Starting phenix.real_space_refine on Fri Jun 6 02:18:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qcp_18331/06_2025/8qcp_18331.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qcp_18331/06_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_18331/06_2025/8qcp_18331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qcp_18331/06_2025/8qcp_18331.map" model { file = "/net/cci-nas-00/data/ceres_data/8qcp_18331/06_2025/8qcp_18331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qcp_18331/06_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-5710/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: 4.43, per 1000 atoms: 0.63 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: 1.76 Conformation dependent library (CDL) restraints added in 631.5 milliseconds 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: 0.72 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: 2.03 Time building geometry restraints manager: 2.03 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: 3.080 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: 0.110 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.110 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.600 ------------------------------------------------------------------------------- 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= 0.704 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 Details of bonding type rmsd hydrogen bonds : bond 0.05400 ( 75) hydrogen bonds : angle 7.61548 ( 225) covalent geometry : bond 0.01111 ( 3489) covalent geometry : angle 1.85898 ( 4668) *********************** 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 : 0.545 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: 0.4861 time to fit residues: 78.3769 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 : 0.552 ------------------------------------------------------------------------------- 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 = 0.131675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.119729 restraints weight = 17927.448| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.16 r_work: 0.3788 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3540 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= 0.253 Angle : 0.724 7.505 4668 Z= 0.379 Chirality : 0.051 0.156 525 Planarity : 0.004 0.025 594 Dihedral : 7.122 27.268 462 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 1.14 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 Details of bonding type rmsd hydrogen bonds : bond 0.02488 ( 75) hydrogen bonds : angle 5.32584 ( 225) covalent geometry : bond 0.00591 ( 3489) covalent geometry : angle 0.72409 ( 4668) *********************** 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 : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.8214 (mttt) cc_final: 0.7747 (tttm) REVERT: B 338 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8029 (mt-10) REVERT: B 340 LYS cc_start: 0.8052 (mttt) cc_final: 0.7592 (mtpt) REVERT: B 345 ASP cc_start: 0.7861 (t0) cc_final: 0.7502 (t0) REVERT: B 347 LYS cc_start: 0.8411 (tttt) cc_final: 0.8057 (mmtt) REVERT: B 370 LYS cc_start: 0.8650 (tttm) cc_final: 0.8392 (tttp) REVERT: D 331 LYS cc_start: 0.8158 (mttt) cc_final: 0.7938 (tttm) REVERT: D 338 GLU cc_start: 0.8664 (mt-10) cc_final: 0.7835 (pm20) REVERT: D 340 LYS cc_start: 0.8727 (mttt) cc_final: 0.8240 (mtpt) REVERT: D 347 LYS cc_start: 0.8352 (tttt) cc_final: 0.7482 (pttm) REVERT: D 372 GLU cc_start: 0.5777 (tp30) cc_final: 0.5526 (tp30) REVERT: F 311 LYS cc_start: 0.8422 (mttm) cc_final: 0.8146 (mmtt) REVERT: F 338 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7802 (mt-10) REVERT: F 340 LYS cc_start: 0.8169 (mttt) cc_final: 0.7701 (mtpt) REVERT: F 343 LYS cc_start: 0.8414 (mtmt) cc_final: 0.8182 (mtmm) REVERT: C 307 GLN cc_start: 0.7664 (mt0) cc_final: 0.6881 (pm20) REVERT: E 311 LYS cc_start: 0.8370 (mttt) cc_final: 0.7133 (mmtt) REVERT: E 340 LYS cc_start: 0.8217 (mttt) cc_final: 0.7902 (tttp) REVERT: E 351 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8224 (tm-30) outliers start: 7 outliers final: 6 residues processed: 101 average time/residue: 0.4508 time to fit residues: 52.2550 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 : 0.531 ------------------------------------------------------------------------------- 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: 0.9990 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 35 optimal weight: 7.9990 chunk 16 optimal weight: 0.0980 chunk 4 optimal weight: 7.9990 chunk 28 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.136740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.125017 restraints weight = 17721.321| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.21 r_work: 0.3864 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3489 Z= 0.092 Angle : 0.537 4.450 4668 Z= 0.277 Chirality : 0.051 0.133 525 Planarity : 0.003 0.023 594 Dihedral : 5.988 23.398 462 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.02 % Allowed : 11.45 % 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: -2.03 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 330 PHE 0.008 0.001 PHE C 346 TYR 0.007 0.001 TYR C 310 ARG 0.002 0.001 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01797 ( 75) hydrogen bonds : angle 4.83829 ( 225) covalent geometry : bond 0.00212 ( 3489) covalent geometry : angle 0.53658 ( 4668) *********************** 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: 4 poor density : 93 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 338 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7881 (mt-10) REVERT: B 340 LYS cc_start: 0.8068 (mttt) cc_final: 0.7613 (mtpt) REVERT: B 345 ASP cc_start: 0.7845 (t0) cc_final: 0.7509 (t0) REVERT: B 347 LYS cc_start: 0.8395 (tttt) cc_final: 0.8048 (mmmt) REVERT: B 369 LYS cc_start: 0.8753 (mttp) cc_final: 0.8421 (mtpp) REVERT: B 370 LYS cc_start: 0.8603 (tttm) cc_final: 0.8379 (tttp) REVERT: D 338 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8284 (mt-10) REVERT: D 340 LYS cc_start: 0.8712 (mttt) cc_final: 0.8220 (mtpt) REVERT: D 347 LYS cc_start: 0.8175 (tttt) cc_final: 0.7303 (pttm) REVERT: D 372 GLU cc_start: 0.5735 (tp30) cc_final: 0.5492 (tp30) REVERT: F 311 LYS cc_start: 0.8394 (mttm) cc_final: 0.8078 (mmtt) REVERT: F 338 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7686 (mt-10) REVERT: F 340 LYS cc_start: 0.8169 (mttt) cc_final: 0.7692 (mtpt) REVERT: F 343 LYS cc_start: 0.8381 (mtmt) cc_final: 0.8121 (mtmm) REVERT: F 353 LYS cc_start: 0.8310 (ttmt) cc_final: 0.7635 (tppt) REVERT: C 314 ASP cc_start: 0.8891 (t0) cc_final: 0.8581 (t0) REVERT: E 311 LYS cc_start: 0.8357 (mttt) cc_final: 0.7092 (mmtt) REVERT: E 351 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8172 (tm-30) outliers start: 4 outliers final: 1 residues processed: 96 average time/residue: 0.4498 time to fit residues: 49.8653 Evaluate side-chains 80 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 324 SER 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: 6.9990 chunk 34 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS B 330 HIS B 368 ASN F 368 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.132097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.120178 restraints weight = 18141.170| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.19 r_work: 0.3800 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3489 Z= 0.178 Angle : 0.553 4.701 4668 Z= 0.285 Chirality : 0.051 0.129 525 Planarity : 0.003 0.026 594 Dihedral : 5.836 22.584 462 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.53 % Allowed : 10.94 % 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: -2.10 (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 0.004 0.001 HIS B 330 PHE 0.003 0.001 PHE A 346 TYR 0.011 0.002 TYR C 310 ARG 0.002 0.001 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01844 ( 75) hydrogen bonds : angle 4.66540 ( 225) covalent geometry : bond 0.00415 ( 3489) covalent geometry : angle 0.55347 ( 4668) *********************** 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 84 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 338 GLU cc_start: 0.8246 (mt-10) cc_final: 0.8014 (mt-10) REVERT: B 347 LYS cc_start: 0.8401 (tttt) cc_final: 0.8032 (mmmt) REVERT: B 369 LYS cc_start: 0.8758 (mttp) cc_final: 0.8510 (ttmm) REVERT: D 338 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8272 (mt-10) REVERT: D 340 LYS cc_start: 0.8735 (mttt) cc_final: 0.8245 (mtpt) REVERT: D 347 LYS cc_start: 0.8292 (tttt) cc_final: 0.7473 (pttm) REVERT: F 311 LYS cc_start: 0.8438 (mttm) cc_final: 0.8110 (mmtt) REVERT: F 338 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7824 (mt-10) REVERT: F 340 LYS cc_start: 0.8194 (mttt) cc_final: 0.7733 (mtpt) REVERT: F 343 LYS cc_start: 0.8468 (mtmt) cc_final: 0.8222 (mtmm) REVERT: F 353 LYS cc_start: 0.8292 (ttmt) cc_final: 0.8084 (tptt) REVERT: C 307 GLN cc_start: 0.7618 (mt0) cc_final: 0.6794 (pm20) REVERT: E 311 LYS cc_start: 0.8340 (mttt) cc_final: 0.7154 (mmtt) REVERT: E 351 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8183 (tm-30) outliers start: 6 outliers final: 5 residues processed: 82 average time/residue: 0.4371 time to fit residues: 41.7552 Evaluate side-chains 79 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 D 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: 0.0570 chunk 4 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 368 ASN F 329 HIS C 351 GLN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.130916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.118977 restraints weight = 17903.970| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.16 r_work: 0.3781 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3489 Z= 0.170 Angle : 0.551 4.484 4668 Z= 0.282 Chirality : 0.051 0.127 525 Planarity : 0.003 0.025 594 Dihedral : 5.702 21.543 462 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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: -2.19 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 329 PHE 0.005 0.001 PHE E 346 TYR 0.012 0.002 TYR E 310 ARG 0.001 0.000 ARG C 349 Details of bonding type rmsd hydrogen bonds : bond 0.01722 ( 75) hydrogen bonds : angle 4.51933 ( 225) covalent geometry : bond 0.00392 ( 3489) covalent geometry : angle 0.55121 ( 4668) *********************** 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 88 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: B 338 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8056 (mt-10) REVERT: B 347 LYS cc_start: 0.8412 (tttt) cc_final: 0.8066 (mmmt) REVERT: B 353 LYS cc_start: 0.8403 (tptt) cc_final: 0.8171 (tptt) REVERT: B 369 LYS cc_start: 0.8795 (mttp) cc_final: 0.8539 (ttmm) REVERT: B 372 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7507 (mt-10) REVERT: D 340 LYS cc_start: 0.8732 (mttt) cc_final: 0.8222 (mtpt) REVERT: D 347 LYS cc_start: 0.8405 (tttt) cc_final: 0.7602 (pttm) REVERT: F 311 LYS cc_start: 0.8402 (mttm) cc_final: 0.8128 (mmtt) REVERT: F 340 LYS cc_start: 0.8181 (mttt) cc_final: 0.7895 (mttm) REVERT: F 343 LYS cc_start: 0.8516 (mtmt) cc_final: 0.8311 (mtmm) REVERT: F 353 LYS cc_start: 0.8289 (ttmt) cc_final: 0.8071 (tptt) REVERT: E 311 LYS cc_start: 0.8276 (mttt) cc_final: 0.7073 (mmtt) REVERT: E 351 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8185 (tm-30) outliers start: 11 outliers final: 10 residues processed: 84 average time/residue: 0.4042 time to fit residues: 40.2612 Evaluate side-chains 83 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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: 2.9990 chunk 21 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.131068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.119235 restraints weight = 17904.102| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.14 r_work: 0.3783 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3489 Z= 0.154 Angle : 0.529 4.392 4668 Z= 0.271 Chirality : 0.051 0.127 525 Planarity : 0.003 0.026 594 Dihedral : 5.499 20.783 462 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % 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: -2.18 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 329 PHE 0.004 0.001 PHE E 346 TYR 0.011 0.002 TYR C 310 ARG 0.001 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01645 ( 75) hydrogen bonds : angle 4.43511 ( 225) covalent geometry : bond 0.00356 ( 3489) covalent geometry : angle 0.52904 ( 4668) *********************** 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 87 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: B 338 GLU cc_start: 0.8237 (mt-10) cc_final: 0.8016 (mt-10) REVERT: B 347 LYS cc_start: 0.8398 (tttt) cc_final: 0.8048 (mmmt) REVERT: B 369 LYS cc_start: 0.8784 (mttp) cc_final: 0.8524 (ttmm) REVERT: B 372 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7422 (mt-10) REVERT: D 340 LYS cc_start: 0.8738 (mttt) cc_final: 0.8264 (mtpt) REVERT: D 347 LYS cc_start: 0.8447 (tttt) cc_final: 0.7584 (pttm) REVERT: F 311 LYS cc_start: 0.8397 (mttm) cc_final: 0.8144 (mmtt) REVERT: F 340 LYS cc_start: 0.8168 (mttt) cc_final: 0.7900 (mttm) REVERT: E 311 LYS cc_start: 0.8265 (mttt) cc_final: 0.7151 (mmtt) REVERT: E 351 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8185 (tm-30) outliers start: 10 outliers final: 9 residues processed: 85 average time/residue: 0.4029 time to fit residues: 40.6641 Evaluate side-chains 82 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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 = 0.3991 r_free = 0.3991 target = 0.132323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.120290 restraints weight = 17663.139| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.12 r_work: 0.3788 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.5352 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= 0.145 Angle : 0.521 4.247 4668 Z= 0.266 Chirality : 0.051 0.126 525 Planarity : 0.003 0.026 594 Dihedral : 5.390 20.508 462 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.80 % Allowed : 9.92 % 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: -2.20 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 329 PHE 0.004 0.001 PHE E 346 TYR 0.010 0.002 TYR C 310 ARG 0.001 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01613 ( 75) hydrogen bonds : angle 4.36630 ( 225) covalent geometry : bond 0.00336 ( 3489) covalent geometry : angle 0.52131 ( 4668) *********************** 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 85 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: B 338 GLU cc_start: 0.8213 (mt-10) cc_final: 0.8004 (mt-10) REVERT: B 347 LYS cc_start: 0.8388 (tttt) cc_final: 0.8068 (mmmt) REVERT: B 369 LYS cc_start: 0.8744 (mttp) cc_final: 0.8499 (ttmm) REVERT: B 372 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7482 (mt-10) REVERT: D 340 LYS cc_start: 0.8715 (mttt) cc_final: 0.8240 (mtpt) REVERT: D 347 LYS cc_start: 0.8451 (tttt) cc_final: 0.7585 (pttm) REVERT: F 311 LYS cc_start: 0.8411 (mttm) cc_final: 0.8151 (mmtt) REVERT: F 340 LYS cc_start: 0.8237 (mttt) cc_final: 0.7986 (mttm) REVERT: F 358 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8082 (m-30) REVERT: E 311 LYS cc_start: 0.8294 (mttt) cc_final: 0.7173 (mmtt) REVERT: E 351 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8176 (tm-30) outliers start: 11 outliers final: 9 residues processed: 81 average time/residue: 0.4115 time to fit residues: 39.8957 Evaluate side-chains 82 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.134004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.121965 restraints weight = 17630.537| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.13 r_work: 0.3809 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3489 Z= 0.114 Angle : 0.493 4.004 4668 Z= 0.251 Chirality : 0.051 0.126 525 Planarity : 0.003 0.027 594 Dihedral : 5.127 20.012 462 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.04 % Allowed : 11.45 % Favored : 86.51 % 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 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 329 PHE 0.003 0.001 PHE E 346 TYR 0.008 0.002 TYR C 310 ARG 0.001 0.000 ARG C 349 Details of bonding type rmsd hydrogen bonds : bond 0.01490 ( 75) hydrogen bonds : angle 4.23849 ( 225) covalent geometry : bond 0.00268 ( 3489) covalent geometry : angle 0.49301 ( 4668) *********************** 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 87 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: B 338 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7913 (mt-10) REVERT: B 347 LYS cc_start: 0.8381 (tttt) cc_final: 0.8113 (mmmt) REVERT: B 372 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7417 (mt-10) REVERT: D 338 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8325 (mt-10) REVERT: D 340 LYS cc_start: 0.8716 (mttt) cc_final: 0.8208 (mtpt) REVERT: D 347 LYS cc_start: 0.8468 (tttt) cc_final: 0.7559 (pttm) REVERT: F 311 LYS cc_start: 0.8423 (mttm) cc_final: 0.8157 (mmtt) REVERT: F 340 LYS cc_start: 0.8187 (mttt) cc_final: 0.7949 (mttm) REVERT: F 358 ASP cc_start: 0.8519 (t70) cc_final: 0.8076 (m-30) REVERT: A 317 LYS cc_start: 0.7930 (mttt) cc_final: 0.7511 (mtmt) REVERT: E 311 LYS cc_start: 0.8264 (mttt) cc_final: 0.7159 (mmtt) REVERT: E 351 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8175 (tm-30) outliers start: 8 outliers final: 7 residues processed: 84 average time/residue: 0.3929 time to fit residues: 39.4980 Evaluate side-chains 80 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 0.0870 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 0.0000 chunk 0 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 overall best weight: 0.9164 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.137224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.125219 restraints weight = 17460.025| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.15 r_work: 0.3849 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3489 Z= 0.078 Angle : 0.475 3.803 4668 Z= 0.240 Chirality : 0.051 0.137 525 Planarity : 0.003 0.029 594 Dihedral : 4.778 19.157 462 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.76 % Allowed : 12.47 % Favored : 86.77 % 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: -2.11 (0.34), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 362 PHE 0.002 0.001 PHE A 346 TYR 0.006 0.001 TYR C 310 ARG 0.001 0.000 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.01279 ( 75) hydrogen bonds : angle 4.02664 ( 225) covalent geometry : bond 0.00195 ( 3489) covalent geometry : angle 0.47466 ( 4668) *********************** 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 80 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: B 338 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7882 (mt-10) REVERT: B 347 LYS cc_start: 0.8378 (tttt) cc_final: 0.8116 (mmmt) REVERT: B 372 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7342 (mt-10) REVERT: D 338 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8308 (mt-10) REVERT: D 340 LYS cc_start: 0.8691 (mttt) cc_final: 0.8181 (mtpt) REVERT: D 347 LYS cc_start: 0.8456 (tttt) cc_final: 0.7577 (pttm) REVERT: F 311 LYS cc_start: 0.8513 (mttm) cc_final: 0.8179 (mmtt) REVERT: F 340 LYS cc_start: 0.8130 (mttt) cc_final: 0.7912 (mttm) REVERT: F 358 ASP cc_start: 0.8498 (t70) cc_final: 0.8062 (m-30) REVERT: E 311 LYS cc_start: 0.8238 (mttt) cc_final: 0.7126 (mmtt) REVERT: E 351 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8145 (tm-30) outliers start: 3 outliers final: 3 residues processed: 79 average time/residue: 0.3844 time to fit residues: 36.2490 Evaluate side-chains 76 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain A 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: 3.9990 chunk 25 optimal weight: 8.9990 chunk 27 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.138944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.126997 restraints weight = 17503.139| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.15 r_work: 0.3876 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3804 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3489 Z= 0.075 Angle : 0.454 3.599 4668 Z= 0.230 Chirality : 0.051 0.125 525 Planarity : 0.002 0.027 594 Dihedral : 4.553 18.452 462 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.51 % Allowed : 13.23 % Favored : 86.26 % 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 0.005 0.001 TYR C 310 ARG 0.001 0.000 ARG F 349 Details of bonding type rmsd hydrogen bonds : bond 0.01261 ( 75) hydrogen bonds : angle 3.84013 ( 225) covalent geometry : bond 0.00185 ( 3489) covalent geometry : angle 0.45410 ( 4668) ********************** 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 78 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: B 338 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7863 (mt-10) REVERT: B 347 LYS cc_start: 0.8393 (tttt) cc_final: 0.8154 (mmmt) REVERT: B 372 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7395 (mt-10) REVERT: D 347 LYS cc_start: 0.8428 (tttt) cc_final: 0.7541 (pttm) REVERT: F 311 LYS cc_start: 0.8512 (mttm) cc_final: 0.8169 (mmtt) REVERT: F 340 LYS cc_start: 0.8105 (mttt) cc_final: 0.7901 (mttp) REVERT: F 345 ASP cc_start: 0.7916 (t0) cc_final: 0.7686 (t0) REVERT: F 358 ASP cc_start: 0.8466 (t70) cc_final: 0.8036 (m-30) REVERT: E 311 LYS cc_start: 0.8238 (mttt) cc_final: 0.7141 (mmtt) REVERT: E 351 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8123 (tm-30) outliers start: 2 outliers final: 2 residues processed: 77 average time/residue: 0.3561 time to fit residues: 32.7454 Evaluate side-chains 74 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain A residue 372 GLU 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: 2.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3996 r_free = 0.3996 target = 0.133202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.121053 restraints weight = 17629.031| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.14 r_work: 0.3790 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3489 Z= 0.165 Angle : 0.517 3.967 4668 Z= 0.262 Chirality : 0.051 0.125 525 Planarity : 0.003 0.024 594 Dihedral : 4.945 18.213 462 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.53 % Allowed : 13.49 % Favored : 84.99 % 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 : -1.61 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 329 PHE 0.006 0.001 PHE E 346 TYR 0.011 0.002 TYR E 310 ARG 0.001 0.000 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.01481 ( 75) hydrogen bonds : angle 4.02289 ( 225) covalent geometry : bond 0.00379 ( 3489) covalent geometry : angle 0.51673 ( 4668) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4573.87 seconds wall clock time: 78 minutes 26.72 seconds (4706.72 seconds total)