Starting phenix.real_space_refine on Wed Feb 12 02:12:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qcp_18331/02_2025/8qcp_18331.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qcp_18331/02_2025/8qcp_18331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qcp_18331/02_2025/8qcp_18331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qcp_18331/02_2025/8qcp_18331.map" model { file = "/net/cci-nas-00/data/ceres_data/8qcp_18331/02_2025/8qcp_18331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qcp_18331/02_2025/8qcp_18331.cif" } resolution = 3.21 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2154 2.51 5 N 630 2.21 5 O 645 1.98 5 H 3567 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7002 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "A" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 4.65, per 1000 atoms: 0.66 Number of scatterers: 7002 At special positions: 0 Unit cell: (138.13, 109.05, 47.255, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 645 8.00 N 630 7.00 C 2154 6.00 H 3567 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 1.6 seconds 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 306 through 310 Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.783A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 319 through 324 removed outlier: 6.316A pdb=" N SER B 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLY F 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYS B 322 " --> pdb=" O GLY F 323 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 337 through 341 Processing sheet with id=AA5, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.599A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 353 through 354 removed outlier: 6.393A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.412A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 368 through 371 removed outlier: 6.409A pdb=" N ASN B 368 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE F 371 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS B 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 374 through 377 removed outlier: 6.629A pdb=" N HIS B 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N THR F 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU B 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 306 through 310 Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.791A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.625A pdb=" N VAL A 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N LYS E 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER A 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 327 through 330 removed outlier: 6.870A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.548A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.151A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 357 through 362 Processing sheet with id=AB8, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.512A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) 75 hydrogen bonds defined for protein. 225 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: 2.48 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 3561 1.11 - 1.29: 573 1.29 - 1.46: 950 1.46 - 1.64: 1966 1.64 - 1.81: 6 Bond restraints: 7056 Sorted by residual: bond pdb=" N GLY E 367 " pdb=" H GLY E 367 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N HIS E 362 " pdb=" H HIS E 362 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N HIS B 362 " pdb=" H HIS B 362 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" NE2 GLN C 336 " pdb="HE21 GLN C 336 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N GLY A 334 " pdb=" H GLY A 334 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 7051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 10908 2.59 - 5.19: 1508 5.19 - 7.78: 421 7.78 - 10.37: 15 10.37 - 12.96: 6 Bond angle restraints: 12858 Sorted by residual: angle pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " pdb=" CD2 HIS C 374 " ideal model delta sigma weight residual 131.20 124.41 6.79 1.30e+00 5.92e-01 2.73e+01 angle pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 131.20 124.70 6.50 1.30e+00 5.92e-01 2.50e+01 angle pdb=" N LYS F 317 " pdb=" CA LYS F 317 " pdb=" C LYS F 317 " ideal model delta sigma weight residual 110.44 116.25 -5.81 1.20e+00 6.94e-01 2.35e+01 angle pdb=" CA ASP E 358 " pdb=" CB ASP E 358 " pdb=" CG ASP E 358 " ideal model delta sigma weight residual 112.60 117.36 -4.76 1.00e+00 1.00e+00 2.26e+01 angle pdb=" C ASP B 348 " pdb=" N ARG B 349 " pdb=" CA ARG B 349 " ideal model delta sigma weight residual 120.90 127.48 -6.58 1.41e+00 5.03e-01 2.18e+01 ... (remaining 12853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.23: 2813 14.23 - 28.45: 228 28.45 - 42.68: 81 42.68 - 56.91: 66 56.91 - 71.13: 64 Dihedral angle restraints: 3252 sinusoidal: 1857 harmonic: 1395 Sorted by residual: dihedral pdb=" CA LYS E 343 " pdb=" C LYS E 343 " pdb=" N LEU E 344 " pdb=" CA LEU E 344 " ideal model delta harmonic sigma weight residual 180.00 150.51 29.49 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA LYS C 343 " pdb=" C LYS C 343 " pdb=" N LEU C 344 " pdb=" CA LEU C 344 " ideal model delta harmonic sigma weight residual 180.00 151.60 28.40 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA LYS A 343 " pdb=" C LYS A 343 " pdb=" N LEU A 344 " pdb=" CA LEU A 344 " ideal model delta harmonic sigma weight residual 180.00 151.67 28.33 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 3249 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.080: 344 0.080 - 0.159: 141 0.159 - 0.238: 33 0.238 - 0.317: 4 0.317 - 0.397: 3 Chirality restraints: 525 Sorted by residual: chirality pdb=" CA LYS F 317 " pdb=" N LYS F 317 " pdb=" C LYS F 317 " pdb=" CB LYS F 317 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CA LEU B 325 " pdb=" N LEU B 325 " pdb=" C LEU B 325 " pdb=" CB LEU B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA LEU C 325 " pdb=" N LEU C 325 " pdb=" C LEU C 325 " pdb=" CB LEU C 325 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 522 not shown) Planarity restraints: 1023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 374 " 0.069 2.00e-02 2.50e+03 3.94e-02 3.50e+01 pdb=" CG HIS C 374 " -0.032 2.00e-02 2.50e+03 pdb=" ND1 HIS C 374 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 HIS C 374 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 HIS C 374 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS C 374 " -0.022 2.00e-02 2.50e+03 pdb=" HD2 HIS C 374 " -0.013 2.00e-02 2.50e+03 pdb=" HE1 HIS C 374 " 0.019 2.00e-02 2.50e+03 pdb=" HE2 HIS C 374 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 346 " -0.081 2.00e-02 2.50e+03 3.37e-02 3.41e+01 pdb=" CG PHE C 346 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 PHE C 346 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 346 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE C 346 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE C 346 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE C 346 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE C 346 " 0.030 2.00e-02 2.50e+03 pdb=" HD2 PHE C 346 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 PHE C 346 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 PHE C 346 " -0.021 2.00e-02 2.50e+03 pdb=" HZ PHE C 346 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.081 2.00e-02 2.50e+03 3.28e-02 3.22e+01 pdb=" CG TYR A 310 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.058 2.00e-02 2.50e+03 pdb=" HD1 TYR A 310 " 0.008 2.00e-02 2.50e+03 pdb=" HD2 TYR A 310 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 TYR A 310 " 0.009 2.00e-02 2.50e+03 pdb=" HE2 TYR A 310 " 0.004 2.00e-02 2.50e+03 ... (remaining 1020 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 585 2.19 - 2.79: 12518 2.79 - 3.39: 18047 3.39 - 4.00: 24454 4.00 - 4.60: 34817 Nonbonded interactions: 90421 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.587 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.603 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.610 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.620 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.638 2.450 ... (remaining 90416 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 304 through 378) selection = chain 'B' selection = (chain 'C' and resid 304 through 378) selection = chain 'D' selection = (chain 'E' and resid 304 through 378) selection = chain 'F' } 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: 3.030 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: 0.120 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.770 Find NCS groups from input model: 0.210 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 : 0.011 0.036 3489 Z= 0.750 Angle : 1.859 7.579 4668 Z= 1.233 Chirality : 0.092 0.397 525 Planarity : 0.009 0.038 594 Dihedral : 11.524 58.039 1332 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.004 HIS A 330 PHE 0.040 0.010 PHE C 346 TYR 0.071 0.020 TYR A 310 ARG 0.003 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.7915 (mttt) cc_final: 0.7644 (tttm) REVERT: B 340 LYS cc_start: 0.7699 (mttt) cc_final: 0.7187 (mtpt) REVERT: B 347 LYS cc_start: 0.8228 (tttt) cc_final: 0.8009 (mmmt) REVERT: D 318 VAL cc_start: 0.7290 (m) cc_final: 0.6957 (m) REVERT: D 331 LYS cc_start: 0.8007 (mttt) cc_final: 0.7713 (tttm) REVERT: D 338 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7469 (pm20) REVERT: D 340 LYS cc_start: 0.8560 (mttt) cc_final: 0.8023 (mtpt) REVERT: D 347 LYS cc_start: 0.8028 (tttt) cc_final: 0.7820 (mtmt) REVERT: D 369 LYS cc_start: 0.8730 (mttt) cc_final: 0.8426 (mtmm) REVERT: F 311 LYS cc_start: 0.8168 (mttm) cc_final: 0.7618 (mmtt) REVERT: F 338 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7309 (mt-10) REVERT: F 340 LYS cc_start: 0.7723 (mttt) cc_final: 0.7192 (mtpt) REVERT: F 343 LYS cc_start: 0.8349 (mtmt) cc_final: 0.8114 (mtmm) REVERT: F 353 LYS cc_start: 0.7707 (tttt) cc_final: 0.7424 (tppt) REVERT: A 321 LYS cc_start: 0.7804 (mttt) cc_final: 0.7516 (mttm) REVERT: A 351 GLN cc_start: 0.7859 (mt0) cc_final: 0.7596 (tt0) REVERT: C 307 GLN cc_start: 0.7493 (mt0) cc_final: 0.6801 (pm20) REVERT: C 321 LYS cc_start: 0.8383 (mttt) cc_final: 0.8122 (mttp) REVERT: C 342 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7003 (pm20) REVERT: C 351 GLN cc_start: 0.8012 (mt0) cc_final: 0.7780 (tt0) REVERT: E 311 LYS cc_start: 0.8089 (mttt) cc_final: 0.6783 (mmtt) REVERT: E 321 LYS cc_start: 0.7921 (mttt) cc_final: 0.7618 (mttp) REVERT: E 338 GLU cc_start: 0.7582 (tt0) cc_final: 0.7382 (tt0) REVERT: E 340 LYS cc_start: 0.7724 (mttt) cc_final: 0.7325 (tttt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.4936 time to fit residues: 79.5395 Evaluate side-chains 93 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.131608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.119648 restraints weight = 17921.183| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.16 r_work: 0.3788 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3489 Z= 0.391 Angle : 0.724 7.501 4668 Z= 0.379 Chirality : 0.051 0.156 525 Planarity : 0.004 0.025 594 Dihedral : 7.124 27.268 462 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.78 % Allowed : 7.63 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.95 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS D 330 PHE 0.009 0.001 PHE E 346 TYR 0.014 0.002 TYR C 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.8217 (mttt) cc_final: 0.7753 (tttm) REVERT: B 338 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8026 (mt-10) REVERT: B 340 LYS cc_start: 0.8052 (mttt) cc_final: 0.7594 (mtpt) REVERT: B 345 ASP cc_start: 0.7860 (t0) cc_final: 0.7504 (t0) REVERT: B 347 LYS cc_start: 0.8411 (tttt) cc_final: 0.8061 (mmtt) REVERT: B 370 LYS cc_start: 0.8651 (tttm) cc_final: 0.8394 (tttp) REVERT: D 331 LYS cc_start: 0.8160 (mttt) cc_final: 0.7942 (tttm) REVERT: D 338 GLU cc_start: 0.8665 (mt-10) cc_final: 0.7835 (pm20) REVERT: D 340 LYS cc_start: 0.8726 (mttt) cc_final: 0.8240 (mtpt) REVERT: D 347 LYS cc_start: 0.8347 (tttt) cc_final: 0.7482 (pttm) REVERT: D 372 GLU cc_start: 0.5777 (tp30) cc_final: 0.5528 (tp30) REVERT: F 311 LYS cc_start: 0.8420 (mttm) cc_final: 0.8146 (mmtt) REVERT: F 338 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7802 (mt-10) REVERT: F 340 LYS cc_start: 0.8171 (mttt) cc_final: 0.7704 (mtpt) REVERT: F 343 LYS cc_start: 0.8413 (mtmt) cc_final: 0.8181 (mtmm) REVERT: C 307 GLN cc_start: 0.7663 (mt0) cc_final: 0.6882 (pm20) REVERT: E 311 LYS cc_start: 0.8371 (mttt) cc_final: 0.7130 (mmtt) REVERT: E 340 LYS cc_start: 0.8218 (mttt) cc_final: 0.7907 (tttp) REVERT: E 351 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8225 (tm-30) outliers start: 7 outliers final: 6 residues processed: 101 average time/residue: 0.4733 time to fit residues: 54.8863 Evaluate side-chains 90 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain E residue 305 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 13 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 0.0270 chunk 4 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS F 330 HIS C 336 GLN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.134501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.122702 restraints weight = 17823.441| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.19 r_work: 0.3834 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3489 Z= 0.174 Angle : 0.554 4.593 4668 Z= 0.286 Chirality : 0.051 0.132 525 Planarity : 0.003 0.023 594 Dihedral : 6.065 23.679 462 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.53 % Allowed : 10.69 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 330 PHE 0.005 0.001 PHE C 346 TYR 0.008 0.002 TYR C 310 ARG 0.003 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 338 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7987 (mt-10) REVERT: B 345 ASP cc_start: 0.7863 (t0) cc_final: 0.7567 (t0) REVERT: B 347 LYS cc_start: 0.8392 (tttt) cc_final: 0.8102 (mmtt) REVERT: B 369 LYS cc_start: 0.8757 (mttp) cc_final: 0.8435 (mtpp) REVERT: D 331 LYS cc_start: 0.8089 (mttt) cc_final: 0.7865 (tttm) REVERT: D 338 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8294 (mt-10) REVERT: D 340 LYS cc_start: 0.8717 (mttt) cc_final: 0.8225 (mtpt) REVERT: D 347 LYS cc_start: 0.8260 (tttt) cc_final: 0.7385 (pttm) REVERT: D 372 GLU cc_start: 0.5505 (tp30) cc_final: 0.5272 (tp30) REVERT: F 311 LYS cc_start: 0.8422 (mttm) cc_final: 0.8101 (mmtt) REVERT: F 338 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7776 (mt-10) REVERT: F 340 LYS cc_start: 0.8183 (mttt) cc_final: 0.7719 (mtpt) REVERT: F 343 LYS cc_start: 0.8430 (mtmt) cc_final: 0.8173 (mtmm) REVERT: F 353 LYS cc_start: 0.8327 (ttmt) cc_final: 0.7597 (tppt) REVERT: C 307 GLN cc_start: 0.7618 (mt0) cc_final: 0.6828 (pm20) REVERT: E 311 LYS cc_start: 0.8327 (mttt) cc_final: 0.7103 (mmtt) REVERT: E 340 LYS cc_start: 0.8244 (mttt) cc_final: 0.8042 (tttp) REVERT: E 351 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8206 (tm-30) outliers start: 6 outliers final: 3 residues processed: 95 average time/residue: 0.4674 time to fit residues: 51.1608 Evaluate side-chains 83 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain A residue 372 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 28 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS A 351 GLN C 351 GLN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.134053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.122284 restraints weight = 17954.739| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.20 r_work: 0.3827 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3489 Z= 0.179 Angle : 0.516 4.322 4668 Z= 0.264 Chirality : 0.051 0.127 525 Planarity : 0.003 0.026 594 Dihedral : 5.578 21.806 462 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.53 % Allowed : 10.69 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 330 PHE 0.002 0.001 PHE A 346 TYR 0.009 0.002 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: B 338 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8036 (mt-10) REVERT: B 347 LYS cc_start: 0.8384 (tttt) cc_final: 0.8041 (mmmt) REVERT: B 369 LYS cc_start: 0.8779 (mttp) cc_final: 0.8561 (ttmm) REVERT: B 372 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7416 (mt-10) REVERT: D 331 LYS cc_start: 0.8104 (mttt) cc_final: 0.7866 (tttm) REVERT: D 338 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8369 (mt-10) REVERT: D 340 LYS cc_start: 0.8729 (mttt) cc_final: 0.8234 (mtpt) REVERT: D 347 LYS cc_start: 0.8278 (tttt) cc_final: 0.7442 (pttm) REVERT: F 311 LYS cc_start: 0.8444 (mttm) cc_final: 0.8118 (mmtt) REVERT: F 340 LYS cc_start: 0.8173 (mttt) cc_final: 0.7883 (mttm) REVERT: F 343 LYS cc_start: 0.8466 (mtmt) cc_final: 0.8234 (mtmm) REVERT: F 353 LYS cc_start: 0.8281 (ttmt) cc_final: 0.8067 (tptt) REVERT: C 314 ASP cc_start: 0.8905 (t0) cc_final: 0.8699 (t0) REVERT: E 311 LYS cc_start: 0.8319 (mttt) cc_final: 0.7108 (mmtt) REVERT: E 340 LYS cc_start: 0.8240 (mttt) cc_final: 0.8029 (tttp) outliers start: 6 outliers final: 5 residues processed: 88 average time/residue: 0.4343 time to fit residues: 44.6645 Evaluate side-chains 82 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain C residue 359 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN D 368 ASN F 329 HIS F 368 ASN A 351 GLN C 351 GLN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.131720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.119881 restraints weight = 17933.829| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.16 r_work: 0.3792 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3489 Z= 0.249 Angle : 0.532 4.390 4668 Z= 0.273 Chirality : 0.051 0.127 525 Planarity : 0.003 0.025 594 Dihedral : 5.558 21.111 462 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.80 % Allowed : 9.41 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.005 0.001 PHE E 346 TYR 0.011 0.002 TYR C 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 338 GLU cc_start: 0.8249 (mt-10) cc_final: 0.8020 (mt-10) REVERT: B 347 LYS cc_start: 0.8394 (tttt) cc_final: 0.8066 (mmmt) REVERT: B 369 LYS cc_start: 0.8774 (mttp) cc_final: 0.8507 (ttmm) REVERT: D 331 LYS cc_start: 0.8117 (mttt) cc_final: 0.7911 (tttm) REVERT: D 340 LYS cc_start: 0.8720 (mttt) cc_final: 0.8214 (mtpt) REVERT: D 347 LYS cc_start: 0.8383 (tttt) cc_final: 0.7564 (pttm) REVERT: F 311 LYS cc_start: 0.8419 (mttm) cc_final: 0.8126 (mmtt) REVERT: F 340 LYS cc_start: 0.8170 (mttt) cc_final: 0.7889 (mttm) REVERT: F 343 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8319 (mtmm) REVERT: E 311 LYS cc_start: 0.8269 (mttt) cc_final: 0.7048 (mmtt) REVERT: E 340 LYS cc_start: 0.8264 (mttt) cc_final: 0.8012 (tttp) outliers start: 11 outliers final: 10 residues processed: 89 average time/residue: 0.4586 time to fit residues: 47.2790 Evaluate side-chains 87 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 372 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 24 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN C 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.132197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.120206 restraints weight = 17772.019| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.15 r_work: 0.3791 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3489 Z= 0.223 Angle : 0.520 4.310 4668 Z= 0.266 Chirality : 0.050 0.127 525 Planarity : 0.003 0.026 594 Dihedral : 5.429 20.682 462 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.29 % Allowed : 10.43 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 329 PHE 0.005 0.001 PHE E 346 TYR 0.010 0.002 TYR C 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: B 338 GLU cc_start: 0.8231 (mt-10) cc_final: 0.8007 (mt-10) REVERT: B 347 LYS cc_start: 0.8387 (tttt) cc_final: 0.8053 (mmmt) REVERT: B 369 LYS cc_start: 0.8797 (mttp) cc_final: 0.8545 (ttmm) REVERT: B 372 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7427 (mt-10) REVERT: D 331 LYS cc_start: 0.8119 (mttt) cc_final: 0.7833 (mtpt) REVERT: D 340 LYS cc_start: 0.8737 (mttt) cc_final: 0.8264 (mtpt) REVERT: D 347 LYS cc_start: 0.8408 (tttt) cc_final: 0.7569 (pttm) REVERT: F 311 LYS cc_start: 0.8396 (mttm) cc_final: 0.8128 (mmtt) REVERT: F 340 LYS cc_start: 0.8187 (mttt) cc_final: 0.7920 (mttm) REVERT: E 311 LYS cc_start: 0.8276 (mttt) cc_final: 0.7103 (mmtt) REVERT: E 340 LYS cc_start: 0.8328 (mttt) cc_final: 0.8059 (tttp) REVERT: E 351 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8258 (tm-30) outliers start: 9 outliers final: 8 residues processed: 85 average time/residue: 0.4730 time to fit residues: 46.4568 Evaluate side-chains 85 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 305 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 0.0000 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN C 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.135809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.123846 restraints weight = 17350.276| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.13 r_work: 0.3829 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3489 Z= 0.141 Angle : 0.475 3.930 4668 Z= 0.242 Chirality : 0.051 0.127 525 Planarity : 0.003 0.028 594 Dihedral : 5.043 19.983 462 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.29 % Allowed : 9.41 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 362 PHE 0.003 0.001 PHE A 346 TYR 0.007 0.001 TYR C 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: B 338 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7952 (mt-10) REVERT: B 347 LYS cc_start: 0.8380 (tttt) cc_final: 0.8069 (mmmt) REVERT: B 369 LYS cc_start: 0.8764 (mttp) cc_final: 0.8561 (ttmm) REVERT: B 372 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7447 (mt-10) REVERT: D 331 LYS cc_start: 0.8066 (mttt) cc_final: 0.7789 (mtpt) REVERT: D 338 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8314 (mt-10) REVERT: D 340 LYS cc_start: 0.8699 (mttt) cc_final: 0.8230 (mtpt) REVERT: D 341 SER cc_start: 0.9258 (m) cc_final: 0.8783 (p) REVERT: D 347 LYS cc_start: 0.8404 (tttt) cc_final: 0.7511 (pttm) REVERT: F 311 LYS cc_start: 0.8446 (mttm) cc_final: 0.8149 (mmtt) REVERT: F 340 LYS cc_start: 0.8159 (mttt) cc_final: 0.7918 (mttm) REVERT: E 311 LYS cc_start: 0.8243 (mttt) cc_final: 0.7102 (mmtt) REVERT: E 340 LYS cc_start: 0.8328 (mttt) cc_final: 0.8074 (tttm) REVERT: E 351 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8239 (tm-30) outliers start: 9 outliers final: 8 residues processed: 87 average time/residue: 0.4294 time to fit residues: 43.6008 Evaluate side-chains 87 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 305 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.133635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.121525 restraints weight = 17606.820| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.13 r_work: 0.3793 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3489 Z= 0.225 Angle : 0.511 4.074 4668 Z= 0.260 Chirality : 0.051 0.125 525 Planarity : 0.003 0.025 594 Dihedral : 5.178 19.517 462 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.54 % Allowed : 9.67 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 329 PHE 0.005 0.001 PHE E 346 TYR 0.011 0.002 TYR C 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: B 338 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7947 (mt-10) REVERT: B 347 LYS cc_start: 0.8363 (tttt) cc_final: 0.8044 (mmmt) REVERT: B 369 LYS cc_start: 0.8750 (mttp) cc_final: 0.8550 (ttmm) REVERT: B 372 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7417 (mt-10) REVERT: D 331 LYS cc_start: 0.8093 (mttt) cc_final: 0.7802 (mtpt) REVERT: D 338 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8206 (mt-10) REVERT: D 340 LYS cc_start: 0.8720 (mttt) cc_final: 0.8228 (mtpt) REVERT: D 347 LYS cc_start: 0.8425 (tttt) cc_final: 0.7529 (pttm) REVERT: F 311 LYS cc_start: 0.8419 (mttm) cc_final: 0.8149 (mmtt) REVERT: F 340 LYS cc_start: 0.8195 (mttt) cc_final: 0.7951 (mttm) REVERT: A 317 LYS cc_start: 0.7941 (mttt) cc_final: 0.7528 (mtmt) REVERT: E 311 LYS cc_start: 0.8290 (mttt) cc_final: 0.7160 (mmtt) REVERT: E 340 LYS cc_start: 0.8370 (mttt) cc_final: 0.8059 (tttp) REVERT: E 351 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8221 (tm-30) REVERT: E 370 LYS cc_start: 0.8923 (ttpt) cc_final: 0.8706 (ttpp) outliers start: 10 outliers final: 10 residues processed: 84 average time/residue: 0.4766 time to fit residues: 46.1908 Evaluate side-chains 86 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 372 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.134933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.122729 restraints weight = 17613.272| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.17 r_work: 0.3811 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3489 Z= 0.157 Angle : 0.480 3.965 4668 Z= 0.243 Chirality : 0.050 0.126 525 Planarity : 0.003 0.027 594 Dihedral : 4.989 19.408 462 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.54 % Allowed : 9.92 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.34), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 329 PHE 0.003 0.001 PHE E 346 TYR 0.008 0.001 TYR C 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.612 Fit side-chains REVERT: B 338 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7929 (mt-10) REVERT: B 347 LYS cc_start: 0.8374 (tttt) cc_final: 0.8063 (mmmt) REVERT: B 372 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7374 (mt-10) REVERT: D 331 LYS cc_start: 0.8085 (mttt) cc_final: 0.7803 (mtpt) REVERT: D 338 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8330 (mt-10) REVERT: D 340 LYS cc_start: 0.8712 (mttt) cc_final: 0.8199 (mtpt) REVERT: D 347 LYS cc_start: 0.8445 (tttt) cc_final: 0.7549 (pttm) REVERT: F 311 LYS cc_start: 0.8438 (mttm) cc_final: 0.8157 (mmtt) REVERT: F 340 LYS cc_start: 0.8161 (mttt) cc_final: 0.7925 (mttm) REVERT: F 358 ASP cc_start: 0.8507 (t70) cc_final: 0.8080 (m-30) REVERT: E 311 LYS cc_start: 0.8284 (mttt) cc_final: 0.7138 (mmtt) REVERT: E 340 LYS cc_start: 0.8359 (mttt) cc_final: 0.8041 (tttm) REVERT: E 351 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8221 (tm-30) REVERT: E 370 LYS cc_start: 0.8918 (ttpt) cc_final: 0.8704 (ttpp) outliers start: 10 outliers final: 10 residues processed: 85 average time/residue: 0.4295 time to fit residues: 42.5368 Evaluate side-chains 85 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 372 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.137357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.125262 restraints weight = 17567.698| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.16 r_work: 0.3843 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.5541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3489 Z= 0.128 Angle : 0.476 5.394 4668 Z= 0.238 Chirality : 0.051 0.126 525 Planarity : 0.003 0.028 594 Dihedral : 4.716 18.725 462 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.78 % Allowed : 10.94 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.34), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 362 PHE 0.002 0.000 PHE A 346 TYR 0.006 0.001 TYR C 310 ARG 0.001 0.000 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.615 Fit side-chains REVERT: B 338 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7876 (mt-10) REVERT: B 347 LYS cc_start: 0.8402 (tttt) cc_final: 0.8113 (mmmt) REVERT: B 372 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7360 (mt-10) REVERT: D 331 LYS cc_start: 0.8081 (mttt) cc_final: 0.7822 (mtpt) REVERT: D 338 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8320 (mt-10) REVERT: D 340 LYS cc_start: 0.8684 (mttt) cc_final: 0.8195 (mtpt) REVERT: D 347 LYS cc_start: 0.8408 (tttt) cc_final: 0.7493 (pttm) REVERT: F 311 LYS cc_start: 0.8506 (mttm) cc_final: 0.8169 (mmtt) REVERT: F 340 LYS cc_start: 0.8120 (mttt) cc_final: 0.7904 (mttp) REVERT: F 345 ASP cc_start: 0.7913 (t0) cc_final: 0.7676 (t0) REVERT: F 358 ASP cc_start: 0.8501 (t70) cc_final: 0.8091 (m-30) REVERT: E 311 LYS cc_start: 0.8232 (mttt) cc_final: 0.7115 (mmtt) REVERT: E 370 LYS cc_start: 0.8911 (ttpt) cc_final: 0.8694 (ttpp) outliers start: 7 outliers final: 6 residues processed: 83 average time/residue: 0.4121 time to fit residues: 40.1923 Evaluate side-chains 80 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 305 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 7 optimal weight: 0.3980 chunk 11 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.135875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.123872 restraints weight = 17413.269| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.14 r_work: 0.3825 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3489 Z= 0.167 Angle : 0.486 4.352 4668 Z= 0.243 Chirality : 0.051 0.124 525 Planarity : 0.003 0.025 594 Dihedral : 4.760 18.486 462 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.29 % Allowed : 10.43 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.34), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 362 PHE 0.003 0.001 PHE E 346 TYR 0.008 0.001 TYR C 310 ARG 0.001 0.000 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4252.51 seconds wall clock time: 75 minutes 39.05 seconds (4539.05 seconds total)