Starting phenix.real_space_refine on Wed Mar 12 03:31:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxr_45009/03_2025/9bxr_45009.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxr_45009/03_2025/9bxr_45009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bxr_45009/03_2025/9bxr_45009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxr_45009/03_2025/9bxr_45009.map" model { file = "/net/cci-nas-00/data/ceres_data/9bxr_45009/03_2025/9bxr_45009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxr_45009/03_2025/9bxr_45009.cif" } resolution = 3.2 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 2202 2.51 5 N 648 2.21 5 O 672 1.98 5 H 3656 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7184 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1198 Classifications: {'peptide': 77} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "F" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1197 Classifications: {'peptide': 77} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1198 Classifications: {'peptide': 77} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "G" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1197 Classifications: {'peptide': 77} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "E" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1197 Classifications: {'peptide': 77} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "H" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1197 Classifications: {'peptide': 77} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Time building chain proxies: 4.32, per 1000 atoms: 0.60 Number of scatterers: 7184 At special positions: 0 Unit cell: (134.274, 107.586, 39.198, 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 672 8.00 N 648 7.00 C 2202 6.00 H 3656 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: 1.79 Conformation dependent library (CDL) restraints added in 608.0 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 804 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 7.064A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL D 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.617A pdb=" N LYS D 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N SER E 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR D 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N CYS E 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS D 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 336 through 340 Processing sheet with id=AA5, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.305A pdb=" N ASP C 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASP D 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 369 through 373 removed outlier: 7.037A pdb=" N LYS C 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLU D 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE C 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LYS D 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N GLU E 372 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE D 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 306 through 310 removed outlier: 6.546A pdb=" N GLN F 307 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N TYR G 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL F 309 " --> pdb=" O TYR G 310 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN G 307 " --> pdb=" O ILE H 308 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N TYR H 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL G 309 " --> pdb=" O TYR H 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 313 through 314 removed outlier: 6.748A pdb=" N VAL F 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL G 313 " --> pdb=" O ASP H 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 317 through 318 removed outlier: 6.372A pdb=" N LYS F 317 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LYS G 317 " --> pdb=" O VAL H 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 328 through 330 Processing sheet with id=AB2, first strand: chain 'F' and resid 336 through 340 Processing sheet with id=AB3, first strand: chain 'F' and resid 343 through 346 Processing sheet with id=AB4, first strand: chain 'F' and resid 356 through 358 Processing sheet with id=AB5, first strand: chain 'F' and resid 361 through 362 Processing sheet with id=AB6, first strand: chain 'F' and resid 369 through 371 49 hydrogen bonds defined for protein. 147 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: 2.09 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3650 1.12 - 1.29: 600 1.29 - 1.46: 1007 1.46 - 1.64: 1975 1.64 - 1.81: 6 Bond restraints: 7238 Sorted by residual: bond pdb=" NE2 GLN E 307 " pdb="HE21 GLN E 307 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" N GLU E 338 " pdb=" H GLU E 338 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N LEU G 357 " pdb=" H LEU G 357 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.74e+01 bond pdb=" CE1 HIS G 362 " pdb=" HE1 HIS G 362 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N LEU H 357 " pdb=" H LEU H 357 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 7233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 10877 2.42 - 4.83: 1806 4.83 - 7.25: 446 7.25 - 9.66: 57 9.66 - 12.08: 6 Bond angle restraints: 13192 Sorted by residual: angle pdb=" CA ASP G 348 " pdb=" CB ASP G 348 " pdb=" CG ASP G 348 " ideal model delta sigma weight residual 112.60 117.21 -4.61 1.00e+00 1.00e+00 2.12e+01 angle pdb=" CA ASP F 348 " pdb=" CB ASP F 348 " pdb=" CG ASP F 348 " ideal model delta sigma weight residual 112.60 117.21 -4.61 1.00e+00 1.00e+00 2.12e+01 angle pdb=" CA ASP H 348 " pdb=" CB ASP H 348 " pdb=" CG ASP H 348 " ideal model delta sigma weight residual 112.60 117.17 -4.57 1.00e+00 1.00e+00 2.09e+01 angle pdb=" CB HIS H 329 " pdb=" CG HIS H 329 " pdb=" CD2 HIS H 329 " ideal model delta sigma weight residual 131.20 125.34 5.86 1.30e+00 5.92e-01 2.03e+01 angle pdb=" CB HIS G 329 " pdb=" CG HIS G 329 " pdb=" CD2 HIS G 329 " ideal model delta sigma weight residual 131.20 125.35 5.85 1.30e+00 5.92e-01 2.03e+01 ... (remaining 13187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 2934 16.79 - 33.58: 241 33.58 - 50.37: 37 50.37 - 67.16: 111 67.16 - 83.96: 3 Dihedral angle restraints: 3326 sinusoidal: 1902 harmonic: 1424 Sorted by residual: dihedral pdb=" CA ILE H 360 " pdb=" C ILE H 360 " pdb=" N THR H 361 " pdb=" CA THR H 361 " ideal model delta harmonic sigma weight residual 180.00 155.96 24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ILE F 360 " pdb=" C ILE F 360 " pdb=" N THR F 361 " pdb=" CA THR F 361 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ILE G 360 " pdb=" C ILE G 360 " pdb=" N THR G 361 " pdb=" CA THR G 361 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 3323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 275 0.065 - 0.129: 200 0.129 - 0.193: 53 0.193 - 0.257: 0 0.257 - 0.322: 6 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA GLU D 380 " pdb=" N GLU D 380 " pdb=" C GLU D 380 " pdb=" CB GLU D 380 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA GLU C 380 " pdb=" N GLU C 380 " pdb=" C GLU C 380 " pdb=" CB GLU C 380 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA GLU E 380 " pdb=" N GLU E 380 " pdb=" C GLU E 380 " pdb=" CB GLU E 380 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 531 not shown) Planarity restraints: 1056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 346 " -0.085 2.00e-02 2.50e+03 3.30e-02 3.27e+01 pdb=" CG PHE G 346 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE G 346 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE G 346 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE G 346 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE G 346 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE G 346 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 PHE G 346 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 PHE G 346 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 PHE G 346 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE G 346 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE G 346 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 346 " -0.085 2.00e-02 2.50e+03 3.30e-02 3.27e+01 pdb=" CG PHE F 346 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE F 346 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE F 346 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE F 346 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE F 346 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE F 346 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 PHE F 346 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 PHE F 346 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 PHE F 346 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE F 346 " -0.008 2.00e-02 2.50e+03 pdb=" HZ PHE F 346 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 346 " -0.085 2.00e-02 2.50e+03 3.30e-02 3.26e+01 pdb=" CG PHE H 346 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE H 346 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE H 346 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE H 346 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE H 346 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE H 346 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 PHE H 346 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 PHE H 346 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 PHE H 346 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE H 346 " -0.008 2.00e-02 2.50e+03 pdb=" HZ PHE H 346 " -0.042 2.00e-02 2.50e+03 ... (remaining 1053 not shown) Histogram of nonbonded interaction distances: 0.32 - 1.18: 20 1.18 - 2.03: 339 2.03 - 2.89: 16323 2.89 - 3.74: 29034 3.74 - 4.60: 46232 Warning: very small nonbonded interaction distances. Nonbonded interactions: 91948 Sorted by model distance: nonbonded pdb=" HG SER G 352 " pdb=" O SER H 352 " model vdw 0.322 2.450 nonbonded pdb=" HG SER F 352 " pdb=" O SER G 352 " model vdw 0.363 2.450 nonbonded pdb="HD23 LEU C 325 " pdb="HD11 LEU D 325 " model vdw 0.718 2.440 nonbonded pdb="HD23 LEU D 325 " pdb="HD11 LEU E 325 " model vdw 0.768 2.440 nonbonded pdb=" HA ILE G 354 " pdb="HD13 ILE H 354 " model vdw 0.797 2.440 ... (remaining 91943 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 'C' and (resid 304 through 329 or (resid 330 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 331 through 380)) selection = (chain 'D' and (resid 304 through 329 or (resid 330 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 331 through 380)) selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.000 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: 0.130 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.570 Find NCS groups from input model: 0.200 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 0.042 3582 Z= 0.782 Angle : 1.867 6.584 4794 Z= 1.214 Chirality : 0.087 0.322 534 Planarity : 0.008 0.035 618 Dihedral : 11.163 83.955 1380 Min Nonbonded Distance : 0.991 Molprobity Statistics. All-atom Clashscore : 32.81 Ramachandran Plot: Outliers : 1.33 % Allowed : 6.67 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % 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: -2.61 (0.28), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.21), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS G 362 PHE 0.058 0.012 PHE F 346 TYR 0.057 0.021 TYR D 310 ARG 0.001 0.000 ARG H 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.606 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: C 338 GLU cc_start: 0.6385 (mp0) cc_final: 0.6061 (mp0) REVERT: C 369 LYS cc_start: 0.8214 (pttt) cc_final: 0.7940 (ptpt) REVERT: F 337 VAL cc_start: 0.7330 (t) cc_final: 0.6935 (t) REVERT: F 338 GLU cc_start: 0.6578 (mp0) cc_final: 0.6244 (mp0) REVERT: F 379 ARG cc_start: 0.6781 (ptp-170) cc_final: 0.5941 (ptm160) REVERT: D 353 LYS cc_start: 0.7642 (mttt) cc_final: 0.7149 (mmtm) REVERT: D 369 LYS cc_start: 0.8059 (pttt) cc_final: 0.7749 (ptpt) REVERT: G 336 GLN cc_start: 0.6780 (mt0) cc_final: 0.5728 (mp-120) REVERT: G 337 VAL cc_start: 0.7166 (t) cc_final: 0.6504 (t) REVERT: G 338 GLU cc_start: 0.6400 (mp0) cc_final: 0.5362 (mp0) REVERT: G 340 LYS cc_start: 0.6194 (mmtm) cc_final: 0.5795 (tptp) REVERT: G 372 GLU cc_start: 0.8434 (tt0) cc_final: 0.8077 (mt-10) REVERT: G 379 ARG cc_start: 0.6391 (ptp-170) cc_final: 0.6026 (ptm-80) REVERT: E 317 LYS cc_start: 0.8090 (ptmt) cc_final: 0.7478 (ptpp) REVERT: E 353 LYS cc_start: 0.7563 (mttt) cc_final: 0.7154 (mmtm) REVERT: E 369 LYS cc_start: 0.8144 (pttt) cc_final: 0.7885 (ptpt) REVERT: E 380 GLU cc_start: 0.5194 (tt0) cc_final: 0.4186 (mp0) REVERT: H 337 VAL cc_start: 0.6658 (t) cc_final: 0.6282 (p) REVERT: H 338 GLU cc_start: 0.6568 (mp0) cc_final: 0.6302 (mp0) REVERT: H 353 LYS cc_start: 0.7436 (mtpt) cc_final: 0.7176 (mttp) REVERT: H 372 GLU cc_start: 0.8377 (tt0) cc_final: 0.7818 (mt-10) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.5715 time to fit residues: 67.2767 Evaluate side-chains 79 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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: 0.9980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN F 330 HIS G 327 ASN G 330 HIS ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.179304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.143502 restraints weight = 11904.413| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 2.44 r_work: 0.4281 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4182 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3582 Z= 0.243 Angle : 0.703 5.317 4794 Z= 0.373 Chirality : 0.050 0.130 534 Planarity : 0.003 0.021 618 Dihedral : 9.197 76.537 480 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.74 % Allowed : 7.71 % Favored : 90.55 % 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: -2.72 (0.27), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.21), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 362 PHE 0.018 0.003 PHE H 346 TYR 0.017 0.003 TYR D 310 ARG 0.003 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: C 338 GLU cc_start: 0.6135 (mp0) cc_final: 0.5623 (mp0) REVERT: C 369 LYS cc_start: 0.8373 (pttt) cc_final: 0.8170 (ptpt) REVERT: F 372 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8100 (mt-10) REVERT: F 379 ARG cc_start: 0.7180 (ptp-170) cc_final: 0.6405 (ptm160) REVERT: F 380 GLU cc_start: 0.7085 (tt0) cc_final: 0.5927 (pm20) REVERT: D 314 ASP cc_start: 0.7743 (m-30) cc_final: 0.7489 (t70) REVERT: G 311 LYS cc_start: 0.8504 (mttt) cc_final: 0.8235 (tmtt) REVERT: G 337 VAL cc_start: 0.7244 (t) cc_final: 0.6660 (t) REVERT: G 338 GLU cc_start: 0.6482 (mp0) cc_final: 0.5750 (mp0) REVERT: G 340 LYS cc_start: 0.6463 (mmtm) cc_final: 0.6127 (tptp) REVERT: G 372 GLU cc_start: 0.8407 (tt0) cc_final: 0.8023 (mt-10) REVERT: G 379 ARG cc_start: 0.6774 (ptp-170) cc_final: 0.6232 (ptm-80) REVERT: E 314 ASP cc_start: 0.7795 (m-30) cc_final: 0.7466 (t0) REVERT: E 317 LYS cc_start: 0.8268 (ptmt) cc_final: 0.7789 (ptpp) REVERT: E 368 ASN cc_start: 0.7971 (m-40) cc_final: 0.7624 (m-40) REVERT: E 369 LYS cc_start: 0.8346 (pttt) cc_final: 0.8134 (ptpt) REVERT: E 375 LYS cc_start: 0.8151 (tttt) cc_final: 0.7781 (mttm) REVERT: H 311 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8377 (mttt) REVERT: H 337 VAL cc_start: 0.6641 (t) cc_final: 0.6352 (t) REVERT: H 338 GLU cc_start: 0.6469 (mp0) cc_final: 0.6200 (mp0) REVERT: H 351 GLN cc_start: 0.6662 (pt0) cc_final: 0.5702 (pm20) REVERT: H 369 LYS cc_start: 0.8394 (ttmt) cc_final: 0.8026 (tttt) REVERT: H 372 GLU cc_start: 0.8264 (tt0) cc_final: 0.7847 (mt-10) REVERT: H 379 ARG cc_start: 0.6470 (ptp-170) cc_final: 0.6258 (ptp90) outliers start: 7 outliers final: 3 residues processed: 95 average time/residue: 0.5011 time to fit residues: 54.3331 Evaluate side-chains 80 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain H residue 358 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 9 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 307 GLN ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 = 0.4662 r_free = 0.4662 target = 0.174921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.140697 restraints weight = 12634.348| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.51 r_work: 0.4234 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4131 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3582 Z= 0.229 Angle : 0.620 4.871 4794 Z= 0.322 Chirality : 0.050 0.133 534 Planarity : 0.003 0.025 618 Dihedral : 8.115 65.031 480 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.49 % Allowed : 10.45 % Favored : 87.06 % 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: -2.84 (0.28), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 329 PHE 0.013 0.002 PHE H 346 TYR 0.017 0.003 TYR C 310 ARG 0.002 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: C 338 GLU cc_start: 0.6223 (mp0) cc_final: 0.5852 (mp0) REVERT: C 369 LYS cc_start: 0.8398 (pttt) cc_final: 0.8124 (ptpt) REVERT: F 311 LYS cc_start: 0.8606 (tptt) cc_final: 0.8043 (tppt) REVERT: F 372 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8166 (mt-10) REVERT: F 379 ARG cc_start: 0.7129 (ptp-170) cc_final: 0.6434 (ptm160) REVERT: F 380 GLU cc_start: 0.7053 (tt0) cc_final: 0.6022 (pm20) REVERT: G 311 LYS cc_start: 0.8540 (mttt) cc_final: 0.8260 (tttt) REVERT: G 337 VAL cc_start: 0.7262 (t) cc_final: 0.6691 (t) REVERT: G 338 GLU cc_start: 0.6632 (mp0) cc_final: 0.5839 (mp0) REVERT: G 340 LYS cc_start: 0.6425 (mmtm) cc_final: 0.6160 (tmtt) REVERT: G 372 GLU cc_start: 0.8514 (tt0) cc_final: 0.8242 (mt-10) REVERT: G 375 LYS cc_start: 0.8459 (tttp) cc_final: 0.8223 (tttp) REVERT: E 317 LYS cc_start: 0.8391 (ptmt) cc_final: 0.7745 (ptpp) REVERT: E 368 ASN cc_start: 0.8026 (m-40) cc_final: 0.7659 (m-40) REVERT: E 369 LYS cc_start: 0.8328 (pttt) cc_final: 0.8026 (ptpp) REVERT: E 375 LYS cc_start: 0.8142 (tttt) cc_final: 0.7798 (mttm) REVERT: H 328 ILE cc_start: 0.8227 (mt) cc_final: 0.7966 (mp) REVERT: H 337 VAL cc_start: 0.6867 (t) cc_final: 0.6485 (t) REVERT: H 338 GLU cc_start: 0.6620 (mp0) cc_final: 0.6413 (mp0) outliers start: 10 outliers final: 6 residues processed: 88 average time/residue: 0.5451 time to fit residues: 54.4107 Evaluate side-chains 79 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 358 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN G 307 GLN ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.176557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.142470 restraints weight = 12620.895| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 2.54 r_work: 0.4260 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4161 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3582 Z= 0.167 Angle : 0.545 4.398 4794 Z= 0.278 Chirality : 0.048 0.128 534 Planarity : 0.003 0.028 618 Dihedral : 7.874 68.848 480 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.24 % Allowed : 11.94 % Favored : 85.82 % 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: -2.72 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 329 PHE 0.009 0.002 PHE H 346 TYR 0.012 0.002 TYR E 310 ARG 0.002 0.000 ARG H 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 338 GLU cc_start: 0.6115 (mp0) cc_final: 0.5732 (mp0) REVERT: C 369 LYS cc_start: 0.8448 (pttt) cc_final: 0.8145 (ptpt) REVERT: F 311 LYS cc_start: 0.8515 (tptt) cc_final: 0.7896 (tppt) REVERT: F 331 LYS cc_start: 0.8272 (mttm) cc_final: 0.7073 (mmtt) REVERT: F 372 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8211 (mt-10) REVERT: F 379 ARG cc_start: 0.7119 (ptp-170) cc_final: 0.6437 (ptm160) REVERT: F 380 GLU cc_start: 0.7088 (tt0) cc_final: 0.5999 (pm20) REVERT: G 311 LYS cc_start: 0.8493 (mttt) cc_final: 0.8195 (tttt) REVERT: G 337 VAL cc_start: 0.7211 (t) cc_final: 0.6793 (t) REVERT: G 338 GLU cc_start: 0.6756 (mp0) cc_final: 0.6054 (mp0) REVERT: G 340 LYS cc_start: 0.6271 (mmtm) cc_final: 0.6028 (tmtt) REVERT: G 372 GLU cc_start: 0.8512 (tt0) cc_final: 0.8224 (mt-10) REVERT: E 317 LYS cc_start: 0.8379 (ptmt) cc_final: 0.7703 (ptpp) REVERT: E 368 ASN cc_start: 0.8074 (m-40) cc_final: 0.7699 (m-40) REVERT: E 369 LYS cc_start: 0.8378 (pttt) cc_final: 0.8045 (ptpp) REVERT: E 375 LYS cc_start: 0.8120 (tttt) cc_final: 0.7767 (mttm) REVERT: H 328 ILE cc_start: 0.8175 (mt) cc_final: 0.7906 (mp) REVERT: H 372 GLU cc_start: 0.8380 (tt0) cc_final: 0.7915 (mt-10) outliers start: 9 outliers final: 5 residues processed: 92 average time/residue: 0.5044 time to fit residues: 53.1428 Evaluate side-chains 84 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 358 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 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 = 0.4675 r_free = 0.4675 target = 0.176009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.142286 restraints weight = 12532.460| |-----------------------------------------------------------------------------| r_work (start): 0.4328 rms_B_bonded: 2.53 r_work: 0.4256 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4155 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3582 Z= 0.163 Angle : 0.529 4.107 4794 Z= 0.268 Chirality : 0.048 0.125 534 Planarity : 0.003 0.030 618 Dihedral : 7.539 67.734 480 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.74 % Allowed : 12.44 % Favored : 84.83 % 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: -2.66 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 329 PHE 0.007 0.001 PHE G 346 TYR 0.012 0.002 TYR E 310 ARG 0.001 0.000 ARG H 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: C 331 LYS cc_start: 0.7214 (ttmt) cc_final: 0.6900 (tttt) REVERT: C 338 GLU cc_start: 0.6021 (mp0) cc_final: 0.5613 (mp0) REVERT: C 369 LYS cc_start: 0.8467 (pttt) cc_final: 0.8181 (ptpt) REVERT: F 311 LYS cc_start: 0.8501 (tptt) cc_final: 0.7765 (tppt) REVERT: F 372 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8190 (mt-10) REVERT: F 380 GLU cc_start: 0.6993 (tt0) cc_final: 0.6021 (pm20) REVERT: G 311 LYS cc_start: 0.8494 (mttt) cc_final: 0.8077 (tptm) REVERT: G 319 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8131 (p) REVERT: G 338 GLU cc_start: 0.6348 (mp0) cc_final: 0.5985 (mp0) REVERT: G 340 LYS cc_start: 0.6236 (mmtm) cc_final: 0.5988 (tmtt) REVERT: G 372 GLU cc_start: 0.8541 (tt0) cc_final: 0.8303 (mt-10) REVERT: G 379 ARG cc_start: 0.6436 (ptp-170) cc_final: 0.6115 (ptm160) REVERT: E 317 LYS cc_start: 0.8385 (ptmt) cc_final: 0.7693 (ptpp) REVERT: E 327 ASN cc_start: 0.8377 (p0) cc_final: 0.8136 (p0) REVERT: E 368 ASN cc_start: 0.8073 (m-40) cc_final: 0.7717 (m-40) REVERT: E 369 LYS cc_start: 0.8371 (pttt) cc_final: 0.8042 (ptpp) REVERT: E 375 LYS cc_start: 0.8094 (tttt) cc_final: 0.7730 (mttm) REVERT: H 328 ILE cc_start: 0.8131 (mt) cc_final: 0.7891 (mp) REVERT: H 369 LYS cc_start: 0.8354 (ttmt) cc_final: 0.7941 (tttt) REVERT: H 372 GLU cc_start: 0.8378 (tt0) cc_final: 0.7908 (mt-10) outliers start: 11 outliers final: 6 residues processed: 89 average time/residue: 0.5330 time to fit residues: 53.9722 Evaluate side-chains 86 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 358 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.4676 r_free = 0.4676 target = 0.176230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.142893 restraints weight = 12516.336| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 2.41 r_work: 0.4281 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4181 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3582 Z= 0.156 Angle : 0.510 3.802 4794 Z= 0.259 Chirality : 0.048 0.128 534 Planarity : 0.003 0.030 618 Dihedral : 7.383 67.242 480 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.49 % Allowed : 13.18 % Favored : 84.33 % 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: -2.60 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 329 PHE 0.006 0.001 PHE G 346 TYR 0.011 0.002 TYR E 310 ARG 0.002 0.000 ARG H 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: C 331 LYS cc_start: 0.7229 (ttmt) cc_final: 0.6936 (tttt) REVERT: C 338 GLU cc_start: 0.6129 (mp0) cc_final: 0.5747 (mp0) REVERT: C 369 LYS cc_start: 0.8450 (pttt) cc_final: 0.8150 (ptpt) REVERT: F 311 LYS cc_start: 0.8496 (tptt) cc_final: 0.7882 (tppt) REVERT: F 372 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8187 (mt-10) REVERT: F 380 GLU cc_start: 0.6999 (tt0) cc_final: 0.6200 (mm-30) REVERT: G 311 LYS cc_start: 0.8470 (mttt) cc_final: 0.8211 (tttt) REVERT: G 319 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8059 (p) REVERT: G 340 LYS cc_start: 0.6313 (mmtm) cc_final: 0.6004 (tmtt) REVERT: G 372 GLU cc_start: 0.8539 (tt0) cc_final: 0.8319 (mt-10) REVERT: G 379 ARG cc_start: 0.6444 (ptp-170) cc_final: 0.6172 (ptm160) REVERT: E 317 LYS cc_start: 0.8383 (ptmt) cc_final: 0.7701 (ptpp) REVERT: E 327 ASN cc_start: 0.8431 (p0) cc_final: 0.8189 (p0) REVERT: E 368 ASN cc_start: 0.8012 (m-40) cc_final: 0.7710 (m-40) REVERT: E 369 LYS cc_start: 0.8434 (pttt) cc_final: 0.8107 (ptpp) REVERT: E 375 LYS cc_start: 0.8044 (tttt) cc_final: 0.7693 (mttm) REVERT: H 328 ILE cc_start: 0.8187 (mt) cc_final: 0.7961 (mp) REVERT: H 369 LYS cc_start: 0.8385 (ttmt) cc_final: 0.7996 (tttt) REVERT: H 372 GLU cc_start: 0.8342 (tt0) cc_final: 0.7931 (mt-10) outliers start: 10 outliers final: 5 residues processed: 89 average time/residue: 0.4944 time to fit residues: 50.4591 Evaluate side-chains 85 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain H residue 358 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.4679 r_free = 0.4679 target = 0.176592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.142998 restraints weight = 12403.846| |-----------------------------------------------------------------------------| r_work (start): 0.4339 rms_B_bonded: 2.46 r_work: 0.4263 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4161 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3582 Z= 0.153 Angle : 0.501 3.767 4794 Z= 0.253 Chirality : 0.048 0.126 534 Planarity : 0.003 0.032 618 Dihedral : 7.196 65.732 480 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.99 % Allowed : 14.68 % Favored : 83.33 % 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: -2.59 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 329 PHE 0.006 0.001 PHE G 346 TYR 0.011 0.002 TYR E 310 ARG 0.001 0.000 ARG H 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 331 LYS cc_start: 0.7269 (ttmt) cc_final: 0.6957 (tttt) REVERT: C 338 GLU cc_start: 0.5978 (mp0) cc_final: 0.5625 (mp0) REVERT: C 369 LYS cc_start: 0.8488 (pttt) cc_final: 0.8191 (ptpt) REVERT: F 311 LYS cc_start: 0.8507 (tptt) cc_final: 0.7872 (tppt) REVERT: F 372 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8218 (mt-10) REVERT: F 380 GLU cc_start: 0.6910 (tt0) cc_final: 0.6104 (mm-30) REVERT: D 349 ARG cc_start: 0.6578 (mtp180) cc_final: 0.5783 (mtt90) REVERT: G 311 LYS cc_start: 0.8456 (mttt) cc_final: 0.8170 (tttt) REVERT: G 319 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7995 (p) REVERT: G 338 GLU cc_start: 0.6537 (mp0) cc_final: 0.6281 (mp0) REVERT: G 340 LYS cc_start: 0.6180 (mmtm) cc_final: 0.5914 (tmtt) REVERT: G 372 GLU cc_start: 0.8569 (tt0) cc_final: 0.8356 (mt-10) REVERT: E 317 LYS cc_start: 0.8372 (ptmt) cc_final: 0.7657 (ptpp) REVERT: E 327 ASN cc_start: 0.8397 (p0) cc_final: 0.8174 (p0) REVERT: E 342 GLU cc_start: 0.3288 (pm20) cc_final: 0.2616 (pm20) REVERT: E 368 ASN cc_start: 0.7969 (m-40) cc_final: 0.7640 (m-40) REVERT: E 369 LYS cc_start: 0.8445 (pttt) cc_final: 0.8092 (ptpp) REVERT: E 375 LYS cc_start: 0.8029 (tttt) cc_final: 0.7677 (mttm) REVERT: H 328 ILE cc_start: 0.8141 (mt) cc_final: 0.7901 (mp) REVERT: H 369 LYS cc_start: 0.8403 (ttmt) cc_final: 0.7974 (tttt) REVERT: H 372 GLU cc_start: 0.8408 (tt0) cc_final: 0.7976 (mt-10) outliers start: 8 outliers final: 7 residues processed: 87 average time/residue: 0.5117 time to fit residues: 51.0688 Evaluate side-chains 88 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain H residue 358 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 9 optimal weight: 0.4980 chunk 11 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4691 r_free = 0.4691 target = 0.177484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.143551 restraints weight = 12502.312| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 2.50 r_work: 0.4275 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4172 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3582 Z= 0.148 Angle : 0.494 3.748 4794 Z= 0.249 Chirality : 0.048 0.127 534 Planarity : 0.003 0.034 618 Dihedral : 7.060 64.840 480 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.99 % Allowed : 14.43 % Favored : 83.58 % 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: -2.53 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 329 PHE 0.006 0.001 PHE G 346 TYR 0.011 0.002 TYR E 310 ARG 0.002 0.000 ARG H 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 331 LYS cc_start: 0.7230 (ttmt) cc_final: 0.6937 (tttt) REVERT: C 338 GLU cc_start: 0.5981 (mp0) cc_final: 0.5626 (mp0) REVERT: C 369 LYS cc_start: 0.8510 (pttt) cc_final: 0.8193 (ptpt) REVERT: F 311 LYS cc_start: 0.8497 (tptt) cc_final: 0.7868 (tppt) REVERT: F 340 LYS cc_start: 0.6518 (tmtt) cc_final: 0.6011 (ttmm) REVERT: F 372 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8229 (mt-10) REVERT: F 380 GLU cc_start: 0.6885 (tt0) cc_final: 0.5882 (pm20) REVERT: D 349 ARG cc_start: 0.6557 (mtp180) cc_final: 0.5761 (mtt90) REVERT: G 311 LYS cc_start: 0.8453 (mttt) cc_final: 0.8172 (tttt) REVERT: G 319 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8026 (p) REVERT: G 338 GLU cc_start: 0.6586 (mp0) cc_final: 0.6147 (mp0) REVERT: G 340 LYS cc_start: 0.6166 (mmtm) cc_final: 0.5869 (tmtt) REVERT: G 372 GLU cc_start: 0.8583 (tt0) cc_final: 0.8326 (mt-10) REVERT: E 317 LYS cc_start: 0.8366 (ptmt) cc_final: 0.7649 (ptpp) REVERT: E 327 ASN cc_start: 0.8440 (p0) cc_final: 0.8219 (p0) REVERT: E 342 GLU cc_start: 0.3130 (pm20) cc_final: 0.2282 (pm20) REVERT: E 368 ASN cc_start: 0.7999 (m-40) cc_final: 0.7695 (m-40) REVERT: E 369 LYS cc_start: 0.8445 (pttt) cc_final: 0.8092 (ptpp) REVERT: E 375 LYS cc_start: 0.8016 (tttt) cc_final: 0.7668 (mttm) REVERT: H 328 ILE cc_start: 0.8131 (mt) cc_final: 0.7901 (mp) outliers start: 8 outliers final: 6 residues processed: 88 average time/residue: 0.4628 time to fit residues: 47.0545 Evaluate side-chains 86 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain H residue 358 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4649 r_free = 0.4649 target = 0.174358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.141005 restraints weight = 12391.284| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 2.37 r_work: 0.4230 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4131 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3582 Z= 0.213 Angle : 0.536 4.242 4794 Z= 0.272 Chirality : 0.048 0.128 534 Planarity : 0.003 0.036 618 Dihedral : 7.130 62.487 480 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 1.74 % Allowed : 14.43 % Favored : 83.83 % 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: -2.69 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 329 PHE 0.009 0.002 PHE G 346 TYR 0.013 0.002 TYR E 310 ARG 0.002 0.000 ARG H 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: C 331 LYS cc_start: 0.7273 (ttmt) cc_final: 0.7006 (tttt) REVERT: C 338 GLU cc_start: 0.6080 (mp0) cc_final: 0.5707 (mp0) REVERT: C 369 LYS cc_start: 0.8488 (pttt) cc_final: 0.8174 (ptpt) REVERT: F 311 LYS cc_start: 0.8508 (tptt) cc_final: 0.7915 (tppt) REVERT: F 372 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8193 (mt-10) REVERT: F 379 ARG cc_start: 0.7121 (ptp-170) cc_final: 0.6645 (ptm160) REVERT: F 380 GLU cc_start: 0.6878 (tt0) cc_final: 0.5977 (pm20) REVERT: D 349 ARG cc_start: 0.6709 (mtp180) cc_final: 0.5913 (mtt90) REVERT: G 311 LYS cc_start: 0.8447 (mttt) cc_final: 0.8217 (tttt) REVERT: G 319 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8141 (p) REVERT: G 340 LYS cc_start: 0.6173 (mmtm) cc_final: 0.5856 (tmtt) REVERT: E 317 LYS cc_start: 0.8389 (ptmt) cc_final: 0.7706 (ptpp) REVERT: E 368 ASN cc_start: 0.7964 (m-40) cc_final: 0.7663 (m-40) REVERT: E 369 LYS cc_start: 0.8395 (pttt) cc_final: 0.8089 (ptpp) REVERT: E 375 LYS cc_start: 0.8061 (tttt) cc_final: 0.7746 (mttm) REVERT: H 328 ILE cc_start: 0.8188 (mt) cc_final: 0.7974 (mp) REVERT: H 369 LYS cc_start: 0.8424 (ttmt) cc_final: 0.8014 (tttt) REVERT: H 372 GLU cc_start: 0.8390 (tt0) cc_final: 0.8080 (mt-10) outliers start: 7 outliers final: 4 residues processed: 87 average time/residue: 0.5449 time to fit residues: 54.3953 Evaluate side-chains 85 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain H residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 4.9990 chunk 34 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.177128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.143787 restraints weight = 12577.511| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 2.49 r_work: 0.4286 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4184 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3582 Z= 0.133 Angle : 0.489 3.778 4794 Z= 0.247 Chirality : 0.048 0.127 534 Planarity : 0.003 0.036 618 Dihedral : 6.959 64.360 480 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.75 % Allowed : 15.67 % Favored : 83.58 % 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: -2.57 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 330 PHE 0.004 0.001 PHE G 346 TYR 0.010 0.002 TYR E 310 ARG 0.002 0.000 ARG H 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 331 LYS cc_start: 0.7208 (ttmt) cc_final: 0.6919 (tttt) REVERT: C 338 GLU cc_start: 0.5995 (mp0) cc_final: 0.5303 (mp0) REVERT: C 369 LYS cc_start: 0.8532 (pttt) cc_final: 0.8204 (ptpt) REVERT: F 311 LYS cc_start: 0.8451 (tptt) cc_final: 0.7835 (tppt) REVERT: F 372 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8211 (mt-10) REVERT: F 379 ARG cc_start: 0.7067 (ptp-170) cc_final: 0.6419 (ptm160) REVERT: F 380 GLU cc_start: 0.6807 (tt0) cc_final: 0.5789 (pm20) REVERT: D 349 ARG cc_start: 0.6594 (mtp180) cc_final: 0.5799 (mtt90) REVERT: G 311 LYS cc_start: 0.8440 (mttt) cc_final: 0.8168 (tttt) REVERT: G 338 GLU cc_start: 0.6633 (mp0) cc_final: 0.6404 (mp0) REVERT: G 340 LYS cc_start: 0.6131 (mmtm) cc_final: 0.5872 (tmtt) REVERT: G 372 GLU cc_start: 0.8551 (tt0) cc_final: 0.8296 (mt-10) REVERT: E 317 LYS cc_start: 0.8375 (ptmt) cc_final: 0.7656 (ptpp) REVERT: E 327 ASN cc_start: 0.8446 (p0) cc_final: 0.7950 (p0) REVERT: E 368 ASN cc_start: 0.7968 (m-40) cc_final: 0.7666 (m-40) REVERT: E 369 LYS cc_start: 0.8393 (pttt) cc_final: 0.8038 (ptpp) REVERT: H 328 ILE cc_start: 0.7958 (mt) cc_final: 0.7715 (mp) REVERT: H 372 GLU cc_start: 0.8410 (tt0) cc_final: 0.8016 (mt-10) outliers start: 3 outliers final: 3 residues processed: 84 average time/residue: 0.5129 time to fit residues: 49.4976 Evaluate side-chains 82 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain H residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4683 r_free = 0.4683 target = 0.177039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.143903 restraints weight = 12464.363| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 2.41 r_work: 0.4285 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4185 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3582 Z= 0.143 Angle : 0.483 3.754 4794 Z= 0.244 Chirality : 0.048 0.125 534 Planarity : 0.003 0.038 618 Dihedral : 6.784 63.122 480 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.00 % Allowed : 15.92 % Favored : 83.08 % 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: -2.51 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 329 PHE 0.006 0.001 PHE G 346 TYR 0.010 0.002 TYR E 310 ARG 0.002 0.000 ARG H 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5476.01 seconds wall clock time: 93 minutes 35.22 seconds (5615.22 seconds total)