Starting phenix.real_space_refine on Wed Feb 12 00:42:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cgz_45589/02_2025/9cgz_45589_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cgz_45589/02_2025/9cgz_45589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cgz_45589/02_2025/9cgz_45589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cgz_45589/02_2025/9cgz_45589.map" model { file = "/net/cci-nas-00/data/ceres_data/9cgz_45589/02_2025/9cgz_45589_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cgz_45589/02_2025/9cgz_45589_neut.cif" } resolution = 2.69 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= 0.001 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 2106 2.51 5 N 606 2.21 5 O 624 1.98 5 H 3480 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6822 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "B" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 4.90, per 1000 atoms: 0.72 Number of scatterers: 6822 At special positions: 0 Unit cell: (146.28, 76.32, 36.04, 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 624 8.00 N 606 7.00 C 2106 6.00 H 3480 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: 1.56 Conformation dependent library (CDL) restraints added in 641.3 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 44.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'A' and resid 320 through 322 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330 removed outlier: 6.948A pdb=" N GLY A 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASN C 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY C 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN E 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 removed outlier: 6.539A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 347 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 356 removed outlier: 6.560A pdb=" N SER A 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N GLY C 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE A 354 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER C 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N GLY E 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ILE C 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.621A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N HIS E 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 375 Processing sheet with id=AB1, first strand: chain 'B' and resid 307 through 310 Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AB3, first strand: chain 'B' and resid 320 through 322 Processing sheet with id=AB4, first strand: chain 'B' and resid 325 through 330 removed outlier: 6.962A pdb=" N GLY B 326 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN D 327 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N HIS F 329 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE D 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.619A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 343 through 347 removed outlier: 6.714A pdb=" N LEU D 344 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N LYS F 347 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE D 346 " --> pdb=" O LYS F 347 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 351 through 356 removed outlier: 6.463A pdb=" N SER B 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLY D 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ILE B 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER D 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N GLY F 355 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ILE D 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.615A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N HIS D 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 369 through 375 79 hydrogen bonds defined for protein. 237 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: 2.23 Time building geometry restraints manager: 1.91 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: 3474 1.12 - 1.29: 558 1.29 - 1.47: 1055 1.47 - 1.64: 1783 1.64 - 1.81: 6 Bond restraints: 6876 Sorted by residual: bond pdb=" N GLU E 338 " pdb=" H GLU E 338 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" NH1 ARG A 349 " pdb="HH12 ARG A 349 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N GLU D 342 " pdb=" H GLU D 342 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N ILE F 360 " pdb=" H ILE F 360 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CZ PHE C 346 " pdb=" HZ PHE C 346 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 6871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 10221 2.34 - 4.68: 1746 4.68 - 7.01: 528 7.01 - 9.35: 45 9.35 - 11.69: 6 Bond angle restraints: 12546 Sorted by residual: angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 119.06 -6.46 1.00e+00 1.00e+00 4.18e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 118.36 -5.76 1.00e+00 1.00e+00 3.32e+01 angle pdb=" CA PHE B 346 " pdb=" CB PHE B 346 " pdb=" CG PHE B 346 " ideal model delta sigma weight residual 113.80 119.51 -5.71 1.00e+00 1.00e+00 3.26e+01 angle pdb=" CA PHE D 346 " pdb=" CB PHE D 346 " pdb=" CG PHE D 346 " ideal model delta sigma weight residual 113.80 119.36 -5.56 1.00e+00 1.00e+00 3.09e+01 angle pdb=" CA ASP D 358 " pdb=" CB ASP D 358 " pdb=" CG ASP D 358 " ideal model delta sigma weight residual 112.60 118.09 -5.49 1.00e+00 1.00e+00 3.02e+01 ... (remaining 12541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 2742 16.10 - 32.20: 230 32.20 - 48.31: 86 48.31 - 64.41: 98 64.41 - 80.51: 12 Dihedral angle restraints: 3168 sinusoidal: 1806 harmonic: 1362 Sorted by residual: dihedral pdb=" CA GLY D 365 " pdb=" C GLY D 365 " pdb=" N GLY D 366 " pdb=" CA GLY D 366 " ideal model delta harmonic sigma weight residual 180.00 151.51 28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA GLY F 365 " pdb=" C GLY F 365 " pdb=" N GLY F 366 " pdb=" CA GLY F 366 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA GLY B 365 " pdb=" C GLY B 365 " pdb=" N GLY B 366 " pdb=" CA GLY B 366 " ideal model delta harmonic sigma weight residual 180.00 153.11 26.89 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 3165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 286 0.070 - 0.140: 178 0.140 - 0.210: 46 0.210 - 0.280: 5 0.280 - 0.350: 1 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA LYS F 369 " pdb=" N LYS F 369 " pdb=" C LYS F 369 " pdb=" CB LYS F 369 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA ARG E 349 " pdb=" N ARG E 349 " pdb=" C ARG E 349 " pdb=" CB ARG E 349 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ARG F 349 " pdb=" N ARG F 349 " pdb=" C ARG F 349 " pdb=" CB ARG F 349 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 513 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 346 " -0.140 2.00e-02 2.50e+03 5.26e-02 8.29e+01 pdb=" CG PHE E 346 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE E 346 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE E 346 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE E 346 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 346 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE E 346 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 PHE E 346 " 0.053 2.00e-02 2.50e+03 pdb=" HD2 PHE E 346 " 0.034 2.00e-02 2.50e+03 pdb=" HE1 PHE E 346 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 PHE E 346 " -0.012 2.00e-02 2.50e+03 pdb=" HZ PHE E 346 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 346 " -0.138 2.00e-02 2.50e+03 5.20e-02 8.10e+01 pdb=" CG PHE C 346 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE C 346 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE C 346 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 PHE C 346 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 346 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE C 346 " -0.019 2.00e-02 2.50e+03 pdb=" HD1 PHE C 346 " 0.050 2.00e-02 2.50e+03 pdb=" HD2 PHE C 346 " 0.049 2.00e-02 2.50e+03 pdb=" HE1 PHE C 346 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE C 346 " -0.016 2.00e-02 2.50e+03 pdb=" HZ PHE C 346 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 330 " 0.085 2.00e-02 2.50e+03 4.96e-02 5.53e+01 pdb=" CG HIS C 330 " -0.061 2.00e-02 2.50e+03 pdb=" ND1 HIS C 330 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS C 330 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 HIS C 330 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS C 330 " -0.038 2.00e-02 2.50e+03 pdb=" HD2 HIS C 330 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 HIS C 330 " 0.047 2.00e-02 2.50e+03 pdb=" HE2 HIS C 330 " 0.056 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 576 2.20 - 2.80: 12440 2.80 - 3.40: 17545 3.40 - 4.00: 24228 4.00 - 4.60: 33709 Nonbonded interactions: 88498 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.596 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.602 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.602 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.607 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.608 2.450 ... (remaining 88493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.600 Find NCS groups from input model: 0.180 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 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 0.040 3396 Z= 0.724 Angle : 1.914 6.574 4548 Z= 1.255 Chirality : 0.087 0.350 516 Planarity : 0.010 0.055 576 Dihedral : 12.927 80.509 1296 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 1.17 % Allowed : 6.81 % Favored : 92.02 % Rotamer: Outliers : 0.26 % Allowed : 5.21 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.35), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.004 HIS F 362 PHE 0.090 0.015 PHE E 346 TYR 0.084 0.026 TYR D 310 ARG 0.008 0.002 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7713 (tttt) cc_final: 0.6490 (tmmt) REVERT: A 321 LYS cc_start: 0.7828 (tttt) cc_final: 0.7358 (ttmt) REVERT: A 331 LYS cc_start: 0.7570 (mttm) cc_final: 0.7355 (mtpp) REVERT: A 338 GLU cc_start: 0.7402 (tt0) cc_final: 0.7191 (tt0) REVERT: A 340 LYS cc_start: 0.8213 (mttt) cc_final: 0.7795 (mmtp) REVERT: B 321 LYS cc_start: 0.7828 (tttt) cc_final: 0.7625 (tttt) REVERT: B 338 GLU cc_start: 0.7653 (tt0) cc_final: 0.7101 (mm-30) REVERT: B 369 LYS cc_start: 0.7747 (mttt) cc_final: 0.7202 (mmtm) REVERT: C 311 LYS cc_start: 0.7102 (tttt) cc_final: 0.6753 (ttmt) REVERT: C 321 LYS cc_start: 0.7083 (tttt) cc_final: 0.6876 (ttmt) REVERT: C 327 ASN cc_start: 0.7483 (m-40) cc_final: 0.7066 (t0) REVERT: C 338 GLU cc_start: 0.6915 (tt0) cc_final: 0.6652 (tt0) REVERT: C 340 LYS cc_start: 0.7572 (mttt) cc_final: 0.7241 (mtmt) REVERT: D 311 LYS cc_start: 0.7860 (tttt) cc_final: 0.7240 (tttp) REVERT: D 321 LYS cc_start: 0.7332 (tttt) cc_final: 0.6077 (tmtm) REVERT: D 327 ASN cc_start: 0.7511 (m-40) cc_final: 0.7145 (t0) REVERT: D 338 GLU cc_start: 0.6957 (tt0) cc_final: 0.6603 (tp30) REVERT: D 353 LYS cc_start: 0.7437 (mttt) cc_final: 0.7003 (mttm) REVERT: E 311 LYS cc_start: 0.7069 (tttt) cc_final: 0.6567 (mmtt) REVERT: E 353 LYS cc_start: 0.7217 (ttmt) cc_final: 0.6772 (ttpp) REVERT: E 356 SER cc_start: 0.8514 (p) cc_final: 0.7946 (t) REVERT: E 358 ASP cc_start: 0.7430 (m-30) cc_final: 0.6988 (m-30) REVERT: F 315 LEU cc_start: 0.8124 (mp) cc_final: 0.7855 (mt) REVERT: F 321 LYS cc_start: 0.7239 (tttt) cc_final: 0.6859 (ttpt) REVERT: F 353 LYS cc_start: 0.7324 (mttt) cc_final: 0.7009 (mtmt) REVERT: F 356 SER cc_start: 0.8475 (p) cc_final: 0.7984 (p) REVERT: F 358 ASP cc_start: 0.7520 (m-30) cc_final: 0.7232 (m-30) outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 2.6578 time to fit residues: 335.4254 Evaluate side-chains 96 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 GLN 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: 0.6980 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 336 GLN B 336 GLN C 351 GLN D 336 GLN E 336 GLN E 351 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.178098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.147688 restraints weight = 9870.773| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 1.79 r_work: 0.4112 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.4017 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3396 Z= 0.265 Angle : 0.661 6.680 4548 Z= 0.347 Chirality : 0.050 0.134 516 Planarity : 0.003 0.020 576 Dihedral : 8.003 54.369 447 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.82 % Allowed : 15.10 % Favored : 83.07 % 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: -2.04 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 374 PHE 0.006 0.001 PHE E 346 TYR 0.011 0.002 TYR E 310 ARG 0.002 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8660 (mttt) cc_final: 0.8386 (mttt) REVERT: B 369 LYS cc_start: 0.7952 (mttt) cc_final: 0.7699 (mmtm) REVERT: C 311 LYS cc_start: 0.7484 (tttt) cc_final: 0.7074 (ttmt) REVERT: C 340 LYS cc_start: 0.8303 (mttt) cc_final: 0.7972 (mtmt) REVERT: C 342 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7182 (mm-30) REVERT: D 311 LYS cc_start: 0.7831 (tttt) cc_final: 0.7432 (tttm) REVERT: D 321 LYS cc_start: 0.8024 (tttt) cc_final: 0.7559 (mtmt) REVERT: D 342 GLU cc_start: 0.7811 (mp0) cc_final: 0.6622 (mp0) REVERT: E 343 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7939 (mtpp) REVERT: E 353 LYS cc_start: 0.8406 (ttmt) cc_final: 0.8197 (ttpp) REVERT: F 315 LEU cc_start: 0.8263 (mp) cc_final: 0.8034 (mt) REVERT: F 356 SER cc_start: 0.9110 (p) cc_final: 0.8891 (p) outliers start: 7 outliers final: 4 residues processed: 107 average time/residue: 2.4001 time to fit residues: 263.9050 Evaluate side-chains 84 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 ASN F 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.171953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.140919 restraints weight = 10107.985| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 1.76 r_work: 0.4037 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3943 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3396 Z= 0.275 Angle : 0.636 4.850 4548 Z= 0.335 Chirality : 0.050 0.125 516 Planarity : 0.004 0.030 576 Dihedral : 6.961 21.751 444 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.12 % Allowed : 19.79 % Favored : 77.08 % 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: -2.35 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.23), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.013 0.002 PHE E 346 TYR 0.018 0.004 TYR D 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.561 Fit side-chains REVERT: A 342 GLU cc_start: 0.7529 (mm-30) cc_final: 0.6879 (pm20) REVERT: B 369 LYS cc_start: 0.8125 (mttt) cc_final: 0.7792 (mttp) REVERT: C 311 LYS cc_start: 0.7478 (tttt) cc_final: 0.6981 (ttmt) REVERT: C 342 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7527 (mm-30) REVERT: D 311 LYS cc_start: 0.7918 (tttt) cc_final: 0.7534 (tttm) REVERT: D 321 LYS cc_start: 0.8044 (tttt) cc_final: 0.7725 (mtmt) REVERT: D 338 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: E 325 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8243 (tp) REVERT: E 353 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8275 (ttpp) REVERT: F 315 LEU cc_start: 0.8314 (mp) cc_final: 0.8068 (mt) REVERT: F 343 LYS cc_start: 0.7985 (mptt) cc_final: 0.6912 (tppt) REVERT: F 351 GLN cc_start: 0.7930 (mt0) cc_final: 0.7649 (mt0) outliers start: 12 outliers final: 5 residues processed: 86 average time/residue: 2.3661 time to fit residues: 209.5593 Evaluate side-chains 74 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 336 GLN Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.0170 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.173130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.142763 restraints weight = 10198.286| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 1.77 r_work: 0.4063 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3968 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 3396 Z= 0.176 Angle : 0.557 4.087 4548 Z= 0.292 Chirality : 0.050 0.129 516 Planarity : 0.003 0.029 576 Dihedral : 6.361 19.736 444 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.34 % Allowed : 21.35 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.23), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 374 PHE 0.006 0.001 PHE E 346 TYR 0.011 0.002 TYR D 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.498 Fit side-chains REVERT: A 338 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8008 (tm-30) REVERT: A 340 LYS cc_start: 0.8577 (mttt) cc_final: 0.8330 (mmtp) REVERT: A 370 LYS cc_start: 0.8450 (tttm) cc_final: 0.8204 (tptp) REVERT: B 369 LYS cc_start: 0.8167 (mttt) cc_final: 0.7836 (mttp) REVERT: C 311 LYS cc_start: 0.7576 (tttt) cc_final: 0.7058 (ttmt) REVERT: C 342 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7540 (mm-30) REVERT: D 311 LYS cc_start: 0.7840 (tttt) cc_final: 0.7453 (tttp) REVERT: D 321 LYS cc_start: 0.8034 (tttt) cc_final: 0.7722 (mtmt) REVERT: D 338 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7999 (mm-30) REVERT: E 325 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8260 (tp) REVERT: E 353 LYS cc_start: 0.8470 (ttmt) cc_final: 0.8268 (ttpp) REVERT: F 315 LEU cc_start: 0.8270 (mp) cc_final: 0.8036 (mt) REVERT: F 343 LYS cc_start: 0.8125 (mptt) cc_final: 0.6964 (tppt) REVERT: F 351 GLN cc_start: 0.7884 (mt0) cc_final: 0.7611 (mt0) outliers start: 9 outliers final: 4 residues processed: 76 average time/residue: 2.4640 time to fit residues: 192.5743 Evaluate side-chains 73 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.170223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.139054 restraints weight = 10132.620| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 1.75 r_work: 0.4030 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3937 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3396 Z= 0.250 Angle : 0.586 4.443 4548 Z= 0.308 Chirality : 0.050 0.122 516 Planarity : 0.004 0.028 576 Dihedral : 6.382 18.980 444 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 3.39 % Allowed : 22.40 % Favored : 74.22 % 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: -2.45 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 374 PHE 0.011 0.001 PHE E 346 TYR 0.018 0.004 TYR D 310 ARG 0.002 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.641 Fit side-chains REVERT: A 338 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7991 (tm-30) REVERT: A 340 LYS cc_start: 0.8553 (mttt) cc_final: 0.8207 (mmtt) REVERT: A 342 GLU cc_start: 0.7683 (mm-30) cc_final: 0.6903 (pm20) REVERT: B 369 LYS cc_start: 0.8186 (mttt) cc_final: 0.7816 (mttp) REVERT: C 311 LYS cc_start: 0.7562 (tttt) cc_final: 0.7004 (ttmt) REVERT: C 342 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7572 (mm-30) REVERT: D 311 LYS cc_start: 0.7829 (tttt) cc_final: 0.7459 (tttp) REVERT: D 321 LYS cc_start: 0.8062 (tttt) cc_final: 0.7670 (mtmt) REVERT: D 338 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: D 342 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7398 (mp0) REVERT: F 315 LEU cc_start: 0.8292 (mp) cc_final: 0.8079 (mt) REVERT: F 343 LYS cc_start: 0.8108 (mptt) cc_final: 0.7882 (mtpp) REVERT: F 351 GLN cc_start: 0.7901 (mt0) cc_final: 0.7630 (mt0) outliers start: 13 outliers final: 8 residues processed: 79 average time/residue: 2.5647 time to fit residues: 208.5077 Evaluate side-chains 72 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 336 GLN Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 362 HIS E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.171149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.140331 restraints weight = 10222.408| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 1.76 r_work: 0.4034 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3941 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3396 Z= 0.203 Angle : 0.555 4.827 4548 Z= 0.289 Chirality : 0.049 0.123 516 Planarity : 0.004 0.029 576 Dihedral : 6.160 18.979 444 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.12 % Allowed : 21.88 % Favored : 75.00 % 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: -2.44 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 374 PHE 0.008 0.001 PHE E 346 TYR 0.015 0.003 TYR D 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.562 Fit side-chains REVERT: A 338 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7979 (tm-30) REVERT: A 340 LYS cc_start: 0.8541 (mttt) cc_final: 0.8179 (mmtt) REVERT: A 342 GLU cc_start: 0.7726 (mm-30) cc_final: 0.6848 (pm20) REVERT: B 369 LYS cc_start: 0.8239 (mttt) cc_final: 0.7841 (mttp) REVERT: C 311 LYS cc_start: 0.7688 (tttt) cc_final: 0.7143 (ttmt) REVERT: C 342 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7621 (mm-30) REVERT: D 311 LYS cc_start: 0.7784 (tttt) cc_final: 0.7404 (tttp) REVERT: D 321 LYS cc_start: 0.8168 (tttt) cc_final: 0.7740 (mtmt) REVERT: D 338 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: F 347 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7797 (mtmt) outliers start: 12 outliers final: 6 residues processed: 72 average time/residue: 2.2201 time to fit residues: 165.0465 Evaluate side-chains 68 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 347 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.171066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.140079 restraints weight = 10113.742| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 1.76 r_work: 0.4036 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3942 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.6163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3396 Z= 0.203 Angle : 0.547 4.220 4548 Z= 0.286 Chirality : 0.049 0.123 516 Planarity : 0.004 0.029 576 Dihedral : 6.041 18.391 444 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.34 % Allowed : 22.92 % Favored : 74.74 % 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: -2.47 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 374 PHE 0.008 0.001 PHE E 346 TYR 0.016 0.003 TYR D 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.547 Fit side-chains REVERT: A 338 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7973 (tm-30) REVERT: A 340 LYS cc_start: 0.8562 (mttt) cc_final: 0.8187 (mmtt) REVERT: A 342 GLU cc_start: 0.7727 (mm-30) cc_final: 0.6848 (pm20) REVERT: B 342 GLU cc_start: 0.8178 (mm-30) cc_final: 0.6404 (mp0) REVERT: B 369 LYS cc_start: 0.8265 (mttt) cc_final: 0.7837 (mttp) REVERT: C 311 LYS cc_start: 0.7773 (tttt) cc_final: 0.7205 (ttmt) REVERT: C 342 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7586 (mm-30) REVERT: D 311 LYS cc_start: 0.7862 (tttt) cc_final: 0.7486 (tttm) REVERT: D 321 LYS cc_start: 0.8191 (tttt) cc_final: 0.7750 (mtmt) REVERT: D 338 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: D 342 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7442 (mp0) REVERT: F 347 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7756 (mtmt) outliers start: 9 outliers final: 4 residues processed: 67 average time/residue: 2.1456 time to fit residues: 148.6727 Evaluate side-chains 67 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.170704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.139723 restraints weight = 10231.245| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 1.76 r_work: 0.4031 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3941 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.6213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3396 Z= 0.210 Angle : 0.546 4.215 4548 Z= 0.286 Chirality : 0.049 0.123 516 Planarity : 0.004 0.029 576 Dihedral : 5.999 18.622 444 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.34 % Allowed : 23.44 % Favored : 74.22 % 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: -2.50 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 374 PHE 0.007 0.001 PHE E 346 TYR 0.017 0.003 TYR D 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.512 Fit side-chains REVERT: A 338 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7967 (tm-30) REVERT: A 340 LYS cc_start: 0.8567 (mttt) cc_final: 0.8247 (mttt) REVERT: A 342 GLU cc_start: 0.7725 (mm-30) cc_final: 0.6834 (pm20) REVERT: B 342 GLU cc_start: 0.8176 (mm-30) cc_final: 0.6399 (mp0) REVERT: B 369 LYS cc_start: 0.8347 (mttt) cc_final: 0.7891 (mttp) REVERT: C 311 LYS cc_start: 0.7786 (tttt) cc_final: 0.7206 (ttmt) REVERT: C 342 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7634 (mm-30) REVERT: D 311 LYS cc_start: 0.7825 (tttt) cc_final: 0.7453 (tttm) REVERT: D 321 LYS cc_start: 0.8190 (tttt) cc_final: 0.7742 (mtmt) REVERT: D 338 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: D 342 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7402 (mp0) REVERT: F 347 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7945 (mtmt) outliers start: 9 outliers final: 6 residues processed: 67 average time/residue: 2.1787 time to fit residues: 151.7260 Evaluate side-chains 68 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 336 GLN Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 347 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 0.0770 chunk 39 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.172454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.141898 restraints weight = 10220.210| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 1.76 r_work: 0.4050 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3961 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.6288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3396 Z= 0.155 Angle : 0.517 4.013 4548 Z= 0.269 Chirality : 0.049 0.124 516 Planarity : 0.003 0.030 576 Dihedral : 5.751 17.680 444 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.08 % Allowed : 23.70 % Favored : 74.22 % 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: -2.42 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.004 0.001 PHE E 346 TYR 0.012 0.002 TYR D 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.590 Fit side-chains REVERT: A 340 LYS cc_start: 0.8541 (mttt) cc_final: 0.8316 (mttt) REVERT: A 342 GLU cc_start: 0.7755 (mm-30) cc_final: 0.6902 (pm20) REVERT: B 342 GLU cc_start: 0.8171 (mm-30) cc_final: 0.6359 (mp0) REVERT: B 369 LYS cc_start: 0.8318 (mttt) cc_final: 0.7852 (mttp) REVERT: C 311 LYS cc_start: 0.7679 (tttt) cc_final: 0.7094 (ttmt) REVERT: C 342 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7635 (mm-30) REVERT: D 311 LYS cc_start: 0.7813 (tttt) cc_final: 0.7438 (tttm) REVERT: D 321 LYS cc_start: 0.8224 (tttt) cc_final: 0.7898 (ttmt) REVERT: D 338 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7729 (tm-30) outliers start: 8 outliers final: 5 residues processed: 68 average time/residue: 1.9895 time to fit residues: 140.4514 Evaluate side-chains 65 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4443 r_free = 0.4443 target = 0.171886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.140804 restraints weight = 10344.313| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 1.79 r_work: 0.4028 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3938 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.6297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3396 Z= 0.195 Angle : 0.551 6.149 4548 Z= 0.287 Chirality : 0.049 0.123 516 Planarity : 0.004 0.031 576 Dihedral : 5.800 17.963 444 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 1.56 % Allowed : 24.74 % Favored : 73.70 % 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: -2.43 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.007 0.001 PHE E 346 TYR 0.017 0.003 TYR D 310 ARG 0.001 0.000 ARG D 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.549 Fit side-chains REVERT: A 340 LYS cc_start: 0.8592 (mttt) cc_final: 0.8367 (mttt) REVERT: A 342 GLU cc_start: 0.7771 (mm-30) cc_final: 0.6917 (pm20) REVERT: B 342 GLU cc_start: 0.8174 (mm-30) cc_final: 0.6416 (mp0) REVERT: B 369 LYS cc_start: 0.8350 (mttt) cc_final: 0.7886 (mttp) REVERT: C 311 LYS cc_start: 0.7793 (tttt) cc_final: 0.7210 (ttmt) REVERT: C 342 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7635 (mm-30) REVERT: D 311 LYS cc_start: 0.7704 (tttt) cc_final: 0.7316 (tttm) REVERT: D 321 LYS cc_start: 0.8230 (tttt) cc_final: 0.7914 (ttmt) REVERT: D 338 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: D 342 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7410 (mp0) outliers start: 6 outliers final: 5 residues processed: 64 average time/residue: 2.0297 time to fit residues: 134.6802 Evaluate side-chains 65 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4433 r_free = 0.4433 target = 0.171454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.140522 restraints weight = 10376.648| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 1.78 r_work: 0.4029 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3940 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3396 Z= 0.201 Angle : 0.549 5.643 4548 Z= 0.287 Chirality : 0.049 0.123 516 Planarity : 0.004 0.031 576 Dihedral : 5.796 17.947 444 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.82 % Allowed : 25.00 % Favored : 73.18 % 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: -2.43 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.007 0.001 PHE E 346 TYR 0.016 0.003 TYR D 310 ARG 0.001 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6353.54 seconds wall clock time: 112 minutes 7.01 seconds (6727.01 seconds total)