Starting phenix.real_space_refine on Fri Oct 10 15:17:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qcp_18331/10_2025/8qcp_18331.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qcp_18331/10_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_18331/10_2025/8qcp_18331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qcp_18331/10_2025/8qcp_18331.map" model { file = "/net/cci-nas-00/data/ceres_data/8qcp_18331/10_2025/8qcp_18331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qcp_18331/10_2025/8qcp_18331.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.42, per 1000 atoms: 0.20 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: 0.52 Conformation dependent library (CDL) restraints added in 189.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.18 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: 1.37 Time building geometry restraints manager: 0.68 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: 0.00 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: 5.290 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: 0.040 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.410 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.210 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.003 0.001 ARG D 349 TYR 0.071 0.020 TYR A 310 PHE 0.040 0.010 PHE C 346 HIS 0.016 0.004 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.01111 ( 3489) covalent geometry : angle 1.85898 ( 4668) hydrogen bonds : bond 0.05400 ( 75) hydrogen bonds : angle 7.61548 ( 225) *********************** 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 : 0.235 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: B 331 LYS cc_start: 0.7915 (mttt) cc_final: 0.7644 (tttm) REVERT: B 340 LYS cc_start: 0.7699 (mttt) cc_final: 0.7186 (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: 0.8022 (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: 0.7492 (tptt) REVERT: A 321 LYS cc_start: 0.7804 (mttt) cc_final: 0.7517 (mttm) REVERT: A 351 GLN cc_start: 0.7859 (mt0) cc_final: 0.7597 (tt0) REVERT: C 307 GLN cc_start: 0.7493 (mt0) cc_final: 0.6802 (pm20) REVERT: C 311 LYS cc_start: 0.8265 (mttt) cc_final: 0.7841 (mtpt) 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: 0.7004 (pm20) REVERT: C 351 GLN cc_start: 0.8012 (mt0) cc_final: 0.7779 (tt0) REVERT: E 311 LYS cc_start: 0.8089 (mttt) cc_final: 0.6781 (mmtt) REVERT: E 321 LYS cc_start: 0.7921 (mttt) cc_final: 0.7618 (mttp) 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: 0.2067 time to fit residues: 33.3258 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 : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.136422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.124449 restraints weight = 17685.720| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.21 r_work: 0.3853 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3489 Z= 0.129 Angle : 0.651 7.197 4668 Z= 0.336 Chirality : 0.051 0.133 525 Planarity : 0.003 0.021 594 Dihedral : 6.930 26.248 462 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.78 % Allowed : 7.38 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 349 TYR 0.009 0.002 TYR C 310 PHE 0.012 0.001 PHE E 346 HIS 0.010 0.002 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3489) covalent geometry : angle 0.65098 ( 4668) hydrogen bonds : bond 0.02303 ( 75) hydrogen bonds : angle 5.21904 ( 225) *********************** 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 108 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.8108 (mttt) cc_final: 0.7778 (tttm) REVERT: B 338 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7954 (mt-10) REVERT: B 340 LYS cc_start: 0.8001 (mttt) cc_final: 0.7564 (mtpt) REVERT: B 345 ASP cc_start: 0.7783 (t0) cc_final: 0.7394 (t0) REVERT: B 347 LYS cc_start: 0.8402 (tttt) cc_final: 0.8050 (mmtt) REVERT: B 358 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8173 (m-30) REVERT: B 369 LYS cc_start: 0.8718 (mttp) cc_final: 0.8447 (mtpp) REVERT: D 331 LYS cc_start: 0.8159 (mttt) cc_final: 0.7884 (tttm) REVERT: D 338 GLU cc_start: 0.8642 (mt-10) cc_final: 0.7803 (pm20) REVERT: D 340 LYS cc_start: 0.8691 (mttt) cc_final: 0.8230 (mtpt) REVERT: D 347 LYS cc_start: 0.8282 (tttt) cc_final: 0.7391 (pttm) REVERT: F 311 LYS cc_start: 0.8439 (mttm) cc_final: 0.8067 (mmtt) REVERT: F 338 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7741 (mt-10) REVERT: F 340 LYS cc_start: 0.8110 (mttt) cc_final: 0.7664 (mtpt) REVERT: F 343 LYS cc_start: 0.8341 (mtmt) cc_final: 0.8084 (mtmm) REVERT: F 353 LYS cc_start: 0.8158 (tttt) cc_final: 0.7781 (tppt) REVERT: E 311 LYS cc_start: 0.8365 (mttt) cc_final: 0.7074 (mmtt) REVERT: E 340 LYS cc_start: 0.8173 (mttt) cc_final: 0.7893 (tttp) outliers start: 7 outliers final: 4 residues processed: 106 average time/residue: 0.1994 time to fit residues: 24.3916 Evaluate side-chains 92 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 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 21 optimal weight: 7.9990 chunk 14 optimal weight: 0.0970 chunk 13 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 overall best weight: 3.3984 ------------------------------------------------------------------------------- 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** B 368 ASN D 368 ASN F 329 HIS F 368 ASN A 351 GLN C 336 GLN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS E 327 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.132381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.120250 restraints weight = 17975.146| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.19 r_work: 0.3796 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3489 Z= 0.174 Angle : 0.583 4.618 4668 Z= 0.303 Chirality : 0.051 0.129 525 Planarity : 0.003 0.025 594 Dihedral : 6.185 23.802 462 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.78 % Allowed : 9.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 379 TYR 0.013 0.002 TYR E 310 PHE 0.004 0.001 PHE B 378 HIS 0.007 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 3489) covalent geometry : angle 0.58339 ( 4668) hydrogen bonds : bond 0.01884 ( 75) hydrogen bonds : angle 4.71012 ( 225) *********************** 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 93 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: B 347 LYS cc_start: 0.8406 (tttt) cc_final: 0.8042 (mmmt) REVERT: B 369 LYS cc_start: 0.8764 (mttp) cc_final: 0.8523 (ttmm) REVERT: D 338 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8441 (mt-10) REVERT: D 340 LYS cc_start: 0.8739 (mttt) cc_final: 0.8219 (mtpt) REVERT: D 347 LYS cc_start: 0.8289 (tttt) cc_final: 0.7414 (pttm) REVERT: F 311 LYS cc_start: 0.8433 (mttm) cc_final: 0.8071 (mmtt) REVERT: F 338 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7797 (mt-10) REVERT: F 340 LYS cc_start: 0.8133 (mttt) cc_final: 0.7688 (mtpt) REVERT: F 343 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8236 (mtmm) REVERT: F 347 LYS cc_start: 0.8566 (mmmt) cc_final: 0.7988 (mmtp) REVERT: C 307 GLN cc_start: 0.7633 (mt0) cc_final: 0.6775 (pm20) REVERT: E 311 LYS cc_start: 0.8337 (mttt) cc_final: 0.7114 (mmtt) REVERT: E 340 LYS cc_start: 0.8243 (mttt) cc_final: 0.7994 (tttp) REVERT: E 351 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8194 (tm-30) outliers start: 7 outliers final: 7 residues processed: 93 average time/residue: 0.1984 time to fit residues: 21.1739 Evaluate side-chains 83 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 320 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain E residue 305 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 28 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.131286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.119210 restraints weight = 18045.732| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.16 r_work: 0.3780 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3709 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.4796 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= 0.178 Angle : 0.565 4.877 4668 Z= 0.291 Chirality : 0.051 0.128 525 Planarity : 0.003 0.026 594 Dihedral : 5.877 22.535 462 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.32), 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 ARG 0.001 0.000 ARG E 379 TYR 0.012 0.002 TYR C 310 PHE 0.004 0.001 PHE E 346 HIS 0.006 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 3489) covalent geometry : angle 0.56524 ( 4668) hydrogen bonds : bond 0.01734 ( 75) hydrogen bonds : angle 4.59532 ( 225) *********************** 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 89 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: B 347 LYS cc_start: 0.8419 (tttt) cc_final: 0.8079 (mmmt) REVERT: B 369 LYS cc_start: 0.8786 (mttp) cc_final: 0.8521 (ttmm) REVERT: D 340 LYS cc_start: 0.8759 (mttt) cc_final: 0.8278 (mtpt) REVERT: D 347 LYS cc_start: 0.8368 (tttt) cc_final: 0.7558 (pttm) REVERT: F 311 LYS cc_start: 0.8390 (mttm) cc_final: 0.8121 (mmtt) REVERT: F 340 LYS cc_start: 0.8206 (mttt) cc_final: 0.7939 (mttp) REVERT: F 353 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7749 (tppt) REVERT: C 307 GLN cc_start: 0.7626 (mt0) cc_final: 0.6790 (pm20) REVERT: E 311 LYS cc_start: 0.8276 (mttt) cc_final: 0.7062 (mmtt) REVERT: E 340 LYS cc_start: 0.8276 (mttt) cc_final: 0.8011 (tttp) REVERT: E 351 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8236 (tm-30) outliers start: 9 outliers final: 6 residues processed: 85 average time/residue: 0.1940 time to fit residues: 19.0793 Evaluate side-chains 81 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 A residue 372 GLU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 372 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** 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 = 0.3963 r_free = 0.3963 target = 0.129792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.117824 restraints weight = 18071.116| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.16 r_work: 0.3759 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3489 Z= 0.200 Angle : 0.571 4.639 4668 Z= 0.294 Chirality : 0.051 0.127 525 Planarity : 0.003 0.026 594 Dihedral : 5.850 21.352 462 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.80 % Allowed : 9.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.29 (0.32), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.013 0.002 TYR C 310 PHE 0.005 0.001 PHE E 346 HIS 0.005 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 3489) covalent geometry : angle 0.57057 ( 4668) hydrogen bonds : bond 0.01754 ( 75) hydrogen bonds : angle 4.56805 ( 225) *********************** 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 91 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: B 347 LYS cc_start: 0.8364 (tttt) cc_final: 0.8033 (mmmt) REVERT: B 369 LYS cc_start: 0.8809 (mttp) cc_final: 0.8564 (ttmm) REVERT: D 340 LYS cc_start: 0.8743 (mttt) cc_final: 0.8261 (mtpt) REVERT: D 347 LYS cc_start: 0.8433 (tttt) cc_final: 0.7584 (pttm) REVERT: F 311 LYS cc_start: 0.8364 (mttm) cc_final: 0.8101 (mmtt) REVERT: F 340 LYS cc_start: 0.8214 (mttt) cc_final: 0.7951 (mttp) REVERT: C 307 GLN cc_start: 0.7615 (mt0) cc_final: 0.6772 (pm20) REVERT: E 311 LYS cc_start: 0.8292 (mttt) cc_final: 0.7130 (mmtt) REVERT: E 340 LYS cc_start: 0.8323 (mttt) cc_final: 0.8010 (tttp) REVERT: E 351 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8240 (tm-30) outliers start: 11 outliers final: 10 residues processed: 87 average time/residue: 0.1852 time to fit residues: 18.7048 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 : 0.174 ------------------------------------------------------------------------------- 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 D residue 341 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 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 30 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.132719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.120843 restraints weight = 17782.080| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.18 r_work: 0.3802 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.5159 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= 0.103 Angle : 0.503 4.118 4668 Z= 0.257 Chirality : 0.051 0.128 525 Planarity : 0.003 0.028 594 Dihedral : 5.455 20.519 462 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.27 % Allowed : 11.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.000 0.000 ARG E 379 TYR 0.008 0.002 TYR E 310 PHE 0.003 0.001 PHE A 346 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 3489) covalent geometry : angle 0.50304 ( 4668) hydrogen bonds : bond 0.01488 ( 75) hydrogen bonds : angle 4.35867 ( 225) *********************** 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 85 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: B 347 LYS cc_start: 0.8367 (tttt) cc_final: 0.8048 (mmmt) REVERT: B 369 LYS cc_start: 0.8757 (mttp) cc_final: 0.8517 (ttmm) REVERT: D 340 LYS cc_start: 0.8711 (mttt) cc_final: 0.8226 (mtpt) REVERT: D 347 LYS cc_start: 0.8414 (tttt) cc_final: 0.7565 (pttm) REVERT: F 311 LYS cc_start: 0.8405 (mttm) cc_final: 0.8129 (mmtt) REVERT: F 340 LYS cc_start: 0.8196 (mttt) cc_final: 0.7924 (mttp) REVERT: F 358 ASP cc_start: 0.8530 (t70) cc_final: 0.8071 (m-30) REVERT: E 311 LYS cc_start: 0.8243 (mttt) cc_final: 0.7102 (mmtt) REVERT: E 340 LYS cc_start: 0.8327 (mttt) cc_final: 0.8030 (tttp) REVERT: E 351 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8247 (tm-30) outliers start: 5 outliers final: 3 residues processed: 82 average time/residue: 0.1921 time to fit residues: 18.1563 Evaluate side-chains 81 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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** ** C 359 ASN ** 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 = 0.3993 r_free = 0.3993 target = 0.132506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.120580 restraints weight = 17815.871| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.19 r_work: 0.3794 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3489 Z= 0.131 Angle : 0.505 4.015 4668 Z= 0.258 Chirality : 0.051 0.125 525 Planarity : 0.003 0.028 594 Dihedral : 5.336 19.717 462 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.29 % Allowed : 9.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.001 0.000 ARG E 379 TYR 0.010 0.002 TYR E 310 PHE 0.003 0.001 PHE E 346 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3489) covalent geometry : angle 0.50466 ( 4668) hydrogen bonds : bond 0.01496 ( 75) hydrogen bonds : angle 4.23547 ( 225) *********************** 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 : 0.230 Fit side-chains revert: symmetry clash REVERT: B 347 LYS cc_start: 0.8374 (tttt) cc_final: 0.8073 (mmmt) REVERT: B 369 LYS cc_start: 0.8739 (mttp) cc_final: 0.8539 (ttmm) REVERT: D 340 LYS cc_start: 0.8730 (mttt) cc_final: 0.8226 (mtpt) REVERT: D 347 LYS cc_start: 0.8425 (tttt) cc_final: 0.7541 (pttm) REVERT: F 311 LYS cc_start: 0.8411 (mttm) cc_final: 0.8138 (mmtt) REVERT: F 340 LYS cc_start: 0.8170 (mttt) cc_final: 0.7921 (mttp) REVERT: F 358 ASP cc_start: 0.8515 (t70) cc_final: 0.8041 (m-30) REVERT: E 311 LYS cc_start: 0.8268 (mttt) cc_final: 0.7131 (mmtt) REVERT: E 340 LYS cc_start: 0.8311 (mttt) cc_final: 0.7986 (tttm) REVERT: E 351 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8198 (tm-30) outliers start: 9 outliers final: 8 residues processed: 86 average time/residue: 0.1905 time to fit residues: 18.9471 Evaluate side-chains 86 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 D residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 372 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 7 optimal weight: 0.0980 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.0970 chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.135872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.124010 restraints weight = 17597.970| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.21 r_work: 0.3838 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3767 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.5447 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= 0.079 Angle : 0.474 3.813 4668 Z= 0.241 Chirality : 0.051 0.129 525 Planarity : 0.003 0.029 594 Dihedral : 4.998 19.408 462 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.001 0.000 ARG A 349 TYR 0.006 0.001 TYR C 310 PHE 0.002 0.001 PHE A 346 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 3489) covalent geometry : angle 0.47409 ( 4668) hydrogen bonds : bond 0.01280 ( 75) hydrogen bonds : angle 4.06862 ( 225) *********************** 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: 6 poor density : 81 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: B 347 LYS cc_start: 0.8349 (tttt) cc_final: 0.8050 (mmmt) REVERT: D 340 LYS cc_start: 0.8726 (mttt) cc_final: 0.8225 (mtpt) REVERT: D 347 LYS cc_start: 0.8391 (tttt) cc_final: 0.7524 (pttm) REVERT: F 311 LYS cc_start: 0.8420 (mttm) cc_final: 0.8135 (mmtt) REVERT: F 340 LYS cc_start: 0.8144 (mttt) cc_final: 0.7910 (mttp) REVERT: F 358 ASP cc_start: 0.8508 (t70) cc_final: 0.8067 (m-30) REVERT: E 311 LYS cc_start: 0.8220 (mttt) cc_final: 0.7124 (mmtt) REVERT: E 340 LYS cc_start: 0.8327 (mttt) cc_final: 0.8002 (tttm) REVERT: E 351 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8182 (tm-30) outliers start: 6 outliers final: 5 residues processed: 85 average time/residue: 0.1748 time to fit residues: 17.2616 Evaluate side-chains 81 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 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 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.134810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.122933 restraints weight = 17664.060| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.20 r_work: 0.3826 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.5560 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= 0.101 Angle : 0.478 3.809 4668 Z= 0.243 Chirality : 0.051 0.125 525 Planarity : 0.003 0.030 594 Dihedral : 4.972 18.873 462 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.27 % Allowed : 11.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.001 0.000 ARG E 379 TYR 0.008 0.001 TYR C 310 PHE 0.003 0.001 PHE E 346 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 3489) covalent geometry : angle 0.47836 ( 4668) hydrogen bonds : bond 0.01328 ( 75) hydrogen bonds : angle 4.01505 ( 225) *********************** 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 83 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: B 347 LYS cc_start: 0.8349 (tttt) cc_final: 0.8058 (mmmt) REVERT: D 340 LYS cc_start: 0.8722 (mttt) cc_final: 0.8221 (mtpt) REVERT: D 347 LYS cc_start: 0.8425 (tttt) cc_final: 0.7554 (pttm) REVERT: F 311 LYS cc_start: 0.8405 (mttm) cc_final: 0.8127 (mmtt) REVERT: F 340 LYS cc_start: 0.8143 (mttt) cc_final: 0.7909 (mttp) REVERT: F 345 ASP cc_start: 0.7901 (t0) cc_final: 0.7649 (t0) REVERT: F 358 ASP cc_start: 0.8497 (t70) cc_final: 0.8057 (m-30) REVERT: A 317 LYS cc_start: 0.7878 (mttt) cc_final: 0.7509 (mtmt) REVERT: E 311 LYS cc_start: 0.8279 (mttt) cc_final: 0.7160 (mmtt) REVERT: E 340 LYS cc_start: 0.8354 (mttt) cc_final: 0.8004 (tttm) REVERT: E 351 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8171 (tm-30) outliers start: 5 outliers final: 5 residues processed: 81 average time/residue: 0.2022 time to fit residues: 18.9286 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 : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain C residue 305 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 329 HIS A 351 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.127536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.115412 restraints weight = 18376.537| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.18 r_work: 0.3718 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 3489 Z= 0.291 Angle : 0.616 4.668 4668 Z= 0.319 Chirality : 0.052 0.124 525 Planarity : 0.003 0.028 594 Dihedral : 5.739 21.571 462 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.04 % Allowed : 10.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.016 0.003 TYR E 310 PHE 0.010 0.001 PHE E 346 HIS 0.006 0.001 HIS F 329 Details of bonding type rmsd covalent geometry : bond 0.00671 ( 3489) covalent geometry : angle 0.61571 ( 4668) hydrogen bonds : bond 0.01819 ( 75) hydrogen bonds : angle 4.50471 ( 225) ********************** 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 79 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.208 Fit side-chains REVERT: B 347 LYS cc_start: 0.8380 (tttt) cc_final: 0.8080 (mmmt) REVERT: D 347 LYS cc_start: 0.8492 (tttt) cc_final: 0.7573 (pttp) REVERT: F 311 LYS cc_start: 0.8419 (mttm) cc_final: 0.8150 (mmtt) REVERT: F 340 LYS cc_start: 0.8224 (mttt) cc_final: 0.7986 (mttm) REVERT: F 345 ASP cc_start: 0.7996 (t0) cc_final: 0.7751 (t0) REVERT: E 351 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8208 (tm-30) outliers start: 8 outliers final: 6 residues processed: 75 average time/residue: 0.1592 time to fit residues: 14.0905 Evaluate side-chains 72 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain C residue 305 SER 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 12 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.131994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.120223 restraints weight = 17753.174| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.19 r_work: 0.3782 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.5741 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= 0.093 Angle : 0.503 4.020 4668 Z= 0.254 Chirality : 0.051 0.128 525 Planarity : 0.002 0.026 594 Dihedral : 5.211 19.238 462 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.27 % Allowed : 11.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.007 0.001 TYR C 310 PHE 0.003 0.001 PHE A 346 HIS 0.002 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 3489) covalent geometry : angle 0.50258 ( 4668) hydrogen bonds : bond 0.01442 ( 75) hydrogen bonds : angle 4.18105 ( 225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2089.67 seconds wall clock time: 36 minutes 9.55 seconds (2169.55 seconds total)