Starting phenix.real_space_refine on Wed Feb 12 02:24:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9o_18287/02_2025/8q9o_18287.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9o_18287/02_2025/8q9o_18287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q9o_18287/02_2025/8q9o_18287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9o_18287/02_2025/8q9o_18287.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9o_18287/02_2025/8q9o_18287.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9o_18287/02_2025/8q9o_18287.cif" } resolution = 3.1 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 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 H 3588 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 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: 7032 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "G" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 4.39, per 1000 atoms: 0.62 Number of scatterers: 7032 At special positions: 0 Unit cell: (168.096, 84.872, 44.496, 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 642 8.00 N 636 7.00 C 2160 6.00 H 3588 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: 1.61 Conformation dependent library (CDL) restraints added in 601.5 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 45.8% 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 removed outlier: 6.402A pdb=" N VAL A 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL C 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.857A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322 removed outlier: 3.647A pdb=" N SER A 320 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS A 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N SER E 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR A 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N CYS E 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS A 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 325 through 330 removed outlier: 6.044A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN A 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 342 Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.480A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 355 Processing sheet with id=AA8, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.452A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 374 removed outlier: 6.426A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N THR C 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU A 372 " --> pdb=" O THR C 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.387A pdb=" N VAL G 306 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N VAL B 309 " --> pdb=" O VAL G 306 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE G 308 " --> pdb=" O VAL B 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.827A pdb=" N VAL G 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 317 through 322 removed outlier: 3.630A pdb=" N SER G 320 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS G 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N SER D 320 " --> pdb=" O LYS G 317 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR G 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N CYS D 322 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LYS G 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 325 through 330 removed outlier: 5.998A pdb=" N GLY G 326 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N HIS B 329 " --> pdb=" O GLY G 326 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE G 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY D 326 " --> pdb=" O LEU G 325 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN G 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 337 through 342 Processing sheet with id=AB6, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.448A pdb=" N ASP G 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 350 through 355 removed outlier: 6.388A pdb=" N VAL G 350 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N LYS B 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER G 352 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N GLY B 355 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE G 354 " --> pdb=" O GLY B 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.458A pdb=" N THR G 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 369 through 374 removed outlier: 6.460A pdb=" N LYS G 370 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N THR B 373 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU G 372 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS G 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N GLU D 372 " --> pdb=" O LYS G 369 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE G 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N HIS D 374 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR G 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 75 hydrogen bonds defined for protein. 225 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.55 - 0.80: 1 0.80 - 1.05: 857 1.05 - 1.31: 3324 1.31 - 1.56: 2898 1.56 - 1.81: 6 Bond restraints: 7086 Sorted by residual: bond pdb=" OG SER A 316 " pdb=" HG SER A 316 " ideal model delta sigma weight residual 0.840 0.549 0.291 2.00e-02 2.50e+03 2.12e+02 bond pdb=" CZ PHE A 378 " pdb=" HZ PHE A 378 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" ND2 ASN B 368 " pdb="HD22 ASN B 368 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CD2 PHE B 378 " pdb=" HD2 PHE B 378 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N ASP D 348 " pdb=" H ASP D 348 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 10761 2.45 - 4.91: 1647 4.91 - 7.36: 472 7.36 - 9.81: 26 9.81 - 12.27: 6 Bond angle restraints: 12912 Sorted by residual: angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.69 117.16 -6.47 1.33e+00 5.65e-01 2.37e+01 angle pdb=" N GLY G 326 " pdb=" CA GLY G 326 " pdb=" C GLY G 326 " ideal model delta sigma weight residual 110.69 117.12 -6.43 1.33e+00 5.65e-01 2.34e+01 angle pdb=" N GLY E 326 " pdb=" CA GLY E 326 " pdb=" C GLY E 326 " ideal model delta sigma weight residual 110.69 117.07 -6.38 1.33e+00 5.65e-01 2.30e+01 angle pdb=" CB HIS B 329 " pdb=" CG HIS B 329 " pdb=" CD2 HIS B 329 " ideal model delta sigma weight residual 131.20 125.17 6.03 1.30e+00 5.92e-01 2.15e+01 angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 110.69 116.76 -6.07 1.33e+00 5.65e-01 2.08e+01 ... (remaining 12907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.46: 2886 13.46 - 26.92: 142 26.92 - 40.38: 74 40.38 - 53.84: 58 53.84 - 67.30: 104 Dihedral angle restraints: 3264 sinusoidal: 1866 harmonic: 1398 Sorted by residual: 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 180.00 158.85 21.15 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ILE A 360 " pdb=" C ILE A 360 " pdb=" N THR A 361 " pdb=" CA THR A 361 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C LYS C 347 " pdb=" N LYS C 347 " pdb=" CA LYS C 347 " pdb=" CB LYS C 347 " ideal model delta harmonic sigma weight residual -122.60 -132.67 10.07 0 2.50e+00 1.60e-01 1.62e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 313 0.070 - 0.140: 157 0.140 - 0.211: 47 0.211 - 0.281: 9 0.281 - 0.351: 2 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS C 347 " pdb=" N LYS C 347 " pdb=" C LYS C 347 " pdb=" CB LYS C 347 " 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 LYS B 347 " pdb=" N LYS B 347 " pdb=" C LYS B 347 " pdb=" CB LYS B 347 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA LYS C 343 " pdb=" N LYS C 343 " pdb=" C LYS C 343 " pdb=" CB LYS C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 525 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 362 " -0.065 2.00e-02 2.50e+03 3.85e-02 3.34e+01 pdb=" CG HIS E 362 " 0.054 2.00e-02 2.50e+03 pdb=" ND1 HIS E 362 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS E 362 " 0.044 2.00e-02 2.50e+03 pdb=" CE1 HIS E 362 " 0.012 2.00e-02 2.50e+03 pdb=" NE2 HIS E 362 " 0.028 2.00e-02 2.50e+03 pdb=" HD2 HIS E 362 " -0.013 2.00e-02 2.50e+03 pdb=" HE1 HIS E 362 " -0.030 2.00e-02 2.50e+03 pdb=" HE2 HIS E 362 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 362 " -0.061 2.00e-02 2.50e+03 3.76e-02 3.18e+01 pdb=" CG HIS A 362 " 0.051 2.00e-02 2.50e+03 pdb=" ND1 HIS A 362 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS A 362 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 HIS A 362 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS A 362 " 0.031 2.00e-02 2.50e+03 pdb=" HD2 HIS A 362 " -0.014 2.00e-02 2.50e+03 pdb=" HE1 HIS A 362 " -0.032 2.00e-02 2.50e+03 pdb=" HE2 HIS A 362 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 362 " 0.057 2.00e-02 2.50e+03 3.47e-02 2.70e+01 pdb=" CG HIS D 362 " -0.050 2.00e-02 2.50e+03 pdb=" ND1 HIS D 362 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS D 362 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 HIS D 362 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS D 362 " -0.028 2.00e-02 2.50e+03 pdb=" HD2 HIS D 362 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 HIS D 362 " 0.030 2.00e-02 2.50e+03 pdb=" HE2 HIS D 362 " 0.037 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 460 2.17 - 2.78: 11993 2.78 - 3.38: 18786 3.38 - 3.99: 24768 3.99 - 4.60: 34581 Nonbonded interactions: 90588 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.560 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.588 2.450 nonbonded pdb=" HZ2 LYS A 370 " pdb=" OE1 GLU A 372 " model vdw 1.677 2.450 nonbonded pdb=" OD2 ASP A 314 " pdb=" HZ1 LYS A 370 " model vdw 1.745 2.450 nonbonded pdb=" OE2 GLU A 372 " pdb=" HE2 HIS A 374 " model vdw 1.747 2.450 ... (remaining 90583 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 'G' } 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: 2.370 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.910 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.012 0.035 3498 Z= 0.790 Angle : 1.866 7.386 4680 Z= 1.237 Chirality : 0.091 0.351 528 Planarity : 0.008 0.032 594 Dihedral : 11.247 58.104 1344 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.03 % Allowed : 3.03 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.004 HIS G 330 PHE 0.050 0.015 PHE D 346 TYR 0.045 0.008 TYR A 310 ARG 0.004 0.001 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: -0.0276 (mt0) cc_final: -0.0658 (tm-30) REVERT: C 313 VAL cc_start: 0.5914 (t) cc_final: 0.5693 (t) REVERT: C 342 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7763 (tt0) REVERT: C 343 LYS cc_start: 0.9032 (mttt) cc_final: 0.8774 (mttm) REVERT: E 320 SER cc_start: 0.6107 (OUTLIER) cc_final: 0.5734 (p) REVERT: G 307 GLN cc_start: -0.0088 (mt0) cc_final: -0.0515 (tm-30) REVERT: G 321 LYS cc_start: 0.8351 (ttmt) cc_final: 0.8136 (mppt) REVERT: G 369 LYS cc_start: 0.7991 (tttt) cc_final: 0.7721 (ttmm) REVERT: B 307 GLN cc_start: -0.0161 (mt0) cc_final: -0.0470 (tp40) REVERT: D 320 SER cc_start: 0.6374 (OUTLIER) cc_final: 0.5973 (p) REVERT: D 369 LYS cc_start: 0.7517 (tttt) cc_final: 0.7316 (ttmm) outliers start: 12 outliers final: 10 residues processed: 126 average time/residue: 0.5043 time to fit residues: 72.5139 Evaluate side-chains 102 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 362 HIS E 362 HIS G 362 HIS G 374 HIS B 362 HIS D 362 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5255 r_free = 0.5255 target = 0.257629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.158294 restraints weight = 8741.108| |-----------------------------------------------------------------------------| r_work (start): 0.4419 rms_B_bonded: 2.71 r_work: 0.4308 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4210 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3498 Z= 0.186 Angle : 0.552 4.129 4680 Z= 0.295 Chirality : 0.052 0.137 528 Planarity : 0.003 0.013 594 Dihedral : 7.847 55.810 480 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.28 % Allowed : 9.09 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.006 0.001 PHE C 346 TYR 0.008 0.001 TYR A 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: -0.0041 (mt0) cc_final: -0.0596 (tm-30) REVERT: A 325 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7499 (tp) REVERT: A 342 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7651 (tt0) REVERT: C 321 LYS cc_start: 0.7744 (mmtt) cc_final: 0.7130 (mmtm) REVERT: C 342 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7574 (tt0) REVERT: C 343 LYS cc_start: 0.9058 (mttt) cc_final: 0.8848 (mttm) REVERT: C 370 LYS cc_start: 0.7615 (tttt) cc_final: 0.7282 (tptp) REVERT: E 320 SER cc_start: 0.6449 (OUTLIER) cc_final: 0.5823 (p) REVERT: G 307 GLN cc_start: -0.0183 (mt0) cc_final: -0.0599 (tm-30) REVERT: G 342 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7531 (tt0) REVERT: G 369 LYS cc_start: 0.7684 (tttt) cc_final: 0.7373 (ttpt) REVERT: G 372 GLU cc_start: 0.6646 (tt0) cc_final: 0.6413 (mt-10) REVERT: B 307 GLN cc_start: 0.0047 (mt0) cc_final: -0.0162 (tp40) REVERT: B 358 ASP cc_start: 0.8457 (m-30) cc_final: 0.8144 (m-30) REVERT: B 370 LYS cc_start: 0.7101 (tptp) cc_final: 0.6203 (tptp) REVERT: D 320 SER cc_start: 0.6536 (OUTLIER) cc_final: 0.6170 (p) REVERT: D 342 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7745 (tt0) REVERT: D 369 LYS cc_start: 0.7122 (tttt) cc_final: 0.6857 (ttmm) outliers start: 13 outliers final: 5 residues processed: 107 average time/residue: 0.4932 time to fit residues: 60.1575 Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 10.0000 chunk 21 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN C 336 GLN G 336 GLN B 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5243 r_free = 0.5243 target = 0.255519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.155830 restraints weight = 8950.271| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 2.66 r_work: 0.4249 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4146 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3498 Z= 0.164 Angle : 0.486 4.992 4680 Z= 0.255 Chirality : 0.051 0.140 528 Planarity : 0.003 0.026 594 Dihedral : 6.083 50.471 473 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.02 % Allowed : 10.86 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 330 PHE 0.006 0.001 PHE A 346 TYR 0.007 0.001 TYR A 310 ARG 0.002 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: -0.0130 (mt0) cc_final: -0.0635 (tm-30) REVERT: A 325 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7413 (tp) REVERT: A 342 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7638 (tt0) REVERT: C 342 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7682 (tt0) REVERT: C 343 LYS cc_start: 0.9098 (mttt) cc_final: 0.8856 (mttm) REVERT: C 347 LYS cc_start: 0.8777 (mmtt) cc_final: 0.8514 (mmtp) REVERT: E 320 SER cc_start: 0.6586 (OUTLIER) cc_final: 0.6108 (p) REVERT: G 307 GLN cc_start: -0.0405 (mt0) cc_final: -0.0800 (tm-30) REVERT: G 342 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7559 (tt0) REVERT: G 369 LYS cc_start: 0.7464 (tttt) cc_final: 0.7090 (ttmm) REVERT: B 325 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7606 (tt) REVERT: B 358 ASP cc_start: 0.8420 (m-30) cc_final: 0.8156 (m-30) REVERT: B 369 LYS cc_start: 0.7440 (ttmt) cc_final: 0.6977 (ttmm) REVERT: D 342 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7755 (tt0) REVERT: D 369 LYS cc_start: 0.7054 (tttt) cc_final: 0.6826 (ttmm) outliers start: 8 outliers final: 3 residues processed: 81 average time/residue: 0.4118 time to fit residues: 39.2493 Evaluate side-chains 77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain D residue 316 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.5241 r_free = 0.5241 target = 0.254820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.153745 restraints weight = 8860.104| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 2.64 r_work: 0.4249 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4151 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3498 Z= 0.175 Angle : 0.463 5.337 4680 Z= 0.240 Chirality : 0.051 0.137 528 Planarity : 0.003 0.024 594 Dihedral : 4.950 41.464 467 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.52 % Allowed : 11.11 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.005 0.001 PHE A 346 TYR 0.005 0.001 TYR A 310 ARG 0.001 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: -0.0120 (mt0) cc_final: -0.0581 (tm-30) REVERT: A 342 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7612 (tt0) REVERT: C 342 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7611 (tt0) REVERT: C 343 LYS cc_start: 0.9042 (mttt) cc_final: 0.8745 (mttm) REVERT: E 320 SER cc_start: 0.6900 (OUTLIER) cc_final: 0.6398 (p) REVERT: G 307 GLN cc_start: -0.0430 (mt0) cc_final: -0.0794 (tm-30) REVERT: G 342 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7508 (tt0) REVERT: G 369 LYS cc_start: 0.7483 (tttt) cc_final: 0.7065 (ttmm) REVERT: B 358 ASP cc_start: 0.8449 (m-30) cc_final: 0.8166 (m-30) REVERT: B 369 LYS cc_start: 0.7420 (ttmt) cc_final: 0.6953 (ttmm) REVERT: D 342 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7857 (tt0) REVERT: D 369 LYS cc_start: 0.6927 (tttt) cc_final: 0.6721 (ttmm) outliers start: 6 outliers final: 3 residues processed: 76 average time/residue: 0.4507 time to fit residues: 39.7968 Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 21 optimal weight: 30.0000 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.5240 r_free = 0.5240 target = 0.254471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.153210 restraints weight = 8720.585| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 2.65 r_work: 0.4244 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4142 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3498 Z= 0.169 Angle : 0.449 4.750 4680 Z= 0.231 Chirality : 0.051 0.134 528 Planarity : 0.002 0.023 594 Dihedral : 4.429 27.257 465 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.76 % Allowed : 11.11 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 329 PHE 0.004 0.001 PHE A 346 TYR 0.003 0.001 TYR A 310 ARG 0.001 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: -0.0248 (mt0) cc_final: -0.0714 (tm-30) REVERT: A 321 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7837 (mmtm) REVERT: A 342 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7600 (tt0) REVERT: C 321 LYS cc_start: 0.7846 (mmtt) cc_final: 0.7447 (mmtm) REVERT: C 342 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7676 (tt0) REVERT: C 370 LYS cc_start: 0.6615 (tptp) cc_final: 0.6247 (mtmt) REVERT: C 372 GLU cc_start: 0.3806 (pp20) cc_final: 0.2420 (mp0) REVERT: E 342 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7685 (tt0) REVERT: G 307 GLN cc_start: -0.0356 (mt0) cc_final: -0.0755 (tm-30) REVERT: G 342 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7552 (tt0) REVERT: G 369 LYS cc_start: 0.7617 (tttt) cc_final: 0.7219 (ttmm) REVERT: B 358 ASP cc_start: 0.8465 (m-30) cc_final: 0.8178 (m-30) REVERT: D 342 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7848 (tt0) outliers start: 3 outliers final: 3 residues processed: 69 average time/residue: 0.4728 time to fit residues: 38.0692 Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 0.0970 chunk 25 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 21 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 0.0020 chunk 15 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 2.0192 ------------------------------------------------------------------------------- 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 = 0.5215 r_free = 0.5215 target = 0.250697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.148452 restraints weight = 8895.590| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 2.68 r_work: 0.4155 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4053 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3498 Z= 0.207 Angle : 0.453 3.973 4680 Z= 0.235 Chirality : 0.050 0.133 528 Planarity : 0.002 0.022 594 Dihedral : 4.247 26.776 464 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.26 % Allowed : 11.11 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.004 0.001 PHE A 346 TYR 0.002 0.001 TYR A 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: -0.0245 (mt0) cc_final: -0.0718 (tm-30) REVERT: A 342 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7647 (tt0) REVERT: C 321 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7383 (mmtm) REVERT: C 342 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7688 (tt0) REVERT: C 370 LYS cc_start: 0.6719 (tptp) cc_final: 0.5848 (mtmt) REVERT: E 342 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7788 (tt0) REVERT: G 307 GLN cc_start: -0.0346 (mt0) cc_final: -0.0727 (tm-30) REVERT: G 342 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7554 (tt0) REVERT: G 369 LYS cc_start: 0.7595 (tttt) cc_final: 0.7207 (ttmm) REVERT: B 358 ASP cc_start: 0.8510 (m-30) cc_final: 0.8254 (m-30) REVERT: B 369 LYS cc_start: 0.7449 (ttmt) cc_final: 0.6996 (ttmm) REVERT: D 342 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7890 (tt0) outliers start: 5 outliers final: 5 residues processed: 68 average time/residue: 0.4681 time to fit residues: 37.0898 Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.5214 r_free = 0.5214 target = 0.251243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.149376 restraints weight = 8886.324| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 2.74 r_work: 0.4157 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4053 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.6445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3498 Z= 0.218 Angle : 0.467 5.635 4680 Z= 0.241 Chirality : 0.050 0.133 528 Planarity : 0.003 0.021 594 Dihedral : 4.269 27.052 464 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.76 % Allowed : 12.12 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 329 PHE 0.004 0.001 PHE A 346 TYR 0.002 0.001 TYR B 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: -0.0176 (mt0) cc_final: -0.0735 (tm-30) REVERT: A 342 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7639 (tt0) REVERT: A 343 LYS cc_start: 0.8596 (mttt) cc_final: 0.8342 (mttm) REVERT: C 321 LYS cc_start: 0.7915 (mmtt) cc_final: 0.7617 (mmtm) REVERT: C 342 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7638 (tt0) REVERT: C 370 LYS cc_start: 0.6764 (tptp) cc_final: 0.5827 (mtmt) REVERT: E 342 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7787 (tt0) REVERT: G 307 GLN cc_start: -0.0399 (mt0) cc_final: -0.0756 (tm-30) REVERT: G 342 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7497 (tt0) REVERT: B 358 ASP cc_start: 0.8488 (m-30) cc_final: 0.8213 (m-30) REVERT: B 369 LYS cc_start: 0.7366 (ttmt) cc_final: 0.6796 (ttmm) REVERT: B 370 LYS cc_start: 0.6641 (tptp) cc_final: 0.6374 (mtmt) REVERT: D 342 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7891 (tt0) outliers start: 3 outliers final: 2 residues processed: 72 average time/residue: 0.4597 time to fit residues: 38.4137 Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain D residue 316 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.5248 r_free = 0.5248 target = 0.254705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.152878 restraints weight = 8921.123| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 2.75 r_work: 0.4211 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4106 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.6602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3498 Z= 0.143 Angle : 0.456 4.542 4680 Z= 0.232 Chirality : 0.050 0.135 528 Planarity : 0.003 0.039 594 Dihedral : 3.915 11.446 462 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.51 % Allowed : 12.37 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 374 PHE 0.002 0.001 PHE A 346 TYR 0.002 0.001 TYR G 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: -0.0117 (mt0) cc_final: -0.0684 (tm-30) REVERT: A 342 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7624 (tt0) REVERT: C 321 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7370 (mmtm) REVERT: C 342 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7642 (tt0) REVERT: C 369 LYS cc_start: 0.7714 (ttmm) cc_final: 0.7447 (ttmm) REVERT: C 370 LYS cc_start: 0.6853 (tptp) cc_final: 0.5840 (mtmt) REVERT: E 342 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7775 (tt0) REVERT: G 307 GLN cc_start: -0.0398 (mt0) cc_final: -0.0784 (tm-30) REVERT: G 342 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7476 (tt0) REVERT: B 358 ASP cc_start: 0.8471 (m-30) cc_final: 0.8153 (m-30) REVERT: D 342 GLU cc_start: 0.8421 (mt-10) cc_final: 0.7885 (tt0) outliers start: 2 outliers final: 2 residues processed: 69 average time/residue: 0.4612 time to fit residues: 36.9690 Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 316 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.5250 r_free = 0.5250 target = 0.254149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.151886 restraints weight = 8851.771| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 2.74 r_work: 0.4210 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4108 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.6699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3498 Z= 0.169 Angle : 0.451 4.315 4680 Z= 0.230 Chirality : 0.050 0.134 528 Planarity : 0.003 0.034 594 Dihedral : 3.841 11.558 462 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.25 % Allowed : 12.12 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.003 0.001 PHE G 346 TYR 0.002 0.001 TYR C 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: -0.0079 (mt0) cc_final: -0.0677 (tm-30) REVERT: A 342 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7654 (tt0) REVERT: C 321 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7406 (mmtm) REVERT: C 342 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7646 (tt0) REVERT: C 369 LYS cc_start: 0.7710 (ttmm) cc_final: 0.7449 (ttmm) REVERT: C 370 LYS cc_start: 0.6926 (tptp) cc_final: 0.5896 (mtmt) REVERT: E 342 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7747 (tt0) REVERT: E 343 LYS cc_start: 0.8889 (mttt) cc_final: 0.8684 (mttp) REVERT: E 372 GLU cc_start: 0.5696 (mt-10) cc_final: 0.5291 (mp0) REVERT: G 342 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7497 (tt0) REVERT: B 358 ASP cc_start: 0.8458 (m-30) cc_final: 0.8156 (m-30) REVERT: D 342 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7892 (tt0) outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.4797 time to fit residues: 36.1147 Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 21 optimal weight: 30.0000 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.5238 r_free = 0.5238 target = 0.253379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.150494 restraints weight = 8931.003| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 2.73 r_work: 0.4180 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4076 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3498 Z= 0.217 Angle : 0.467 4.777 4680 Z= 0.239 Chirality : 0.050 0.133 528 Planarity : 0.003 0.033 594 Dihedral : 3.928 12.386 462 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.51 % Allowed : 12.12 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.003 0.001 PHE G 346 TYR 0.002 0.001 TYR D 310 ARG 0.001 0.000 ARG A 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: -0.0027 (mt0) cc_final: -0.0641 (tm-30) REVERT: A 342 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7691 (tt0) REVERT: C 321 LYS cc_start: 0.7918 (mmtt) cc_final: 0.7615 (mmtm) REVERT: C 342 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7641 (tt0) REVERT: E 342 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7802 (tt0) REVERT: B 343 LYS cc_start: 0.8962 (mttt) cc_final: 0.8749 (mttm) REVERT: B 358 ASP cc_start: 0.8471 (m-30) cc_final: 0.8183 (m-30) REVERT: B 369 LYS cc_start: 0.7266 (ttmt) cc_final: 0.6767 (ttmm) REVERT: D 342 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7956 (tt0) outliers start: 2 outliers final: 2 residues processed: 67 average time/residue: 0.4662 time to fit residues: 36.2513 Evaluate side-chains 66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 316 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 0.0770 chunk 36 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.5290 r_free = 0.5290 target = 0.258754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.156728 restraints weight = 8863.855| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 2.74 r_work: 0.4260 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4153 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.6939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3498 Z= 0.129 Angle : 0.451 4.772 4680 Z= 0.224 Chirality : 0.050 0.132 528 Planarity : 0.003 0.044 594 Dihedral : 3.602 10.405 462 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.51 % Allowed : 12.63 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.84 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 330 PHE 0.001 0.000 PHE C 346 TYR 0.003 0.001 TYR G 310 ARG 0.001 0.000 ARG A 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5209.99 seconds wall clock time: 92 minutes 43.97 seconds (5563.97 seconds total)