Starting phenix.real_space_refine on Wed Sep 17 07:59:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cgz_45589/09_2025/9cgz_45589_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cgz_45589/09_2025/9cgz_45589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cgz_45589/09_2025/9cgz_45589_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cgz_45589/09_2025/9cgz_45589_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cgz_45589/09_2025/9cgz_45589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cgz_45589/09_2025/9cgz_45589.map" } resolution = 2.69 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2106 2.51 5 N 606 2.21 5 O 624 1.98 5 H 3480 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6822 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "B" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 1.67, per 1000 atoms: 0.24 Number of scatterers: 6822 At special positions: 0 Unit cell: (146.28, 76.32, 36.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 624 8.00 N 606 7.00 C 2106 6.00 H 3480 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 299.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 44.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'A' and resid 320 through 322 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330 removed outlier: 6.948A pdb=" N GLY A 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASN C 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY C 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN E 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 removed outlier: 6.539A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 347 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 356 removed outlier: 6.560A pdb=" N SER A 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N GLY C 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE A 354 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER C 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N GLY E 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ILE C 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.621A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N HIS E 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 375 Processing sheet with id=AB1, first strand: chain 'B' and resid 307 through 310 Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AB3, first strand: chain 'B' and resid 320 through 322 Processing sheet with id=AB4, first strand: chain 'B' and resid 325 through 330 removed outlier: 6.962A pdb=" N GLY B 326 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN D 327 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N HIS F 329 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE D 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.619A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 343 through 347 removed outlier: 6.714A pdb=" N LEU D 344 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N LYS F 347 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE D 346 " --> pdb=" O LYS F 347 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 351 through 356 removed outlier: 6.463A pdb=" N SER B 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLY D 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ILE B 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER D 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N GLY F 355 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ILE D 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.615A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N HIS D 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 369 through 375 79 hydrogen bonds defined for protein. 237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3474 1.12 - 1.29: 558 1.29 - 1.47: 1055 1.47 - 1.64: 1783 1.64 - 1.81: 6 Bond restraints: 6876 Sorted by residual: bond pdb=" N GLU E 338 " pdb=" H GLU E 338 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" NH1 ARG A 349 " pdb="HH12 ARG A 349 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N GLU D 342 " pdb=" H GLU D 342 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N ILE F 360 " pdb=" H ILE F 360 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CZ PHE C 346 " pdb=" HZ PHE C 346 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 6871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 10221 2.34 - 4.68: 1746 4.68 - 7.01: 528 7.01 - 9.35: 45 9.35 - 11.69: 6 Bond angle restraints: 12546 Sorted by residual: angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 119.06 -6.46 1.00e+00 1.00e+00 4.18e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 118.36 -5.76 1.00e+00 1.00e+00 3.32e+01 angle pdb=" CA PHE B 346 " pdb=" CB PHE B 346 " pdb=" CG PHE B 346 " ideal model delta sigma weight residual 113.80 119.51 -5.71 1.00e+00 1.00e+00 3.26e+01 angle pdb=" CA PHE D 346 " pdb=" CB PHE D 346 " pdb=" CG PHE D 346 " ideal model delta sigma weight residual 113.80 119.36 -5.56 1.00e+00 1.00e+00 3.09e+01 angle pdb=" CA ASP D 358 " pdb=" CB ASP D 358 " pdb=" CG ASP D 358 " ideal model delta sigma weight residual 112.60 118.09 -5.49 1.00e+00 1.00e+00 3.02e+01 ... (remaining 12541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 2742 16.10 - 32.20: 230 32.20 - 48.31: 86 48.31 - 64.41: 98 64.41 - 80.51: 12 Dihedral angle restraints: 3168 sinusoidal: 1806 harmonic: 1362 Sorted by residual: dihedral pdb=" CA GLY D 365 " pdb=" C GLY D 365 " pdb=" N GLY D 366 " pdb=" CA GLY D 366 " ideal model delta harmonic sigma weight residual 180.00 151.51 28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA GLY F 365 " pdb=" C GLY F 365 " pdb=" N GLY F 366 " pdb=" CA GLY F 366 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA GLY B 365 " pdb=" C GLY B 365 " pdb=" N GLY B 366 " pdb=" CA GLY B 366 " ideal model delta harmonic sigma weight residual 180.00 153.11 26.89 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 3165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 286 0.070 - 0.140: 178 0.140 - 0.210: 46 0.210 - 0.280: 5 0.280 - 0.350: 1 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA LYS F 369 " pdb=" N LYS F 369 " pdb=" C LYS F 369 " pdb=" CB LYS F 369 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA ARG E 349 " pdb=" N ARG E 349 " pdb=" C ARG E 349 " pdb=" CB ARG E 349 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ARG F 349 " pdb=" N ARG F 349 " pdb=" C ARG F 349 " pdb=" CB ARG F 349 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 513 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 346 " -0.140 2.00e-02 2.50e+03 5.26e-02 8.29e+01 pdb=" CG PHE E 346 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE E 346 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE E 346 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE E 346 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 346 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE E 346 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 PHE E 346 " 0.053 2.00e-02 2.50e+03 pdb=" HD2 PHE E 346 " 0.034 2.00e-02 2.50e+03 pdb=" HE1 PHE E 346 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 PHE E 346 " -0.012 2.00e-02 2.50e+03 pdb=" HZ PHE E 346 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 346 " -0.138 2.00e-02 2.50e+03 5.20e-02 8.10e+01 pdb=" CG PHE C 346 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE C 346 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE C 346 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 PHE C 346 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 346 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE C 346 " -0.019 2.00e-02 2.50e+03 pdb=" HD1 PHE C 346 " 0.050 2.00e-02 2.50e+03 pdb=" HD2 PHE C 346 " 0.049 2.00e-02 2.50e+03 pdb=" HE1 PHE C 346 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE C 346 " -0.016 2.00e-02 2.50e+03 pdb=" HZ PHE C 346 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 330 " 0.085 2.00e-02 2.50e+03 4.96e-02 5.53e+01 pdb=" CG HIS C 330 " -0.061 2.00e-02 2.50e+03 pdb=" ND1 HIS C 330 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS C 330 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 HIS C 330 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS C 330 " -0.038 2.00e-02 2.50e+03 pdb=" HD2 HIS C 330 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 HIS C 330 " 0.047 2.00e-02 2.50e+03 pdb=" HE2 HIS C 330 " 0.056 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 576 2.20 - 2.80: 12440 2.80 - 3.40: 17545 3.40 - 4.00: 24228 4.00 - 4.60: 33709 Nonbonded interactions: 88498 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.596 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.602 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.602 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.607 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.608 2.450 ... (remaining 88493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.980 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.160 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:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.040 3396 Z= 0.680 Angle : 1.914 6.574 4548 Z= 1.255 Chirality : 0.087 0.350 516 Planarity : 0.010 0.055 576 Dihedral : 12.927 80.509 1296 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 1.17 % Allowed : 6.81 % Favored : 92.02 % Rotamer: Outliers : 0.26 % Allowed : 5.21 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.13 (0.35), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG D 349 TYR 0.084 0.026 TYR D 310 PHE 0.090 0.015 PHE E 346 HIS 0.016 0.004 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.01071 ( 3396) covalent geometry : angle 1.91435 ( 4548) hydrogen bonds : bond 0.09819 ( 79) hydrogen bonds : angle 7.06534 ( 237) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7713 (tttt) cc_final: 0.6489 (tmmt) REVERT: A 321 LYS cc_start: 0.7828 (tttt) cc_final: 0.7358 (ttmt) REVERT: A 331 LYS cc_start: 0.7570 (mttm) cc_final: 0.7355 (mtpp) REVERT: A 338 GLU cc_start: 0.7402 (tt0) cc_final: 0.7191 (tt0) REVERT: A 340 LYS cc_start: 0.8213 (mttt) cc_final: 0.7795 (mmtp) REVERT: B 321 LYS cc_start: 0.7828 (tttt) cc_final: 0.7620 (tttt) REVERT: B 338 GLU cc_start: 0.7653 (tt0) cc_final: 0.7101 (mm-30) REVERT: B 369 LYS cc_start: 0.7747 (mttt) cc_final: 0.7202 (mmtm) REVERT: C 311 LYS cc_start: 0.7102 (tttt) cc_final: 0.6753 (ttmt) REVERT: C 321 LYS cc_start: 0.7083 (tttt) cc_final: 0.6876 (ttmt) REVERT: C 327 ASN cc_start: 0.7483 (m-40) cc_final: 0.7066 (t0) REVERT: C 338 GLU cc_start: 0.6915 (tt0) cc_final: 0.6651 (tt0) REVERT: C 340 LYS cc_start: 0.7572 (mttt) cc_final: 0.7241 (mtmt) REVERT: D 311 LYS cc_start: 0.7860 (tttt) cc_final: 0.7240 (tttp) REVERT: D 321 LYS cc_start: 0.7332 (tttt) cc_final: 0.6932 (ttmt) REVERT: D 327 ASN cc_start: 0.7511 (m-40) cc_final: 0.7145 (t0) REVERT: D 338 GLU cc_start: 0.6957 (tt0) cc_final: 0.6603 (tp30) REVERT: D 353 LYS cc_start: 0.7437 (mttt) cc_final: 0.7003 (mttm) REVERT: E 311 LYS cc_start: 0.7069 (tttt) cc_final: 0.6567 (mmtt) REVERT: E 353 LYS cc_start: 0.7217 (ttmt) cc_final: 0.6771 (ttpp) REVERT: E 356 SER cc_start: 0.8514 (p) cc_final: 0.7933 (t) REVERT: E 358 ASP cc_start: 0.7430 (m-30) cc_final: 0.6962 (m-30) REVERT: F 315 LEU cc_start: 0.8124 (mp) cc_final: 0.7855 (mt) REVERT: F 321 LYS cc_start: 0.7239 (tttt) cc_final: 0.6459 (tmtt) REVERT: F 343 LYS cc_start: 0.7498 (mptt) cc_final: 0.6130 (tppt) REVERT: F 353 LYS cc_start: 0.7324 (mttt) cc_final: 0.7009 (mtmt) REVERT: F 356 SER cc_start: 0.8475 (p) cc_final: 0.7984 (p) REVERT: F 358 ASP cc_start: 0.7520 (m-30) cc_final: 0.7231 (m-30) outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 1.3961 time to fit residues: 175.6746 Evaluate side-chains 96 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 336 GLN B 336 GLN C 351 GLN E 336 GLN E 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.179460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.149425 restraints weight = 9977.446| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 1.77 r_work: 0.4137 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.4045 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3396 Z= 0.146 Angle : 0.658 5.732 4548 Z= 0.348 Chirality : 0.051 0.139 516 Planarity : 0.003 0.023 576 Dihedral : 7.952 53.190 447 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.82 % Allowed : 15.10 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.00 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 349 TYR 0.010 0.002 TYR E 310 PHE 0.008 0.001 PHE E 346 HIS 0.004 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 3396) covalent geometry : angle 0.65848 ( 4548) hydrogen bonds : bond 0.03333 ( 79) hydrogen bonds : angle 4.49872 ( 237) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8631 (mttt) cc_final: 0.8377 (mttt) REVERT: A 348 ASP cc_start: 0.8215 (t0) cc_final: 0.7980 (t70) REVERT: A 369 LYS cc_start: 0.8074 (mttp) cc_final: 0.7711 (mttp) REVERT: B 369 LYS cc_start: 0.7970 (mttt) cc_final: 0.7709 (mmtm) REVERT: C 311 LYS cc_start: 0.7358 (tttt) cc_final: 0.7017 (ttmt) REVERT: C 340 LYS cc_start: 0.8276 (mttt) cc_final: 0.7912 (mtmt) REVERT: C 342 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7143 (mm-30) REVERT: D 311 LYS cc_start: 0.7856 (tttt) cc_final: 0.7490 (tttp) REVERT: D 321 LYS cc_start: 0.7984 (tttt) cc_final: 0.7245 (tptt) REVERT: D 348 ASP cc_start: 0.8002 (t0) cc_final: 0.7739 (t0) REVERT: E 343 LYS cc_start: 0.8012 (mtpp) cc_final: 0.7766 (mtpt) REVERT: F 315 LEU cc_start: 0.8202 (mp) cc_final: 0.7982 (mt) REVERT: F 343 LYS cc_start: 0.7779 (mptt) cc_final: 0.6516 (tppt) REVERT: F 356 SER cc_start: 0.9106 (p) cc_final: 0.8855 (p) outliers start: 7 outliers final: 5 residues processed: 105 average time/residue: 1.3498 time to fit residues: 145.2279 Evaluate side-chains 83 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 ASN F 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.173990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.144426 restraints weight = 10069.254| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 1.75 r_work: 0.4080 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3396 Z= 0.143 Angle : 0.610 4.430 4548 Z= 0.322 Chirality : 0.051 0.130 516 Planarity : 0.003 0.024 576 Dihedral : 6.683 21.444 444 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.65 % Allowed : 19.53 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.19 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.014 0.003 TYR D 310 PHE 0.017 0.001 PHE C 346 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 3396) covalent geometry : angle 0.61000 ( 4548) hydrogen bonds : bond 0.02821 ( 79) hydrogen bonds : angle 4.21840 ( 237) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 342 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6951 (pm20) REVERT: B 369 LYS cc_start: 0.8063 (mttt) cc_final: 0.7715 (mttp) REVERT: C 311 LYS cc_start: 0.7433 (tttt) cc_final: 0.6958 (ttmt) REVERT: C 319 THR cc_start: 0.7880 (p) cc_final: 0.7674 (p) REVERT: C 342 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7486 (mm-30) REVERT: D 311 LYS cc_start: 0.7877 (tttt) cc_final: 0.7510 (tttp) REVERT: D 342 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: D 348 ASP cc_start: 0.8055 (t0) cc_final: 0.7807 (t0) REVERT: E 325 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8127 (tp) REVERT: E 343 LYS cc_start: 0.8058 (mtpp) cc_final: 0.7786 (mtpt) REVERT: F 315 LEU cc_start: 0.8348 (mp) cc_final: 0.8137 (mt) REVERT: F 321 LYS cc_start: 0.8448 (tttt) cc_final: 0.8191 (ttmt) REVERT: F 343 LYS cc_start: 0.7929 (mptt) cc_final: 0.6622 (tppt) REVERT: F 345 ASP cc_start: 0.7654 (t0) cc_final: 0.7303 (m-30) REVERT: F 351 GLN cc_start: 0.7873 (mt0) cc_final: 0.7602 (mt0) REVERT: F 369 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8009 (mttm) outliers start: 14 outliers final: 5 residues processed: 89 average time/residue: 1.1910 time to fit residues: 108.9825 Evaluate side-chains 75 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4455 r_free = 0.4455 target = 0.172392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.141346 restraints weight = 10214.884| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 1.79 r_work: 0.4050 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3953 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3396 Z= 0.150 Angle : 0.588 4.260 4548 Z= 0.308 Chirality : 0.050 0.123 516 Planarity : 0.003 0.026 576 Dihedral : 6.397 19.503 444 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.08 % Allowed : 22.66 % Favored : 75.26 % 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: -2.25 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.021 0.003 TYR C 310 PHE 0.006 0.001 PHE E 346 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3396) covalent geometry : angle 0.58803 ( 4548) hydrogen bonds : bond 0.02636 ( 79) hydrogen bonds : angle 4.19674 ( 237) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.235 Fit side-chains REVERT: B 369 LYS cc_start: 0.8162 (mttt) cc_final: 0.7820 (mttp) REVERT: C 311 LYS cc_start: 0.7552 (tttt) cc_final: 0.7039 (ttmt) REVERT: C 342 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7475 (mm-30) REVERT: D 311 LYS cc_start: 0.7988 (tttt) cc_final: 0.7602 (tttp) REVERT: D 338 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7843 (tm-30) REVERT: D 342 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: E 325 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8249 (tp) REVERT: F 315 LEU cc_start: 0.8322 (mp) cc_final: 0.8104 (mt) REVERT: F 321 LYS cc_start: 0.8491 (tttt) cc_final: 0.8189 (ttmt) REVERT: F 345 ASP cc_start: 0.7665 (t0) cc_final: 0.7313 (m-30) REVERT: F 351 GLN cc_start: 0.7833 (mt0) cc_final: 0.7555 (mt0) REVERT: F 369 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7994 (mttm) outliers start: 8 outliers final: 3 residues processed: 75 average time/residue: 1.2199 time to fit residues: 94.1446 Evaluate side-chains 64 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.173003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.140776 restraints weight = 10208.467| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 1.81 r_work: 0.4046 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3950 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3396 Z= 0.121 Angle : 0.550 3.866 4548 Z= 0.287 Chirality : 0.049 0.126 516 Planarity : 0.004 0.028 576 Dihedral : 6.072 17.806 444 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.60 % Allowed : 22.66 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.27 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.013 0.002 TYR C 310 PHE 0.004 0.001 PHE E 346 HIS 0.002 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 3396) covalent geometry : angle 0.55024 ( 4548) hydrogen bonds : bond 0.02405 ( 79) hydrogen bonds : angle 4.05721 ( 237) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.199 Fit side-chains REVERT: A 338 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: B 369 LYS cc_start: 0.8118 (mttt) cc_final: 0.7764 (mttp) REVERT: C 342 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7512 (mm-30) REVERT: D 311 LYS cc_start: 0.7901 (tttt) cc_final: 0.7530 (tttp) REVERT: D 338 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7982 (mm-30) REVERT: D 342 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: D 356 SER cc_start: 0.8946 (p) cc_final: 0.8638 (t) REVERT: E 325 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8282 (tp) REVERT: E 343 LYS cc_start: 0.7968 (mtpp) cc_final: 0.7511 (mmpt) REVERT: F 345 ASP cc_start: 0.7668 (t0) cc_final: 0.7353 (m-30) REVERT: F 351 GLN cc_start: 0.7828 (mt0) cc_final: 0.7568 (mt0) outliers start: 10 outliers final: 5 residues processed: 67 average time/residue: 1.0534 time to fit residues: 72.8836 Evaluate side-chains 66 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.172807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.140518 restraints weight = 10237.953| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 1.81 r_work: 0.4042 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3946 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3396 Z= 0.123 Angle : 0.542 3.833 4548 Z= 0.283 Chirality : 0.049 0.124 516 Planarity : 0.003 0.028 576 Dihedral : 5.918 17.701 444 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.86 % Allowed : 22.14 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.29 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.013 0.003 TYR D 310 PHE 0.004 0.001 PHE E 346 HIS 0.002 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 3396) covalent geometry : angle 0.54171 ( 4548) hydrogen bonds : bond 0.02324 ( 79) hydrogen bonds : angle 4.00170 ( 237) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.191 Fit side-chains REVERT: B 369 LYS cc_start: 0.8123 (mttt) cc_final: 0.7737 (mttp) REVERT: C 311 LYS cc_start: 0.7652 (tttt) cc_final: 0.7095 (ttmt) REVERT: C 342 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7566 (mm-30) REVERT: D 311 LYS cc_start: 0.7890 (tttt) cc_final: 0.7501 (tttp) REVERT: D 338 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: D 342 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: D 356 SER cc_start: 0.8907 (p) cc_final: 0.8608 (t) REVERT: E 325 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8346 (tp) REVERT: E 343 LYS cc_start: 0.7942 (mtpp) cc_final: 0.7484 (mmpt) REVERT: F 345 ASP cc_start: 0.7620 (t0) cc_final: 0.7344 (m-30) REVERT: F 351 GLN cc_start: 0.7848 (mt0) cc_final: 0.7586 (mt0) REVERT: F 369 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7994 (mttm) outliers start: 11 outliers final: 4 residues processed: 68 average time/residue: 1.1014 time to fit residues: 77.2716 Evaluate side-chains 68 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.171678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.139335 restraints weight = 10150.626| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 1.80 r_work: 0.4027 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3931 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.6067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3396 Z= 0.139 Angle : 0.550 3.893 4548 Z= 0.288 Chirality : 0.049 0.122 516 Planarity : 0.004 0.029 576 Dihedral : 5.908 17.190 444 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.65 % Allowed : 22.40 % Favored : 73.96 % 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: -2.30 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.015 0.003 TYR D 310 PHE 0.006 0.001 PHE E 346 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3396) covalent geometry : angle 0.55018 ( 4548) hydrogen bonds : bond 0.02324 ( 79) hydrogen bonds : angle 3.97329 ( 237) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.206 Fit side-chains REVERT: A 338 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7857 (tm-30) REVERT: A 342 GLU cc_start: 0.7751 (mm-30) cc_final: 0.6968 (pm20) REVERT: B 369 LYS cc_start: 0.8210 (mttt) cc_final: 0.7770 (mttp) REVERT: C 311 LYS cc_start: 0.7715 (tttt) cc_final: 0.7141 (ttmt) REVERT: C 342 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7606 (mm-30) REVERT: D 311 LYS cc_start: 0.7876 (tttt) cc_final: 0.7496 (tttp) REVERT: D 338 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7881 (tm-30) REVERT: D 342 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: D 356 SER cc_start: 0.8908 (p) cc_final: 0.8610 (t) REVERT: E 343 LYS cc_start: 0.8004 (mtpp) cc_final: 0.7525 (mmpt) REVERT: F 345 ASP cc_start: 0.7639 (t0) cc_final: 0.7355 (m-30) REVERT: F 369 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8039 (mttm) outliers start: 14 outliers final: 6 residues processed: 72 average time/residue: 1.0515 time to fit residues: 78.1666 Evaluate side-chains 73 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 336 GLN Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.172444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.140184 restraints weight = 10259.375| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 1.82 r_work: 0.4039 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3942 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.6226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3396 Z= 0.123 Angle : 0.535 4.435 4548 Z= 0.277 Chirality : 0.049 0.124 516 Planarity : 0.004 0.029 576 Dihedral : 5.778 17.030 444 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.60 % Allowed : 23.44 % Favored : 73.96 % 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: -2.28 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.013 0.002 TYR D 310 PHE 0.004 0.001 PHE A 346 HIS 0.002 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 3396) covalent geometry : angle 0.53528 ( 4548) hydrogen bonds : bond 0.02196 ( 79) hydrogen bonds : angle 3.93501 ( 237) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.216 Fit side-chains REVERT: A 338 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: A 342 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7013 (pm20) REVERT: B 369 LYS cc_start: 0.8204 (mttt) cc_final: 0.7760 (mttp) REVERT: C 311 LYS cc_start: 0.7688 (tttt) cc_final: 0.7143 (ttmt) REVERT: C 342 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7609 (mm-30) REVERT: D 311 LYS cc_start: 0.7848 (tttt) cc_final: 0.7478 (tttp) REVERT: D 338 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7963 (mm-30) REVERT: D 342 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: D 356 SER cc_start: 0.8903 (p) cc_final: 0.8624 (t) REVERT: F 345 ASP cc_start: 0.7612 (t0) cc_final: 0.7404 (m-30) REVERT: F 369 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8037 (mttm) outliers start: 10 outliers final: 6 residues processed: 70 average time/residue: 1.2010 time to fit residues: 86.4728 Evaluate side-chains 71 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.170937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.138861 restraints weight = 10461.763| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 1.81 r_work: 0.4010 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3916 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.6245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3396 Z= 0.162 Angle : 0.562 4.207 4548 Z= 0.294 Chirality : 0.049 0.122 516 Planarity : 0.004 0.028 576 Dihedral : 5.897 17.241 444 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.39 % Allowed : 22.66 % Favored : 73.96 % 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: -2.37 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG E 349 TYR 0.018 0.003 TYR D 310 PHE 0.007 0.001 PHE E 346 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 3396) covalent geometry : angle 0.56229 ( 4548) hydrogen bonds : bond 0.02319 ( 79) hydrogen bonds : angle 3.96862 ( 237) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: A 342 GLU cc_start: 0.7777 (mm-30) cc_final: 0.6963 (pm20) REVERT: B 369 LYS cc_start: 0.8252 (mttt) cc_final: 0.7781 (mttp) REVERT: C 343 LYS cc_start: 0.8354 (mmtp) cc_final: 0.7962 (mmtm) REVERT: D 311 LYS cc_start: 0.7843 (tttt) cc_final: 0.7486 (tttp) REVERT: D 338 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7978 (mm-30) REVERT: D 342 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: D 356 SER cc_start: 0.8949 (p) cc_final: 0.8640 (t) REVERT: F 345 ASP cc_start: 0.7702 (t0) cc_final: 0.7397 (m-30) REVERT: F 369 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8048 (mttm) outliers start: 13 outliers final: 6 residues processed: 64 average time/residue: 1.0834 time to fit residues: 71.5025 Evaluate side-chains 66 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 0.1980 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4449 r_free = 0.4449 target = 0.171108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.138772 restraints weight = 10294.617| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 1.81 r_work: 0.4020 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3926 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.6296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3396 Z= 0.142 Angle : 0.546 3.996 4548 Z= 0.284 Chirality : 0.049 0.123 516 Planarity : 0.004 0.029 576 Dihedral : 5.820 17.126 444 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.34 % Allowed : 23.70 % Favored : 73.96 % 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: -2.36 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.015 0.003 TYR D 310 PHE 0.005 0.001 PHE E 346 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3396) covalent geometry : angle 0.54638 ( 4548) hydrogen bonds : bond 0.02247 ( 79) hydrogen bonds : angle 3.98251 ( 237) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: A 342 GLU cc_start: 0.7804 (mm-30) cc_final: 0.6977 (pm20) REVERT: A 369 LYS cc_start: 0.7979 (mttp) cc_final: 0.7647 (mttp) REVERT: B 369 LYS cc_start: 0.8271 (mttt) cc_final: 0.7800 (mttp) REVERT: C 342 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7769 (mm-30) REVERT: D 311 LYS cc_start: 0.7810 (tttt) cc_final: 0.7470 (tttp) REVERT: D 338 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7964 (mm-30) REVERT: D 342 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: D 356 SER cc_start: 0.8927 (p) cc_final: 0.8622 (t) REVERT: F 345 ASP cc_start: 0.7651 (t0) cc_final: 0.7373 (m-30) REVERT: F 369 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8031 (mttm) outliers start: 9 outliers final: 5 residues processed: 66 average time/residue: 1.0883 time to fit residues: 74.1539 Evaluate side-chains 66 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 369 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4441 r_free = 0.4441 target = 0.170621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.138190 restraints weight = 10262.578| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 1.81 r_work: 0.4010 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3917 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.6387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3396 Z= 0.157 Angle : 0.557 4.223 4548 Z= 0.290 Chirality : 0.049 0.123 516 Planarity : 0.004 0.028 576 Dihedral : 5.839 17.112 444 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.60 % Allowed : 24.48 % Favored : 72.92 % 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: -2.41 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.017 0.003 TYR D 310 PHE 0.007 0.001 PHE E 346 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 3396) covalent geometry : angle 0.55658 ( 4548) hydrogen bonds : bond 0.02277 ( 79) hydrogen bonds : angle 4.01191 ( 237) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3495.09 seconds wall clock time: 60 minutes 0.59 seconds (3600.59 seconds total)