Starting phenix.real_space_refine on Fri Aug 22 18:59:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9o_18287/08_2025/8q9o_18287.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9o_18287/08_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_18287/08_2025/8q9o_18287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9o_18287/08_2025/8q9o_18287.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9o_18287/08_2025/8q9o_18287.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9o_18287/08_2025/8q9o_18287.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.42, per 1000 atoms: 0.20 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: 0.58 Conformation dependent library (CDL) restraints added in 183.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.20 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: 1.37 Time building geometry restraints manager: 0.79 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: 0.00 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: 4.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.300 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.850 ------------------------------------------------------------------------------- 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= 0.727 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (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 ARG 0.004 0.001 ARG E 379 TYR 0.045 0.008 TYR A 310 PHE 0.050 0.015 PHE D 346 HIS 0.015 0.004 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.01165 ( 3498) covalent geometry : angle 1.86560 ( 4680) hydrogen bonds : bond 0.09938 ( 75) hydrogen bonds : angle 7.16299 ( 225) *********************** 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 : 0.200 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 369 LYS cc_start: 0.7991 (tttt) cc_final: 0.7720 (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: 0.5964 (p) REVERT: D 369 LYS cc_start: 0.7517 (tttt) cc_final: 0.7241 (ttmm) outliers start: 12 outliers final: 10 residues processed: 126 average time/residue: 0.2167 time to fit residues: 31.0740 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 : 0.196 ------------------------------------------------------------------------------- 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 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.5261 r_free = 0.5261 target = 0.258362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.159701 restraints weight = 8808.200| |-----------------------------------------------------------------------------| r_work (start): 0.4432 rms_B_bonded: 2.72 r_work: 0.4321 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4224 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3498 Z= 0.119 Angle : 0.545 4.255 4680 Z= 0.289 Chirality : 0.052 0.142 528 Planarity : 0.003 0.014 594 Dihedral : 7.843 55.798 480 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.28 % Allowed : 8.84 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.008 0.001 TYR A 310 PHE 0.005 0.001 PHE A 346 HIS 0.004 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3498) covalent geometry : angle 0.54505 ( 4680) hydrogen bonds : bond 0.03292 ( 75) hydrogen bonds : angle 4.54500 ( 225) *********************** 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 106 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: -0.0052 (mt0) cc_final: -0.0600 (tm-30) REVERT: A 321 LYS cc_start: 0.7963 (mmtt) cc_final: 0.7725 (mmtm) REVERT: A 325 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7468 (tp) REVERT: A 342 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7647 (tt0) REVERT: C 321 LYS cc_start: 0.7730 (mmtt) cc_final: 0.7262 (mmtm) REVERT: C 342 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7561 (tt0) REVERT: C 343 LYS cc_start: 0.9049 (mttt) cc_final: 0.8837 (mttm) REVERT: C 370 LYS cc_start: 0.7603 (tttt) cc_final: 0.7342 (tptp) REVERT: E 320 SER cc_start: 0.6418 (OUTLIER) cc_final: 0.5794 (p) REVERT: G 307 GLN cc_start: -0.0190 (mt0) cc_final: -0.0602 (tm-30) REVERT: G 342 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7527 (tt0) REVERT: G 369 LYS cc_start: 0.7695 (tttt) cc_final: 0.7401 (ttpt) REVERT: G 372 GLU cc_start: 0.6652 (tt0) cc_final: 0.6439 (mt-10) REVERT: B 307 GLN cc_start: 0.0036 (mt0) cc_final: -0.0165 (tp40) REVERT: D 320 SER cc_start: 0.6497 (OUTLIER) cc_final: 0.6129 (p) REVERT: D 342 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7739 (tt0) outliers start: 13 outliers final: 5 residues processed: 106 average time/residue: 0.2018 time to fit residues: 24.3544 Evaluate side-chains 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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 6 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 374 HIS C 336 GLN G 336 GLN B 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5175 r_free = 0.5175 target = 0.248044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.146431 restraints weight = 8939.963| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 2.67 r_work: 0.4158 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4059 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3498 Z= 0.225 Angle : 0.543 5.395 4680 Z= 0.291 Chirality : 0.052 0.142 528 Planarity : 0.003 0.026 594 Dihedral : 6.432 51.513 473 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.77 % Allowed : 11.62 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 349 TYR 0.006 0.001 TYR A 310 PHE 0.009 0.001 PHE A 346 HIS 0.005 0.001 HIS G 329 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 3498) covalent geometry : angle 0.54310 ( 4680) hydrogen bonds : bond 0.02859 ( 75) hydrogen bonds : angle 4.36931 ( 225) *********************** 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 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: -0.0086 (mt0) cc_final: -0.0625 (tm-30) REVERT: A 342 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7620 (tt0) REVERT: C 342 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7589 (tt0) REVERT: C 343 LYS cc_start: 0.8981 (mttt) cc_final: 0.8728 (mttm) REVERT: E 320 SER cc_start: 0.6579 (OUTLIER) cc_final: 0.6065 (p) REVERT: G 307 GLN cc_start: -0.0412 (mt0) cc_final: -0.0813 (tm-30) REVERT: G 369 LYS cc_start: 0.7592 (tttt) cc_final: 0.7227 (ttmm) REVERT: B 307 GLN cc_start: 0.0128 (mt0) cc_final: -0.0101 (tp40) REVERT: D 342 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7975 (tt0) outliers start: 7 outliers final: 2 residues processed: 71 average time/residue: 0.1689 time to fit residues: 14.1237 Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 320 SER 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 21 optimal weight: 30.0000 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 = 0.5204 r_free = 0.5204 target = 0.250908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.149462 restraints weight = 8934.233| |-----------------------------------------------------------------------------| r_work (start): 0.4311 rms_B_bonded: 2.67 r_work: 0.4190 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4086 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5706 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= 0.156 Angle : 0.483 4.128 4680 Z= 0.252 Chirality : 0.051 0.138 528 Planarity : 0.003 0.024 594 Dihedral : 5.147 44.891 465 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.76 % Allowed : 11.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.006 0.001 TYR A 310 PHE 0.005 0.001 PHE A 346 HIS 0.002 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 3498) covalent geometry : angle 0.48261 ( 4680) hydrogen bonds : bond 0.02339 ( 75) hydrogen bonds : angle 4.12518 ( 225) *********************** 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 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: -0.0162 (mt0) cc_final: -0.0614 (tm-30) REVERT: A 342 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7702 (tt0) REVERT: C 342 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7649 (tt0) REVERT: C 343 LYS cc_start: 0.9050 (mttt) cc_final: 0.8753 (mttm) REVERT: E 320 SER cc_start: 0.6870 (OUTLIER) cc_final: 0.6352 (p) REVERT: G 307 GLN cc_start: -0.0543 (mt0) cc_final: -0.0922 (tm-30) REVERT: G 342 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7554 (tt0) REVERT: G 369 LYS cc_start: 0.7655 (tttt) cc_final: 0.7221 (ttmm) REVERT: B 307 GLN cc_start: 0.0183 (mt0) cc_final: -0.0048 (tp40) REVERT: B 369 LYS cc_start: 0.7457 (ttmt) cc_final: 0.6968 (ttmm) REVERT: D 342 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7906 (tt0) outliers start: 3 outliers final: 2 residues processed: 69 average time/residue: 0.1958 time to fit residues: 15.7107 Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain D residue 316 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.5207 r_free = 0.5207 target = 0.251010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.150202 restraints weight = 8855.039| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 2.66 r_work: 0.4197 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4094 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5962 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= 0.132 Angle : 0.469 4.728 4680 Z= 0.241 Chirality : 0.050 0.132 528 Planarity : 0.003 0.024 594 Dihedral : 4.689 32.543 465 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.01 % Allowed : 11.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.005 0.001 TYR G 310 PHE 0.004 0.001 PHE A 346 HIS 0.002 0.001 HIS G 329 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 3498) covalent geometry : angle 0.46932 ( 4680) hydrogen bonds : bond 0.02084 ( 75) hydrogen bonds : angle 3.84716 ( 225) *********************** 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 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: -0.0216 (mt0) cc_final: -0.0685 (tm-30) REVERT: A 342 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7667 (tt0) REVERT: C 321 LYS cc_start: 0.7850 (mmtt) cc_final: 0.7404 (mmtm) REVERT: C 342 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7681 (tt0) REVERT: C 370 LYS cc_start: 0.7369 (tttt) cc_final: 0.6420 (mtmt) REVERT: E 320 SER cc_start: 0.7022 (OUTLIER) cc_final: 0.6610 (p) REVERT: E 342 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7755 (tt0) REVERT: G 307 GLN cc_start: -0.0378 (mt0) cc_final: -0.0738 (tm-30) REVERT: G 321 LYS cc_start: 0.8252 (mppt) cc_final: 0.8034 (mppt) REVERT: G 342 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7544 (tt0) REVERT: B 307 GLN cc_start: 0.0074 (mt0) cc_final: -0.0146 (tp40) REVERT: B 358 ASP cc_start: 0.8558 (m-30) cc_final: 0.8296 (m-30) REVERT: B 369 LYS cc_start: 0.7420 (ttmt) cc_final: 0.6837 (ttmm) REVERT: D 342 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7884 (tt0) outliers start: 4 outliers final: 3 residues processed: 68 average time/residue: 0.1799 time to fit residues: 14.3331 Evaluate side-chains 66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.0040 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 32 optimal weight: 0.0770 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 overall best weight: 0.8156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5238 r_free = 0.5238 target = 0.253567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.152843 restraints weight = 8960.148| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 2.74 r_work: 0.4227 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4125 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.6241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3498 Z= 0.079 Angle : 0.439 4.119 4680 Z= 0.224 Chirality : 0.050 0.136 528 Planarity : 0.002 0.023 594 Dihedral : 4.272 28.760 465 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.76 % Allowed : 12.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.003 0.001 TYR G 310 PHE 0.002 0.001 PHE A 346 HIS 0.002 0.000 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00185 ( 3498) covalent geometry : angle 0.43923 ( 4680) hydrogen bonds : bond 0.02061 ( 75) hydrogen bonds : angle 3.59783 ( 225) *********************** 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 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: -0.0182 (mt0) cc_final: -0.0666 (tm-30) REVERT: A 342 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7625 (tt0) REVERT: C 321 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7313 (mmtm) REVERT: C 342 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7651 (tt0) REVERT: C 370 LYS cc_start: 0.7384 (tttt) cc_final: 0.6443 (mtmt) REVERT: E 342 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7780 (tt0) REVERT: G 307 GLN cc_start: -0.0400 (mt0) cc_final: -0.0749 (tm-30) REVERT: G 321 LYS cc_start: 0.8232 (mppt) cc_final: 0.7682 (mmtt) REVERT: G 342 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7485 (tt0) REVERT: B 358 ASP cc_start: 0.8524 (m-30) cc_final: 0.8277 (m-30) REVERT: B 369 LYS cc_start: 0.7244 (ttmt) cc_final: 0.6731 (ttmm) REVERT: D 342 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7862 (tt0) outliers start: 3 outliers final: 2 residues processed: 68 average time/residue: 0.1696 time to fit residues: 13.6853 Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 316 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.5226 r_free = 0.5226 target = 0.252074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.150721 restraints weight = 8948.811| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 2.72 r_work: 0.4191 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4090 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.6440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 3498 Z= 0.112 Angle : 0.444 4.069 4680 Z= 0.228 Chirality : 0.050 0.132 528 Planarity : 0.002 0.022 594 Dihedral : 3.914 11.422 462 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.76 % Allowed : 13.13 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.003 0.001 TYR G 310 PHE 0.003 0.001 PHE A 346 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 3498) covalent geometry : angle 0.44443 ( 4680) hydrogen bonds : bond 0.02068 ( 75) hydrogen bonds : angle 3.55441 ( 225) *********************** 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 74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: -0.0170 (mt0) cc_final: -0.0650 (tm-30) REVERT: A 342 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7618 (tt0) REVERT: A 343 LYS cc_start: 0.8616 (mttt) cc_final: 0.8331 (mttm) REVERT: C 321 LYS cc_start: 0.7854 (mmtt) cc_final: 0.7347 (mmtm) REVERT: C 342 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7653 (tt0) REVERT: E 342 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7814 (tt0) REVERT: G 307 GLN cc_start: -0.0392 (mt0) cc_final: -0.0746 (tm-30) REVERT: G 321 LYS cc_start: 0.8234 (mppt) cc_final: 0.7711 (mmtt) REVERT: G 342 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7507 (tt0) REVERT: B 358 ASP cc_start: 0.8528 (m-30) cc_final: 0.8285 (m-30) REVERT: B 369 LYS cc_start: 0.7338 (ttmt) cc_final: 0.6771 (ttmm) REVERT: D 342 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7890 (tt0) outliers start: 3 outliers final: 3 residues processed: 72 average time/residue: 0.1697 time to fit residues: 14.0925 Evaluate side-chains 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain B residue 315 LEU 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 21 optimal weight: 30.0000 chunk 26 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.5245 r_free = 0.5245 target = 0.253840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.152309 restraints weight = 8958.889| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 2.74 r_work: 0.4197 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4091 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.6565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3498 Z= 0.093 Angle : 0.448 4.361 4680 Z= 0.229 Chirality : 0.050 0.132 528 Planarity : 0.003 0.041 594 Dihedral : 3.811 11.072 462 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.76 % Allowed : 13.13 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.002 0.001 TYR G 310 PHE 0.002 0.001 PHE A 346 HIS 0.001 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 3498) covalent geometry : angle 0.44825 ( 4680) hydrogen bonds : bond 0.01932 ( 75) hydrogen bonds : angle 3.45459 ( 225) *********************** 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 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: -0.0113 (mt0) cc_final: -0.0682 (tm-30) REVERT: A 342 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7590 (tt0) REVERT: A 343 LYS cc_start: 0.8612 (mttt) cc_final: 0.8336 (mttm) REVERT: C 321 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7329 (mmtm) REVERT: C 342 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7645 (tt0) REVERT: E 342 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7803 (tt0) REVERT: G 307 GLN cc_start: -0.0435 (mt0) cc_final: -0.0772 (tm-30) REVERT: G 321 LYS cc_start: 0.8214 (mppt) cc_final: 0.7711 (mmtt) REVERT: G 342 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7475 (tt0) REVERT: G 369 LYS cc_start: 0.7184 (ttpt) cc_final: 0.6583 (tttm) REVERT: B 321 LYS cc_start: 0.7739 (mmtt) cc_final: 0.7496 (mmtt) REVERT: B 358 ASP cc_start: 0.8532 (m-30) cc_final: 0.8289 (m-30) REVERT: B 369 LYS cc_start: 0.7263 (ttmt) cc_final: 0.6764 (ttmm) REVERT: D 342 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7871 (tt0) outliers start: 3 outliers final: 3 residues processed: 71 average time/residue: 0.2157 time to fit residues: 17.5889 Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain B 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 24 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.5197 r_free = 0.5197 target = 0.249431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.147390 restraints weight = 8995.779| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 2.74 r_work: 0.4141 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4040 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.6664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3498 Z= 0.174 Angle : 0.473 4.271 4680 Z= 0.247 Chirality : 0.050 0.132 528 Planarity : 0.003 0.039 594 Dihedral : 4.062 13.074 462 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.01 % Allowed : 13.13 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 379 TYR 0.002 0.001 TYR D 310 PHE 0.005 0.001 PHE A 346 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 3498) covalent geometry : angle 0.47267 ( 4680) hydrogen bonds : bond 0.02254 ( 75) hydrogen bonds : angle 3.65923 ( 225) *********************** 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 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: -0.0090 (mt0) cc_final: -0.0663 (tm-30) REVERT: A 342 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7708 (tt0) REVERT: C 321 LYS cc_start: 0.7889 (mmtt) cc_final: 0.7371 (mmtm) REVERT: C 342 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7654 (tt0) REVERT: E 342 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7841 (tt0) REVERT: G 342 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7523 (tt0) REVERT: G 369 LYS cc_start: 0.7232 (ttpt) cc_final: 0.6613 (tttm) REVERT: B 321 LYS cc_start: 0.7825 (mmtt) cc_final: 0.7227 (mppt) REVERT: B 358 ASP cc_start: 0.8527 (m-30) cc_final: 0.8275 (m-30) REVERT: B 369 LYS cc_start: 0.7279 (ttmt) cc_final: 0.6825 (ttmm) REVERT: D 342 GLU cc_start: 0.8493 (mt-10) cc_final: 0.7945 (tt0) outliers start: 4 outliers final: 4 residues processed: 62 average time/residue: 0.2002 time to fit residues: 14.4073 Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain B 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 27 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 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 = 0.5228 r_free = 0.5228 target = 0.252168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.150640 restraints weight = 8954.160| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.74 r_work: 0.4185 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4083 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.6772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3498 Z= 0.107 Angle : 0.451 4.520 4680 Z= 0.230 Chirality : 0.050 0.130 528 Planarity : 0.003 0.038 594 Dihedral : 3.886 12.518 462 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.76 % Allowed : 14.14 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.002 0.001 TYR G 310 PHE 0.002 0.001 PHE A 346 HIS 0.001 0.000 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 3498) covalent geometry : angle 0.45086 ( 4680) hydrogen bonds : bond 0.01937 ( 75) hydrogen bonds : angle 3.51639 ( 225) ********************** 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 66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: -0.0075 (mt0) cc_final: -0.0679 (tm-30) REVERT: A 342 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7616 (tt0) REVERT: A 343 LYS cc_start: 0.8608 (mttt) cc_final: 0.8330 (mttm) REVERT: C 321 LYS cc_start: 0.7922 (mmtt) cc_final: 0.7403 (mmtm) REVERT: C 342 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7654 (tt0) REVERT: C 370 LYS cc_start: 0.7298 (tttt) cc_final: 0.6791 (tttm) REVERT: E 342 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7816 (tt0) REVERT: G 342 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7483 (tt0) REVERT: G 369 LYS cc_start: 0.7199 (ttpt) cc_final: 0.6587 (tttm) REVERT: B 321 LYS cc_start: 0.7807 (mmtt) cc_final: 0.7214 (mppt) REVERT: B 358 ASP cc_start: 0.8534 (m-30) cc_final: 0.8274 (m-30) REVERT: B 369 LYS cc_start: 0.7255 (ttmt) cc_final: 0.6826 (ttmm) REVERT: D 342 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7889 (tt0) outliers start: 3 outliers final: 3 residues processed: 64 average time/residue: 0.1894 time to fit residues: 13.9435 Evaluate side-chains 66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain B 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 39 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 30.0000 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.5200 r_free = 0.5200 target = 0.249431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.147017 restraints weight = 8879.038| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 2.75 r_work: 0.4141 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4039 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.6840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3498 Z= 0.173 Angle : 0.469 4.402 4680 Z= 0.245 Chirality : 0.050 0.131 528 Planarity : 0.003 0.036 594 Dihedral : 4.058 13.808 462 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.76 % Allowed : 14.14 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 379 TYR 0.002 0.001 TYR C 310 PHE 0.005 0.001 PHE G 346 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 3498) covalent geometry : angle 0.46930 ( 4680) hydrogen bonds : bond 0.02204 ( 75) hydrogen bonds : angle 3.67283 ( 225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2433.21 seconds wall clock time: 41 minutes 51.69 seconds (2511.69 seconds total)