Starting phenix.real_space_refine on Tue Sep 24 09:12:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u65_41944/09_2024/8u65_41944.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u65_41944/09_2024/8u65_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u65_41944/09_2024/8u65_41944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u65_41944/09_2024/8u65_41944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u65_41944/09_2024/8u65_41944.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u65_41944/09_2024/8u65_41944.cif" } resolution = 3.01 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= 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 6.89, per 1000 atoms: 0.90 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: 2.11 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.91 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: 2.27 Time building geometry restraints manager: 2.37 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 512 or resid 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: 19.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.330 Find NCS groups from input model: 0.360 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.520 ------------------------------------------------------------------------------- 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 : 0.002 0.056 7793 Z= 0.164 Angle : 0.585 7.527 10592 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 : 12.11 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (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 TRP 0.015 0.001 TRP B 391 HIS 0.004 0.001 HIS A 179 PHE 0.010 0.001 PHE A 102 TYR 0.017 0.001 TYR A 172 ARG 0.003 0.000 ARG A 500 *********************** 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 fitting. rotamer outliers: 3 poor density : 160 time to evaluate : 0.787 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: 0.2098 time to fit residues: 44.2915 Evaluate side-chains 157 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 81 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 0.0770 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN A 302 GLN A 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7793 Z= 0.286 Angle : 0.626 6.846 10592 Z= 0.327 Chirality : 0.043 0.165 1189 Planarity : 0.005 0.051 1377 Dihedral : 7.386 82.575 1087 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.47 % Allowed : 27.29 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.28), residues: 953 helix: 0.39 (0.25), residues: 401 sheet: -1.81 (0.41), residues: 142 loop : -1.01 (0.33), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 391 HIS 0.006 0.001 HIS B 30 PHE 0.012 0.002 PHE B 199 TYR 0.021 0.002 TYR A 172 ARG 0.003 0.000 ARG B 371 *********************** 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 203 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 166 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: B 95 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.6862 (mpp) REVERT: B 163 MET cc_start: 0.6228 (ptp) cc_final: 0.5891 (ptm) REVERT: B 332 GLN cc_start: 0.6567 (pp30) cc_final: 0.6214 (pp30) REVERT: A 304 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7623 (mt) outliers start: 37 outliers final: 19 residues processed: 186 average time/residue: 0.2038 time to fit residues: 50.5619 Evaluate side-chains 179 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 284 SER Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 322 ARG 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 202 SER Chi-restraints excluded: chain A residue 252 VAL 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 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 441 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 59 optimal weight: 0.1980 chunk 24 optimal weight: 0.0970 chunk 87 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 70 optimal weight: 0.0470 overall best weight: 0.3476 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7793 Z= 0.222 Angle : 0.576 6.335 10592 Z= 0.301 Chirality : 0.042 0.206 1189 Planarity : 0.005 0.048 1377 Dihedral : 7.155 81.957 1084 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.35 % Allowed : 27.54 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.28), residues: 953 helix: 0.47 (0.25), residues: 407 sheet: -1.84 (0.41), residues: 144 loop : -1.12 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 476 HIS 0.005 0.001 HIS B 30 PHE 0.011 0.001 PHE B 199 TYR 0.015 0.001 TYR A 172 ARG 0.006 0.000 ARG A 500 *********************** 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 192 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 156 time to evaluate : 0.813 Fit side-chains REVERT: B 163 MET cc_start: 0.6221 (ptp) cc_final: 0.5990 (ptm) REVERT: B 206 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6511 (mm-30) REVERT: A 139 MET cc_start: 0.7717 (ptm) cc_final: 0.7507 (ptm) REVERT: A 263 MET cc_start: 0.6501 (tmm) cc_final: 0.6087 (tmm) REVERT: A 304 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7776 (mt) REVERT: A 335 HIS cc_start: 0.6305 (OUTLIER) cc_final: 0.6039 (t70) outliers start: 36 outliers final: 22 residues processed: 176 average time/residue: 0.1964 time to fit residues: 46.9223 Evaluate side-chains 176 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL 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 B residue 425 MET 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 335 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 390 THR 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 86 optimal weight: 0.8980 chunk 65 optimal weight: 0.0470 chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN B 374 HIS ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7793 Z= 0.261 Angle : 0.593 6.584 10592 Z= 0.308 Chirality : 0.043 0.214 1189 Planarity : 0.005 0.046 1377 Dihedral : 7.245 80.824 1084 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.28), residues: 953 helix: 0.47 (0.25), residues: 407 sheet: -1.84 (0.41), residues: 143 loop : -1.16 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 391 HIS 0.007 0.001 HIS B 30 PHE 0.014 0.002 PHE B 199 TYR 0.015 0.002 TYR A 172 ARG 0.002 0.000 ARG A 470 *********************** 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 199 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 156 time to evaluate : 0.840 Fit side-chains REVERT: B 10 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6973 (mm-30) REVERT: B 95 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6859 (mpp) REVERT: B 206 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6587 (mm-30) REVERT: A 263 MET cc_start: 0.6549 (tmm) cc_final: 0.6128 (tmm) REVERT: A 335 HIS cc_start: 0.6323 (OUTLIER) cc_final: 0.5960 (t70) REVERT: A 338 MET cc_start: 0.6441 (mmm) cc_final: 0.6175 (mmm) outliers start: 43 outliers final: 24 residues processed: 181 average time/residue: 0.1982 time to fit residues: 48.1354 Evaluate side-chains 179 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 153 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 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 359 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 40 GLU 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 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 420 SER 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 52 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 332 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 7793 Z= 0.408 Angle : 0.689 7.054 10592 Z= 0.360 Chirality : 0.045 0.221 1189 Planarity : 0.005 0.048 1377 Dihedral : 7.811 75.364 1084 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 6.04 % Allowed : 26.93 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.27), residues: 953 helix: 0.21 (0.25), residues: 398 sheet: -1.96 (0.43), residues: 135 loop : -1.25 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 391 HIS 0.009 0.001 HIS B 30 PHE 0.020 0.002 PHE B 199 TYR 0.017 0.002 TYR B 259 ARG 0.004 0.000 ARG A 500 *********************** 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 213 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 163 time to evaluate : 0.821 Fit side-chains REVERT: B 10 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7058 (mm-30) REVERT: B 32 LEU cc_start: 0.6804 (mt) cc_final: 0.6566 (mm) REVERT: B 95 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.6855 (mpp) REVERT: B 118 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6134 (mt-10) REVERT: B 206 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6760 (mm-30) REVERT: A 53 VAL cc_start: 0.5358 (OUTLIER) cc_final: 0.5084 (t) REVERT: A 171 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7781 (mt) REVERT: A 333 GLN cc_start: 0.6889 (mp10) cc_final: 0.6687 (pm20) REVERT: A 338 MET cc_start: 0.6467 (mmm) cc_final: 0.6203 (mmm) outliers start: 50 outliers final: 30 residues processed: 192 average time/residue: 0.2050 time to fit residues: 53.0025 Evaluate side-chains 199 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 206 GLU 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 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 23 PHE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 90 VAL 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 224 ASN Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 291 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 0.0020 chunk 92 optimal weight: 0.1980 chunk 77 optimal weight: 0.4980 chunk 43 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7793 Z= 0.214 Angle : 0.613 6.564 10592 Z= 0.319 Chirality : 0.043 0.234 1189 Planarity : 0.005 0.050 1377 Dihedral : 7.541 77.488 1084 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.83 % Allowed : 29.23 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.28), residues: 953 helix: 0.33 (0.25), residues: 416 sheet: -1.94 (0.41), residues: 148 loop : -1.21 (0.34), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 437 HIS 0.005 0.001 HIS B 30 PHE 0.010 0.001 PHE A 102 TYR 0.016 0.002 TYR A 172 ARG 0.002 0.000 ARG A 213 *********************** 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 fitting. rotamer outliers: 40 poor density : 156 time to evaluate : 0.816 Fit side-chains REVERT: B 10 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7017 (mm-30) REVERT: B 118 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.5990 (mt-10) REVERT: B 206 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6560 (mm-30) REVERT: B 379 CYS cc_start: 0.6787 (OUTLIER) cc_final: 0.6570 (p) REVERT: A 120 GLN cc_start: 0.5882 (OUTLIER) cc_final: 0.5576 (mt0) REVERT: A 263 MET cc_start: 0.6560 (tmm) cc_final: 0.6219 (tmm) outliers start: 40 outliers final: 26 residues processed: 182 average time/residue: 0.1934 time to fit residues: 47.1204 Evaluate side-chains 180 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 151 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 269 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 301 CYS 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 379 CYS 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 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 159 GLU 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 374 HIS Chi-restraints excluded: chain A residue 390 THR 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 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 0.0970 chunk 92 optimal weight: 0.5980 chunk 57 optimal weight: 0.0000 chunk 56 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 332 GLN A 433 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7793 Z= 0.261 Angle : 0.628 7.070 10592 Z= 0.325 Chirality : 0.043 0.199 1189 Planarity : 0.005 0.052 1377 Dihedral : 7.544 78.100 1084 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.95 % Allowed : 28.50 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.28), residues: 953 helix: 0.43 (0.25), residues: 412 sheet: -1.93 (0.41), residues: 148 loop : -1.18 (0.34), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 391 HIS 0.007 0.001 HIS B 30 PHE 0.013 0.002 PHE B 199 TYR 0.019 0.002 TYR A 172 ARG 0.003 0.000 ARG A 250 *********************** 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 189 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 148 time to evaluate : 0.942 Fit side-chains REVERT: B 10 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7058 (mm-30) REVERT: B 118 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.5982 (mt-10) REVERT: B 206 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6609 (mm-30) REVERT: B 379 CYS cc_start: 0.6781 (OUTLIER) cc_final: 0.6550 (p) REVERT: B 486 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6828 (mtmm) REVERT: A 120 GLN cc_start: 0.5891 (OUTLIER) cc_final: 0.5586 (mt0) REVERT: A 218 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7474 (tpt170) REVERT: A 263 MET cc_start: 0.6598 (tmm) cc_final: 0.6054 (tmm) REVERT: A 284 SER cc_start: 0.7726 (p) cc_final: 0.7429 (p) outliers start: 41 outliers final: 27 residues processed: 178 average time/residue: 0.2113 time to fit residues: 49.6630 Evaluate side-chains 178 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL 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 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 379 CYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 408 VAL 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 120 GLN Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 433 ASN 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 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 chunk 17 optimal weight: 0.0980 chunk 58 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 72 optimal weight: 0.3980 chunk 84 optimal weight: 0.0270 chunk 88 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 overall best weight: 0.2838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 329 GLN A 433 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7793 Z= 0.217 Angle : 0.640 16.819 10592 Z= 0.325 Chirality : 0.043 0.231 1189 Planarity : 0.005 0.052 1377 Dihedral : 7.481 78.768 1084 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.95 % Allowed : 28.86 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.28), residues: 953 helix: 0.37 (0.25), residues: 422 sheet: -1.86 (0.41), residues: 148 loop : -1.24 (0.34), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 391 HIS 0.005 0.001 HIS B 30 PHE 0.010 0.001 PHE A 102 TYR 0.014 0.002 TYR B 376 ARG 0.004 0.000 ARG A 250 *********************** 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 190 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 149 time to evaluate : 1.098 Fit side-chains REVERT: B 10 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7027 (mm-30) REVERT: B 118 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.5966 (mt-10) REVERT: B 206 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6547 (mm-30) REVERT: B 379 CYS cc_start: 0.6736 (OUTLIER) cc_final: 0.6509 (p) REVERT: A 120 GLN cc_start: 0.5878 (OUTLIER) cc_final: 0.5629 (mm-40) REVERT: A 263 MET cc_start: 0.6493 (tmm) cc_final: 0.6001 (tmm) REVERT: A 284 SER cc_start: 0.7694 (p) cc_final: 0.7443 (p) REVERT: A 338 MET cc_start: 0.6331 (OUTLIER) cc_final: 0.6041 (mmm) outliers start: 41 outliers final: 27 residues processed: 178 average time/residue: 0.2363 time to fit residues: 55.3908 Evaluate side-chains 180 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 149 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 69 VAL 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 338 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 408 VAL 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 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 333 GLN Chi-restraints excluded: chain A residue 338 MET 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 433 ASN 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 86 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 51 optimal weight: 0.0060 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 77 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 0.3980 chunk 56 optimal weight: 0.0870 chunk 91 optimal weight: 0.0370 overall best weight: 0.1852 ------------------------------------------------------------------------------- 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 433 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7793 Z= 0.199 Angle : 0.614 7.683 10592 Z= 0.317 Chirality : 0.043 0.215 1189 Planarity : 0.005 0.050 1377 Dihedral : 7.340 80.982 1084 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.71 % Allowed : 28.50 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.28), residues: 953 helix: 0.50 (0.25), residues: 422 sheet: -1.66 (0.43), residues: 141 loop : -1.23 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 476 HIS 0.005 0.001 HIS A 179 PHE 0.010 0.001 PHE A 102 TYR 0.013 0.001 TYR B 376 ARG 0.005 0.000 ARG A 250 *********************** 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 188 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 149 time to evaluate : 0.800 Fit side-chains REVERT: B 118 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.5930 (mt-10) REVERT: B 379 CYS cc_start: 0.6702 (OUTLIER) cc_final: 0.6485 (p) REVERT: A 95 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.7016 (mmm) REVERT: A 149 LEU cc_start: 0.8312 (mt) cc_final: 0.8108 (mp) REVERT: A 185 GLU cc_start: 0.7879 (pm20) cc_final: 0.7506 (mp0) REVERT: A 263 MET cc_start: 0.6404 (tmm) cc_final: 0.5859 (tmm) REVERT: A 284 SER cc_start: 0.7714 (p) cc_final: 0.7453 (p) REVERT: A 335 HIS cc_start: 0.6248 (OUTLIER) cc_final: 0.5855 (t70) REVERT: A 338 MET cc_start: 0.6271 (mmm) cc_final: 0.5894 (mmm) outliers start: 39 outliers final: 29 residues processed: 178 average time/residue: 0.2185 time to fit residues: 51.3723 Evaluate side-chains 176 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 69 VAL 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 335 HIS Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 408 VAL 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 115 LEU 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 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 433 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 95 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 81 optimal weight: 0.0070 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7793 Z= 0.271 Angle : 0.677 7.868 10592 Z= 0.346 Chirality : 0.044 0.217 1189 Planarity : 0.005 0.055 1377 Dihedral : 7.487 79.664 1084 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.71 % Allowed : 27.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.28), residues: 953 helix: 0.38 (0.25), residues: 424 sheet: -1.77 (0.41), residues: 148 loop : -1.30 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 391 HIS 0.006 0.001 HIS B 30 PHE 0.015 0.002 PHE B 199 TYR 0.016 0.002 TYR B 376 ARG 0.005 0.000 ARG A 250 ********************** 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 185 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 146 time to evaluate : 0.838 Fit side-chains REVERT: B 10 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7021 (mm-30) REVERT: B 118 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.5936 (mt-10) REVERT: B 136 MET cc_start: 0.8023 (tpt) cc_final: 0.7773 (mmm) REVERT: B 139 MET cc_start: 0.7209 (ttm) cc_final: 0.6925 (ttm) REVERT: B 379 CYS cc_start: 0.6722 (OUTLIER) cc_final: 0.6495 (p) REVERT: A 263 MET cc_start: 0.6581 (tmm) cc_final: 0.6095 (tmm) REVERT: A 335 HIS cc_start: 0.6342 (OUTLIER) cc_final: 0.6040 (t70) REVERT: A 338 MET cc_start: 0.6316 (mmm) cc_final: 0.5977 (mmm) outliers start: 39 outliers final: 31 residues processed: 173 average time/residue: 0.2172 time to fit residues: 49.5705 Evaluate side-chains 180 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 69 VAL 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 203 ASP 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 332 GLN Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET 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 115 LEU 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 335 HIS Chi-restraints excluded: chain A residue 337 MET 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 433 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 14 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.180475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.162619 restraints weight = 11335.181| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 2.33 r_work: 0.4073 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 7793 Z= 0.384 Angle : 1.061 59.199 10592 Z= 0.626 Chirality : 0.046 0.285 1189 Planarity : 0.007 0.151 1377 Dihedral : 7.500 79.653 1084 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.59 % Allowed : 28.14 % Favored : 67.27 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.28), residues: 953 helix: 0.36 (0.25), residues: 424 sheet: -1.81 (0.41), residues: 148 loop : -1.31 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 391 HIS 0.006 0.001 HIS B 30 PHE 0.014 0.002 PHE B 199 TYR 0.014 0.002 TYR B 376 ARG 0.004 0.000 ARG A 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2454.78 seconds wall clock time: 45 minutes 48.66 seconds (2748.66 seconds total)