Starting phenix.real_space_refine on Thu Nov 14 19:33:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bxr_45009/11_2024/9bxr_45009.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bxr_45009/11_2024/9bxr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bxr_45009/11_2024/9bxr_45009.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bxr_45009/11_2024/9bxr_45009.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bxr_45009/11_2024/9bxr_45009.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bxr_45009/11_2024/9bxr_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-5513/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: 3.99, per 1000 atoms: 0.56 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: 1.85 Conformation dependent library (CDL) restraints added in 638.8 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: 0.68 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: 2.25 Time building geometry restraints manager: 2.21 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: 0.00 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.750 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.190 ------------------------------------------------------------------------------- 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 : 0.656 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: 0.5723 time to fit residues: 67.2172 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 : 0.600 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 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 : 0.624 Fit side-chains revert: symmetry clash REVERT: C 338 GLU cc_start: 0.6038 (mp0) cc_final: 0.5500 (mp0) REVERT: C 369 LYS cc_start: 0.8348 (pttt) cc_final: 0.8079 (ptpt) REVERT: F 372 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8365 (mt-10) REVERT: F 379 ARG cc_start: 0.6977 (ptp-170) cc_final: 0.6188 (ptm160) REVERT: F 380 GLU cc_start: 0.6752 (tt0) cc_final: 0.5726 (pm20) REVERT: D 314 ASP cc_start: 0.7624 (m-30) cc_final: 0.7247 (t70) REVERT: D 369 LYS cc_start: 0.8117 (pttt) cc_final: 0.7903 (ptpt) REVERT: G 311 LYS cc_start: 0.8450 (mttt) cc_final: 0.8134 (tmtt) REVERT: G 337 VAL cc_start: 0.7034 (t) cc_final: 0.6421 (t) REVERT: G 338 GLU cc_start: 0.6340 (mp0) cc_final: 0.5572 (mp0) REVERT: G 340 LYS cc_start: 0.6360 (mmtm) cc_final: 0.6033 (tptp) REVERT: G 372 GLU cc_start: 0.8545 (tt0) cc_final: 0.8133 (mt-10) REVERT: G 379 ARG cc_start: 0.6622 (ptp-170) cc_final: 0.6022 (ptm-80) REVERT: E 314 ASP cc_start: 0.7804 (m-30) cc_final: 0.7312 (t0) REVERT: E 317 LYS cc_start: 0.8200 (ptmt) cc_final: 0.7654 (ptpp) REVERT: E 368 ASN cc_start: 0.7792 (m-40) cc_final: 0.7438 (m-40) REVERT: E 369 LYS cc_start: 0.8306 (pttt) cc_final: 0.8013 (ptpt) REVERT: E 375 LYS cc_start: 0.8289 (tttt) cc_final: 0.7884 (mttm) REVERT: H 311 LYS cc_start: 0.8508 (ttmt) cc_final: 0.8242 (mttt) REVERT: H 337 VAL cc_start: 0.6432 (t) cc_final: 0.6143 (t) REVERT: H 338 GLU cc_start: 0.6375 (mp0) cc_final: 0.6121 (mp0) REVERT: H 351 GLN cc_start: 0.5886 (pt0) cc_final: 0.5247 (pm20) REVERT: H 369 LYS cc_start: 0.8396 (ttmt) cc_final: 0.7995 (tttt) REVERT: H 372 GLU cc_start: 0.8390 (tt0) cc_final: 0.7933 (mt-10) REVERT: H 379 ARG cc_start: 0.6346 (ptp-170) cc_final: 0.6110 (ptp90) outliers start: 7 outliers final: 3 residues processed: 95 average time/residue: 0.5177 time to fit residues: 56.5826 Evaluate side-chains 81 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 31 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 307 GLN G 359 ASN ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3582 Z= 0.346 Angle : 0.708 5.479 4794 Z= 0.372 Chirality : 0.051 0.135 534 Planarity : 0.003 0.031 618 Dihedral : 8.466 62.552 480 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.23 % Allowed : 11.44 % Favored : 85.32 % 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: -3.09 (0.28), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.21), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 329 PHE 0.017 0.003 PHE H 346 TYR 0.021 0.004 TYR C 310 ARG 0.002 0.001 ARG G 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 92 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: C 338 GLU cc_start: 0.6132 (mp0) cc_final: 0.5667 (mp0) REVERT: C 369 LYS cc_start: 0.8349 (pttt) cc_final: 0.8139 (ptpt) REVERT: F 311 LYS cc_start: 0.8597 (tptt) cc_final: 0.8054 (tptm) REVERT: F 372 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8400 (mt-10) REVERT: F 379 ARG cc_start: 0.6903 (ptp-170) cc_final: 0.6207 (ptm160) REVERT: F 380 GLU cc_start: 0.6868 (tt0) cc_final: 0.5812 (pm20) REVERT: D 314 ASP cc_start: 0.7649 (m-30) cc_final: 0.7404 (t70) REVERT: D 369 LYS cc_start: 0.8311 (pttt) cc_final: 0.8050 (ptpt) REVERT: G 311 LYS cc_start: 0.8483 (mttt) cc_final: 0.8206 (tttt) REVERT: G 337 VAL cc_start: 0.7006 (t) cc_final: 0.6406 (t) REVERT: G 338 GLU cc_start: 0.6528 (mp0) cc_final: 0.5730 (mp0) REVERT: G 340 LYS cc_start: 0.6272 (mmtm) cc_final: 0.6040 (tmtt) REVERT: G 372 GLU cc_start: 0.8624 (tt0) cc_final: 0.8311 (mt-10) REVERT: E 317 LYS cc_start: 0.8316 (ptmt) cc_final: 0.7640 (ptpp) REVERT: E 327 ASN cc_start: 0.8123 (p0) cc_final: 0.7836 (p0) REVERT: E 368 ASN cc_start: 0.7761 (m-40) cc_final: 0.7387 (m-40) REVERT: E 369 LYS cc_start: 0.8319 (pttt) cc_final: 0.7975 (ptpp) REVERT: E 375 LYS cc_start: 0.8301 (tttt) cc_final: 0.7939 (mttm) REVERT: H 328 ILE cc_start: 0.8169 (mt) cc_final: 0.7927 (mp) REVERT: H 337 VAL cc_start: 0.6704 (t) cc_final: 0.6355 (t) REVERT: H 338 GLU cc_start: 0.6546 (mp0) cc_final: 0.6330 (mp0) REVERT: H 369 LYS cc_start: 0.8455 (ttmt) cc_final: 0.8078 (tttt) outliers start: 13 outliers final: 7 residues processed: 88 average time/residue: 0.5455 time to fit residues: 54.5007 Evaluate side-chains 82 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 G residue 359 ASN 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 4 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.0670 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4768 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= 0.222 Angle : 0.600 4.706 4794 Z= 0.310 Chirality : 0.049 0.132 534 Planarity : 0.003 0.033 618 Dihedral : 8.153 66.323 480 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.49 % Allowed : 11.69 % 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: -3.09 (0.28), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 329 PHE 0.010 0.002 PHE H 346 TYR 0.015 0.003 TYR E 310 ARG 0.001 0.000 ARG H 349 *********************** 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: 10 poor density : 84 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 338 GLU cc_start: 0.6056 (mp0) cc_final: 0.5600 (mp0) REVERT: C 369 LYS cc_start: 0.8361 (pttt) cc_final: 0.8160 (ptpt) REVERT: F 311 LYS cc_start: 0.8576 (tptt) cc_final: 0.7951 (tppt) REVERT: F 372 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8408 (mt-10) REVERT: F 379 ARG cc_start: 0.6913 (ptp-170) cc_final: 0.6232 (ptm160) REVERT: F 380 GLU cc_start: 0.6777 (tt0) cc_final: 0.5833 (pm20) REVERT: D 369 LYS cc_start: 0.8259 (pttt) cc_final: 0.8014 (ptpt) REVERT: G 311 LYS cc_start: 0.8499 (mttt) cc_final: 0.8182 (tttt) REVERT: G 319 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8161 (p) REVERT: G 337 VAL cc_start: 0.6989 (t) cc_final: 0.6472 (t) REVERT: G 338 GLU cc_start: 0.6545 (mp0) cc_final: 0.5739 (mp0) REVERT: G 372 GLU cc_start: 0.8609 (tt0) cc_final: 0.8312 (mt-10) REVERT: E 317 LYS cc_start: 0.8296 (ptmt) cc_final: 0.7617 (ptpp) REVERT: E 327 ASN cc_start: 0.8141 (p0) cc_final: 0.7707 (p0) REVERT: E 368 ASN cc_start: 0.7791 (m-40) cc_final: 0.7466 (m-40) REVERT: E 369 LYS cc_start: 0.8337 (pttt) cc_final: 0.8000 (ptpp) REVERT: E 375 LYS cc_start: 0.8245 (tttt) cc_final: 0.7847 (mttm) REVERT: H 328 ILE cc_start: 0.8176 (mt) cc_final: 0.7908 (mp) REVERT: H 337 VAL cc_start: 0.6824 (t) cc_final: 0.6429 (t) REVERT: H 338 GLU cc_start: 0.6568 (mp0) cc_final: 0.6330 (mp0) REVERT: H 369 LYS cc_start: 0.8435 (ttmt) cc_final: 0.8053 (tttt) REVERT: H 372 GLU cc_start: 0.8420 (tt0) cc_final: 0.7928 (mt-10) outliers start: 10 outliers final: 5 residues processed: 90 average time/residue: 0.5152 time to fit residues: 52.8862 Evaluate side-chains 86 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 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 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.0770 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.5165 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= 0.143 Angle : 0.524 3.836 4794 Z= 0.266 Chirality : 0.048 0.127 534 Planarity : 0.003 0.032 618 Dihedral : 7.738 69.358 480 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.99 % Allowed : 12.19 % 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: -2.84 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 330 PHE 0.005 0.001 PHE H 346 TYR 0.010 0.002 TYR E 310 ARG 0.001 0.000 ARG H 349 *********************** 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 92 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 338 GLU cc_start: 0.6039 (mp0) cc_final: 0.5622 (mp0) REVERT: F 311 LYS cc_start: 0.8488 (tptt) cc_final: 0.7827 (tppt) REVERT: F 372 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8400 (mt-10) REVERT: F 380 GLU cc_start: 0.6739 (tt0) cc_final: 0.5898 (pm20) REVERT: D 369 LYS cc_start: 0.8264 (pttt) cc_final: 0.7932 (ptpt) REVERT: G 311 LYS cc_start: 0.8457 (mttt) cc_final: 0.8156 (tttt) REVERT: G 340 LYS cc_start: 0.6132 (tmtt) cc_final: 0.5890 (tptp) REVERT: G 372 GLU cc_start: 0.8593 (tt0) cc_final: 0.8258 (mt-10) REVERT: E 317 LYS cc_start: 0.8302 (ptmt) cc_final: 0.7621 (ptpp) REVERT: E 327 ASN cc_start: 0.8173 (p0) cc_final: 0.7755 (p0) REVERT: E 368 ASN cc_start: 0.7845 (m-40) cc_final: 0.7548 (m-40) REVERT: E 369 LYS cc_start: 0.8297 (pttt) cc_final: 0.7986 (ptpp) REVERT: E 375 LYS cc_start: 0.8171 (tttt) cc_final: 0.7779 (mttm) REVERT: H 328 ILE cc_start: 0.8152 (mt) cc_final: 0.7891 (mp) REVERT: H 338 GLU cc_start: 0.6637 (mp0) cc_final: 0.6422 (mp0) REVERT: H 372 GLU cc_start: 0.8385 (tt0) cc_final: 0.7968 (mt-10) outliers start: 8 outliers final: 6 residues processed: 89 average time/residue: 0.4968 time to fit residues: 50.8156 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 : 0.662 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain H residue 361 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3582 Z= 0.302 Angle : 0.620 5.237 4794 Z= 0.319 Chirality : 0.049 0.131 534 Planarity : 0.004 0.035 618 Dihedral : 7.781 64.355 480 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.99 % Allowed : 13.68 % 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: -3.05 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 329 PHE 0.011 0.002 PHE G 346 TYR 0.017 0.003 TYR E 310 ARG 0.002 0.000 ARG F 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: 12 poor density : 80 time to evaluate : 0.688 Fit side-chains REVERT: C 338 GLU cc_start: 0.6053 (mp0) cc_final: 0.5578 (mp0) REVERT: F 311 LYS cc_start: 0.8573 (tptt) cc_final: 0.7900 (tppt) REVERT: F 372 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8443 (mt-10) REVERT: F 380 GLU cc_start: 0.6749 (tt0) cc_final: 0.5884 (pm20) REVERT: D 316 SER cc_start: 0.9135 (p) cc_final: 0.8692 (m) REVERT: D 349 ARG cc_start: 0.6895 (mtp180) cc_final: 0.6066 (mtt90) REVERT: D 369 LYS cc_start: 0.8315 (pttt) cc_final: 0.7920 (ptpt) REVERT: G 311 LYS cc_start: 0.8457 (mttt) cc_final: 0.8152 (tttt) REVERT: G 319 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8268 (p) REVERT: E 317 LYS cc_start: 0.8319 (ptmt) cc_final: 0.7612 (ptpp) REVERT: E 327 ASN cc_start: 0.8206 (p0) cc_final: 0.7738 (p0) REVERT: E 342 GLU cc_start: 0.3215 (pm20) cc_final: 0.1810 (mt-10) REVERT: E 368 ASN cc_start: 0.7814 (m-40) cc_final: 0.7481 (m-40) REVERT: E 369 LYS cc_start: 0.8316 (pttt) cc_final: 0.8006 (ptpp) REVERT: E 375 LYS cc_start: 0.8261 (tttt) cc_final: 0.7907 (mttm) REVERT: H 328 ILE cc_start: 0.8097 (mt) cc_final: 0.7855 (mp) REVERT: H 338 GLU cc_start: 0.6653 (mp0) cc_final: 0.6410 (mp0) REVERT: H 353 LYS cc_start: 0.6406 (mtpt) cc_final: 0.6010 (mttp) REVERT: H 369 LYS cc_start: 0.8371 (ttmt) cc_final: 0.7997 (tttt) outliers start: 12 outliers final: 6 residues processed: 89 average time/residue: 0.5307 time to fit residues: 53.9059 Evaluate side-chains 84 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 0.0670 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.5752 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= 0.141 Angle : 0.518 4.364 4794 Z= 0.262 Chirality : 0.048 0.126 534 Planarity : 0.003 0.033 618 Dihedral : 7.477 69.281 480 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.49 % Allowed : 13.68 % 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: -2.84 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 330 PHE 0.004 0.001 PHE G 346 TYR 0.010 0.002 TYR E 310 ARG 0.001 0.000 ARG H 349 *********************** 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 92 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: C 338 GLU cc_start: 0.6025 (mp0) cc_final: 0.5613 (mp0) REVERT: F 311 LYS cc_start: 0.8470 (tptt) cc_final: 0.7710 (tppt) REVERT: F 340 LYS cc_start: 0.5578 (tmtt) cc_final: 0.5303 (ttmm) REVERT: F 372 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8406 (mt-10) REVERT: F 380 GLU cc_start: 0.6720 (tt0) cc_final: 0.5844 (pm20) REVERT: D 349 ARG cc_start: 0.6847 (mtp180) cc_final: 0.6047 (mtt90) REVERT: D 369 LYS cc_start: 0.8261 (pttt) cc_final: 0.7908 (ptpt) REVERT: G 311 LYS cc_start: 0.8424 (mttt) cc_final: 0.8085 (tptm) REVERT: G 319 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8110 (p) REVERT: G 340 LYS cc_start: 0.6102 (tmtt) cc_final: 0.5825 (tptp) REVERT: G 372 GLU cc_start: 0.8664 (tt0) cc_final: 0.8395 (mt-10) REVERT: G 379 ARG cc_start: 0.6407 (ptp-170) cc_final: 0.5974 (ptm-80) REVERT: E 317 LYS cc_start: 0.8322 (ptmt) cc_final: 0.7621 (ptpp) REVERT: E 327 ASN cc_start: 0.8144 (p0) cc_final: 0.7745 (p0) REVERT: E 342 GLU cc_start: 0.3006 (pm20) cc_final: 0.2403 (pm20) REVERT: E 368 ASN cc_start: 0.7736 (m-40) cc_final: 0.7447 (m-40) REVERT: E 369 LYS cc_start: 0.8273 (pttt) cc_final: 0.7972 (ptpp) REVERT: E 375 LYS cc_start: 0.8159 (tttt) cc_final: 0.7768 (mttm) REVERT: H 328 ILE cc_start: 0.8141 (mt) cc_final: 0.7910 (mp) REVERT: H 338 GLU cc_start: 0.6766 (mp0) cc_final: 0.6547 (mp0) REVERT: H 369 LYS cc_start: 0.8389 (ttmt) cc_final: 0.7994 (tttt) outliers start: 10 outliers final: 7 residues processed: 88 average time/residue: 0.5100 time to fit residues: 51.3777 Evaluate side-chains 89 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 358 ASP Chi-restraints excluded: chain H residue 361 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3582 Z= 0.176 Angle : 0.523 4.316 4794 Z= 0.266 Chirality : 0.048 0.128 534 Planarity : 0.003 0.036 618 Dihedral : 7.267 66.097 480 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.74 % Allowed : 13.43 % 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: -2.79 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 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 F 349 *********************** 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 92 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: C 338 GLU cc_start: 0.6054 (mp0) cc_final: 0.5646 (mp0) REVERT: F 311 LYS cc_start: 0.8477 (tptt) cc_final: 0.7812 (tppt) REVERT: F 372 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8426 (mt-10) REVERT: F 380 GLU cc_start: 0.6707 (tt0) cc_final: 0.5825 (pm20) REVERT: D 349 ARG cc_start: 0.6870 (mtp180) cc_final: 0.6081 (mtt90) REVERT: D 369 LYS cc_start: 0.8278 (pttt) cc_final: 0.7813 (ptpt) REVERT: G 311 LYS cc_start: 0.8429 (mttt) cc_final: 0.8148 (tttt) REVERT: G 319 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8105 (p) REVERT: G 340 LYS cc_start: 0.6010 (tmtt) cc_final: 0.5652 (tptp) REVERT: G 372 GLU cc_start: 0.8680 (tt0) cc_final: 0.8367 (mt-10) REVERT: G 379 ARG cc_start: 0.6406 (ptp-170) cc_final: 0.5978 (ptm-80) REVERT: E 317 LYS cc_start: 0.8315 (ptmt) cc_final: 0.7603 (ptpp) REVERT: E 327 ASN cc_start: 0.8146 (p0) cc_final: 0.7718 (p0) REVERT: E 368 ASN cc_start: 0.7872 (m-40) cc_final: 0.7611 (m-40) REVERT: E 369 LYS cc_start: 0.8271 (pttt) cc_final: 0.7676 (ptmm) REVERT: E 375 LYS cc_start: 0.8158 (tttt) cc_final: 0.7778 (mttm) REVERT: H 328 ILE cc_start: 0.8113 (mt) cc_final: 0.7876 (mp) REVERT: H 369 LYS cc_start: 0.8410 (ttmt) cc_final: 0.8009 (tttt) outliers start: 11 outliers final: 9 residues processed: 87 average time/residue: 0.5046 time to fit residues: 50.4389 Evaluate side-chains 89 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 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 325 LEU Chi-restraints excluded: chain H residue 358 ASP Chi-restraints excluded: chain H residue 361 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3582 Z= 0.202 Angle : 0.536 4.347 4794 Z= 0.273 Chirality : 0.048 0.128 534 Planarity : 0.003 0.037 618 Dihedral : 7.262 65.366 480 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.49 % Allowed : 14.18 % 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: -2.85 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 329 PHE 0.008 0.001 PHE G 346 TYR 0.013 0.002 TYR E 310 ARG 0.001 0.000 ARG F 349 *********************** 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 91 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: C 338 GLU cc_start: 0.6064 (mp0) cc_final: 0.5660 (mp0) REVERT: F 311 LYS cc_start: 0.8487 (tptt) cc_final: 0.7835 (tppt) REVERT: F 372 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8423 (mt-10) REVERT: F 379 ARG cc_start: 0.6935 (ptp-170) cc_final: 0.6496 (ptm160) REVERT: F 380 GLU cc_start: 0.6535 (tt0) cc_final: 0.5651 (pm20) REVERT: D 316 SER cc_start: 0.9171 (p) cc_final: 0.8704 (m) REVERT: D 349 ARG cc_start: 0.6860 (mtp180) cc_final: 0.6055 (mtt90) REVERT: D 369 LYS cc_start: 0.8369 (pttt) cc_final: 0.7877 (ptpt) REVERT: G 311 LYS cc_start: 0.8433 (mttt) cc_final: 0.8154 (tttt) REVERT: G 319 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8137 (p) REVERT: G 340 LYS cc_start: 0.5926 (tmtt) cc_final: 0.5560 (tptp) REVERT: G 372 GLU cc_start: 0.8694 (tt0) cc_final: 0.8358 (mt-10) REVERT: G 379 ARG cc_start: 0.6407 (ptp-170) cc_final: 0.5943 (ptm-80) REVERT: E 317 LYS cc_start: 0.8304 (ptmt) cc_final: 0.7637 (ptpp) REVERT: E 327 ASN cc_start: 0.8173 (p0) cc_final: 0.7755 (p0) REVERT: E 368 ASN cc_start: 0.7845 (m-40) cc_final: 0.7575 (m-40) REVERT: E 369 LYS cc_start: 0.8284 (pttt) cc_final: 0.7729 (ptmm) REVERT: E 375 LYS cc_start: 0.8171 (tttt) cc_final: 0.7784 (mttm) REVERT: H 328 ILE cc_start: 0.8096 (mt) cc_final: 0.7859 (mp) REVERT: H 353 LYS cc_start: 0.6409 (mtpt) cc_final: 0.6137 (mttp) REVERT: H 369 LYS cc_start: 0.8421 (ttmt) cc_final: 0.8013 (tttt) outliers start: 10 outliers final: 8 residues processed: 87 average time/residue: 0.5699 time to fit residues: 56.5897 Evaluate side-chains 89 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain H residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.6143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3582 Z= 0.127 Angle : 0.480 3.768 4794 Z= 0.242 Chirality : 0.048 0.126 534 Planarity : 0.003 0.036 618 Dihedral : 6.971 67.974 480 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.49 % Allowed : 14.93 % 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: -2.64 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 330 PHE 0.003 0.001 PHE G 378 TYR 0.008 0.001 TYR E 310 ARG 0.001 0.000 ARG F 349 ********************** 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 92 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: C 331 LYS cc_start: 0.7676 (mtpp) cc_final: 0.7077 (tttt) REVERT: C 338 GLU cc_start: 0.6070 (mp0) cc_final: 0.5191 (mp0) REVERT: F 311 LYS cc_start: 0.8396 (tptt) cc_final: 0.7906 (tptm) REVERT: F 368 ASN cc_start: 0.8860 (m-40) cc_final: 0.8660 (m-40) REVERT: F 372 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8364 (mt-10) REVERT: F 379 ARG cc_start: 0.6812 (ptp-170) cc_final: 0.6277 (ptm160) REVERT: F 380 GLU cc_start: 0.6505 (tt0) cc_final: 0.5608 (pm20) REVERT: D 316 SER cc_start: 0.9159 (p) cc_final: 0.8718 (m) REVERT: D 349 ARG cc_start: 0.6837 (mtp180) cc_final: 0.6051 (mtt90) REVERT: D 369 LYS cc_start: 0.8355 (pttt) cc_final: 0.8030 (ptpt) REVERT: G 311 LYS cc_start: 0.8419 (mttt) cc_final: 0.8155 (tttt) REVERT: G 319 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.8088 (p) REVERT: G 340 LYS cc_start: 0.5878 (tmtt) cc_final: 0.5621 (tptp) REVERT: G 372 GLU cc_start: 0.8604 (tt0) cc_final: 0.8346 (mt-10) REVERT: G 379 ARG cc_start: 0.6351 (ptp-170) cc_final: 0.5913 (ptm-80) REVERT: E 317 LYS cc_start: 0.8318 (ptmt) cc_final: 0.7652 (ptpp) REVERT: E 327 ASN cc_start: 0.8123 (p0) cc_final: 0.7733 (p0) REVERT: E 368 ASN cc_start: 0.7759 (m-40) cc_final: 0.7514 (m-40) REVERT: E 369 LYS cc_start: 0.8238 (pttt) cc_final: 0.7987 (ptpp) REVERT: H 328 ILE cc_start: 0.7979 (mt) cc_final: 0.7740 (mp) REVERT: H 369 LYS cc_start: 0.8416 (ttmt) cc_final: 0.7977 (tttt) REVERT: H 372 GLU cc_start: 0.8392 (tt0) cc_final: 0.8101 (mt-10) outliers start: 6 outliers final: 4 residues processed: 90 average time/residue: 0.5581 time to fit residues: 58.2053 Evaluate side-chains 89 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4654 r_free = 0.4654 target = 0.174150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.140957 restraints weight = 12551.082| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 2.47 r_work: 0.4231 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4129 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.6147 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= 0.197 Angle : 0.524 4.155 4794 Z= 0.266 Chirality : 0.048 0.126 534 Planarity : 0.003 0.038 618 Dihedral : 6.978 64.031 480 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 1.49 % Allowed : 14.93 % 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: -2.71 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.25), 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 0.013 0.002 TYR E 310 ARG 0.001 0.000 ARG E 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3006.61 seconds wall clock time: 57 minutes 59.72 seconds (3479.72 seconds total)