: 234 3.01 - 4.52: 47 4.52 - 6.02: 14 6.02 - 7.53: 4 Bond angle restraints: 10592 Sorted by residual: angle pdb=" N VAL A 422 " pdb=" CA VAL A 422 " pdb=" C VAL A 422 " ideal model delta sigma weight residual 106.53 110.51 -3.98 1.41e+00 5.03e-01 7.97e+00 angle pdb=" CA LYS B 56 " pdb=" CB LYS B 56 " pdb=" CG LYS B 56 " ideal model delta sigma weight residual 114.10 119.47 -5.37 2.00e+00 2.50e-01 7.22e+00 angle pdb=" CA GLU B 381 " pdb=" CB GLU B 381 " pdb=" CG GLU B 381 " ideal model delta sigma weight residual 114.10 119.34 -5.24 2.00e+00 2.50e-01 6.88e+00 angle pdb=" CB MET B 263 " pdb=" CG MET B 263 " pdb=" SD MET B 263 " ideal model delta sigma weight residual 112.70 119.91 -7.21 3.00e+00 1.11e-01 5.77e+00 angle pdb=" CA GLN B 329 " pdb=" CB GLN B 329 " pdb=" CG GLN B 329 " ideal model delta sigma weight residual 114.10 118.85 -4.75 2.00e+00 2.50e-01 5.63e+00 ... (remaining 10587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.30: 3996 18.30 - 36.60: 527 36.60 - 54.89: 143 54.89 - 73.19: 49 73.19 - 91.49: 12 Dihedral angle restraints: 4727 sinusoidal: 1929 harmonic: 2798 Sorted by residual: dihedral pdb=" CB CYS B 375 " pdb=" SG CYS B 375 " pdb=" SG CYS B 379 " pdb=" CB CYS B 379 " ideal model delta sinusoidal sigma weight residual -86.00 -148.61 62.61 1 1.00e+01 1.00e-02 5.18e+01 dihedral pdb=" CA GLY A 55 " pdb=" C GLY A 55 " pdb=" N LYS A 56 " pdb=" CA LYS A 56 " ideal model delta harmonic sigma weight residual -180.00 -161.08 -18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA GLU B 381 " pdb=" C GLU B 381 " pdb=" N PRO B 382 " pdb=" CA PRO B 382 " ideal model delta harmonic sigma weight residual -180.00 -163.37 -16.63 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 4724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 809 0.033 - 0.067: 253 0.067 - 0.100: 89 0.100 - 0.134: 35 0.134 - 0.167: 3 Chirality restraints: 1189 Sorted by residual: chirality pdb=" CB VAL B 155 " pdb=" CA VAL B 155 " pdb=" CG1 VAL B 155 " pdb=" CG2 VAL B 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.00e-01 chirality pdb=" CG LEU A 331 " pdb=" CB LEU A 331 " pdb=" CD1 LEU A 331 " pdb=" CD2 LEU A 331 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" CB VAL A 155 " pdb=" CA VAL A 155 " pdb=" CG1 VAL A 155 " pdb=" CG2 VAL A 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 1186 not shown) Planarity restraints: 1377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 429 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO A 430 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 430 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 430 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 188 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO A 189 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 57 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A 58 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " -0.022 5.00e-02 4.00e+02 ... (remaining 1374 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 257 2.71 - 3.26: 7623 3.26 - 3.81: 12501 3.81 - 4.35: 15795 4.35 - 4.90: 25870 Nonbonded interactions: 62046 Sorted by model distance: nonbonded pdb=" O THR A 326 " pdb=" OG1 THR A 330 " model vdw 2.164 3.040 nonbonded pdb=" O GLY A 305 " pdb=" OG SER A 309 " model vdw 2.164 3.040 nonbonded pdb=" O THR B 326 " pdb=" OG1 THR B 330 " model vdw 2.176 3.040 nonbonded pdb=" O ILE A 160 " pdb=" OG1 THR A 164 " model vdw 2.206 3.040 nonbonded pdb=" O ILE B 160 " pdb=" OG1 THR B 164 " model vdw 2.218 3.040 ... (remaining 62041 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' and (resid 2 through 120 or resid 135 through 900)) selection = (chain 'B' and (resid 2 through 120 or resid 135 through 342 or resid 345 throug \ h 512 or resid 900)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.490 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 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 : 0.003 0.066 7796 Z= 0.151 Angle : 0.585 7.527 10594 Z= 0.299 Chirality : 0.041 0.167 1189 Planarity : 0.005 0.062 1377 Dihedral : 18.680 91.490 2908 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.36 % Allowed : 31.88 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: -0.65 (0.29), residues: 953 helix: 0.63 (0.28), residues: 375 sheet: -1.92 (0.44), residues: 131 loop : -0.79 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 500 TYR 0.017 0.001 TYR A 172 PHE 0.010 0.001 PHE A 102 TRP 0.015 0.001 TRP B 391 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 7793) covalent geometry : angle 0.58475 (10592) SS BOND : bond 0.00753 ( 1) SS BOND : angle 1.29168 ( 2) hydrogen bonds : bond 0.22099 ( 367) hydrogen bonds : angle 8.03843 ( 1047) Misc. bond : bond 0.06475 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8465 (mp) cc_final: 0.8126 (tt) outliers start: 3 outliers final: 2 residues processed: 160 average time/residue: 0.0993 time to fit residues: 21.1472 Evaluate side-chains 157 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain A residue 374 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.0030 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 0.0770 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.1506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 505 ASN A 275 GLN ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.185150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.167773 restraints weight = 11627.307| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.38 r_work: 0.4115 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7796 Z= 0.121 Angle : 0.565 5.759 10594 Z= 0.293 Chirality : 0.042 0.164 1189 Planarity : 0.005 0.050 1377 Dihedral : 7.078 87.470 1087 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.23 % Allowed : 27.42 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: -0.66 (0.28), residues: 953 helix: 0.59 (0.25), residues: 404 sheet: -1.64 (0.42), residues: 137 loop : -0.94 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 500 TYR 0.018 0.001 TYR A 172 PHE 0.008 0.001 PHE A 473 TRP 0.011 0.001 TRP A 476 HIS 0.004 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7793) covalent geometry : angle 0.56471 (10592) SS BOND : bond 0.00449 ( 1) SS BOND : angle 1.31366 ( 2) hydrogen bonds : bond 0.04502 ( 367) hydrogen bonds : angle 5.44167 ( 1047) Misc. bond : bond 0.00006 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: B 36 LEU cc_start: 0.3284 (OUTLIER) cc_final: 0.2880 (mt) REVERT: B 163 MET cc_start: 0.5996 (ptp) cc_final: 0.5772 (ptp) REVERT: B 211 LEU cc_start: 0.7727 (mp) cc_final: 0.7287 (mt) REVERT: B 332 GLN cc_start: 0.6471 (pp30) cc_final: 0.6224 (pp30) REVERT: A 263 MET cc_start: 0.6352 (tmm) cc_final: 0.5741 (tmm) outliers start: 35 outliers final: 15 residues processed: 177 average time/residue: 0.0956 time to fit residues: 22.7208 Evaluate side-chains 164 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 435 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 85 optimal weight: 1.9990 chunk 71 optimal weight: 0.1980 chunk 92 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 HIS A 275 GLN ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.178614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.160730 restraints weight = 11535.390| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.38 r_work: 0.4061 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7796 Z= 0.176 Angle : 0.592 6.283 10594 Z= 0.308 Chirality : 0.042 0.208 1189 Planarity : 0.005 0.044 1377 Dihedral : 7.054 83.947 1084 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.71 % Allowed : 25.85 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: -0.72 (0.28), residues: 953 helix: 0.64 (0.25), residues: 402 sheet: -1.75 (0.41), residues: 142 loop : -1.04 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 250 TYR 0.018 0.002 TYR A 172 PHE 0.015 0.002 PHE B 199 TRP 0.009 0.002 TRP A 391 HIS 0.006 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 7793) covalent geometry : angle 0.59215 (10592) SS BOND : bond 0.00643 ( 1) SS BOND : angle 0.50086 ( 2) hydrogen bonds : bond 0.04455 ( 367) hydrogen bonds : angle 5.30831 ( 1047) Misc. bond : bond 0.00009 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.279 Fit side-chains REVERT: B 95 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.6854 (mpp) REVERT: B 163 MET cc_start: 0.6209 (ptp) cc_final: 0.5973 (ptm) REVERT: B 446 VAL cc_start: 0.8620 (p) cc_final: 0.8283 (m) REVERT: A 118 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7174 (mt-10) REVERT: A 172 TYR cc_start: 0.7664 (m-80) cc_final: 0.7316 (m-80) REVERT: A 185 GLU cc_start: 0.7928 (pm20) cc_final: 0.7681 (pm20) REVERT: A 304 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7776 (mt) REVERT: A 325 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6712 (tm-30) REVERT: A 329 GLN cc_start: 0.7465 (mt0) cc_final: 0.7179 (mt0) outliers start: 39 outliers final: 23 residues processed: 179 average time/residue: 0.0915 time to fit residues: 22.0847 Evaluate side-chains 179 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 19 optimal weight: 0.0020 chunk 79 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN A 224 ASN A 302 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.176849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.158949 restraints weight = 11666.652| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 2.35 r_work: 0.4059 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7796 Z= 0.220 Angle : 0.625 6.601 10594 Z= 0.325 Chirality : 0.043 0.211 1189 Planarity : 0.005 0.044 1377 Dihedral : 7.397 79.575 1084 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.92 % Allowed : 25.72 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: -0.92 (0.28), residues: 953 helix: 0.43 (0.25), residues: 407 sheet: -1.85 (0.41), residues: 137 loop : -1.13 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 250 TYR 0.014 0.002 TYR A 172 PHE 0.017 0.002 PHE B 199 TRP 0.012 0.002 TRP A 391 HIS 0.007 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 7793) covalent geometry : angle 0.62501 (10592) SS BOND : bond 0.00662 ( 1) SS BOND : angle 0.47328 ( 2) hydrogen bonds : bond 0.04448 ( 367) hydrogen bonds : angle 5.37059 ( 1047) Misc. bond : bond 0.00007 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 0.302 Fit side-chains REVERT: B 10 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7015 (mm-30) REVERT: B 95 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.6843 (mpp) REVERT: B 206 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6502 (mm-30) REVERT: B 446 VAL cc_start: 0.8585 (p) cc_final: 0.8272 (m) REVERT: A 118 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7273 (mt-10) REVERT: A 263 MET cc_start: 0.6653 (tmm) cc_final: 0.6125 (tmm) REVERT: A 335 HIS cc_start: 0.6266 (OUTLIER) cc_final: 0.5915 (t70) outliers start: 49 outliers final: 26 residues processed: 189 average time/residue: 0.0941 time to fit residues: 23.9224 Evaluate side-chains 185 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 67 optimal weight: 0.5980 chunk 64 optimal weight: 0.1980 chunk 41 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 378 ASN A 433 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.180256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.162464 restraints weight = 11553.117| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 2.36 r_work: 0.4048 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7796 Z= 0.186 Angle : 0.612 6.422 10594 Z= 0.317 Chirality : 0.043 0.219 1189 Planarity : 0.005 0.047 1377 Dihedral : 7.395 79.342 1084 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.47 % Allowed : 27.78 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: -0.91 (0.28), residues: 953 helix: 0.49 (0.25), residues: 411 sheet: -1.81 (0.42), residues: 137 loop : -1.22 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 250 TYR 0.015 0.002 TYR A 172 PHE 0.014 0.002 PHE B 199 TRP 0.016 0.002 TRP B 437 HIS 0.006 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 7793) covalent geometry : angle 0.61244 (10592) SS BOND : bond 0.00606 ( 1) SS BOND : angle 0.46921 ( 2) hydrogen bonds : bond 0.04183 ( 367) hydrogen bonds : angle 5.23356 ( 1047) Misc. bond : bond 0.00002 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: B 10 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7027 (mm-30) REVERT: B 95 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.6877 (mpp) REVERT: B 206 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6536 (mm-30) REVERT: B 446 VAL cc_start: 0.8576 (p) cc_final: 0.8247 (m) REVERT: A 118 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7239 (mt-10) REVERT: A 263 MET cc_start: 0.6604 (tmm) cc_final: 0.6109 (tmm) outliers start: 37 outliers final: 29 residues processed: 178 average time/residue: 0.0954 time to fit residues: 22.7910 Evaluate side-chains 182 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 79 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.177299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.159396 restraints weight = 11523.760| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.36 r_work: 0.4061 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7796 Z= 0.200 Angle : 0.620 6.932 10594 Z= 0.321 Chirality : 0.043 0.223 1189 Planarity : 0.005 0.047 1377 Dihedral : 7.484 78.726 1084 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.83 % Allowed : 27.42 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: -0.86 (0.28), residues: 953 helix: 0.58 (0.25), residues: 405 sheet: -1.75 (0.42), residues: 139 loop : -1.24 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 250 TYR 0.016 0.002 TYR A 172 PHE 0.016 0.002 PHE B 199 TRP 0.013 0.002 TRP A 391 HIS 0.007 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 7793) covalent geometry : angle 0.61986 (10592) SS BOND : bond 0.00613 ( 1) SS BOND : angle 0.47054 ( 2) hydrogen bonds : bond 0.04186 ( 367) hydrogen bonds : angle 5.23815 ( 1047) Misc. bond : bond 0.00003 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: B 10 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7034 (mm-30) REVERT: B 95 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.6841 (mpp) REVERT: B 118 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.5960 (mt-10) REVERT: B 206 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6608 (mm-30) REVERT: B 446 VAL cc_start: 0.8580 (p) cc_final: 0.8247 (m) REVERT: A 263 MET cc_start: 0.6661 (tmm) cc_final: 0.6177 (tmm) REVERT: A 335 HIS cc_start: 0.6361 (OUTLIER) cc_final: 0.6033 (t70) outliers start: 40 outliers final: 28 residues processed: 184 average time/residue: 0.0778 time to fit residues: 19.2730 Evaluate side-chains 182 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.177170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.159191 restraints weight = 11481.515| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 2.36 r_work: 0.4061 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7796 Z= 0.211 Angle : 0.637 6.963 10594 Z= 0.329 Chirality : 0.044 0.200 1189 Planarity : 0.005 0.050 1377 Dihedral : 7.587 77.664 1084 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.19 % Allowed : 27.29 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: -1.02 (0.28), residues: 953 helix: 0.46 (0.25), residues: 415 sheet: -1.82 (0.41), residues: 142 loop : -1.37 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.016 0.002 TYR A 172 PHE 0.016 0.002 PHE B 199 TRP 0.013 0.002 TRP A 391 HIS 0.007 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 7793) covalent geometry : angle 0.63678 (10592) SS BOND : bond 0.00611 ( 1) SS BOND : angle 0.46700 ( 2) hydrogen bonds : bond 0.04237 ( 367) hydrogen bonds : angle 5.28494 ( 1047) Misc. bond : bond 0.00003 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 0.337 Fit side-chains REVERT: B 10 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7065 (mm-30) REVERT: B 95 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.6865 (mpp) REVERT: B 118 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6015 (mt-10) REVERT: B 206 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6645 (mm-30) REVERT: B 446 VAL cc_start: 0.8572 (p) cc_final: 0.8251 (m) REVERT: B 486 LYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6863 (mtmm) REVERT: A 120 GLN cc_start: 0.5882 (OUTLIER) cc_final: 0.5576 (mt0) REVERT: A 263 MET cc_start: 0.6670 (tmm) cc_final: 0.6138 (tmm) REVERT: A 335 HIS cc_start: 0.6339 (OUTLIER) cc_final: 0.5975 (t70) outliers start: 43 outliers final: 31 residues processed: 182 average time/residue: 0.0937 time to fit residues: 22.9110 Evaluate side-chains 190 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 486 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 441 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 26 optimal weight: 0.3980 chunk 67 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.177044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.159049 restraints weight = 11604.079| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 2.38 r_work: 0.4055 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7796 Z= 0.212 Angle : 0.645 7.199 10594 Z= 0.335 Chirality : 0.044 0.198 1189 Planarity : 0.005 0.050 1377 Dihedral : 7.640 76.735 1084 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 5.92 % Allowed : 26.81 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: -1.08 (0.28), residues: 953 helix: 0.34 (0.25), residues: 416 sheet: -1.79 (0.42), residues: 142 loop : -1.35 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.016 0.002 TYR A 172 PHE 0.016 0.002 PHE B 199 TRP 0.014 0.002 TRP A 391 HIS 0.007 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 7793) covalent geometry : angle 0.64480 (10592) SS BOND : bond 0.00594 ( 1) SS BOND : angle 0.49593 ( 2) hydrogen bonds : bond 0.04244 ( 367) hydrogen bonds : angle 5.32047 ( 1047) Misc. bond : bond 0.00003 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 150 time to evaluate : 0.298 Fit side-chains REVERT: B 10 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7070 (mm-30) REVERT: B 95 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.6839 (mpp) REVERT: B 118 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.5936 (mt-10) REVERT: B 206 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6672 (mm-30) REVERT: B 446 VAL cc_start: 0.8581 (p) cc_final: 0.8258 (m) REVERT: B 486 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6884 (mtmm) REVERT: A 95 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.7007 (mmt) REVERT: A 120 GLN cc_start: 0.5900 (OUTLIER) cc_final: 0.5596 (mt0) REVERT: A 172 TYR cc_start: 0.7686 (m-80) cc_final: 0.7193 (m-80) REVERT: A 185 GLU cc_start: 0.7938 (pm20) cc_final: 0.7548 (mp0) REVERT: A 263 MET cc_start: 0.6710 (tmm) cc_final: 0.6224 (tmm) REVERT: A 335 HIS cc_start: 0.6372 (OUTLIER) cc_final: 0.6087 (t70) REVERT: A 393 MET cc_start: 0.2564 (ttm) cc_final: 0.2218 (tpp) outliers start: 49 outliers final: 35 residues processed: 180 average time/residue: 0.0992 time to fit residues: 23.7341 Evaluate side-chains 188 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 486 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 441 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 29 optimal weight: 0.6980 chunk 64 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 27 optimal weight: 0.3980 chunk 60 optimal weight: 0.0870 chunk 42 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.183243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.165344 restraints weight = 11576.678| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 2.37 r_work: 0.4082 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7796 Z= 0.155 Angle : 0.623 7.396 10594 Z= 0.320 Chirality : 0.043 0.192 1189 Planarity : 0.005 0.050 1377 Dihedral : 7.532 78.303 1084 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.31 % Allowed : 27.54 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: -0.92 (0.28), residues: 953 helix: 0.43 (0.25), residues: 420 sheet: -1.58 (0.44), residues: 130 loop : -1.33 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.019 0.002 TYR A 172 PHE 0.011 0.001 PHE B 199 TRP 0.012 0.002 TRP B 391 HIS 0.006 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 7793) covalent geometry : angle 0.62341 (10592) SS BOND : bond 0.00443 ( 1) SS BOND : angle 0.38956 ( 2) hydrogen bonds : bond 0.03874 ( 367) hydrogen bonds : angle 5.12225 ( 1047) Misc. bond : bond 0.00007 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.321 Fit side-chains REVERT: B 10 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6999 (mm-30) REVERT: B 118 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.5856 (mt-10) REVERT: B 206 GLU cc_start: 0.6824 (mm-30) cc_final: 0.6604 (mm-30) REVERT: B 446 VAL cc_start: 0.8584 (p) cc_final: 0.8230 (m) REVERT: B 486 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6870 (mtmm) REVERT: A 95 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6963 (mmt) REVERT: A 120 GLN cc_start: 0.5892 (OUTLIER) cc_final: 0.5593 (mt0) REVERT: A 172 TYR cc_start: 0.7653 (m-80) cc_final: 0.7194 (m-80) REVERT: A 185 GLU cc_start: 0.7936 (pm20) cc_final: 0.7562 (mp0) REVERT: A 263 MET cc_start: 0.6593 (tmm) cc_final: 0.6136 (tmm) REVERT: A 335 HIS cc_start: 0.6365 (OUTLIER) cc_final: 0.6104 (t70) REVERT: A 393 MET cc_start: 0.2716 (ttm) cc_final: 0.2167 (tpp) REVERT: A 500 ARG cc_start: 0.8110 (tmm-80) cc_final: 0.7886 (tmm-80) outliers start: 44 outliers final: 34 residues processed: 177 average time/residue: 0.1011 time to fit residues: 23.6831 Evaluate side-chains 186 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 486 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 441 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 22 optimal weight: 0.0770 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 0.2980 chunk 60 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.0470 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.179648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.161916 restraints weight = 11474.075| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 2.32 r_work: 0.4088 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7796 Z= 0.150 Angle : 0.631 8.398 10594 Z= 0.321 Chirality : 0.043 0.188 1189 Planarity : 0.005 0.051 1377 Dihedral : 7.474 79.909 1084 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.95 % Allowed : 27.78 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: -0.88 (0.28), residues: 953 helix: 0.48 (0.25), residues: 420 sheet: -1.54 (0.42), residues: 143 loop : -1.30 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.016 0.002 TYR A 172 PHE 0.011 0.001 PHE B 199 TRP 0.012 0.002 TRP A 476 HIS 0.005 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7793) covalent geometry : angle 0.63076 (10592) SS BOND : bond 0.00422 ( 1) SS BOND : angle 0.38075 ( 2) hydrogen bonds : bond 0.03792 ( 367) hydrogen bonds : angle 5.04313 ( 1047) Misc. bond : bond 0.00008 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.272 Fit side-chains REVERT: B 10 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7051 (mm-30) REVERT: B 118 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.5856 (mt-10) REVERT: B 446 VAL cc_start: 0.8598 (p) cc_final: 0.8248 (m) REVERT: B 486 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6850 (mtmm) REVERT: A 95 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6961 (mmt) REVERT: A 120 GLN cc_start: 0.5884 (OUTLIER) cc_final: 0.5560 (mt0) REVERT: A 172 TYR cc_start: 0.7600 (m-80) cc_final: 0.7215 (m-80) REVERT: A 185 GLU cc_start: 0.7897 (pm20) cc_final: 0.7535 (mp0) REVERT: A 263 MET cc_start: 0.6562 (tmm) cc_final: 0.6071 (tmm) REVERT: A 335 HIS cc_start: 0.6257 (OUTLIER) cc_final: 0.5992 (t70) REVERT: A 393 MET cc_start: 0.2861 (ttm) cc_final: 0.2498 (tpp) REVERT: A 500 ARG cc_start: 0.8084 (tmm-80) cc_final: 0.7879 (tmm-80) outliers start: 41 outliers final: 32 residues processed: 171 average time/residue: 0.0990 time to fit residues: 22.6050 Evaluate side-chains 180 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 486 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 441 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 chunk 26 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 90 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.179162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.161426 restraints weight = 11445.959| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.30 r_work: 0.4080 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7796 Z= 0.178 Angle : 0.653 9.167 10594 Z= 0.335 Chirality : 0.044 0.199 1189 Planarity : 0.005 0.051 1377 Dihedral : 7.523 79.677 1084 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 5.07 % Allowed : 27.54 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: -0.97 (0.28), residues: 953 helix: 0.42 (0.25), residues: 420 sheet: -1.77 (0.41), residues: 149 loop : -1.26 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.017 0.002 TYR A 172 PHE 0.014 0.002 PHE B 199 TRP 0.012 0.002 TRP A 391 HIS 0.006 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 7793) covalent geometry : angle 0.65274 (10592) SS BOND : bond 0.00963 ( 1) SS BOND : angle 2.29104 ( 2) hydrogen bonds : bond 0.03934 ( 367) hydrogen bonds : angle 5.10973 ( 1047) Misc. bond : bond 0.00004 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2224.87 seconds wall clock time: 39 minutes 0.74 seconds (2340.74 seconds total)